Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome

Forster, Samuel C.; Liu, Junyan; Kumar, Nitin; Gulliver, Emily; Gould, Jodee; Escobar‐Zepeda, Alejandra; Mkandawire, Tapoka T.; Pike, Lindsay J.; Shao, Yan; Stares, Mark; Browne, Hilary P.; Neville, Bridget A.; Lawley, Trevor D.

doi:10.1038/s41467-022-29096-9

Cited by 89 publications

(32 citation statements)

References 52 publications

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“…Movement within the genome is often mediated by specific MGEs, such as insertion sequences and transposons [3]. Others like plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs) are key vectors for intercellular mobility, being responsible for a large fraction of the variability observed between bacterial species [4][5][6][7]. Bacteria undergo extensive horizontal gene transfer (HGT), and some estimates suggest that more than 80% of bacterial genes were horizontally transferred at some point in their evolutionary history [8].…”

Section: Introductionmentioning

confidence: 99%

The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

Botelho

Cazares

Schulenburg

2022

Preprint

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Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance genes in human pathogens, including the particularly problematic group of ESKAPE pathogens, such as Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), in the ESKAPE pathogens. We characterized over 1700 complete ESKAPE genomes and found that different MGE types are asymmetrically distributed across these pathogens. While some MGEs are capable of exchanging DNA beyond the genus (and phylum) barrier, horizontal gene transfer (HGT) is mainly restricted by phylum or genus. We further observed that most genes on MGEs have unknown functions and show intricate distribution patterns. Moreover, AMR genes and anti-CRISPRs are overrepresented in the ESKAPE mobilome. Our results also underscored species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we found that CRISPR targets vary according to MGE type: while plasmid CRISPRs almost exclusively target other plasmids, ICEs/IME CRISPRs preferentially target ICEs/IMEs and prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.

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Section: Introductionmentioning

confidence: 99%

The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

Botelho

Cazares

Schulenburg

2022

Preprint

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“…Notably, almost all bacteria (99.2%) containing ARGs had mobile genetic elements (Supplementary Table 14 and Supplementary Fig. 5 ), suggesting frequent horizontal gene transfer [ 20 ]. Consistently, VFG abundance (copy number/cell) in Wuhan was also significantly higher in May–June 2020 than that in other periods (Fig.…”

Section: Resultsmentioning

confidence: 99%

Disruption and recovery of river planktonic community during and after the COVID-19 outbreak in Wuhan, China

Chen

Wang

et al. 2022

ISME Communications

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During the COVID-19 outbreak in Wuhan, large amounts of anti-coronavirus chemicals, such as antiviral drugs and disinfectants were discharged into the surrounding aquatic ecosystem, causing potential ecological damage. Here, we investigated plankton in the Wuhan reaches of the Yangtze River, before, during, and after COVID-19, with the river reaches of three adjacent cities sampled for comparison. During the COVID-19, planktonic microbial density declined significantly. Correspondingly, the eukaryotic and prokaryotic community compositions and functions shifted markedly, with increasing abundance of chlorine-resistant organisms. Abundance of antibiotic resistance genes, virulence factor genes, and bacteria containing both genes increased by 2.3-, 2.7-, and 7.9-fold, respectively, compared to other periods. After COVID-19, all measured plankton community compositional and functional traits recovered in the Yangtze River.

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“…Any strains with all these three elements may increase the dissemination rate of ARG, which is a crucial trait for AR development for clinical pathogen bacteria. In a recent large-scale genome mining study, a group of MGE with TA and ARG detected gut pathogens and symbionts in which mobiles cross taxa at the phylum level ( Forster et al, 2022 ). A summary table of all ARG annotations is provided in Supplementary Table 9 .…”

Section: Discussionmentioning

confidence: 99%

Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa

Dai

et al. 2022

Front. Microbiol.

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The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in P. aeruginosa. Moreover, manual inspection revealed several TA systems that were not yet reported in P. aeruginosa including the hok-sok, cptA-cptB, cbeA-cbtA, tomB-hha, and ryeA-sdsR. Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored P. aeruginosa pan-genomes, expanded the knowledge on P. aeruginosa, and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination.

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Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome

Cited by 89 publications

References 52 publications

The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements

Disruption and recovery of river planktonic community during and after the COVID-19 outbreak in Wuhan, China

Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa

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