key: cord-0428740-fssv5hy9
authors: Sekyere, John Osei; Faife, Sara Lino
title: Pathogens, Virulence and Resistance Genes Surveillance with Metagenomics Can Pre-empt Dissemination and Escalation of Untreatable Infections: A Systematic Review and Meta-analyses
date: 2021-06-30
journal: bioRxiv
DOI: 10.1101/2021.06.30.450418
sha: 212d2807073b971a9d0f0abc2f417e6c1cb5af7a
doc_id: 428740
cord_uid: fssv5hy9

Background The dissemination of pathogens carrying genetic elements such as antimicrobial resistance genes (ARGs), mobile-genetic elements (MGEs), virulome and methylome have a negative impact on food and environment safety, water quality and animal and human health. The applications of metagenomics to monitor and identify the prevalence/endemicity and emergence of these pathogenic agents from different sources were examined. Methods Articles published in English language up to October 2020 were searched for on PubMed. Qualitative and quantitative data extracted from the included articles were translated into charts and maps. GraphPad Prism 9.0.2 was used to undertake statistical analysis using descriptive and column statistics, Chi-square, ANOVA, Wilcoxon’s signed-rank, and one-sample t-test. Results In all, 143 articles from 39 countries from Europe, America, Asia, and Africa were quantitatively analysed. Metagenomes from sewage/wastewater, surface water samples (ocean, sea, river lake, stream and tap water), WWTP, effluents and sludge samples contained pathogenic bacteria (Aeromonas, Acinetobacter, Pseudomonas, Streptococcus, Bacteroides, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae and Acinetobacter baumannii), viruses (Adenovirus, Enterovirus, Hepatovirus, Mamastrovirus and Rotavirus) and parasites (Acanthamoeba, Giardia, Entamoeba, Blastocystis and Naegleria). Integrons, plasmids, transposons, insertion sequences, prophages and integrative and conjugative elements were identified. ARGs mediating resistance to important antibiotics, including β-lactams, aminoglycosides, fluoroquinolones, and tetracycline, and virulence factors such as secretion system, adherence, antiphagocytosis, capsule, invasion, iron uptake, hemolysin, and flagella. Conclusion Clinically important pathogens, ARGs, and MGEs were identified in diverse clinical, environmental, and animal sources through metagenomics, which can be used to determine the prevalence and emergence of known and unknown pathogens and ARGs. Importance/significance Global metagenomic analyses of drinking water, effluents, influents, un/-treated sewage, WWTPs, sludge, rivers, lakes, soil, sediments, biosolid, air and plants. showed the global distribution of diverse clinically important ARGs on mobile genetic elements, antimicrobial-resistant bacteria (ARB) and pathogens, metal resistance genes, and virulence genes in almost all environments. These depict the importance of shot-gun metagenomics as a surveillance tool for AMR and infectious disease control to safeguard water & food quality as well as public health from water- and food-borne outbreaks of pathogenic and ARB infections. More concerning was the identification of ARGs to last-resort antibiotics i.e., carbapenems, colistin, & tigecycline.

Metagenomic studies elucidating how this technology has been used to explore the 1 0 2 dissemination of pathogens harbouring MGEs and ARGs exist. However, systematic reviews Worryingly, the presence of Mamastrovirus in drinking water leads to diarrhoea, particularly The presence of these protozoa in irrigation water is a concern for public health as they cause whilst Acanthamoeba castellanii can enter from skin ulcers or traumatic penetration. Worryingly, Giardia can survive in water for up to 3 months and it is not killed by normal that the water disinfection process did not have any action against Acinetobacter, Bordetella, Burkholderia, and Pseudomonas, which harboured genes encoding resistance to 4 2 7 aminoglycosides, carbapenems, cephalosporins, fluoroquinolones, glycopeptides, 4 2 8 glycylcyclines, macrolides, monobactams, oxazolidinones, penems, and peptides (29). As with surface water, underground water is mainly used for drinking and irrigation. Metagenomic studies showed that this source of water can pose risks for humans and 4 3 2 animals. Enterococcus, Escherichia coli and E. coli O157 isolates were detected in 4 3 3 groundwater from wells in the USA (58), constituting a concern as, generally, wells are normally found in rural area where in many cases, the population does not focus on water 4 3 5 treatment. Moreover, the shiga-like producing E. coli (E. coli O157), which may lead to a harmful antibiotic-resistant pathogens. process). In these WWTPs effluents, Acinetobacter, Aeromonas, and Pseudomonas were identified. Furthermore, the effluents were identified as a reservoir of ARGs to bacitracin, water by seeping into underground water (62).

The use of metagenomic technology allowed the identification of Helicobacter pylori, Helicobacter species rarely infect the gastric mucosa (53). Notably, many viruses were identified in sewage samples. Airport toilet waste was a target sewage samples constitutes a public health concern as well because sewage pathogenic 4 9 0 microorganisms are derived from human and animal faeces, and its contact is associated with ciprofloxacin, and tetracycline than that normally found in the environment significantly metagenomic assembly tools were compared, the three above assemblers were considered the 8 3 5

best assemblers, due to their performance. In the same study, it was observed that their use

should be based on the aim of the study, advising that MEGAHIT and IDBA-UD should be 8 3 7

applied for micro diversity and Spades for binning and bacterial genome reconstruction RAST is considered a robust tool, used for processing, analysing, sharing and disseminating these binning tools is related to their good capacity of grouping reads or contigs into 8 4 8

individual genomes and assigning the groups to specific genus, species, or subspecies, based 8 4 9

either on composition or similarity.

In the annotation process, bioinformatic tools allowed the identification of genes, proteins, applied tool and its performance was comparable or better than other methods i.e., BLAST is commonly used and considered 'gold standard' for sequence comparison (147). The SILVA database was mostly used for taxonomic assignment and was considered a and BLASTX tools and noticed that both had the same degree of sensitivity, albeit

DIAMOND, an open-source algorithm based on double indexing, was 20,000 times faster

than BLASTX on short reads (149). Bayesian classifier (RDP Classifier, Rtax and Uclust), it was observed that METAXA2 often had good performance than other tools in terms of making correct predictions whilst

maintaining a low misclassification rate (151). alignments. Additionally, it had a potential to quickly identify contaminant sequences (155).

The application of ARGs-OAP in ARGs identification allowed classification and annotation of ARG-8 7 6

like sequences within a short time (156). This pipeline can analyse many sample and return a general 8 7 7 were analysed and visualized using R (66,90,160) , an open-source statistical programming language 8 8 4

and environment for data analysis and graphics (161). R supports several specific packages including 8 8 5

vegan and igraph, which are selected according to the focus of the metagenomic study to assess 8 8 6

functional differences between samples(130). FASTQC and Trimmomatic were mostly used for 8 8 7

quality control in metagenomic studies (162) to assess the quality of the data generated by the 8 8 8

sequencing pipelines, filter and remove shorter and poorer sequences, and remove ambiguous base 8 8 9

pairs and chimeras (163). 

Genomic analysis of hospital plumbing reveals