cord-000347-gdra8xhj	2011	
cord-000820-5b29wtim	2012	RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The current study investigated the intestinal contents collected from 248 water buffalo calves affected by gastroenteritis with lethal outcome to: (i) evaluate the prevalence of Salmonella spp., and (ii) perform a polyphasic characterization of the collected isolates of S. The genetic characterization (Table 2) included five loci (avrA, ssaQ, mgtC, siiD, and sopB) located on SPI 1-5, respectively [8] , eight loci (gipA, gtgB, sopE, sodC1, gtgE, gogB, sspH1, and sspH2) of prophage origin [9] [10] [11] [12] [13] , the gene spvC, located on a virulence plasmid [12] , and nine genes (stfE, safC, csgA, ipfD, bcfC, stbD, pefA, fimA, and agfA) coding for bacterial fimbriae, involved in surface adhesion and gut colonization [5] .
cord-002561-7j43yic1	2017	
cord-003908-wbawzbhz	2019	
cord-004116-ckms25na	2020	
cord-004751-4vl0cvyq	1973	
cord-005057-deq5tv1d	1990	
cord-007890-bie1veti	2002	Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children''s Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections.
cord-008777-i2reanan	2005	Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins.
cord-009664-kb9fnbgy	2014	Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically.
cord-009764-m9flptcv	2019	
cord-010187-ymhcfyxx	2005	
cord-010641-hk90qx1k	2020	
cord-012054-bpgb7tgo	2008	
cord-014461-2ubh9u8r	2012	
cord-018061-jy3km0fr	2016	rhamnosus GG (LGG), a famous probiotic strain, was evaluated and showed an anti-infl uenza virus activity on intranasal and oral administration [ 26 , 27 ] . Moreover, the antiviral effect of probiotics by immunomodulatory mechanisms depends on the immune system status, which can be explained in the study conducted by Lehtoranta et al., who showed that the combination of four probiotic strains worked very well in children but not in the elderly [ 61 ] . The role of commensal bacteria in the persistence of enteric viral infections has previously been shown in a series of recent studies published in 2011, using poliovirus, reovirus and mouse mammary tumor virus (MMTV) as EnV models [ 99 -101 ] . Differential effects of Escherichia coli Nissle and Lactobacillus rhamnosus Strain GG on human rotavirus binding, infection, and B cell immunity
cord-019490-m1cuuehi	2015	Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control.
cord-022383-pz0htccp	2013	The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats.
cord-022501-9wnmdvg5	2015	Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing).
cord-023592-w96h4rir	2015	Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined.
cord-255137-utg8k7qs	2019	
cord-255857-y9wjp0aj	2001	Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. However, the cluster of amino acid mutations located near the carboxyl terminal end suggests that the replicase region was altered during passage to result in a more fit virus for replication in cell culture, as evidenced by the in vitro one-step growth curve comparison shown in Fig. 4 . Sequence analysis of strains VR-2332 and RespPRRS indicated that there were 15 nucleotide changes in this region, and all but one of which resulted in amino acid alterations. Attenuation can result from changes in many areas of viral genomes and the 41 nucleotide mutations described include alterations in several key PRRSV regions.
cord-259959-qzd3hf8y	2020	
cord-267189-xq70rn1j	2016	
cord-267671-ys43n672	2015	Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases.
cord-269892-bmdpbkni	2011	Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. The first group of sponges (Aplysina fistularis, Plakortis sp., Amphimedon compressa, Aiolochroia crassa, Agelas clathrodes, Agelas cerebrum, Ircinia felix, Scopalina ruetzleri, Erylus formosus, Chondrilla nucula, and Aplysina archeri) was collected by SCUBA diving at depths of 3-20 m in Bahamas in July 2008 (GPS-26°27′3.25″ N, 77°5 4′14.59″ W). In terms of actinomycete diversity, the 79 cultivated strains are represented by 20 different genera namely Microbacterium (21 isolates), Rhodococcus (10), Streptomyces (5), Mycobacterium (6), Micromonospora (5), Knoellia (4), Gordonia (4), Curtobacterium (4), Arthrobacter (4) Salinispora (3), Saccharopolyspora (2), Nocardioides (2), Citromicrobium (2), Sanguibacter (1), Lapillicoccus (1), Kocuria (1), Dietzia (1), Cellulosimicrobium (1) Cellulomonas (1), and Agrococcus (1; Supplementary Table 1) . A family of aeruginosin inhibitors is active against human serine proteases and was isolated from marine sponges and cyanobacterial waterblooms (Ersmark et al. Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes
cord-271897-9oqzsd70	2020	
cord-279495-zxerb7de	2012	Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus
cord-280334-7b7rvr25	2020	
cord-281172-7di6eub3	2016	
cord-288451-npefpo3t	2016	
cord-289623-7oc1ykds	2020	
cord-291510-jh2fdks4	2020	
cord-291930-n7wq09rq	2010	
cord-294509-txk1qic1	2016	
cord-296611-ma32oz4o	2019	
cord-299763-ttb7o8lv	2016	Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains
cord-301301-ilsenpus	2017	
cord-301347-22lt6h40	2016	Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene
cord-306976-p2521bl4	2016	
cord-323463-osf6t7cw	2008	This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. Although predictions during the 20th century indicated that the incidence of infectious diseases would diminish as a result of improvements in sanitation and by the introduction of many vaccines and antibiotics, at the beginning of the 21st century the rates of infections produced by new pathogens or by reemerging microorganisms possessing new virulence or resistance phenotypes is increasing, threatening the overall human health [1] [2] [3] [4] [5] . It is in this scenario where community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as the most common pathogen isolated from patients with skin and soft-tissue infections attending to the emergency departments in many United States and Australian cities 8, 9 , and at present, its incidence is increasing in other parts of the world 10, 11 .
cord-347644-4qenzjiu	2019	
cord-353190-7qcoxl81	2012	This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine.
cord-355119-sdg9zdc1	2016	
cord-355492-0zvqvumc	2006