# ent

id: cord-024652-4i6kktl0
type: GGP
entity:
  cis 2 4 dimethylthiane S S dioxide cyclopentane butanoic acid 2 methyl methyl ester 1 butanol 3 methyl acetate


id: cord-024652-4i6kktl0
type: CL
entity:
  spp Trichoderma spp Phomopsis spp and Oxyporus latemarginatus are reported to produce VOCs that inhibit mycelial growth of phytopathogenic fungi


id: cord-024652-4i6kktl0
type: CL
entity:
  kelp an iodine rich substance needed for the normal functioning of thyroid gland Laminaria produces laminarin glucan polysaccharide


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  dicotyledonous plants Apiaceae Asteraceae Convolvulaceae Chenopodiaceae Euphorbiaceae Linaceae Moraceae Piperaceae Rosaceae Rutaceae


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  quinones phenols phenolic esters steroids terpenoids cytochalasins benzopyranone alkaloids isocoumarins


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  S 5 methyl 1 heptanol ethyl acetate propanoic acid 2 methyl methyl ester cis 2 4 dimethylthiane S S dioxide cyclopentane butanoic acid 2 methyl methyl ester 1 butanol 3 methyl acetate


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  methyl 1 butanol 1 methyl 1 3 cyclohexadiene 1 methyl 1 4 cyclohexadiene 4 heptanone isoamyl acetate 4 heptyn 2 ol 2 octenal octanal β


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  alkylated phenols anthraquinones coumarins phenolic acid phenols phenylpropanoids quinines xanthones hydroxycinnamic acid p coumaric acid ferulic acid


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  Asparagus racemosus Willd Insecticidal secondary metabolic products from the entomogenous fungus Fusarium larvarum 12 Heptadecenyl resorcinol


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  dem Sachalin Staudenknoterich Reynoutria sachalinensis F Schmidt Nakai gegen Plizkrankheiten insbesondere Echte Mehltauplize Production of


id: cord-024652-4i6kktl0
type: CHEMICAL
entity:
  Cinnamomum camphora Muscodor kashayum sp nov a new volatile antimicrobial producing endophytic fungus Muscodor


id: cord-255351-vp19ydce
type: DISEASE
entity:
  typhi Shigella Campylobacter Giardia lamblia Vibrio Cryptosporidium Entamoeba norovirus calicivirus Norwalk


id: cord-320295-k2i52wgs
type: ORG
entity:
  the International Committee on Taxonomy of Viruses the National Centre for Biotechnology Information the CAB International Bioscience


id: cord-018101-zd4v222b
type: ORG
entity:
  Bell and World Health Organization Working Group on Prevention of International and Community Transmission of SARS


id: cord-018101-zd4v222b
type: ORG
entity:
  Bell and World Health Organization Working Group on Prevention of International and Community Transmission of SARS 2004


id: cord-018101-zd4v222b
type: LAW
entity:
  Chap 5 World Health Organization World Health Organization Working Group on Prevention of International and Community Transmission of SARS


id: cord-297621-xunyqlr5
type: GGP
entity:
  Staphylococcus epidermidis 4 6 0 5 127 Streptococcus bovis 7 0 0 3 134 Streptococcus dysgalactiae 3 5 0 3


id: cord-297621-xunyqlr5
type: LAW
entity:
  transfusion Treatment of Platelet Concentrates with the MIRASOL Pathogen Inactivation System Modulates Platelet


id: cord-297621-xunyqlr5
type: ORG
entity:
  the Hemostatic Efficacy of Pathogen Reduced Platelets vs Untreated Platelets in Patients With Thrombocytopenia


id: cord-297621-xunyqlr5
type: DISEASE
entity:
  Nukleinsäuren ist nicht sequenz spezifisch Die Reaktion erfolgt bevorzugt mit den Pyrimidinbasen Thymidin


id: cord-297621-xunyqlr5
type: CHEMICAL
entity:
  Propionibacterium acnes 4 53 1 13 121 Staphylococcus aureus 6 6 0 4 134 Staphylococcus epidermidis 4 6 0 5 127 Streptococcus bovis 7 0 0 3 134 Streptococcus dysgalactiae 3 5 0 3 134 Streptococcus pyogenes 4 4 0 8 134 Streptococcus pyogenes 4 1 0 9 127


id: cord-297621-xunyqlr5
type: CHEMICAL
entity:
  verwendeten TK Bei einer Aktualisierung des Reviews konnten zwei weitere abgeschlossene Studien mit zusammen 559 Teilnehmern einbezogen werden drei weitere werden aktuell durchgeführt diese wurden aber noch nicht


id: cord-297621-xunyqlr5
type: CHEMICAL
entity:
  toxikologischen Studien sowie der vorliegenden klinischen Studien s Tab Auch bei Einsatz von PI Verfahren sind Übertragungen


id: cord-282610-zim7nond
type: DISEASE
entity:
  Epstein Barr Virus infected lymphoblastoid cell lines 128 Figure 4 HIV M tuberculosis Cytomegalovirus Borrelia burgdorferi


id: cord-289443-46w52de3
type: PROTEIN
entity:
  ankyrin repeat domain 30A ANKRD30A CD4 microtubule associated protein 4 MAP4 nucleoporin 153 kDa NUP153


id: cord-289443-46w52de3
type: PROTEIN
entity:
  proteolytic fragments B2M β2 microglobulin BLMH bleomycin hydrolase CALR calreticulin CD40LG CD40 ligand


id: cord-289443-46w52de3
type: PROTEIN
entity:
  cellular proteases ACE2 angiotensin converting enzyme 2 DARC Duffy blood group atypical chemokine receptor MX1 myxovirus resistance 1 SSD sterol sensing domain TFRC transferrin receptor TLR4 Toll


id: cord-289443-46w52de3
type: CL
entity:
  natural killer T iTCR invariant TCR LGMN legumain LNPEP leucyl cystinyl aminopeptidase NCF neutrophil cytosol


id: cord-289443-46w52de3
type: DISEASE
entity:
  HIV 1 replication HIV 1 capsid cyclophilin interactions determine nuclear import pathway integration targeting and replication efficiency This


id: cord-269607-xh1hu3k4
type: CHEMICAL
entity:
  Typha latifolia Cyperus papyrus Cyperus alternifolius Phragmites mauritianus Pistia stratiotes Lemna paucicostata Spirodela polyrhiza Eichhornia


id: cord-339886-th1da1bb
type: ORG
entity:
  Committee on Achieving Sustainable Global Capacity for Surveillance and Response to Emerging Diseases of Zoonotic Origin


id: cord-031017-xjnbmah5
type: EVENT
entity:
  Multistate Outbreak of Salmonella Anatum Infections Linked to Imported Hot Peppers United States Investigation


id: cord-031017-xjnbmah5
type: ORG
entity:
  Hamburg LimeSurvey Project Sharing Data for Global Infectious Disease Surveillance and Outbreak Detection Considerations


id: cord-263484-afcgqjwq
type: GGP
entity:
  Alzheimer s disease An electrocardiogram based analysis evaluating sleep quality in patients with obstructive sleep apnea Large scale objective association of


id: cord-260420-4s7akmdp
type: ORG
entity:
  the Canadian Institutes of Health Research the Natural Sciences and Engineering Research Council of Canada


id: cord-260420-4s7akmdp
type: DISEASE
entity:
  influenza s seasonality Physico chemical characteristics of evaporating respiratory fluid droplets Isoelectric points of viruses Nanoscale aerovirology an efficient yet simple method to analyze the viral distribution of single bioaerosols The Pollution Particulate Concentrator PoPCon


id: cord-280107-tulne0v3
type: WORK_OF_ART
entity:
  The Vietnam Initiative on Zoonotic Infections VIZIONS A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases


id: cord-292031-weiwksh6
type: WORK_OF_ART
entity:
  Drinking Water Quality Volume 1 Recommendations World Health Organization WHO Geneva Switzwerland Towards


id: cord-292031-weiwksh6
type: ORG
entity:
  Quantitative Microbial Risk Assessment of Waterborne Disease Guidelines for Safe Recreational Water Environments


id: cord-295469-5an7836u
type: DISEASE
entity:
  Stachybotrys chartarum enteric viruses noro and rotaviruses respiratory viruses influenza and coronaviruses mycobacteria tuberculous


id: cord-279376-0x4zrfw3
type: GGP
entity:
  r 0 80 1 00 Seasonality and weather correlation results were summarised and discussed in terms of differences between weather variables and within the


id: cord-348819-gq7lp931
type: DISEASE
entity:
  human immunodeficiency virus 44 and royalsocietypublishing org journal rstb Phil Trans R Soc B 374 20190014


id: cord-260679-tm1s6wvj
type: DISEASE
entity:
  COPD cancer diabetes chronic liver disease renal impairment Immunosuppressive disorders HIV Solid organ


id: cord-346053-mk1mzc5z
type: CL
entity:
  stem rust of wheat Recent research in medical epidemiology has elucidated the impact of pathogen ecology in environmental reservoirs on the evolution of novel or enhanced pathogen virulence In contrast the evolution of virulence in plant pathogens has been investigated from a predominantly agro centric


id: cord-310439-z0bxsjug
type: ORG
entity:
  The Association of Official Seed Analysts Association of Official Seed Certifying Agencies International Seed Trade Association


id: cord-337219-d81v8b4j
type: LAW
entity:
  Guidelines for Design and Construction of Hospitals and Health Care Facilities Isolation Rooms Design Assessment


id: cord-337219-d81v8b4j
type: ORG
entity:
  Korea Centers for Disease Control Prevention Plan for Extended Installation of Negative Pressure Units


id: cord-354254-89vjfkfd
type: GGP
entity:
  sources 1 1 1 1 12 12 12 Reynolds transportation law calculates the source quantity in control volume at time t which


id: cord-301767-1jv20em8
type: CL
entity:
  enterohemorrhagic Escherichia coli O157 H7 in soil and on leaf lettuce and parsley grown in fields treated with contaminated manure composts or irrigation water


id: cord-301767-1jv20em8
type: DISEASE
entity:
  enteroviruses echovirus type 7 strain Wallace coxsackievirus B3 strain Nancy and poliovirus type 1 strain LSc


id: cord-322120-wtu04r2j
type: WORK_OF_ART
entity:
  The Role of Influenza and Pollution The Changing Paradigm of Air Pollution Monitoring Towards a Unified System


id: cord-322120-wtu04r2j
type: ORG
entity:
  the Standard Gravimetric Methods to Measure Personal Exposure and Kitchen Concentrations to Fine Particulate Matter


id: cord-322120-wtu04r2j
type: ORG
entity:
  the Total Coliform Rule WHO Guidelines for Drinking Water Quality A Systematic Review of the Health Outcomes Related to Household Water Quality in Developing Countries Coliform Bacteria


id: cord-322120-wtu04r2j
type: WORK_OF_ART
entity:
  the Bacteriology of the Coliform Group Their Suitability as Markers of Microbial Water Safety Presence and Growth of Naturalized Escherichia Coli in Temperate Soils


id: cord-322120-wtu04r2j
type: FAC
entity:
  Lake Superior Watersheds Microbial Source Tracking Current Methodology and Future Directions Microbial Source Tracking Markers for Detection of Fecal Contamination


id: cord-322120-wtu04r2j
type: FAC
entity:
  Detecting Viral Diversity in Water Environments Metagenomic Analysis Reveals Wastewater Treatment Plants


id: cord-322120-wtu04r2j
type: ORG
entity:
  Quantitative Molecular Diagnostic Methods to Identify Causes of Diarrhoea in Children A Reanalysis of the GEMS Case Control Study Specific Burdens of Community Diarrhoea in Developing Countries


id: cord-322120-wtu04r2j
type: ORG
entity:
  Rationale Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection


# bib

id: cord-001387-2g9dc5z4
title: A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe
author: McIntyre, K. Marie
date: 2014-08-19
txt: ./txt/cord-001387-2g9dc5z4.txt
cache: ./cache/cord-001387-2g9dc5z4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138073/
doi: 10.1371/journal.pone.0103529
summary:
  By coupling the H-index method with the EID2, the primary aim of this study was to establish priority lists of human and domestic animal pathogens (including zoonoses) present in Europe. Its potential as a quantitative One Health indicator (i.e. a single measure applicable to both human and animal diseases) was investigated by comparing scores for human-only, zoonotic, and animal-only pathogen groups, including emerging status as this would likely drive research impact. We investigated its value as a proxy for animal disease impact by comparing domestic animal pathogen H-indices with other measures of impact including presence on the OIE list [10] , and inclusion in DISCONTOOLS [11] . The study establishes priority lists of human and domestic animal pathogens (including zoonoses) present in Europe, using the H-index as a proxy measure for impact.

abstract:
  Disease or pathogen risk prioritisations aid understanding of infectious agent impact within surveillance or mitigation and biosecurity work, but take significant development. Previous work has shown the H-(Hirsch-)index as an alternative proxy. We present a weighted risk analysis describing infectious pathogen impact for human health (human pathogens) and well-being (domestic animal pathogens) using an objective, evidence-based, repeatable approach; the H-index. This study established the highest H-index European pathogens. Commonalities amongst pathogens not included in previous surveillance or risk analyses were examined. Differences between host types (humans/animals/zoonotic) in pathogen H-indices were explored as a One Health impact indicator. Finally, the acceptability of the H-index proxy for animal pathogen impact was examined by comparison with other measures. 57 pathogens appeared solely in the top 100 highest H-indices (1) human or (2) animal pathogens list, and 43 occurred in both. Of human pathogens, 66 were zoonotic and 67 were emerging, compared to 67 and 57 for animals. There were statistically significant differences between H-indices for host types (humans, animal, zoonotic), and there was limited evidence that H-indices are a reasonable proxy for animal pathogen impact. This work addresses measures outlined by the European Commission to strengthen climate change resilience and biosecurity for infectious diseases. The results include a quantitative evaluation of infectious pathogen impact, and suggest greater impacts of human-only compared to zoonotic pathogens or scientific under-representation of zoonoses. The outputs separate high and low impact pathogens, and should be combined with other risk assessment methods relying on expert opinion or qualitative data for priority setting, or could be used to prioritise diseases for which formal risk assessments are not possible because of data gaps.


id: cord-004914-cnz61qjy
title: Cross-Species Pathogen Transmission and Disease Emergence in Primates
author: Pedersen, Amy B.
date: 2010-03-16
txt: ./txt/cord-004914-cnz61qjy.txt
cache: ./cache/cord-004914-cnz61qjy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087625/
doi: 10.1007/s10393-010-0284-3
summary:
  This analysis provides the first quantitative attempt to assess the risk of pathogens host-shifting to humans from wildlife populations, a critical step toward predicting disease emergence. Following Davies and Pedersen (2008) , we derived the relationship between evolutionary divergence (representing time to most recent common ancestor from the dated phylogenetic tree of Bininda-Emonds et al., 2007) , and pathogen community similarity (as described above) between each primate pair using generalized linear modeling (GLM) with binomial errors and a logit link function in the statistical package R (R: a programming environment for data analysis and graphics, v. Next, to provide an estimate of the cross-species pathogen transmission risk from wild primates to humans, we constructed a second hotspot map, weighting each primate distribution in proportion to its evolutionary distance from humans, using the nonlinear transformation determined from the GLM model coefficients described above. Population centers in close proximity to regions with high phylogenetic risk of host shifts and human population growth are likely to be foci of disease emergence.

