Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater

Zhi, Shuai; Banting, Graham; Stothard, Paul; Ashbolt, Nicholas J.; Checkley, Sylvia; Meyer, Kelsey; Otto, Simon J. G.; Neumann, Norman F.

doi:10.1016/j.watres.2019.03.024

Cited by 46 publications

(66 citation statements)

References 66 publications

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“…Thereby, our findings regarding the low ARG prevalence in viruses are consistent with data obtained for the analyses of 1181 phage isolate genomes (Enault et al, 2017). The amount of ARGs per bacterial genome estimated in our samples (10-32 ARGs/genome) is lower than the average calculated (≈51 ARGs/genome) for 26 strains of E. coli isolated from wastewater from different geographic points (Zhi et al, 2019).…”

Section: Discussionsupporting

confidence: 91%

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Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Maestre‐Carballa

Gomez

Navarro

et al. 2019

Environmental Microbiology

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Summary Wastewater treatment plants effluents are considered as hotspots for the dispersion of antibiotic resistance genes (ARGs) into natural ecosystems. The bacterial resistome (ARG collection in a metagenome) analyses have provided clues on antibacterial resistance dynamics. However, viruses and vesicles are frequently ignored. Here, we addressed the bacterial, viral and vesicle resistomes from a representative wastewater effluent in natural conditions and amended with polymyxin, which is used as a last resort antibiotic. Metagenomics showed that the natural prokaryotic resistome was vast (9000 ARG hits/Gb metagenome) and diverse, while viral resistome was two orders of magnitude lower (50 ARG hits/Gb metagenome) suggesting that viruses rarely encoded ARGs. After polymyxin amendment, data showed no ARG enrichment – including to polymyxin – in the microbiome. Remarkably, microbiomes responded to polymyxin with a vast release of putative vesicles (threefold increase compared with the control), which might be used as 'traps' to decrease the antibiotic concentration. Intriguingly, although polymyxin resistance genes (PRGs) were rare in the microbiome (0.018% of total ARG found), in the viral and vesicle fractions, PRGs were more abundant (0.5%–0.8% of total ARG found). Our data suggest that vesicles could have a more active role in the context of transmission of antibiotic resistances.

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Section: Discussionsupporting

confidence: 91%

“…The amount of ARGs per bacterial genome estimated in our samples (10–32 ARGs/genome) is lower than the average calculated (≈51 ARGs/genome) for 26 strains of E . coli isolated from wastewater from different geographic points (Zhi et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Maestre‐Carballa

Gomez

Navarro

et al. 2019

Environmental Microbiology

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“…There 326 is however no absolute correlation between phylogenetic lineage and any given niche, 327 and overlaps are observed. Interestingly, in our study, more than half of the E. coli sink 328 isolates cultured were ST635, which has been recently described as a highly adapted, 329 resistance-and virulence gene-enriched wastewater-associated strain thought to be 330 globally distributed, but is also found in humans, animals and other environments 331 (16). Of note, it has been observed in association with several clinically relevant trans-332 missible resistance genes, including ESBLs, carbapenemases, and rRNA methylases, 333 and was one of only two E. coli STs in our study that harboured an ESBL (bla CTX-M-15 ).…”

Section: Metagenomic Assignments To Bacterial Speciesmentioning

confidence: 71%

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

Constantinides

Chau

Quan

et al. 2020

Preprint

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Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonised with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole genome sequencing (WGS) of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies which may vary as a result of different inputs and selection pressures. WGS of 46 contemporaneous patient isolates identified one (2%; 95% CI 0.05-11%) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10% of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including blaCTX-M, blaSHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention.IMPORTANCEEscherichia coli and Klebsiella spp. cause a wide range of bacterial infections, including bloodstream, urine and lung infections. Previous studies have shown that sink drains in hospitals may be part of transmission chains in outbreaks of antimicrobial-resistant E. coli and Klebsiella spp., leading to colonisation and clinical disease in patients. We show that even in non-outbreak settings, contamination of sink drains by these bacteria is common across hospital wards, and that many antimicrobial resistance genes can be found and potentially exchanged in these sink drain sites. Our findings demonstrate that the colonisation of handwashing sink drains by these bacteria in hospitals is likely contributing to some infections in patients, and that additional work is needed to further quantify this risk, and to consider appropriate mitigating interventions.

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“…Nonetheless, general reliance on culturable E. coli to assess enteric bacterial water quality has proven to be of pragmatic value. As with most indicators, however, limits need to be understood, such as order of magnitude increases in disinfection resistance of some environmental strains of E. coli following up-regulation of stress-related genes (Zhi et al, 2019) and actual environmental growth under some conditions (Nanayakkara et al, 2019). The transfer of these attributes to pathogenic bacteria is always a possibility, thus it is important to anticipate such microbial dynamics and reduce environments where antibiotic resistant strains may mix with human bacterial pathogens.…”

Section: Bacterial Pathogens In Water and Sanitation Systems: Defininmentioning

confidence: 99%

Overview of issues for water bacterial pathogens

Pruden¹,

Ashbolt²,

Miller³

2019

Water and Sanitation for the 21st Century: Health and Microbiological Aspects of Excreta and Wastewater Management (Global Wate

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Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater

Cited by 46 publications

References 66 publications

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

Overview of issues for water bacterial pathogens

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