Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

Mentzer, Astrid von; Connor, Thomas R.; Wieler, Lothar H.; Semmler, Torsten; Iguchi, Atsushi; Thomson, Nicholas R.; Rasko, David A.; Joffré, Enrique; Corander, Jukka; Pickard, Derek; Wiklund, Gudrun; Svennerholm, Ann‐Mari; Sjöling, Åsa; Dougan, Gordon

doi:10.1038/ng.3145

Cited by 204 publications

(314 citation statements)

References 47 publications

Supporting

Mentioning

279

Contrasting

Order By: Relevance

“…Studies have characterized ST131 in detail and highlighted genetic events leading to the success of this lineage. Two studies investigating the origin of enteropathogenic E. coli (EPEC) and atypical enteropathogenic E. coli (aEPEC) and the association of genetic factors with clinical disease severity illustrated the power of WGS by showing that aEPEC and EPEC emerged several times in different lineages (Hazen et al 2016;Ingle et al 2016), and a further study analyzed a global collection of 362 enterotoxigenic E. coli (ETEC) (von Mentzer et al 2014). Smaller studies of local epidemics have concentrated on other pathotypes and single STs.…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

et al. 2017

Self Cite

View full text Add to dashboard Cite

Escherichia coli associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader E. coli population associated with disease, we used genomics to analyze a systematic 11-yr hospital-based survey of E. coli associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful lineages identified the emergence of ST131 and ST69 and their establishment as two of the five most common lineages along with ST73, ST95, and ST12. The most frequently identified lineage was ST73. Compared to ST131, ST73 was susceptible to most antibiotics, indicating that multidrug resistance was not the dominant reason for prevalence of E. coli lineages in this population. Temporal phylogenetic analysis of the emergence of ST69 and ST131 identified differences in the dynamics of emergence and showed that expansion of ST131 in this population was not driven by sequential emergence of increasingly resistant subclades. We showed that over time, the E. coli population was only transiently disturbed by the introduction of new lineages before a new equilibrium was rapidly achieved. Together, these findings suggest that the frequency of E. coli lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche.

show abstract

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Isolates included in this study involve various species of the Enterobacteriaceae collected for eight different studies (268)(269)(270)(271)(272)(273)(274). Each study lies within a 'global' or 'geographical/region specific' scope according to the list of countries covered by their strain collection (Appendix C; Table S3).…”

Section: Methodsmentioning

confidence: 99%

“…Contigs from each isolate were obtained as previously described (268)(269)(270)(271)(272)(273)(274). A collective total of 1683 isolates passed QC based on total alignment length and number of contigs.…”

Section: Methodsmentioning

confidence: 99%

“…Here, we perform an investigation of 1683 isolates of different species within the Enterobacteriaceae using an opportunistic and non-selective approach of existing sequencing data from several global and regional studies (268)(269)(270)(271)(272)(273)(274). Three studies were designed to capture the global diversity of Klebsiella pneumoniae (271), the Yersinia genus (273), and Enterotoxigenic E. coli (ETEC) (274) were included, as well as five regional studies looking …”

Section: Introductionmentioning

confidence: 99%

“…Three studies were designed to capture the global diversity of Klebsiella pneumoniae (271), the Yersinia genus (273), and Enterotoxigenic E. coli (ETEC) (274) were included, as well as five regional studies looking …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The genetic analysis of Enterobacteriaceae plasmids to provide insights into the acquisition and spread of the blaNDM gene

Wailan¹

View full text Add to dashboard Cite

Treatment options for infections caused by pathogenic Gram-negative bacteria, especially those of the Enterobacteriaceae family, are becoming limited with the increase of antimicrobial resistance (AMR). β-lactamases are a major mechanism for AMR within the Enterobacteriaeae. The most problematic β-lactamases are carbapenemases, which confer resistance to carbapenems, the major last-line antimicrobial. A recently emerged carbapenemase that has globally disseminated is the NDM carbapenemase, provided by blaNDM genes. These blaNDM genes (and other AMR genes) are able to transmit between strains when inserted on extrachromosomal self-replicating DNA molecules known as 'plasmids'. AMR genes within Enterobacteriacae are frequently associated with specific bacterial species, clonal lineage, plasmid Incompatibility (Inc) types or transposable elements. The blaNDM genes however do not have this association when oberserved in the Enterobacteriaceae family. To address and characterise this new paradigm presented by blaNDM genes, this thesis presents the bioinformatic analysis of plasmids associated with the Enterobacteriaceae to provide insights into the acquisition and spread of the blaNDM gene and an epidemiological approach to assess its plasmid-mediated dissemination between genetically unrelated species.Specifically these aims were achieved by; firstly, the establishment of a recent account of the blaNDM gene from an epidemiological perspective using a novel genetic/molecular approach. This would identify the spread of individual plasmids carrying blaNDM across multiple species and patients, both within a single facility and across multiple national facilities. The approach combined in-depth bioinformatic analysis of blaNDM genetic contexts (NGCs) with common molecular epidemiology techniques. IncN2 (n=4) and IncA/C (n=3) were identified as the most common plasmids types carrying blaNDM across four patients within a Pakistani military hospital. These patients harboured between two and four NDM-1 producing Gram-negative bacilli of different ii species coresident in their stool samples. IncFII-types (n=7) and IncX3 (n=4) were the most common plasmid types carrying blaNDM amongst 12 Enterobacteriaceae isolates, each from different patients across multiple Australian healthcare facilities. These isolates each carried one plasmid harbouring blaNDM but only five different blaNDM genetic contexts were identified, indicating five particular plasmids with a specific NGC had disseminated amongst these 12 isolates.Secondly, to investigate transposable elements involved for insertion of the blaNDM gene into different plasmid types, the complete sequence of four plasmids carrying blaNDM (two IncA/C2 and two IncFIIY) was bioinformatically analysed. These plasmids were from four different clinical samples of four patients, comprised of Klebsiella pneumoniae, Enterobacter cloacae, and Escherichia coli. Each plasmid was observed to acquire blaNDM by different mechanisms on very similar plasmid backbones. Transposable elements ...

show abstract

Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label‐Free Quantitative Proteomics

2020

View full text Add to dashboard Cite

Escherichia coli and Shigella spp. causing illnesses in humans represent a genotypically and phenotypically diverse group of pathogens. Although E. coli diversity has been studied by comparative genomics, the intra‐species variation at the proteome level is currently unknown. The proteomes of 16 pathogenic E. coli, 2 non‐pathogenic E. coli, and 5 Shigella strains originating from 18 phylogenetic lineages are investigated. By applying label‐free quantitative proteomics on trypsin‐digested cell extracts from bacteria grown on blood agar, 4018 proteins are detected, 3285 of which arequantified, and 261 represented virulence factors. Of 753 proteins quantified in all strains, the levels of 153 vary substantially between strains and are functionally associated mostly with stress response and peripheral metabolism. The levels of proteins associated with the central metabolism vary considerably less than the levels of proteins from other metabolic pathways. Hierarchical clustering analysis based on the protein levels results in strains grouping that differ from that obtained by gene‐based phylogenetic analysis. Finally, strains of some E. coli pathotypes have more similar protein profiles even when the strains are not genetically closely related. The results suggest that the degree of genetic relatedness may not necessarily be a good predictor of E. coli phenotypic characteristics.

show abstract

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

Cited by 204 publications

References 47 publications

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

The genetic analysis of Enterobacteriaceae plasmids to provide insights into the acquisition and spread of the blaNDM gene

Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label‐Free Quantitative Proteomics

Contact Info

Product

Resources

About