abstract:
  Many of the most virulent emerging infectious diseases in humans, e.g., AIDS and Ebola, are zoonotic, having shifted from wildlife populations. Critical questions for predicting disease emergence are: (1) what determines when and where a disease will first cross from one species to another, and (2) which factors facilitate emergence after a successful host shift. In wild primates, infectious diseases most often are shared between species that are closely related and inhabit the same geographic region. Therefore, humans may be most vulnerable to diseases from the great apes, which include chimpanzees and gorillas, because these species represent our closest relatives. Geographic overlap may provide the opportunity for cross-species transmission, but successful infection and establishment will be determined by the biology of both the host and pathogen. We extrapolate the evolutionary relationship between pathogen sharing and divergence time between primate species to generate “hotspot” maps, highlighting regions where the risk of disease transfer between wild primates and from wild primates to humans is greatest. We find that central Africa and Amazonia are hotspots for cross-species transmission events between wild primates, due to a high diversity of closely related primate species. Hotspots of host shifts to humans will be most likely in the forests of central and west Africa, where humans come into frequent contact with their wild primate relatives. These areas also are likely to sustain a novel epidemic due to their rapidly growing human populations, close proximity to apes, and population centers with high density and contact rates among individuals.


id: cord-009394-3jeexu27
title: Modern Approaches in Probiotics Research to Control Foodborne Pathogens
author: Amalaradjou, Mary Anne Roshni
date: 2012-09-30
txt: ./txt/cord-009394-3jeexu27.txt
cache: ./cache/cord-009394-3jeexu27.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150249/
doi: 10.1016/b978-0-12-394598-3.00005-8
summary:
  Although probiotics have been demonstrated to be effective in antagonizing foodborne pathogens, challenges exist in the characterization and elucidation of underlying molecular mechanisms of action and in the development of potential delivery strategies that could maintain the viability and functionality of the probiotic in the target organ. Those include lactose metabolism and food digestion, production of antimicrobial peptides and control of enteric infections, antimycotic effects, anticarcinogenic properties, immunologic enhancement, enhancement of short-chain fatty acid (SCFA) production, antiatherogenic and cholesterol-lowering attributes, regulatory role in allergy (Thomas et al., 2011) , protection against vaginal or urinary tract infections, increased nutritional value, maintenance of epithelial integrity and barrier, stimulation of repair mechanism in cells, and maintenance and reestablishment of a well-balanced indigenous intestinal and respiratory microbial communities.

abstract:
  Foodborne illness is a serious public health concern. There are over 200 known microbial, chemical, and physical agents that are known to cause foodborne illness. Efforts are made for improved detection, control and prevention of foodborne pathogen in food, and pathogen associated diseases in the host. Several commonly used approaches to control foodborne pathogens include antibiotics, natural antimicrobials, bacteriophages, bacteriocins, ionizing radiations, and heat. In addition, probiotics offer a potential intervention strategy for the prevention and control of foodborne infections. This review focuses on the use of probiotics and bioengineered probiotics to control foodborne pathogens, their antimicrobial actions, and their delivery strategies. Although probiotics have been demonstrated to be effective in antagonizing foodborne pathogens, challenges exist in the characterization and elucidation of underlying molecular mechanisms of action and in the development of potential delivery strategies that could maintain the viability and functionality of the probiotic in the target organ.


id: cord-015484-t1zbpyin
title: Emerging Pathogens: What Are the Sources and How Can They Be Spotted Quickly?
author: nan
date: 2003-05-01
txt: ./txt/cord-015484-t1zbpyin.txt
cache: ./cache/cord-015484-t1zbpyin.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107543/
doi: 10.1309/nm113vcpd3pgvgcl
abstract: nan
summary:
  Top priorities of the 4 major sections include: í í Surveillance: The CDC with state health departments and other task force members began planning a coordinated surveillance system, such that all entities would use similar methodology and develop patterns of use for antimicrobial drug used in human medicine, agriculture, and other consumer products. A case in point was published in the March 2003 issue of Emerging Infectious Diseases as a letter to the editor, describing a multi-drug resistant Shigella dysenteriae type 1 organism, first seen in India in 1984, where it was sensitive to nalidixic acid. Hooper (Massachusetts General Hospital, Harvard Medical School, Boston, MA), writing in a special issue of Emerging Pathogens (Mar-April, 2001), drug resistance in Streptococcus pneumoniae, which is currently low, will require close monitoring as fluoroquinolones are used more extensively for treating respiratory tract infections.


id: cord-016588-f8uvhstb
title: Informatics for Infectious Disease Research and Control
author: Sintchenko, Vitali
date: 2009-10-03
txt: ./txt/cord-016588-f8uvhstb.txt
cache: ./cache/cord-016588-f8uvhstb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120928/
doi: 10.1007/978-1-4419-1327-2_1
summary:
  The goal of infectious disease informatics is to optimize the clinical and public health management of infectious diseases through improvements in the development and use of antimicrobials, the design of more effective vaccines, the identification of biomarkers for life-threatening infections, a better understanding of host-pathogen interactions, and biosurveillance and clinical decision support. "New Age" infectious disease informatics rests on advances in microbial genomics, the sequencing and comparative study of the genomes of pathogens, and proteomics or the identification and characterization of their protein related properties and reconstruction of metabolic and regulatory pathways (Bansal 2005) . The figure was produced using Artemis software (The Wellcome Trust Sanger Institute, UK) 1 Informatics for Infectious Disease Research and Control evidence-based gene calling or translating alignments of the DNA sequence to known proteins; and (3) aligning cDNAs from the same or related species.

abstract:
  The goal of infectious disease informatics is to optimize the clinical and public health management of infectious diseases through improvements in the development and use of antimicrobials, the design of more effective vaccines, the identification of biomarkers for life-threatening infections, a better understanding of host-pathogen interactions, and biosurveillance and clinical decision support. Infectious disease informatics can lead to more targeted and effective approaches for the prevention, diagnosis and treatment of infections through a comprehensive review of the genetic repertoire and metabolic profiles of a pathogen. The developments in informatics have been critical in boosting the translational science and in supporting both reductionist and integrative research paradigms.


id: cord-016717-2twm4hmc
title: How Does Biodiversity Influence the Ecology of Infectious Disease?
author: Vourc’h, Gwenaël
date: 2011-06-28
txt: ./txt/cord-016717-2twm4hmc.txt
cache: ./cache/cord-016717-2twm4hmc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121084/
doi: 10.1007/978-94-007-2114-2_13
summary:
  To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. In this chapter, we investigate how biodiversity influences the ecology of infectious diseases at the intraspecific level (genetic variability of pathogens and hosts) and at the level of communities (species composition). The hypothesis underlying the amplification and dilution effect is that for many diseases, the competence of reservoirs, i.e. the ability to become infected and retransmit the pathogen, varies according to the host species (Haydon et al.

abstract:
  Over the past years, biodiversity has been reduced on an unprecedented scale, while new infectious diseases are emerging at an increasing rate. Greater overall biodiversity could lead to a greater diversity of hosts and thus of pathogens. Yet disease regulation – due to the buffering role of host diversity – is considered to be one of the services provided by biodiversity. In this chapter, we ask how biodiversity is linked to infectious disease. First, we investigate the influence of the biodiversity of pathogens. We highlight that the number of pathogen species is not well known but that new findings are facilitated by the rapid expansion of molecular techniques. We show that, although there is a trend to find higher pathogen richness toward the equator, identifying a global pattern between the richness of all pathogen species and their latitudinal distribution is challenging. We emphasize that pathogen intraspecific diversity is a crucial factor in disease emergence and allows pathogens to adapt to the selective pressures they face. In addition, the selective pressure acting on hosts due to parasite, and reinforced by parasite diversity within hosts seems to be a major evolutionary and ecological force shaping hosts biodiversity. Second, we investigate how the diversity of hosts influences infectious disease ecology. For multi-host diseases, a change in host species richness or abundance can modify the dynamics of local infectious diseases by either reducing (“dilution effect”) or increasing (“amplification effect”) the risk of transmission to the targeted host species. The underlying hypothesis is that, the competence of reservoirs varies according to the host species. The dilution effect has been demonstrated mainly through theoretical work and there have been only few case studies. Regarding the genetic diversity of host, an important issue is: to what extent does a reduction of this diversity impact the ability of the host population to response to infectious diseases? Third, we rapidly examine the role of biodiversity in the treatment of infectious diseases. To conclude, we consider that the consequences of the loss of species biodiversity on infectious diseases is still largely unknown, notably due to the lack of knowledge on the dynamics of host-pathogen relationships, especially at the population and at the community level.. We highlight that work on multi-host/ ulti-pathogen systems should be fostered and that new approaches, such as metagenomic investigations that does not require a priori assumptions, are promising to describe a community of pathogens and their interactions.


id: cord-018101-zd4v222b
title: Disease Outbreaks: Critical Biological Factors and Control Strategies
author: Kawashima, Kent
date: 2016-05-31
txt: ./txt/cord-018101-zd4v222b.txt
cache: ./cache/cord-018101-zd4v222b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122892/
doi: 10.1007/978-3-319-39812-9_10
summary:
  We will briefly describe some pathogens that cause human disease and their transmission mechanisms before analyzing the SARS 2002-2003 epidemic as a case study of a modern urban epidemic. In general, fecal-oral and vector-borne diseases are infections transmitted through an environmental (water, food) or a biological (animal) carrier that extends transmission range to large distances, but other routes are also possible depending on the specific pathogen. In the following three subsections, we discuss theoretical results on three important aspect of disease outbreak: (1) the effect of "superspreaders" on the probability of outbreak, (2) the impact of control strategies such as isolation and quarantine, and (3) factors that affect the evolution of pathogen virulence. When the host population has a highly heterogeneously connected network, emergence of disease may be rare, but infections that survive stochastic extinction produce "explosive" epidemics similar to the case of SARS in 2002.

abstract:
  Disease outbreaks remain a major threat to human health and welfare especially in urban areas in both developed and developing countries. A large body of theoretical work has been devoted to modeling disease emergence, and critical factors that predict outbreak occurrence and severity have been proposed. In this chapter, we focus on biological factors that underlie both theoretical models and urban planning. We describe the SARS 2002–2003 pandemic as a case study of epidemic control of a human infectious disease. We then describe theoretical analyses of disease dynamics and control strategies. An important conclusion is that epidemic control will be strongly dependent on particular aspects of pathogen biology including host breadth, virulence, incubation time, and/or mutation rate. The probability, and potential cost, of future outbreaks, may be high and lessons from both past cases and theoretical work should inform urban design and policy. Interdisciplinary collaboration in planning, swiftness of information dissemination and response, and willingness to forgo personal liberties during a crisis may be key factors in resilience to infectious disease outbreaks.


id: cord-021966-5m21bsrw
title: Vaccines
author: Shaw, Alan R.
date: 2009-05-15
txt: ./txt/cord-021966-5m21bsrw.txt
cache: ./cache/cord-021966-5m21bsrw.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152278/
doi: 10.1016/b978-0-323-04404-2.10092-2
abstract: nan
summary:
  Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination?


id: cord-023830-w218ogsk
title: Rapid Detection of Bioterrorism Pathogens
author: Perlin, David
date: 2008-09-10
txt: ./txt/cord-023830-w218ogsk.txt
cache: ./cache/cord-023830-w218ogsk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176176/
doi: 10.1007/978-1-59745-326-4_16
abstract: nan
summary:
  The inadequacy of phenotypic-based diagnostic assays is illustrated graphically by the ''''gold standard'''' public health laboratory-testing algorithm that was in place for positive identification of Bacillus anthracis from environmental samples during the October 2001 anthrax outbreak (Fig. 16.1a) . Genomic differences between microbes offer an alternative to culturing for detection and identification of pathogens by providing species-specific DNA targets that can be accurately resolved by molecular methodology. Polymerase chain reaction (PCR)-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for identification of bacterial, fungal and many viral pathogenic agents. Most importantly, these genetic probing systems offer rapid turn around time (1-6 h) and are suitable for high throughput, automated multiplex operations critical for use in clinical diagnostic laboratories. Rapid diagnostic assays in the genomic biology era: detection and identification of infectious disease and biological weapon agents


id: cord-024652-4i6kktl0
title: Natural Products as Fungicide and Their Role in Crop Protection
author: Santra, Hiran Kanti
date: 2020-05-12
txt: ./txt/cord-024652-4i6kktl0.txt
cache: ./cache/cord-024652-4i6kktl0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212785/
doi: 10.1007/978-981-15-3024-1_9
summary:
  A large number of bioactive compounds ranging from direct plant (both cryptogams algae and moss and phanerogams)-derived natural extracts, essential oil of aromatic plants, and low-molecular-weight antimicrobial compounds known as phytoalexins to secondary metabolites that are both volatile and nonvolatile organic compounds of microbes (fungal and actinobacterial members) residing inside the host tissue, called endophyte, are widely used as agricultural bioweapons. Endophytic culture extracts are also known to be rich sources of phenolics; usually they are directly proportional to the antioxidative property of any fungal isolate, but in some particular cases, they are characterized with their antifungal potentials against phytopathogenic fungus. So it is a great opportunity to use the unique mixture of volatile organic compounds of the endophytic isolate to reduce the crop loss caused by the pathogenic infection on the commercially valuable plant of cherry tomato worldwide.

abstract:
  Seeking solutions from nature for solving one and all problems is the age-old practice for mankind, and natural products are proved to be the most effective one for keeping up the balance of development as well as the “healthy, wealthy, and well” condition of mother nature. Fungal pathogens are proved to be a common and popular contaminant of agroecosystem that approximately causes 70–80% of total microbial crop loss. To meet the proper global increasing need of food products as a result of population explosion, managing agricultural system in an eco-friendly and profitable manner is the prime target; thus the word “sustainable agriculture” plays it part, and this package is highly effective when coupled with nature-derived fungicidal products that can minimize the event of fungal infections in agrarian ecosystem. Present study enlists the most common and effective natural products that might be of plant or microbial origin, their mode of action, day-by-day development of phytopathogenic resistance against the prevailing fungicides, and also their role in maintenance of sustainability of agricultural practices with special emphasis on their acceptance over the synthetic or chemical one. A large number of bioactive compounds ranging from direct plant (both cryptogams algae and moss and phanerogams)-derived natural extracts, essential oil of aromatic plants, and low-molecular-weight antimicrobial compounds known as phytoalexins to secondary metabolites that are both volatile and nonvolatile organic compounds of microbes (fungal and actinobacterial members) residing inside the host tissue, called endophyte, are widely used as agricultural bioweapons. The rhizospheric partners of plant, mycorrhizae, are also a prime agent of this chemical warfare and protect their green partners from fungal invaders and emphasize the concept of “sustainable agriculture.”


