Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Shaw, Liam P.; Chau, Kevin; Kavanagh, James; AbuOun, Manal; Stubberfield, Emma; Gweon, Hyun S.; Barker, Leanne; Rodger, Gillian; Bowes, Michael J.; Hubbard, Alasdair T. M.; Pickford, Hayleah; Swann, Jeremy; Gilson, Daniel; Smith, Richard P.; Hoosdally, Sarah; Sebra, Robert; Brett, Howard; Peto, Tim; Bailey, Mark; Crook, Derrick W.; Read, Daniel S.; Anjum, Muna F.; Walker, A Sarah; Stoesser, Nicole

doi:10.1126/sciadv.abe3868

Cited by 56 publications

(60 citation statements)

References 75 publications

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“…Our study indicates that performing screening on plates supplemented with ceftazidime increases the probability of finding MDR Enterobacterales in vegetable samples. Therefore, this antibiotic could be used as a marker for multidrug resistance in Enterobacterales in our region, agreeing with data from other regions, such as Europe, where cefotaxime is used as a marker of resistance (Shaw et al, 2021). Before this study, it was thought that supplementing with ciprofloxacin could have a similar effect on the detection of MDR Enterobacterales, as in this region a high prevalence of resistance to this antibiotic is reported (ISP, Instituto de Salud Publica, 2015;Durán, 2018).…”

Section: Seasons Is Associated With the Isolation Of Mdr And Third-generation Cephalosporins Enterobacterales In Vegetables And Watersupporting

confidence: 91%

Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type

et al. 2021

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The dissemination of antibiotic-resistant bacteria (ARB) from water used for crop irrigation to vegetables is poorly studied. During a year, five farmer markets in a city in Central Chile were visited, and 478 vegetable samples (parsleys, corianders, celeries, lettuces, chards, and beets) were collected. Simultaneously, 32 water samples were collected from two rivers which are used to irrigate the vegetables produced in the area. Resistant Enterobacterales were isolated and identified. Colistin resistance gene mcr-1 and extended spectrum β-lactamases (ESBL) were molecularly detected. The association of environmental factors was evaluated, with the outcomes being the presence of Enterobacterales resistant to four antibiotic families and the presence of multidrug resistance (MDR) phenotypes. Parsley, coriander, and celery showed the highest prevalence of resistant Enterobacterales (41.9% for ciprofloxacin and 18.5% for ceftazidime). A total of 155 isolates were obtained, including Escherichia coli (n=109), Citrobacter sp. (n=20), Enterobacter cloacae complex (n=8), Klebsiella pneumoniae (n=8), and Klebsiella aerogenes (n=1). Resistance to ampicillin (63.2%) and ciprofloxacin (74.2%) was most frequently found; 34.5% of the isolates showed resistance to third-generation cephalosporins, and the MDR phenotype represented 51.6% of the isolates. In two E. coli isolates (1.29%), the gene mcr-1 was found and ESBL genes were found in 23/62 isolates (37%), with blaCTX-M being the most frequently found in 20 isolates (32%). Resistant Enterobacterales isolated during the rainy season were less likely to be MDR as compared to the dry season. Understanding environmental associations represent the first step toward an improved understanding of the public health impact of ARB in vegetables and water.

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Section: Seasons Is Associated With the Isolation Of Mdr And Third-generation Cephalosporins Enterobacterales In Vegetables And Watersupporting

confidence: 91%

Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type

et al. 2021

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“…Our study was limited by the inability to reconstruct closed genomes/plasmids using short-read sequencing data and our plasmidome analysis should therefore be interpreted with caution. The widely used PlasmidFinder database allows some inferences to be made using short read data; however, there are many untypeable plasmids that are not reflected in this database [ 64 ]. Similarly the MLplasmids classification algorithm used is trained on a limited reference set which may lead to some erroneous contig classifications.…”

Section: Discussionmentioning

confidence: 99%

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

et al. 2021

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Background The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design. Methods In this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression. Results We demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs). Conclusions Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks.

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“…Firstly, ARG-plasmids usually carry a high number of repeated sequences [ 49 , 50 , 51 , 52 ], and therefore exhibit highly entangled assembly graphs. Secondly, ARGs are frequently located on large plasmids with low copy number, and therefore have coverage values that are similar to chromosomes [ 48 , 52 ]. Consequently, finding plasmid-walks with differential coverage in the assembly graphs could be challenging for all tools relying on this strategy.…”

Section: Discussionmentioning

confidence: 99%

“…Thirdly, ARG-plasmids are frequently built as mosaic-like structures, containing mobile components that can be found in different plasmid backbones [ 48 , 52 , 53 , 54 , 55 ]. This type of genomic organization also complicates their reconstruction using reference-based methods, since databases might contain very similar fragments that are shared by a variety of plasmids.…”

Section: Discussionmentioning

confidence: 99%

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Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

et al. 2021

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The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.

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Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Cited by 56 publications

References 75 publications

Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type

Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data

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