id: cord-031017-xjnbmah5
author: Van Goethem, N.
date: 2020-08-31
txt: ./txt/cord-031017-xjnbmah5.txt
cache: ./cache/cord-031017-xjnbmah5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456758/
doi: 10.1186/s12889-020-09428-4
summary:
  METHODS: In May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. The following criteria were included (top to bottom): clinical and/or public health significance, priority with respect to preventing the spread of antimicrobial resistance, local/national/international policy surveillance priorities or obligations, importance of prevention and control programs (e.g. vaccination), utility of WGS for diagnostics and/or treatment decisions (individual patient care), utility of increased resolution to infer relatedness that would not be obtained via conventional methods, availability of high-quality/complete/standardized epidemiological and/or clinical data to provide context to the WGS results, possibility to link genomic data from different sources (food-animalhuman-environment), cost-effectiveness (e.g. replacing multiple tests), time-saving compared to conventional testing methods, impact on outcomes for patients and populations (translation into actionable results), availability of WGS typing schemes and reference databases (e.g. for antimicrobial resistance), availability of validated (quality-controlled) WGS workflows (both wet and dry laboratory), availability of expertise to generate, analyze and interpret WGS data, and availability of the appropriate infrastructure (sequence technology, high-performance computing, data storage, etc.).

title:
  Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019

abstract:
  BACKGROUND: Pathogen genomics is increasingly being translated from the research setting into the activities of public health professionals operating at different levels. This survey aims to appraise the literacy level and gather the opinions of public health experts and allied professionals working in the field of infectious diseases in Belgium concerning the implementation of next-generation sequencing (NGS) in public health practice. METHODS: In May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. Descriptive statistics were used to report on the frequency distribution of multiple choice responses whereas thematic analysis was used to analyze free text responses. A multivariable logistic regression model was constructed to identify important predictors for a positive attitude towards the implementation of pathogen genomics in public health practice. RESULTS: 146 out of the 753 invited public health professionals completed the survey. 63% of respondents indicated that public health agencies should be using genomics to understand and control infectious diseases. Having a high level of expertise in the field of pathogen genomics was the strongest predictor of a positive attitude (OR = 4.04, 95% CI = 1.11 – 17.23). A significantly higher proportion of data providers indicated to have followed training in the field of pathogen genomics compared to data end-users (p < 0.001). Overall, 79% of participants expressed interest in receiving further training. Main concerns were related to the cost of sequencing technologies, data sharing, data integration, interdisciplinary working, and bioinformatics expertise. CONCLUSIONS: Belgian health professionals expressed favorable views about implementation of pathogen genomics in their work activities related to infectious disease surveillance and control. They expressed the need for suitable training initiatives to strengthen their competences in the field. Their perception of the utility and feasibility of pathogen genomics for public health purposes will be a key driver for its further implementation.


id: cord-211735-qqm4fbor
author: Gulec, Fatih
date: 2020-11-02
txt: ./txt/cord-211735-qqm4fbor.txt
cache: ./cache/cord-211735-qqm4fbor.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2011.00884v1.pdf
doi: nan
summary:
  To this end, we propose a communication engineering approach that melts different disciplines such as epidemiology, biology, medicine, and fluid dynamics in the same pot to model airborne pathogen transmission among humans. The aim of this article is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases among humans through airborne pathogen transmission. By utilizing this analogy, we propose an approach to modeling interhuman airborne pathogen transmission with communication engineering perspective where mobile humans forming a group are considered as a mobile human ad hoc network (MoHANET). In this section, we present a framework with communication engineering perspective to model the spread of infectious diseases through airborne pathogen transmission. In the networking layer, the details of the MoHANET architecture are presented in order to model the spread of infectious diseases in a large scale (km) within the communication engineering framework as shown in Fig. 2.

title:
  Mobile Human Ad Hoc Networks: A Communication Engineering Viewpoint on Interhuman Airborne Pathogen Transmission

abstract:
  Pathogens such as viruses and bacteria play a vital role in human life, since they cause infectious diseases which can lead to epidemics. Recent coronavirus disease 2019 epidemic has shown that taking effective prevention measures such as wearing masks are important to reduce the human deaths and side effects of the epidemic. It is therefore requisite to accurately model the spread of infectious diseases whose one of the most crucial routes of transmission is airborne transmission. The transmission models in the literature are proposed independently from each other, at different scales and by the researchers from various disciplines. Thus, there is a need to merge all these research attempts. To this end, we propose a communication engineering approach that melts different disciplines such as epidemiology, biology, medicine, and fluid dynamics in the same pot to model airborne pathogen transmission among humans. In this approach, we introduce the concept of mobile human ad hoc networks (MoHANETs). This concept exploits the similarity of airborne transmission-driven human groups with mobile ad hoc networks and uses molecular communication as the enabling paradigm. The aim of this article is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases among humans through airborne pathogen transmission. In this article, we first review the airborne pathogen transmission mechanisms. Then, the MoHANET is given with a layered structure. In these layers, the infectious human emitting pathogen-laden droplets through air and the exposed human to these droplets are considered as the transmitter and receiver, respectively. Moreover, the experimental methods for the proposed approach are reviewed and discussed.


id: cord-255230-i6q73bhs
title: Capturing Fluctuations in Pathogen Avoidance: the Situational Pathogen Avoidance Scale
author: Makhanova, Anastasia
date: 2020-08-13
txt: ./txt/cord-255230-i6q73bhs.txt
cache: ./cache/cord-255230-i6q73bhs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s40806-020-00256-8
doi: 10.1007/s40806-020-00256-8
summary:
  Across six studies, we demonstrate the reliability and validity of the SPA scale, show that the scale is influenced by situational activation of pathogen avoidance motives, and demonstrate that it mediates the association between pathogen avoidance motives (both chronic and situational) and social biases against obese and foreign targets. Study 1 is a preliminary study intended to establish the reliability and factor structure of the scale and examine predictive validity by assessing the association between the SPA scale and aversive reactions toward an obese target (a heuristic cue associated with pathogen avoidance). Study 1 provides initial evidence for the reliability and the one-factor structure of the SPA scale and examined whether SPA scores were associated with bias against a target linked to heuristic pathogen threat (an obese target). Additionally, individuals who reported higher (relative to lower) SPA scores also reported more aversive reactions toward an obese target, consistent with prior research linking pathogen avoidance to prejudice against targets heuristically associated with illness.

abstract:
  Pathogen avoidance is an important motive underlying human behavior and is associated with numerous psychological processes—including biases against social groups heuristically associated with illness. Although there are reliable measurement scales to assess chronic dispositional levels of pathogen avoidance, no measurement scale currently exists to directly assess moment-to-moment fluctuations in pathogen avoidance. This paper presents the Situational Pathogen Avoidance (SPA) scale, which assesses situational variability in pathogen avoidance, especially as it pertains to avoidance of social stimuli. Across six studies, we demonstrate the reliability and validity of the SPA scale, show that the scale is influenced by situational activation of pathogen avoidance motives, and demonstrate that it mediates the association between pathogen avoidance motives (both chronic and situational) and social biases against obese and foreign targets. The SPA scale provides a valuable measurement tool for researchers who study pathogen avoidance and to those who study social biases more generally. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40806-020-00256-8) contains supplementary material, which is available to authorized users.


id: cord-255351-vp19ydce
title: Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review
author: Lanata, Claudio F.
date: 2013-09-04
txt: ./txt/cord-255351-vp19ydce.txt
cache: ./cache/cord-255351-vp19ydce.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0072788
doi: 10.1371/journal.pone.0072788
summary:
  We present the results of a systematic literature review of studies of diarrhea etiology in hospitalized children and use these results to estimate the global burden of diarrhea mortality by pathogen for children under 5 years of age for 2011. From 22 643 citations identified in the electronic search, 1 003 articles were selected for further evaluation (Fig. 1) ; 840 articles were excluded because they had one or more of the exclusion criteria (About 35% because they were not longitudinal studies or inappropriate laboratory methods were used, 31% because no data was given for children ,5 years of age, 23% for studies that lasted less than 12 months of duration, and the rest because data were reported after rotavirus vaccine introduction, duplicate publications or reporting results on a pathogen not included in our list).

abstract:
  Estimation of pathogen-specific causes of child diarrhea deaths is needed to guide vaccine development and other prevention strategies. We did a systematic review of articles published between 1990 and 2011 reporting at least one of 13 pathogens in children <5 years of age hospitalized with diarrhea. We included 2011 rotavirus data from the Rotavirus Surveillance Network coordinated by WHO. We excluded studies conducted during diarrhea outbreaks that did not discriminate between inpatient and outpatient cases, reporting nosocomial infections, those conducted in special populations, not done with adequate methods, and rotavirus studies in countries where the rotavirus vaccine was used. Age-adjusted median proportions for each pathogen were calculated and applied to 712 000 deaths due to diarrhea in children under 5 years for 2011, assuming that those observed among children hospitalized for diarrhea represent those causing child diarrhea deaths. 163 articles and WHO studies done in 31 countries were selected representing 286 inpatient studies. Studies seeking only one pathogen found higher proportions for some pathogens than studies seeking multiple pathogens (e.g. 39% rotavirus in 180 single-pathogen studies vs. 20% in 24 studies with 5–13 pathogens, p<0·0001). The percentage of episodes for which no pathogen could be identified was estimated to be 34%; the total of all age-adjusted percentages for pathogens and no-pathogen cases was 138%. Adjusting all proportions, including unknowns, to add to 100%, we estimated that rotavirus caused 197 000 [Uncertainty range (UR) 110 000–295 000], enteropathogenic E. coli 79 000 (UR 31 000–146 000), calicivirus 71 000 (UR 39 000–113 000), and enterotoxigenic E. coli 42 000 (UR 20 000–76 000) deaths. Rotavirus, calicivirus, enteropathogenic and enterotoxigenic E. coli cause more than half of all diarrheal deaths in children <5 years in the world.


id: cord-256543-7kfi2yvu
title: Sustained fecal-oral human-to-human transmission following a zoonotic event
author: de Graaf, Miranda
date: 2016-11-23
txt: ./txt/cord-256543-7kfi2yvu.txt
cache: ./cache/cord-256543-7kfi2yvu.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1879625716301687
doi: 10.1016/j.coviro.2016.11.001
summary:
  Using a comparative approach including parasites, bacteria and viruses that transmit via the fecal-oral route, the meeting aimed at identifying the key drivers of sustained human-to-human transmission after a zoonotic event, taking into account the host, the pathogen and the interface (transmission amplifiers). Enteric pathogens can be transmitted between humans by the fecal-oral route via direct contact or indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites ( Figure 1 ). After shedding from the host enteric pathogens can be transmitted between humans by the fecal-oral route via direct contact between humans, or via indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites. A human reservoir for non-typhoid Salmonella (NTS) transmission of multiple serotypes was demonstrated in a study of NTS-infected patients who continued to shed NTS for months up to years, and strains of these patients acquired antimicrobial resistance genes and virulence genes that possibly affected host-pathogen interactions [34 ] .

abstract:
  Bacterial, viral and parasitic zoonotic pathogens that transmit via the fecal-oral route have a major impact on global health. However, the mechanisms underlying the emergence of such pathogens from the animal reservoir and their persistence in the human population are poorly understood. Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment. We discuss current data gaps and propose future research directions.


id: cord-256615-gvq8uyfk
title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans
author: Rosenberg, Ronald
date: 2014-11-22
txt: ./txt/cord-256615-gvq8uyfk.txt
cache: ./cache/cord-256615-gvq8uyfk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00018-014-1785-y
doi: 10.1007/s00018-014-1785-y
summary:
  RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans.

abstract:
  RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. Despite great advances made in diagnostic technology since the 1950s, the annual rate at which novel virulent viruses have been found has remained at 2–3. Most emerging viruses are zoonoses; they have jumped from mammal or bird hosts to humans. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations.


id: cord-257802-vgizgq2y
title: Applications of microarrays in pathogen detection and biodefence
author: Uttamchandani, Mahesh
date: 2008-11-12
txt: ./txt/cord-257802-vgizgq2y.txt
cache: ./cache/cord-257802-vgizgq2y.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.tibtech.2008.09.004
doi: 10.1016/j.tibtech.2008.09.004
summary:
  Advances in miniaturizing this initial PCR step, for instance the development of Review Glossary Biodefence: defensive measures against biological threats, including natural/ emerging pathogens and bioterror agents, that have significant potential to endanger public health Detection: identifying the presence of target pathogen(s) from clinical or environmental samples. (b) Antibody microarrays can be used to detect pathogen proteins or antigens that might be present in environmental samples as an indication of contamination or for diagnostic purposes to determine pathogen infection in human tissues. fabricated a customized Affymetrix microarray containing 53 660 probes to detect DNA amplified from 18 different pathogenic microorganisms simultaneously, including pathogens from the US CDC''s list of bioterrorism agents, such as Bacillus anthracis (which causes anthrax), Clostridium botulinum (which generates the botulinum toxin), Yersinia pestis (which causes bubonic plague) and the Ebola virus [17] .

abstract:
  The microarray is a platform with wide-ranging potential in biodefence. Owing to the high level of throughput attainable through miniaturization, microarrays have accelerated the ability to respond in an epidemic or crisis. Extending beyond diagnostics, recent studies have applied microarrays as a research tool towards understanding the etiology and pathogenicity of dangerous pathogens, as well as in vaccine development. The original emphasis was on DNA microarrays, but the range now includes protein, antibody and carbohydrate microarrays, and research groups have exploited this diversity to further extend microarray applications in the area of biodefence. Here, we discuss the impact and contributions of the growing range of microarrays and emphasize the concepts that might shape the future of biodefence research.


id: cord-258139-x4js9vqe
title: Biosecurity and bovine respiratory disease
author: Callan, Robert J
date: 2005-03-04
txt: ./txt/cord-258139-x4js9vqe.txt
cache: ./cache/cord-258139-x4js9vqe.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S074907200200004X
doi: 10.1016/s0749-0720(02)00004-x
summary:
  Alternatively, when the causative pathogens are endemic in a population and individual susceptibility is dependent on numerous interrelated factors, the management of animal resistance and risk factors may be proportionally more important for disease prevention than biosecurity practices. The authors emphasize five areas of biosecurity management that should be more rigorously applied for the reduction of respiratory disease prevalence in cattle, including (1) strategic vaccination, (2) calf biosecurity, (3) housing ventilation, (4) commingling and animal contact, and (5) bovine viral diarrhea virus control. Airborne pathogen concentration is a function of many factors, including animal type, housing system, stocking rate, bedding, humidity, dust particle density and size, and finally, elimination through ventilation. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical.

abstract:
  Although biosecurity practices play a role in minimizing respiratory disease in cattle, they must be used in combination with other management strategies that address the many other risk factors. Because the pathogens involved in bovine respiratory disease are enzootic in the general cattle population, biosecurity practices aimed at the complete elimination of exposure are currently impractical. Several animal husbandry and production management practices can be used to minimize pathogen shedding, exposure, and transmission within a given population, however. Various combinations of these control measures can be applied to individual farms to help decrease the morbidity and mortality attributed to respiratory disease.


id: cord-260420-4s7akmdp
title: Bioaerosols and Transmission, a Diverse and Growing Community of Practice
author: Mubareka, Samira
date: 2019-02-21
txt: ./txt/cord-260420-4s7akmdp.txt
cache: ./cache/cord-260420-4s7akmdp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30847337/
doi: 10.3389/fpubh.2019.00023
summary:
  There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate interand intra-species pathogen transmission via bioaerosols. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter-and intra-species pathogen transmission via bioaerosols. A network approach has proven successful in other cross-disciplinary fields, including One Health and eco-health whereby wildlife, computational and evolutionary biologists, microbiologists, virologists, epidemiologists, ecologists, environmental scientists, climatologists, and human, animal, and public health practitioners are collaborating to address challenges in zoonotic diseases research and control (17, 18) .

abstract:
  The transmission of infectious microbes via bioaerosols is of significant concern for both human and animal health. However, gaps in our understanding of respiratory pathogen transmission and methodological heterogeneity persist. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. Collaborative initiatives support advances in topics such as bioaerosol behavior, dispersion models, risk assessment, risk/exposure effects, and mitigation strategies in clinical, experimental, agricultural, and other field settings. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter- and intra-species pathogen transmission via bioaerosols.


id: cord-260679-tm1s6wvj
title: Pneumonia—Overview
author: Lim, Wei Shen
date: 2020-05-20
txt: ./txt/cord-260679-tm1s6wvj.txt
cache: ./cache/cord-260679-tm1s6wvj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780128012383116368
doi: 10.1016/b978-0-12-801238-3.11636-8
summary:
  Within the grouping of hospital-acquired pneumonia (HAP), further distinction is usually made according to whether the patient was on an intensive care unit, or intubated (ventilator-acquired pneumonia (VAP)) at the time of infection (Torres et al., 2017; Kalil et al., 2016) . A definitive diagnosis of pneumonia comprises four aspects: (i) symptoms and signs of a respiratory tract infection, (ii) radiological changes, (iii) identification of a putative pathogen and (iv) a treatment response, or clinical course, consistent with pneumonia. A meta-analysis of individual participant data from 26 RCTs found that PCT-directed treatment in the management of acute respiratory tract infections (of varying types and severity, including CAP and HAP) was associated with a reduction in antibiotic exposure (5.0 vs. The respiratory pathogens commonly implicated in patients with CAP remain important aetiological agents in all other types of pneumonia, including HAP and pneumonia in the immunocompromised host (Table 8 ).

abstract:
  Pneumonia is very common and continues to exact a high burden on health. The Global Burden of Disease Study 2015 found lower respiratory infections (LRIs) were the leading infectious cause of death and the fifth leading cause of death overall. Pneumococcal pneumonia caused 55% of LRI deaths in all ages (1.5 million deaths). Novel pathogens, particularly viruses, continue to emerge as causes of pneumonia. The rise of drug-resistance among common respiratory pathogens is a further challenge. Pneumonia is commonly classified according to patient location at the time of infection, leading to the categories of community-acquired, hospital-acquired and ventilator-acquired pneumonia.


id: cord-263484-afcgqjwq
title: Precision epidemiology for infectious disease control
author: Ladner, Jason T.
date: 2019-02-06
txt: ./txt/cord-263484-afcgqjwq.txt
cache: ./cache/cord-263484-afcgqjwq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30728537/
doi: 10.1038/s41591-019-0345-2
summary:
  With sufficient sampling, relevant metadata (such as location and date) and an appropriate statistical framework, pathogen genomes can reveal patterns of epidemic transmission at a fine-scale resolution, thus enabling the design of targeted interventions that are more precise than those based on traditional epidemiological data alone. Through near-real-time genome sequencing and public data deposition of clinical, environmental, and foodrelated bacterial isolates, this network is streamlining the process of recognizing, investigating, and reducing the impact of foodborne disease outbreaks 42, 43 . This includes changes to research practice regarding the benefits for rapid and open sharing of data and results as well as a focus on building capacity for sequencing and analysis within public health agencies and the regions most severely impacted by infectious disease 57, 58 . One important approach to accelerating responses in the future is to build genome sequencing and analysis capabilities within public health agencies and hospitals as well as in developing countries disproportionately impacted by infectious disease outbreaks.

abstract:
  Advances in genomics and computing are transforming the capacity for the characterization of biological systems, and researchers are now poised for a precision-focused transformation in the way they prepare for, and respond to, infectious diseases. This includes the use of genome-based approaches to inform molecular diagnosis and individual-level treatment regimens. In addition, advances in the speed and granularity of pathogen genome generation have improved the capability to track and understand pathogen transmission, leading to potential improvements in the design and implementation of population-level public health interventions. In this Perspective, we outline several trends that are driving the development of precision epidemiology of infectious disease and their implications for scientists’ ability to respond to outbreaks.


id: cord-269124-oreg7rnj
title: Ancient pathogen genomics as an emerging tool for infectious disease research
author: Spyrou, Maria A.
date: 2019-04-05
txt: ./txt/cord-269124-oreg7rnj.txt
cache: ./cache/cord-269124-oreg7rnj.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41576-019-0119-1
doi: 10.1038/s41576-019-0119-1
summary:
  Examples of tools that have shown their effectiveness with ancient metagenomic DNA include the widely used Basic Local Alignment Search Tool (BLAST) 68 ; the MEGAN Alignment Tool (MALT) 41 , which involves a taxonomic binning algorithm that can use whole genome databases (such as the National Center for Biotechnical Information (NCBI) Reference Sequence (RefSeq) database 69 ); Metagenomic Phylogenetic Analysis (MetaPhlAn) 70 , which is also integrated into the metagenomic pipeline MetaBIT 71 and uses thousands (or millions) of marker genes for the distinction of specific microbial clades; or Kraken 72 , an alignment free sequence classifier that is based on k-mer matching of a query to a constructed database. Similar limitations can arise when the evolutionary history of a microorganism is vastly affected by recombination, as observed for HBV 44, 53 , although HBV molecular dating was recently attempted using a different genomic data set and suggested that the currently explored diversity of Old and New World pri mate lineages (including all human genotypes) may have emerged within the last 20,000 years 43 .

abstract:
  Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.


id: cord-269607-xh1hu3k4
title: Effective control of waterborne pathogens by aquatic plants
author: Dhir, Bhupinder
date: 2020-02-14
txt: ./txt/cord-269607-xh1hu3k4.txt
cache: ./cache/cord-269607-xh1hu3k4.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780128187838000177
doi: 10.1016/b978-0-12-818783-8.00017-7
summary:
  Both dispersed growth and attached growth biological wastewater treatment systems assist in removal of pathogens but require high hydraulic retention time (HRT) (average time water molecules stay in the system) and continuous feeding of organic matter and nutrients. Biofilms present in the plant roots are believed to supply a more effective substrate for removal of bacteria through various methods such as mechanical filtration, sedimentation, adsorption, die-off, predation, and antibiotic excretion (Soto et al., 1999; Karathanasis et al., 2003) Removal (83%e94%) of pathogen especially coliform and enteric bacteria by surface flow constructed wetlands has been reported earlier (Perkins and Hunter, 2000) . Predation is another mechanism that plays an important role in the removal of bacteria, protozoan (oocysts), and fecal coliforms from wastewater in constructed wetlands (Mandi et al., 1993; Green et al., 1997) . High removal efficiency 2 to 4 log 10 (99% to 100%) of pathogens particularly bacteria, viruses, protozoa (cysts), and helminths (eggs) from wastewater has been noted in vegetated constructed wetlands.

abstract:
  The role of aquatic plants in treating wastewater contaminated with inorganic and organic pollutants is well established. Recent studies have shown that aquatic plants possess potential to remove pathogens from wastewater. High removal (90%) of pathogenic microbes such as Enterococci, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Clostridium perfringens, Staphylococcus aureus, and Salmonella have been achieved using aquatic plant species viz. Typha latifolia, Cyperus papyrus, Cyperus alternifolius, Phragmites mauritianus, Pistia stratiotes, Lemna paucicostata, Spirodela polyrhiza, Eichhornia crassipes. Pathogen removal by aquatic plants mainly occurs because of toxicity exerted by exudates produced by them or attachment of pathogens to plant roots followed by filtration. Constructed wetlands have proved very efficient in treating pathogen-contaminated water. More studies are required to find out the exact mechanism of pathogen removal by these plants so that their role in phytoremediation technologies can be emphasized.


id: cord-276966-wmelyonk
title: A proposed treatment for pathogenic enveloped viruses having high rates of mutation or replication
author: Roe, Kevin
date: 2020-07-08
txt: ./txt/cord-276966-wmelyonk.txt
cache: ./cache/cord-276966-wmelyonk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32640050/
doi: 10.1111/sji.12928
summary:
  In targeting specific viral pathogens, dual-protein ligand masks (for brevity, henceforth called dualprotein ligands) should be able to create a quick and powerful immune memory response with existing memory immune cells against some viral pathogens or virus infected cells, without some of the practical limitations of vaccines. Dual-protein ligands could induce an immune response by mimicking the key parts of antigens that activate existing immune memory cells or innate immune cells to attack tagged viral pathogens. All rights reserved One treatment option injects dual-protein ligands into the blood stream or localized regions to mask pathogenic surface proteins used by viruses to infect mammalian cells. Targeted dual-protein ligands could mask viral surface proteins to quickly treat some untreatable virus infections by using already existing immune cells.

abstract:
  Several enveloped viruses, particularly some RNA viruses, have high rates of mutation or replication, which can make them virulent pathogens in humans and other mammals. A proposed treatment could use synthesized proteins to mask pathogenic viral surface proteins to quickly induce an immune attack on specific enveloped viruses by using existing immune cells. One treatment could inject dual‐protein ligand masks into patients' blood streams to mask pathogenic surface proteins used to infect mammalian cells. The mammalian immune system already uses an analogous, more complex structure called a pentraxin to neutralize some pathogens by connecting their surface proteins to immune cells. And several types of antiviral peptides have already experimentally demonstrated effectiveness in blocking various viral pathogen infections. These treatments offer advantages, especially for currently untreatable viral pathogens. Furthermore, using dual‐protein ligands and the antigenic memory of some subpopulations of NK cells would also allow the creation of defacto vaccines based on a host's NK cells, instead of vaccines utilizing CD4 and CD8 α:β T cells, which are limited by the requirement of MHC presentation of the target antigens to α:β T cells. Targeted NK cell vaccines could attack host cells latently or actively infected by intracellular pathogens, even host cells having pathogen downregulated MHC antigen presentation. Eight postulates concerning the effects of pathogen mutation, or change in phenotype from genetic recombination or rearrangement, and replication rates on pathogen versus host dominance are also listed, which should be applicable to viral and non‐viral pathogens.


id: cord-279376-0x4zrfw3
title: Pathogen seasonality and links with weather in England and Wales: a big data time series analysis
author: Cherrie, Mark P. C.
date: 2018-08-28
txt: ./txt/cord-279376-0x4zrfw3.txt
cache: ./cache/cord-279376-0x4zrfw3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12889-018-5931-6
doi: 10.1186/s12889-018-5931-6
summary:
  We aimed to systematically document the seasonality of several human infectious disease pathogens in England and Wales, highlighting those organisms that appear weather-sensitive and therefore may be influenced by climate change in the future. A systematic approach to the analysis of the potential seasonality of common pathogen serotypes and their associations with multiple weather variables is required to help narrow the focus on candidate pathogens in addition to those that have been studied in depth previously. The aim of the analysis was to use several data mining techniques to identify pathogens that display a seasonal component, and describe their associations with meteorological factors as an aid to future analytical work (including forecasting) and public health planning. In this large database of infectious diseases in England and Wales, we have provided an analysis of the seasonality of common pathogens and their correlation with meteorological data.

abstract:
  BACKGROUND: Many infectious diseases of public health importance display annual seasonal patterns in their incidence. We aimed to systematically document the seasonality of several human infectious disease pathogens in England and Wales, highlighting those organisms that appear weather-sensitive and therefore may be influenced by climate change in the future. METHODS: Data on infections in England and Wales from 1989 to 2014 were extracted from the Public Health England (PHE) SGSS surveillance database. We conducted a weekly, monthly and quarterly time series analysis of 277 pathogen serotypes. Each organism’s time series was forecasted using the TBATS package in R, with seasonality detected using model fit statistics. Meteorological data hosted on the MEDMI Platform were extracted at a monthly resolution for 2001–2011. The organisms were then clustered by K-means into two groups based on cross correlation coefficients with the weather variables. RESULTS: Examination of 12.9 million infection episodes found seasonal components in 91/277 (33%) organism serotypes. Salmonella showed seasonal and non-seasonal serotypes. These results were visualised in an online Rshiny application. Seasonal organisms were then clustered into two groups based on their correlations with weather. Group 1 had positive correlations with temperature (max, mean and min), sunshine and vapour pressure and inverse correlations with mean wind speed, relative humidity, ground frost and air frost. Group 2 had the opposite but also slight positive correlations with rainfall (mm, > 1 mm, > 10 mm). CONCLUSIONS: The detection of seasonality in pathogen time series data and the identification of relevant weather predictors can improve forecasting and public health planning. Big data analytics and online visualisation allow the relationship between pathogen incidence and weather patterns to be clarified. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12889-018-5931-6) contains supplementary material, which is available to authorized users.


id: cord-280107-tulne0v3
author: Rabaa, Maia A.
date: 2015-09-24
txt: ./txt/cord-280107-tulne0v3.txt
cache: ./cache/cord-280107-tulne0v3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s10393-015-1061-0
doi: 10.1007/s10393-015-1061-0
summary:
  This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence. Here, we describe a project that is currently underway in communities across Vietnam in which we are collecting clinical samples and associated clinical, epidemiological, and demographic data, which will be combined with high-throughput viral genome sequences and qualitative social sciences data to address key onehealth questions with the aim of better understanding the origins, risks, and emergence of zoonotic infections. To estimate the burden of disease (focusing on viral and zoonotic diseases), and investigate the disease epidemiology in patients hospitalized with specified clinical syndromes and infections in a cohort of high-risk individuals occupationally exposed to animals; with targeted sampling from domestic animals and wildlife in association with these individuals 3. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance the understanding of viral cross-species transmission events, and allow us to identify the relevant risk factors and drivers of zoonotic disease emergence.

title:
  The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases

abstract:
  The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.


id: cord-282610-zim7nond
author: Proal, Amy
date: 2018-12-04
txt: ./txt/cord-282610-zim7nond.txt
cache: ./cache/cord-282610-zim7nond.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3389/fped.2018.00373
doi: 10.3389/fped.2018.00373
summary:
  title: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. The gut microbiome can initiate and promote colorectal cancer at all stages of tumorigenesis by acting as an inducer of DNA damage, generating epigenetic changes, regulating cell growth, and modulating host immune responses (80) . If ME/CFS is driven by successive infection, treatments that support or activate the human immune system could improve microbiome health by allowing patients to better target persistent pathogens. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to many of these persistent microbiome pathogens. In ME/CFS, the immune response, metabolism, central nervous system, and human gene expression are all linked by the activity of the microbiome and its associated proteins/metabolites.

title:
  Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity

abstract:
  The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.


id: cord-282628-6uoberfu
title: Future impacts and trends in treatment of hospital wastewater
author: Tiwari, Bhagyashree
date: 2020-05-01
txt: ./txt/cord-282628-6uoberfu.txt
cache: ./cache/cord-282628-6uoberfu.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B9780128197226000171
doi: 10.1016/b978-0-12-819722-6.00017-1
summary:
  The causative agent of most emerging infectious diseases is viruses; every year approximately more than two novel viral pathogens are identified, which can cause illness in a human. Factors for emergence include natural process (evolution of pathogen), infectious agents transfer from vertebrate to mammals, antimicrobial resistance (AMR), and climate change. The factors responsible for the emergence of infectious diseases such as (1) the evolution of new strain, (2) the introduction of a host to enzootic, (3) translocation of infected wildlife, (4) farming practices, and (5) others were provided. Due to emergence of antibiotic-resistant pathogens and unavoidable use of antibiotics, concomitant environmental perturbation caused by climate change might make the earth is not suitable for humans and other livings. Increasing resistance to antibiotics and the emergence of "superbugs" that are resistant to drugs of last resort have highlighted the great need for alternative treatments of bacterial disease. Furthermore, development of drug-resistant organisms and increased pathogen survival rate, only raising panic about the human, animal, and environmental health.

abstract:
  The world’s population growth and economic development result in the increased requirement of land, water, and energy. This increased demand leads to the deforestation, loss in biodiversity, imbalance in agriculture and food supply, climate change, and increase in food and travel trade, which result in emergence and reemergence of infectious diseases. This chapter discussed various emerging infectious diseases and their causative agents (Buruli ulcer and Bunyvirus). Furthermore, this chapter further illustrates the emergence of superbugs and the associated threat due to the presence of pharmaceutical compounds in the environment. The prevalence of pharmaceuticals in the environment exerts ecotoxic effects on living organisms and causes thousands of death every year. The threats associated with the pharmaceutical presence in the environment were briefly discussed in this chapter. Finally, this chapter provides the alternative methods to avoid the use of antibiotics and to develop novel treatment technologies (such as Phage therapy) to degrade and remove the pharmaceutical compounds.


id: cord-285778-80baxwgc
title: Introduction to the Immune Response
author: nan
date: 2014-10-10
txt: ./txt/cord-285778-80baxwgc.txt
cache: ./cache/cord-285778-80baxwgc.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/B9780123852458000017
doi: 10.1016/b978-0-12-385245-8.00001-7
summary:
  Some innate mechanisms require no induction and are completely non-specific, whereas others are inducible and involve broad receptor-mediated recognition of a limited number of pathogen-associated or damage-associated molecular patterns (PAMPs/DAMPs). When invaders breach anatomical and physiological barriers, innate leukocytes start to take action as a result of pattern recognition mediated by the binding of PRMs to PAMPs furnished by pathogens and to DAMPs emanating from damaged host cells. If the pathogen manages to enter the underlying cell layer, mechanisms mediated by complement and innate leukocytes are induced due to relatively broad recognition of PAMPs. If a more targeted, pathogen-specific response becomes necessary, elements of innate immunity then facilitate induction of highly specific adaptive responses initiated by engagement of the antigen receptors of B, Th or Tc lymphocytes. Innate leukocytes activated by the binding of PRRs to PAMPs provided by the attacking pathogen, or to DAMPs present due to host cell injury or death, work quickly to eliminate the invader using the mechanisms of inflammation, phagocytosis and target cell lysis.

abstract:
  In this chapter we provide an overview of the immune system and its vital role maintaining human health. Immune responses require the coordinated action of leukocytes that travel the body to eliminate threats posed by trauma, infection, toxins, and cancer. Leukocytes communicate via direct contact and via production and receipt of soluble proteins and intercellular messenger proteins called cytokines. Complete clearance of unwanted entities may involve both innate and adaptive leukocyte responses, which influence each other. Some innate mechanisms require no induction and are completely non-specific, whereas others are inducible and involve broad receptor-mediated recognition of a limited number of pathogen-associated or damage-associated molecular patterns (PAMPs/DAMPs). Adaptive responses involve the selective activation of lymphocytes via engagement of their antigen receptors by a specific foreign antigen. The three major subsets of lymphocytes are T helper cells (Th), cytotoxic T cells (Tc) and B cells, which use distinct mechanisms to recognize antigen and carry out different effector functions. Immune system malfunction can contribute to many clinical illnesses including autoimmune disorders, allergies, immunodeficiencies, chronic inflammation and cancer.


id: cord-288170-i01pdngb
title: Chapter 9 Pathogenic agents
author: Böhm, R.
date: 2007-12-31
txt: ./txt/cord-288170-i01pdngb.txt
cache: ./cache/cord-288170-i01pdngb.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1478748207800121
doi: 10.1016/s1478-7482(07)80012-1
summary:
  Nevertheless, inadequate technical design and improper management of the composting process may result in survival and transmission of the pathogens involved; therefore, only treatment in a validated process under steady supervision will lead to a hygienically safe product. The capability of a process to inactivate pathogens causing risks that depend on the raw material cannot be judged simply by analysis of presence or absence of indicators (bacterial, viral, fungal, or parasitic) in the final product. If either the thermophilic process itself or if an additional thermal treatment shall provide the inactivation of pathogens belonging to the indicated level of thermoand chemo-resistance, representative test-organisms must be exposed in a similar matrix as that being treated in a suitable test-body in a defined validation experiment. It could be demonstrated that if dealing with a moderate epidemiological risk, e.g., given in composting source-separated biowastes, Salmonella senftenberg W775 will cover the most relevant viral pathogens causing notifiable diseases in farm animals and which may be present in low concentrations in the raw material.

abstract:
  Publisher Summary This chapter describes the pathogens of humans, animals, and plants that may be present in organic wastes. The recycling of biological wastes by aerobic or anaerobic biotechnological treatment is necessary to protect the environment and to save natural resources. The recycling process may be conducted either in large-scale plants operated mostly in urban industrial areas, or in small plants operated primarily in the rural environment to improve the farmer's income. A relatively large number of pathogens are found in solid and liquid organic wastes and the most prevalent are bacteria, viruses, fungi, and parasites. Fungi present in wastes and materials used for composting are mainly of interest from the point of view of occupational health and phytohygiene. The presence of parasites or their infective stages in wastes or residues of plant, animal, or human origin depends on the nature of the wastes and the level of pretreatment. Parasites are of veterinary and medical importance if the raw materials used for composting are generated in wastewater treatment facilities or in slaughterhouses. Plant pathogenic parasites must also be considered, even if some of them are highly specialized on certain plants, which limit their epidemiological importance. Cyst-forming nematodes are the most relevant because these cysts may survive in the soil for several years.


id: cord-289443-46w52de3
title: Evolutionary insights into host–pathogen interactions from mammalian sequence data
author: Sironi, Manuela
date: 2015-03-18
txt: ./txt/cord-289443-46w52de3.txt
cache: ./cache/cord-289443-46w52de3.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/nrg3905
doi: 10.1038/nrg3905
summary:
  Nevertheless, natural selection signatures have been described at several mammalian genes that interact with recently emerged human infectious agents (for example, HIV-1), possibly as a result of the pressure imposed by extinct pathogens or because these agents have established long-lasting interactions with non-human hosts. Thus, as observed for ACE2, MERS-CoV and related viruses (for example, coronavirus HKU4) are likely to act as drivers of molecular evolution on mammalian DPP4 genes; it will be especially interesting to evaluate the contribution of positively selected sites in ferrets because these animals are resistant to MERS-CoV infection. In the host-pathogen arms race, these molecules represent one of the foremost detection-defence systems; consistently, several studies have reported adaptive evolution at genes encoding mammalian PRRs. Analyses in primates, rodents and representative mammalian species indicate that positive selection shaped nucleotide diversity at most TLRs, with the strongest pressure acting on TLR4 (REFS 35, 48, 49) .

abstract:
  Infections are one of the major selective pressures acting on humans, and host-pathogen interactions contribute to shaping the genetic diversity of both organisms. Evolutionary genomic studies take advantage of experiments that natural selection has been performing over millennia. In particular, inter-species comparative genomic analyses can highlight the genetic determinants of infection susceptibility or severity. Recent examples show how evolution-guided approaches can provide new insights into host–pathogen interactions, ultimately clarifying the basis of host range and explaining the emergence of different diseases. We describe the latest developments in comparative immunology and evolutionary genetics, showing their relevance for understanding the molecular determinants of infection susceptibility in mammals. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrg3905) contains supplementary material, which is available to authorized users.


id: cord-292031-weiwksh6
title: Waterborne Pathogens: Detection Methods and Challenges
author: Ramírez-Castillo, Flor Yazmín
date: 2015-05-21
txt: ./txt/cord-292031-weiwksh6.txt
cache: ./cache/cord-292031-weiwksh6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26011827/
doi: 10.3390/pathogens4020307
summary:
  Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. Molecular techniques, such as nucleic acid amplification procedures, offer sensitive and analytical tools for detecting a variety of pathogens, including new emerging strains, present the possibility of automation, and real-time analysis to provide information for microbial risk assessment purposes [33] . Limitations of DNA based methods such as PCR include the inability to discriminate between viable from non-viable cells that both contain DNA, the low concentration of several pathogens in water such as Cryptosporidium, Giardia and viruses, and the lack of data to indicate the real infectious risk to a population. Oligonucleotide microarrays are a powerful genomic technology that is widely utilized to monitor gene expression under different cell growth conditions, detecting specific mutations in DNA sequences and characterizing microorganisms in environmental samples [76] .

abstract:
  Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.


id: cord-294585-dl5v9p50
title: Pathogen‐reduction methods: advantages and limits
author: Klein, H. G.
date: 2009-02-13
txt: ./txt/cord-294585-dl5v9p50.txt
cache: ./cache/cord-294585-dl5v9p50.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32328162/
doi: 10.1111/j.1751-2824.2009.01224.x
summary:
  However, because blood contains numerous labile proteins and fragile cells, and because there is a wide array of potentially infectious agents, no single method of pathogen-inactivation will likely preserve all blood components, yet effectively remove all viruses, bacteria, spores, protozoa and prions. Riboflavin/ultraviolet light treatment has been evaluated in preclinical studies and found to result in reduction of infectivity by many pathogens including west Nile virus, intracellular HIV, bacteria and protozoa. Therapeutic efficacy and safety of platelets treated with a photochemical process for pathogen inactivation: the SPRINT Trial Clinical safety of platelets photochemically treated with amotosalen HCl and ultraviolet A light for pathogen inactivation: the SPRINT trial Fresh frozen plasma prepared with amotosalen HCl (S-59) photochemical pathogen inactivation: transfusion of patients with congenital coagulation factor deficiencies Therapeutic efficacy and safety of red blood cells treated with a chemical process (S-303) for pathogen inactivation: a Phase III clinical trial in cardiac surgery patients

abstract:
  Pathogen‐reduction (inactivation) provides a proactive approach to reducing transfusion‐transmitted infection. Pathogen‐reduction technologies have been successfully implemented by plasma fractionators resulting in no transmission of human immunodeficiency, hepatitis C, or hepatitis B viruses by US‐licensed plasma derivatives since 1987. Fractionation technologies cannot be used to treat cellular blood components. Although blood donor screening, deferral and disease testing have drastically reduced the incidence of transfusion‐transmitted diseases, the threat of new or re‐emerging pathogens remains. Of particular concern is the silent emergence of a new agent with a prolonged latent period in which asymptomatic infected carriers would donate and spread infection. The ultimate goal of pathogen‐inactivation is to reduce transmission of potential pathogens without significantly compromising the therapeutic efficacy of the cellular and protein constituents of blood. The acceptable technology must not introduce toxicities into the blood supply nor result in neoantigen formation and subsequent antibody production. Several promising pathogen‐inactivation technologies are being developed and tested, and others are currently in use, but all of them have limits. Pathogen‐reduction promises an additional ‘layer of protection’ from infectious agents and has the potential to impact the safety of blood transfusions worldwide.


id: cord-295469-5an7836u
author: Ijaz, M. Khalid
date: 2016-09-02
txt: ./txt/cord-295469-5an7836u.txt
cache: ./cache/cord-295469-5an7836u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.ajic.2016.06.008
doi: 10.1016/j.ajic.2016.06.008
summary:
  The following groups of human pathogens are covered because of their known or potential airborne spread: vegetative bacteria (staphylococci and legionellae), fungi (Aspergillus, Penicillium, and Cladosporium spp and Stachybotrys chartarum), enteric viruses (noroand rotaviruses), respiratory viruses (influenza and coronaviruses), mycobacteria (tuberculous and nontuberculous), and bacterial spore formers (Clostridium difficile and Bacillus anthracis). The following groups of human pathogens are covered because of their known or potential airborne spread: vegetative bacteria (staphylococci and legionellae), fungi (Aspergillus, Penicillium, and Cladosporium spp and Stachybotrys chartarum), enteric viruses (noro-and rotaviruses), respiratory viruses (influenza and coronaviruses), mycobacteria (tuberculous and nontuberculous), and bacterial spore formers (Clostridium difficile and Bacillus anthracis). 71 Based on our considerable experience in the study of airborne human pathogens, 13, 25, 39, 43, 72 we have built an aerobiology chamber (Fig 2) designed to meet the requirements of the EPA guidelines and have used this to study the effects that a variety of air decontamination technologies have on the airborne survival and inactivation of vegetative bacteria, viruses (bacteriophage), and bacterial spore-formers (Sattar et al, unpublished data) .

title:
  Generic aspects of the airborne spread of human pathogens indoors and emerging air decontamination technologies

abstract:
  Indoor air can be an important vehicle for a variety of human pathogens. This review provides examples of airborne transmission of infectious agents from experimental and field studies and discusses how airborne pathogens can contaminate other parts of the environment to give rise to secondary vehicles leading air-surface-air nexus with possible transmission to susceptible hosts. The following groups of human pathogens are covered because of their known or potential airborne spread: vegetative bacteria (staphylococci and legionellae), fungi (Aspergillus, Penicillium, and Cladosporium spp and Stachybotrys chartarum), enteric viruses (noro- and rotaviruses), respiratory viruses (influenza and coronaviruses), mycobacteria (tuberculous and nontuberculous), and bacterial spore formers (Clostridium difficile and Bacillus anthracis). An overview of methods for experimentally generating and recovering airborne human pathogens is included, along with a discussion of factors that influence microbial survival in indoor air. Available guidelines from the U.S. Environmental Protection Agency and other global regulatory bodies for the study of airborne pathogens are critically reviewed with particular reference to microbial surrogates that are recommended. Recent developments in experimental facilities to contaminate indoor air with microbial aerosols are presented, along with emerging technologies to decontaminate indoor air under field-relevant conditions. Furthermore, the role that air decontamination may play in reducing the contamination of environmental surfaces and its combined impact on interrupting the risk of pathogen spread in both domestic and institutional settings is discussed.


id: cord-297203-f3f31h4r
title: Emerging viruses and current strategies for vaccine intervention
author: Afrough, B.
date: 2019-04-16
txt: ./txt/cord-297203-f3f31h4r.txt
cache: ./cache/cord-297203-f3f31h4r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30993690/
doi: 10.1111/cei.13295
summary:
  While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Modified vaccinia virus Ankara (MVA) is licensed as a third-generation vaccinia type vaccine against smallpox and serves as a potent vector system for the development of new candidate vaccines against a range of infectious diseases, including those caused by emerging pathogens. Additionally, MVA elicits a strong immunological response against a range of other orthopoxviruses (OPXVs) (including Variola), and vaccines based on this platform can be considered as providing added value, as human immunity to OPXVs is low (after the cessation of the smallpox vaccination campaign) opening a gap for OPXV emergence, as evidenced by the recent occurrence of monkeypox virus in West Africa and onward cross boarder transmissions [39, 40] .

abstract:
  During the past decade several notable viruses have suddenly emerged from obscurity or anonymity to become serious global health threats, provoking concern regarding their sustained epidemic transmission in immunologically naive human populations. With each new threat comes the call for rapid vaccine development. Indeed, vaccines are considered a critical component of disease prevention for emerging viral infections because, in many cases, other medical options are limited or non‐existent, or that infections result in such a rapid clinical deterioration that the effectiveness of therapeutics is limited. While classic approaches to vaccine development are still amenable to emerging viruses, the application of molecular techniques in virology has profoundly influenced our understanding of virus biology, and vaccination methods based on replicating, attenuated and non‐replicating virus vector approaches have become useful vaccine platforms. Together with a growing understanding of viral disease emergence, a range of vaccine strategies and international commitment to underpin development, vaccine intervention for new and emerging viruses may become a possibility.


id: cord-297440-uw263cfc
title: Microbial sequencing to improve individual and population health
author: Peacock, Sharon J
date: 2014-11-19
txt: ./txt/cord-297440-uw263cfc.txt
cache: ./cache/cord-297440-uw263cfc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s13073-014-0103-5
doi: 10.1186/s13073-014-0103-5
summary:
  Personalized anti-infective therapies and surveillance of emergent pathogen outbreaks are just two examples of the potential benefits of merging the fields of genomics and infectious diseases. Sequencing will bring improvements in the detection and control of outbreaks associated with multidrugresistant and other pathogens in hospitals and the community [1] . Passive surveillance using sequence data generated for clinical use would provide an overview of the emergence and spread of antimicrobial resistance. Active genomic surveillance of key human pathogens would provide an early warning system for outbreaks, inform vaccine strategies through tracking of vaccine escape, and detect the emergence of new clones that harbor known or novel virulence determinants. New methods to handle and process everexpanding pathogen-specific microbial genome databases will also be needed, including global and region-specific listings of gene mutations associated with drug resistance. Further technological advances are also required to reduce the turnaround time between taking a clinical sample and generating sequence data.

abstract:
  Recent advances in sequencing technologies are changing the face of infectious disease investigation and control. Personalized anti-infective therapies and surveillance of emergent pathogen outbreaks are just two examples of the potential benefits of merging the fields of genomics and infectious diseases.


id: cord-297621-xunyqlr5
title: Pathogen-Inaktivierungssysteme für Thrombozytenkonzentrate: Stellungnahme
author: nan
date: 2018-06-21
txt: ./txt/cord-297621-xunyqlr5.txt
cache: ./cache/cord-297621-xunyqlr5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00103-018-2766-3
doi: 10.1007/s00103-018-2766-3
abstract: nan
summary:
  Die Daten aus den Hämovigilanzberichten 2013/14 und 2015 [7, 8] zeigen, dass in Deutschland sowohl das Risiko einer Übertragung von viralen Erregern als auch das Risiko einer Transfusions-bedingten bakteriellen Infektion durch TK [9] sehr gering ist. Interstrang-Reaktionen sind möglich, so dass ein breites Spektrum von Nukleinsäuren einschließlich der von Viren und anderen Pathogenen inaktiviert werden kann [10] In einem Hämostase-Globaltest (RO-TEM®) war die Gerinnungszeit nach 5 Tagen Lagerung verglichen mit den Kontrollen nur leicht verkürzt [60] . Die Wirkung von THERAFLEX auf Protozoen wurde mit Trypanosoma cruzi, Leishmania infantum, Plasmodium falciparum und Babesia divergens untersucht [135] [136] [137] . Pathogen inactivation of double-dose buffy-coat platelet concentrates photochemically treated with amotosalen and UVA light: preservation of in vitro function Pathogen reduction technology treatment of platelets, plasma and whole blood using riboflavin and UV light Pathogen inactivation of Trypanosoma cruzi in plasma and platelet concentrates using riboflavin and ultraviolet light Pathogen reduction by ultraviolet C light effectively inactivates human white blood cells in platelet products


id: cord-299790-vciposnk
author: Ho, Zheng Jie Marc
date: 2015-06-09
txt: ./txt/cord-299790-vciposnk.txt
cache: ./cache/cord-299790-vciposnk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25827870/
doi: 10.1111/irv.12312
summary:
  Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. For instance, one study showed that 15.3% of ambulatory patients with influenza-like illness had two viruses detected, 6 and another found that in 28.2% of children with community-acquired pneumonia, the illness was due to mixed viral-bacterial infections. 7 Others also previously described respiratory viral 8, 9 and bacterial co-infections 10, 11 in various settings, although most focus on specific pathogen combinations, especially of the synergism between influenza and Streptococcus pneumoniae (S. Mean proportion for dual infections with nasal symptoms lay in between at 0.748, statistically different from both viral (P = 0.002) and bacterial (P < 0.001) mono-pathogen levels.

title:
  Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness

abstract:
  BACKGROUND: Although it is known that febrile respiratory illnesses (FRI) may be caused by multiple respiratory pathogens, there are no population-level studies describing its impact on clinical disease. METHODS: Between May 2009 and October 2012, 7733 FRI patients and controls in the Singapore military had clinical data and nasal wash samples collected prospectively and sent for PCR testing. Patients with one pathogen detected (mono-pathogen) were compared with those with two pathogens (dual pathogen) for differences in basic demographics and clinical presentation. RESULTS: In total, 45.8% had one pathogen detected, 20.2% had two pathogens detected, 30.9% had no pathogens detected, and 3.1% had more than two pathogens. Multiple pathogens were associated with recruits, those with asthma and non-smokers. Influenza A (80.0%), influenza B (73.0%) and mycoplasma (70.6%) were most commonly associated with mono-infections, while adenovirus was most commonly associated with dual infections (62.9%). Influenza A paired with S. pneumoniae had higher proportions of chills and rigors than their respective mono-pathogens (P = 0.03, P = 0.009). H. influenzae paired with either enterovirus or parainfluenzae had higher proportions of cough with phlegm than their respective mono-pathogens. Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. CONCLUSION: A substantial number of FRI patients have multiple pathogens detected. Observed clinical differences between patients of dual pathogen and mono-pathogen indicate the likely presence of complex microbial interactions between the various pathogens.


id: cord-301767-1jv20em8
author: Alegbeleye, Oluwadara Oluwaseun
date: 2018-02-03
txt: ./txt/cord-301767-1jv20em8.txt
cache: ./cache/cord-301767-1jv20em8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29526204/
doi: 10.1016/j.fm.2018.01.003
summary:
  Primarily, pathogens may contaminate produce ''on-field'' via various routes including; atmospheric deposition, uptake from contaminated soils and groundwater (Harris et al., 2003; Lynch et al., 2009; Mei Soon et al., 2012) , use of raw (or poorly treated) manure and compost, exposure to contaminated water (irrigation or flooding), transfer by insects, or by fecal contamination generated by livestock or wild Table 1 The most commonly implicated etiological agents in fresh produce borne illnesses (Brackett, 1994; Buck et al., 2003; Heaton and Jones, 2008; Jung et al., 2014; Callej on et al., 2015) . Epidemiological investigations of food poisoning outbreaks, experimental studies examining pathogen contamination of fruits and vegetables as well as observations of increased incidence of disease in areas practicing wastewater irrigation with little or no wastewater treatment indicate that contaminated irrigation water might indeed be a source of foodborne pathogens on fresh produce (Norman and Kabler, 1953; Hern andez et al., 1997; Steele and Odumeru, 2004) .

title:
  Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review

abstract:
  Foodborne illness resulting from the consumption of contaminated fresh produce is a common phenomenon and has severe effects on human health together with severe economic and social impacts. The implications of foodborne diseases associated with fresh produce have urged research into the numerous ways and mechanisms through which pathogens may gain access to produce, thereby compromising microbiological safety. This review provides a background on the various sources and pathways through which pathogenic bacteria contaminate fresh produce; the survival and proliferation of pathogens on fresh produce while growing and potential methods to reduce microbial contamination before harvest. Some of the established bacterial contamination sources include contaminated manure, irrigation water, soil, livestock/ wildlife, and numerous factors influence the incidence, fate, transport, survival and proliferation of pathogens in the wide variety of sources where they are found. Once pathogenic bacteria have been introduced into the growing environment, they can colonize and persist on fresh produce using a variety of mechanisms. Overall, microbiological hazards are significant; therefore, ways to reduce sources of contamination and a deeper understanding of pathogen survival and growth on fresh produce in the field are required to reduce risk to human health and the associated economic consequences.


id: cord-307803-rlvk6bcx
title: Q&A: What are pathogens, and what have they done to and for us?
author: Balloux, Francois
date: 2017-10-19
txt: ./txt/cord-307803-rlvk6bcx.txt
cache: ./cache/cord-307803-rlvk6bcx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12915-017-0433-z
doi: 10.1186/s12915-017-0433-z
summary:
  Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. Conversely, Yersinia pestis, another intracellular obligate bacterium and the agent of plague, has a natural life cycle involving alternating infections of rodents and fleas, but can infect essentially any mammalian host. Apart from a few putative ancestral pathogens, including Helicobacter pylori [15] , that might have co-speciated with their human host, the infectious diseases afflicting us were acquired through host jumps from other wild or domesticated animal hosts or sometimes from the wider environment. We might also speculate that the evolutionary potential and high genetic diversity of most pathogens limits our ability to detect protective variants in the human genome, particularly so if these were only effective against a subset of lineages within a pathogenic species.

abstract:
  Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many play essential roles in plant, animal and human health. Others, however, are either obligate or facultative pathogens exerting a spectrum of deleterious effects on their hosts. Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. From the dawn of humanity and throughout history, infectious diseases have shaped human evolution, demography, migrations and history.


id: cord-307874-0obomty2
title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis?
author: Pardon, Bart
date: 2020-05-23
txt: ./txt/cord-307874-0obomty2.txt
cache: ./cache/cord-307874-0obomty2.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0749072020300220
doi: 10.1016/j.cvfa.2020.03.005
summary:
  Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity.

abstract:
  When it is desired to identify infectious agents involved in an outbreak of bovine respiratory disease, a variety of possible sampling methods may be used. For field use, the deep nasopharyngeal swab, transtracheal wash, and nonendoscopic bronchoalveolar lavage are most feasible. At present, bacterial culture and polymerase chain reaction testing are most commonly used to identify infectious agents. Interpretation of test results can be challenging, particularly for opportunistic pathogens. Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented.


id: cord-308089-q2w9fb0i
title: Evolution of virulence
author: Ewald, Paul W.
date: 2005-03-01
txt: ./txt/cord-308089-q2w9fb0i.txt
cache: ./cache/cord-308089-q2w9fb0i.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15081500/
doi: 10.1016/s0891-5520(03)00099-0
summary:
  This new germ theory is emphasizing how environments and human activities influence the characteristics of infectious agents and the broader role of infection as a cause of chronic diseases. The association between vector-borne transmission and virulence explains why diseases such as malaria, yellow fever, dengue, sleeping sickness, and visceral leishmaniasis are so severe, whereas most of the respiratory-tract pathogens of humans are relatively benign. Evolutionary management of the virulence of vector-borne diseases requires interventions that elevate the immobilization of hosts more costly to the infecting pathogens. Although sexually transmitted pathogens are molded by natural selection to be benign over the short run, this long-term persistence within hosts raises the possibility of long-term damage, even though there is low probability of severe damage during any small period of time during the first years of infection. The theoretical framework for understanding the evolution of virulence of sexually transmitted pathogens provides clues about which infectious agents are the most likely causes of these illnesses.

abstract:
  At the close of the 19th century, the germ theory had generated a new understanding of the causes of acute infectious diseases and revealed new directions for study. This understanding contributed to the greatest improvements in health in the history of medicine. At the end of the 20th century, the second stage of this disciplinary development is occurring. The old germ theory is being expanded into a new germ theory, which, by integrated the full spectrum of biologic disciplines. This new germ theory is emphasizing how environments and human activities influence the characteristics of infectious agents and the broader role of infection as a cause of chronic diseases.


id: cord-310439-z0bxsjug
title: Pathogen-Tested Planting Material
author: Martin, R. R.
date: 2014-12-31
txt: ./txt/cord-310439-z0bxsjug.txt
cache: ./cache/cord-310439-z0bxsjug.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/B978044452512300173X
doi: 10.1016/b978-0-444-52512-3.00173-x
summary:
  Buffer zone An area surrounding or adjacent to an area for production of plants in a certification scheme designed to minimize the probability of spread of the target pathogens, pollen, or seed into or out of the block, to meet phytosanitary or other control measures as defined in a certification standard. Many certification programs are based on a published standard that defines site selection and preparation, isolation distances from plants of the same species and other vegetation, number of inspections, record keeping on plant traceability so that tracebacks or traceforwards can be done if a problem should arise, a pest and disease management plan, records of all pest management activities, the conditions and protocols to be followed during plant or seed production, and types and amount of testing that needs to be done at each level in the propagation cycle.

abstract:
  Abstract Certification programs have been developed to provide plant material that meets a predetermined level of plant health. The primary objectives of these programs are to limit pathogen incidence in plant material in order to minimize losses by growers and prevent movement of harmful pests and pathogens that may harm the environment. For many fruit and nut crops, orchards are expected to remain productive for years or decades; thus, starting with plants of high health status is essential. The components of certification programs in terms of plant health will be outlined, along with the benefits of harmonizing these programs where possible to facilitate plant movement without increasing trade in plant pathogens.


id: cord-312161-egwo19oc
title: Detection of pathogens in water: from phylochips to qPCR to pyrosequencing
author: Aw, Tiong Gim
date: 2011-12-05
txt: ./txt/cord-312161-egwo19oc.txt
cache: ./cache/cord-312161-egwo19oc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.copbio.2011.11.016
doi: 10.1016/j.copbio.2011.11.016
summary:
  Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ''molecular revolution'' are at present emerging rapidly as tools of pathogen detection and discovery. The limitations in detecting and identifying pathogens directly from environmental water samples by culture or microscopy can now be addressed by integrating concentration techniques with molecular tools to provide sensitive, specific and quantitative data on any pathogens of interest. Pyrosequencing technology is revolutionizing the study of microbial ecology as well as direct metagenomic detection Detection of pathogens in water Aw and Rose 425 High levels of several classes of resistance genes in bacterial communities exposed to antibiotic were identified.

abstract:
  Waterborne pathogens pose a significant threat to human health and a proper assessment of microbial water quality is important for decision making regarding water infrastructure and treatment investments and eventually to provide early warning of disease, particularly given increasing global disasters associated with severe public health risks. Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. Future challenges lie in integrating these molecular tools with concentration techniques and bioinformatics platforms for unbiased guide of pathogen surveillance in water and developing standardized protocols.


id: cord-316999-712rit8h
title: Invasive alien species and disease risk: An open challenge in public and animal health
author: Chinchio, Eleonora
date: 2020-10-22
txt: ./txt/cord-316999-712rit8h.txt
cache: ./cache/cord-316999-712rit8h.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33091094/
doi: 10.1371/journal.ppat.1008922
abstract: nan
summary:
  To this aim, we provide here an overview of how animal IAS may affect local disease dynamics both directly and indirectly, i.e., acting as pathogen hosts or disrupting the recipient ecosystem structure, through real-case examples from the ecological literature, and, in the last paragraph, we propose future initiatives aimed at improving our capacity for targeted actions toward the IAS most likely to threaten human and animal health, calling for an increased involvement of people working in the fields of animal and public health in a new invasion epidemiology field. IAS may host pathogens that are absent in the area of release and cause their establishment and subsequent spillover to local species, possibly resulting in an increase of disease risk for humans, domestic animals, and native wildlife.


id: cord-320295-k2i52wgs
title: Host Range and Emerging and Reemerging Pathogens
author: Woolhouse, Mark E.J.
date: 2005-12-17
txt: ./txt/cord-320295-k2i52wgs.txt
cache: ./cache/cord-320295-k2i52wgs.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16485468/
doi: 10.3201/eid1112.050997
summary:
  However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population. All the defined host types are potential sources of zoonotic infections, but differences occurred in their importance (ranked by number of pathogen species supported) across viruses, bacteria, fungi, protozoa, and helminths and no 1 type consistently dominates ( Figure 1A) , although ungulates are the most important overall, supporting over 250 species of human pathogen. However, when the fraction of emerging and reemerging species is compared with the breadth of host range (as the number of host types other than humans), a pattern becomes apparent (Figure 2) . Relationship between breadth of host range (as number of nonhuman host types, as listed in Figure 1 ) and the fraction of pathogen species regarded as emerging or reemerging.

abstract:
  An updated literature survey identified 1,407 recognized species of human pathogen, 58% of which are zoonotic. Of the total, 177 are regarded as emerging or reemerging. Zoonotic pathogens are twice as likely to be in this category as are nonzoonotic pathogens. Emerging and reemerging pathogens are not strongly associated with particular types of nonhuman hosts, but they are most likely to have the broadest host ranges. Emerging and reemerging zoonoses are associated with a wide range of drivers, but changes in land use and agriculture and demographic and societal changes are most commonly cited. However, although zoonotic pathogens do represent the most likely source of emerging and reemerging infectious disease, only a small minority have proved capable of causing major epidemics in the human population.


id: cord-322120-wtu04r2j
author: Goddard, Frederick G. B.
date: 2020-08-19
txt: ./txt/cord-322120-wtu04r2j.txt
cache: ./cache/cord-322120-wtu04r2j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32813503/
doi: 10.1021/acs.est.0c02421
summary:
  Systematic reviews of water, sanitation, and hygiene (WaSH) evaluations, conducted to identify the health effects of interventions designed to reduce enteric pathogen exposure, have generally found improved WaSH to be protective against diarrhea, 24 soil-transmitted helminthiasis, 25 and malnutrition. A systematic review of the effects of sanitation interventions on fecal−oral transmission pathways identified the following approaches used: enteric pathogens or indicator bacteria in environmental samples (drinking water, hands, sentinel toys, food, household and latrine surfaces, and soil); the presence or abundance of flies; and observations of human and animal feces. 68 There are a number of factors to consider when measuring enteric pathogen prevalence in the environment, including environmental sampling strategies, the use of indicators as proxies for enteric pathogens, differentiating between human and animal sources of contamination, detection limits, and selecting which specific pathogens to target.

title:
  Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group

abstract:
  [Image: see text] Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.


id: cord-325052-7vlxa0i7
title: Vaccines for emerging pathogens: prospects for licensure
author: Williamson, E. D.
date: 2019-04-11
txt: ./txt/cord-325052-7vlxa0i7.txt
cache: ./cache/cord-325052-7vlxa0i7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/cei.13284
doi: 10.1111/cei.13284
summary:
  However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. While approval of vaccines for diseases caused by such pathogens would Clinical and Experimental Immunology REvIEw ARtIClE Series Editor: E Diane williamson make a significant impact on disease outbreaks, taking niche vaccines into clinical development, including Phase III clinical trials for efficacy, requires a large investment in time and money. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or an alternative status in the United States, Canada and European Union (EU) making use of a considerable number of alternative regulatory mechanisms that are available prior to licensing, so that the products are deployable at the first indications of a disease outbreak.

abstract:
  Globally, there are a number of emerging pathogens. For most, there are no licensed vaccines available for human use, although there is ongoing research and development. However, given the extensive and increasing list of emerging pathogens and the investment required to bring vaccines into clinical use, the task is huge. Overlaid on this task is the risk of anti‐microbial resistance (AMR) acquisition by micro‐organisms which can endow a relatively harmless organism with pathogenic potential. Furthermore, climate change also introduces a challenge by causing some of the insect vectors and environmental conditions prevalent in tropical regions to begin to spread out from these traditional areas, thus increasing the risk of migration of zoonotic disease. Vaccination provides a defence against these emerging pathogens. However, vaccines for pathogens which cause severe, but occasional, disease outbreaks in endemic pockets have suffered from a lack of commercial incentive for development to a clinical standard, encompassing Phase III clinical trials for efficacy. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or equivalent status in the United States, Canada and the European Union, making use of a considerable number of regulatory mechanisms that are available prior to licensing. This review covers the status of vaccine development for some of the emerging pathogens, the hurdles that need to be overcome to achieve EUA or an equivalent regional or national status and how these considerations may impact vaccine development for the future, such that a more comprehensive stockpile of promising vaccines can be achieved.


id: cord-329149-1giy1fow
title: Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions
author: Martinez-Martin, Nadia
date: 2017-02-22
txt: ./txt/cord-329149-1giy1fow.txt
cache: ./cache/cord-329149-1giy1fow.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28321417/
doi: 10.1155/2017/2197615
summary:
  Despite SPR and related methods offering higher sensitivity for detection of transient Biochemical and MS PDGFR identified as a high affinity cell surface receptor for the CMV gHgLgO protein complex [21] Herpes simplex viruses (HSVs) Biophysical Secreted and plasma membrane-expressed glycoprotein G targets a specific set of human chemokines with high affinity [22] Human immunodeficiency virus type 1 (HIV) Despite the undoubted importance of the biochemical and biophysical approaches to the study of host-pathogen interactions, the aforementioned limitations have motivated the development of alternative technologies for large-scale analysis of ePPIs. From the initial utilization of microarrays for detection of PPI over a decade ago, human proteome chips containing thousands of recombinant proteins have been generated, some of which are now commercially available.

abstract:
  Pathogens have evolved unique mechanisms to breach the cell surface barrier and manipulate the host immune response to establish a productive infection. Proteins exposed to the extracellular environment, both cell surface-expressed receptors and secreted proteins, are essential targets for initial invasion and play key roles in pathogen recognition and subsequent immunoregulatory processes. The identification of the host and pathogen extracellular molecules and their interaction networks is fundamental to understanding tissue tropism and pathogenesis and to inform the development of therapeutic strategies. Nevertheless, the characterization of the proteins that function in the host-pathogen interface has been challenging, largely due to the technical challenges associated with detection of extracellular protein interactions. This review discusses available technologies for the high throughput study of extracellular protein interactions between pathogens and their hosts, with a focus on mammalian viruses and bacteria. Emerging work illustrates a rich landscape for extracellular host-pathogen interaction and points towards the evolution of multifunctional pathogen-encoded proteins. Further development and application of technologies for genome-wide identification of extracellular protein interactions will be important in deciphering functional host-pathogen interaction networks, laying the foundation for development of novel therapeutics.


id: cord-330463-j4cf7vzs
title: Indoor air as a vehicle for human pathogens: Introduction, objectives, and expectation of outcome
author: Sattar, Syed A.
date: 2016-09-02
txt: ./txt/cord-330463-j4cf7vzs.txt
cache: ./cache/cord-330463-j4cf7vzs.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0196655316305387
doi: 10.1016/j.ajic.2016.06.010
summary:
  In this international workshop, a panel of 6 experts will expound on the following: (1) the potential for indoor air to spread a wide range of human pathogens, plus engineering controls to reduce the risk for exposure to airborne infectious agents; (2) the behavior of aerosolized infectious agents indoors and the use of emerging air decontamination technologies; (3) a survey of quantitative methods to recover infectious agents and their surrogates from indoor air with regard to survival and inactivation of airborne pathogens; (4) mathematical models to predict the movement of pathogens indoors and the use of such information to optimize the benefits of air decontamination technologies; and (5) synergy between different infectious agents, such as legionellae and fungi, in the built environment predisposing to possible transmission-related health impacts of aerosolized biofilm-based opportunistic pathogens.

abstract:
  Airborne spread of pathogens can be rapid, widespread, and difficult to prevent. In this international workshop, a panel of 6 experts will expound on the following: (1) the potential for indoor air to spread a wide range of human pathogens, plus engineering controls to reduce the risk for exposure to airborne infectious agents; (2) the behavior of aerosolized infectious agents indoors and the use of emerging air decontamination technologies; (3) a survey of quantitative methods to recover infectious agents and their surrogates from indoor air with regard to survival and inactivation of airborne pathogens; (4) mathematical models to predict the movement of pathogens indoors and the use of such information to optimize the benefits of air decontamination technologies; and (5) synergy between different infectious agents, such as legionellae and fungi, in the built environment predisposing to possible transmission-related health impacts of aerosolized biofilm-based opportunistic pathogens. After the presentations, the panel will address a set of preformulated questions on selection criteria for surrogate microbes to study the survival and inactivation of airborne human pathogens, desirable features of technologies for microbial decontamination of indoor air, knowledge gaps, and research needs. It is anticipated that the deliberations of the workshop will provide the attendees with an update on the significance of indoor air as a vehicle for transmitting human pathogens with a brief on what is currently being done to mitigate the risks from airborne infectious agents.


id: cord-337219-d81v8b4j
author: Cheong, Chang Heon
date: 2018-03-13
txt: ./txt/cord-337219-d81v8b4j.txt
cache: ./cache/cord-337219-d81v8b4j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29534043/
doi: 10.3390/ijerph15030510
summary:
  Simulation cases for analysis were established, as shown in Table 3 , to conduct a case study that analyzed the range of airborne pathogen dispersion according to the location of diffusers in the bed area of the ED, the ventilation rate, and the installation of partitions between beds. Simulation cases for analysis were established, as shown in Table 3 , to conduct a case study that analyzed the range of airborne pathogen dispersion according to the location of diffusers in the bed area of the ED, the ventilation rate, and the installation of partitions between beds. Simulation cases for analysis were established, as shown in Table 3 , to conduct a case study that analyzed the range of airborne pathogen dispersion according to the location of diffusers in the bed area of the ED, the ventilation rate, and the installation of partitions between beds.

title:
  Case Study of Airborne Pathogen Dispersion Patterns in Emergency Departments with Different Ventilation and Partition Conditions

abstract:
  The prevention of airborne infections in emergency departments is a very important issue. This study investigated the effects of architectural features on airborne pathogen dispersion in emergency departments by using a CFD (computational fluid dynamics) simulation tool. The study included three architectural features as the major variables: increased ventilation rate, inlet and outlet diffuser positions, and partitions between beds. The most effective method for preventing pathogen dispersion and reducing the pathogen concentration was found to be increasing the ventilation rate. Installing partitions between the beds and changing the ventilation system’s inlet and outlet diffuser positions contributed only minimally to reducing the concentration of airborne pathogens.


id: cord-339886-th1da1bb
title: Towards a genomics-informed, real-time, global pathogen surveillance system
author: Gardy, Jennifer L.
date: 2017-11-13
txt: ./txt/cord-339886-th1da1bb.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29129921/
doi: 10.1038/nrg.2017.88
summary:
  Given that outbreaks of emerging infectious diseases (EIDs) most often occur in settings with minimal laboratory capacity, where routine culture and bench-top sequencing are simply not feasible, the need for a portable diagnostic platform capable of in situ clinical metagenomics and outbreak surveillance is evident. Portable genome sequencing technology and digital epidemiology platforms form the foundation for both real-time pathogen and disease surveillance systems and outbreak response efforts, all of which exist within the One Health context, in which surveillance, outbreak detection and response span the human, animal and environmental health domains. For example, genome sequences from a raccoon-associated variant of rabies virus (RRV), when paired with fine-scale geographic information and data from Canadian and US wildlife rabies vaccination programmes, demonstrated that multiple cross-border incursions were responsible for the expansion of RRV into Canada and sustained outbreaks in several provinces 70 ; this finding led to renewed concern about and action against rabies on the part of public health authorities 71 .

abstract:
  The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes — now a staple of the public health microbiology laboratory in well-resourced settings — can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrg.2017.88) contains supplementary material, which is available to authorized users.


id: cord-341672-k5pa3n2l
title: Units for vigilance of emerging diseases based on wastewater treatment plants (WWTP‐UVED)
author: Barros‐Rodríguez, Adoración
date: 2020-07-27
txt: ./txt/cord-341672-k5pa3n2l.txt
cache: ./cache/cord-341672-k5pa3n2l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32715638/
doi: 10.1111/1751-7915.13635
summary:
  Here, we propose the development of Units for Vigilance of Emerging Diseases based on the screening of pathogens released to wastewater treatment plants to follow the spread of the infectious agent to determine the location of infected people. bs_bs_banner Today, we have enough culture-independent techniques for the extraction and massive sequencing of nucleic acids (e.g. Illumina or Ion Torrent) and through specific amplification of pathogen genes by qPCR, to monitor the unusual presence of pathogens at any population''s WWTPs. We therefore suggest the creation of Units for Vigilance of Emerging Diseases (UVEDs) based on the continuous analysis of pathogens in WWTPs in potentially affected areas and especially during epidemics and pandemics. Therefore, we believe that the creation of such UVEDs for WWTPs under the coordination of a central service to analyse countrywide nucleic acid samples would greatly benefit our society and should be implemented by future legislation similarly to the analysis of other pathogens in the treated wastewater.

abstract:
  Pandemics deeply affect the health and economy of the world population. A precise determination of affected communities is of great importance to establish containment measures and reduce the economic impact. Here, we propose the development of Units for Vigilance of Emerging Diseases based on the screening of pathogens released to wastewater treatment plants to follow the spread of the infectious agent to determine the location of infected people.


id: cord-345583-3auz7gi6
title: Bacteriophage Based Biosensors: Trends, Outcomes and Challenges
author: Aliakbar Ahovan, Zahra
date: 2020-03-11
txt: ./txt/cord-345583-3auz7gi6.txt
cache: ./cache/cord-345583-3auz7gi6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32168802/
doi: 10.3390/nano10030501
summary:
  Consequently, the bacteriophage used like bio-probe in biosensor devises offer several advantages, such as (1) specificity to host bacteria, consequently efficient bacteria screening [15] , (2) easy to generate mass quantities of progeny phages, due to their short replication time, (3) ability to tolerate critical conditions, such as organic solvents and large range of pH and temperature [16] . Consequently, the bacteriophage used like bio-probe in biosensor devises offer several advantages, such as (1) specificity to host bacteria, consequently efficient bacteria screening [15] , (2) easy to generate mass quantities of progeny phages, due to their short replication time, (3) ability to tolerate critical conditions, such as organic solvents and large range of pH and temperature [16] . In phage-based biosensors, bacteriophage is Nanomaterials 2020, 10, 501 8 of 16 attached to the sensor surface, and consequently, it can detect the pathogen in the sample [38] .

abstract:
  Foodborne pathogens are one of the main concerns in public health, which can have a serious impact on community health and health care systems. Contamination of foods by bacterial pathogens (such as Staphylococcus aureus, Streptococci, Legionella pneumophila, Escherichia coli, Campylobacter jejuni and Salmonella typhimurium) results in human infection. A typical example is the current issue with Coronavirus, which has the potential for foodborne transmission and ruling out such concerns is often difficult. Although, the possible dissemination of such viruses via the food chain has been raised. Standard bacterial detection methods require several hours or even days to obtain the results, and the delay may result in food poisoning to eventuate. Conventional biochemical and microbiological tests are expensive, complex, time-consuming and not always reliable. Therefore, there are urgent demands to develop simple, cheap, quick, sensitive, specific and reliable tests for the detection of these pathogens in foods. Recent advances in smart materials, nanomaterials and biomolecular modeling have been a quantum leap in the development of biosensors in overcoming the limitations of a conventional standard laboratory assay. This research aimed to critically review bacteriophage-based biosensors, used for the detection of foodborne pathogens, as well as their trends, outcomes and challenges are discussed. The future perspective in the use of simple and cheap biosensors is in the development of lab-on-chips, and its availability in every household to test the quality of their food.


id: cord-345799-i0j6tctr
title: Co-detection of Pandemic (H1N1) 2009 Virus and Other Respiratory Pathogens
author: Koon, Kassi
date: 2010-12-17
txt: ./txt/cord-345799-i0j6tctr.txt
cache: ./cache/cord-345799-i0j6tctr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21122236/
doi: 10.3201/eid1612.091697
summary:
  From May through October 2009, a total of 10,624 clinical samples from 23 US states were screened for multiple respiratory pathogen gene targets. The main fi nding of this large-scale clinical study was the co-detection of multiple pathogens with the pandemic infl uenza virus strain. Pandemic (H1N1) 2009 virus and multiple other pathogens are often detected during autopsy (1,2), indicating that co-infection may play a major role in the disease process. Our fi ndings suggest that multiplex screening for respiratory pathogens is useful for providing rapid surveillance information to inform physicians who would otherwise base decisions on clinical signs and symptoms alone. Electronic reporting of empirical laboratory respiratory pathogen detection provided by a Clinical Laboratory Improvement Amendments-approved laboratory can greatly enhance surveillance data collection (10) . Development and evaluation of a novel multiplex PCR technology for molecular differential detection of bacterial respiratory disease pathogens

abstract:
  From May through October 2009, a total of 10,624 clinical samples from 23 US states were screened for multiple respiratory pathogen gene targets. Of 3,110 (29.3%) samples positive for pandemic (H1N1) 2009 virus, 28% contained >1 other pathogen, most commonly Staphylococcus aureus (14.7%), Streptococcus pneumoniae (10.2%), and Haemophilus influenzae (3.5%).


id: cord-346053-mk1mzc5z
author: Morris, Cindy E.
date: 2009-12-24
txt: ./txt/cord-346053-mk1mzc5z.txt
cache: ./cache/cord-346053-mk1mzc5z.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20041212/
doi: 10.1371/journal.ppat.1000693
abstract: nan
summary:
  We present numerous examples of virulence traits in plant pathogenic microorganisms that also have a function in their survival and growth in nonagricultural and nonplant habitats. Adaptation to biotic and abiotic stresses, within or outside of agricultural habitats, likely plays as important a role in the evolution of parasitic fitness of plant pathogens as it does for human pathogens. As illustrated above, traits that confer fitness in response to biotic and abiotic environmental stress can have dual-use as virulence factors in human pathogens. In plant pathogens, the transport systems for toxins and antimicrobials can have broad spectrum activity, leading to resistance to agricultural fungicides and also contributing to virulence [12] . The examples listed above that describe traits that play roles in both environmental fitness and virulence to plants provide a compelling incentive to expand our paradigms concerning the forces that drive evolution of plant pathogenicity.

title:
  Expanding the Paradigms of Plant Pathogen Life History and Evolution of Parasitic Fitness beyond Agricultural Boundaries


id: cord-347946-i6kx3n6m
author: Raison, Charles L
date: 2016-09-15
txt: ./txt/cord-347946-i6kx3n6m.txt
cache: ./cache/cord-347946-i6kx3n6m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27629366/
doi: 10.1038/npp.2016.194
summary:
  Like sickness behavior, depression in response to immune activation aided in host defense both directly (ie, raised body temperature and energy conservation behaviors) and indirectly (social avoidance, energy conservation, and hypervigilance; Raison and Miller, pathogenhost defense theory of depression [PATHOS-D]) Adaptive explanations for associations between MDD and altered immune functioning are not considered (frequent unexamined assumption of researchers working on proximal mechanisms) Toll-like receptor (TLR) mRNA and protein have been reported to be elevated in both the periphery and CNS of individuals with MDD (Hung et al, 2014 (Hung et al, , 2015 Keri et al, 2014; van Dooren et al, 2016) , with some evidence suggesting that successful pharmaco-or psychotherapy reduces peripheral TLR activity (Keri et al, 2014; Hung et al, 2015) .

title:
  Pathogen–Host Defense in the Evolution of Depression: Insights into Epidemiology, Genetics, Bioregional Differences and Female Preponderance

abstract:
  Significant attention has been paid to the potential adaptive value of depression as it relates to interactions with people in the social world. However, in this review, we outline the rationale of why certain features of depression including its environmental and genetic risk factors, its association with the acute phase response and its age of onset and female preponderance appear to have evolved from human interactions with pathogens in the microbial world. Approaching the relationship between inflammation and depression from this evolutionary perspective yields a number of insights that may reveal important clues regarding the origin and epidemiology of the disorder as well as the persistence of its risk alleles in the modern human genome.


id: cord-348819-gq7lp931
title: Dynamic and integrative approaches to understanding pathogen spillover
author: Becker, Daniel J.
date: 2019-08-12
txt: ./txt/cord-348819-gq7lp931.txt
cache: ./cache/cord-348819-gq7lp931.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1098/rstb.2019.0014
doi: 10.1098/rstb.2019.0014
abstract: nan
summary:
  The second set of manuscripts focuses on in-depth analysis of each of the factors affecting cross-species transmission: infection dynamics in reservoir hosts, pathogen survival in the environment, recipient host exposure, dose -response relationships and establishment of infection in recipient hosts. The authors show how modelling cross-species transmission as a percolation process, in which pathogens move from infected reservoirs to recipient hosts along a graph representing various spillover pathways [18, 19] , reveals first principles for how such datasets will behave and how common statistical tools can produce misleading inferences and poor predictions. This inclusive approach to confronting epidemiological models with longitudinal data in poorly understood reservoir host systems holds promise for elucidating spatio-temporal risk of pathogen spillover. Through several case studies (e.g. Lyme disease [63] , Hendra virus [64] , Plasmodium knowlesi [65] ), the authors further demonstrate how ecologically focused research has facilitated predicting spillover of particular pathogens in space and time and facilitated design of intervention strategies.


id: cord-348841-qxkmngyk
author: Kozakiewicz, Christopher P.
date: 2018-07-28
txt: ./txt/cord-348841-qxkmngyk.txt
cache: ./cache/cord-348841-qxkmngyk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30459828/
doi: 10.1111/eva.12678
summary:
  Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. We excluded reviews (n = 15), meeting abstracts (n = 1), purely methods-based papers (n = 6) and articles that identified as or mentioned landscape genetics but did not sufficiently incorporate landscape factors or genetic data into the study (n = 32), studies that referred to any of our pathogen-related search terms without it being a primary motivation for the study (n = 21), and studies that used words like "transmit" or "parasite" outside of the context of infectious agents (such as the transmission of behaviours) (n = 6). Spatial variation in pathogen prevalence or infection risk can be represented in much the same way as any landscape variable , making spatial data relating to presence of an infectious agent well-suited for incorporation into host landscape genetic models.

title:
  Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

abstract:
  Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free‐living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host‐vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross‐disciplinary advances.


id: cord-354254-89vjfkfd
author: Peng, Shanbi
date: 2020-08-31
txt: ./txt/cord-354254-89vjfkfd.txt
cache: ./cache/cord-354254-89vjfkfd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33027870/
doi: 10.1016/j.scitotenv.2020.142090
summary:
  Inspired by the impact of COVID-19, this review summarizes research works of pathogen transmission based on CFD methods with different models and algorithms. Defining the pathogen as the particle or gaseous in CFD simulation is a common method and epidemic models are used in some investigations to rise the authenticity of calculation. The Re-Normalization Group (RNG) k-ε was used in simulation in order to solve the turbulence with the good performance of accuracy, efficiency and robustness; In Gao and Niu [45] study, RNG k-ε model including the effect of low-Reynolds-number is used to solve the airflow and the diffusion of tracer gas which can represent the contaminant transmission are calculated by the equation below: Gao, et.al [102] combined the use of experiment and CFD method to study airborne transmission in different flats of a high-rise building and to verify their simulation, the data of tracer gas experiment from Denmark Aalborg University [103] is used.

title:
  The role of computational fluid dynamics tools on investigation of pathogen transmission: Prevention and control

abstract:
  Transmission mechanics of infectious pathogen in various environments are of great complexity and has always been attracting many researchers' attention. As a cost-effective and powerful method, Computational Fluid Dynamics (CFD) plays an important role in numerically solving environmental fluid mechanics. Besides, with the development of computer science, an increasing number of researchers start to analyze pathogen transmission by using CFD methods. Inspired by the impact of COVID-19, this review summarizes research works of pathogen transmission based on CFD methods with different models and algorithms. Defining the pathogen as the particle or gaseous in CFD simulation is a common method and epidemic models are used in some investigations to rise the authenticity of calculation. Although it is not so difficult to describe the physical characteristics of pathogens, how to describe the biological characteristics of it is still a big challenge in the CFD simulation. A series of investigations which analyzed pathogen transmission in different environments (hospital, teaching building, etc) demonstrated the effect of airflow on pathogen transmission and emphasized the importance of reasonable ventilation. Finally, this review presented three advanced methods: LBM method, Porous Media method, and Web-based forecasting method. Although CFD methods mentioned in this review may not alleviate the current pandemic situation, it helps researchers realize the transmission mechanisms of pathogens like viruses and bacteria and provides guidelines for reducing infection risk in epidemic or pandemic situations.


id: cord-355165-xc6ythgp
title: Validation of Syndromic Surveillance for Respiratory Pathogen Activity
author: van den Wijngaard, Cees
date: 2008-06-17
txt: ./txt/cord-355165-xc6ythgp.txt
cache: ./cache/cord-355165-xc6ythgp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3201/eid1406.071467
doi: 10.3201/eid1406.071467
summary:
  We defi ned syndrome data as data in health-related registries that refl ect infectious disease activity without identifying causative pathogen(s) or focusing on pathogenspecifi c symptoms (such as routine surveillance data for infl uenza-like illness [11] or surveillance of acute fl accid paralysis for polio [12] ). Six registries were selected ( Table 1 ) that collected data on work absenteeism, general practice (GP) consultations, prescription medications dispensed by pharmacies, diagnostic test requests (laboratory submissions) (13), hospital diagnoses, and deaths. As a reference for the syndrome data, we included specifi c pathogen counts for 1999-2004 from the following sources: 1) Weekly Sentinel Surveillance System of the Dutch Working Group on Clinical Virology (which covers 38%-73% of the population of the Netherlands [14] respiratory disease-related counts of Streptococcus pneumoniae (data in 2003-2004 were interpolated for 2 laboratories during short periods of missing data; total coverage 24%); and 3) national mandatory notifi cations of pertussis.

abstract:
  Syndromic surveillance is increasingly used to signal unusual illness events. To validate data-source selection, we retrospectively investigated the extent to which 6 respiratory syndromes (based on different medical registries) reflected respiratory pathogen activity. These syndromes showed higher levels in winter, which corresponded with higher laboratory counts of Streptococcus pneumoniae, respiratory syncytial virus, and influenza virus. Multiple linear regression models indicated that most syndrome variations (up to 86%) can be explained by counts of respiratory pathogens. Absenteeism and pharmacy syndromes might reflect nonrespiratory conditions as well. We also observed systematic syndrome elevations in the fall, which were unexplained by pathogen counts but likely reflected rhinovirus activity. Earliest syndrome elevations were observed in absenteeism data, followed by hospital data (+1 week), pharmacy/general practitioner consultations (+2 weeks), and deaths/laboratory submissions (test requests) (+3 weeks). We conclude that these syndromes can be used for respiratory syndromic surveillance, since they reflect patterns in respiratory pathogen activity.


