Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates

Stoppe, Nancy de Castro; Silva, Juliana Saragiotto; Carlos, Camila; Sato, Maria Inês Z.; Saraiva, Antônio Mauro; Ottoboni, Laura Maria Mariscal; Torres, Tatiana Teixeira

doi:10.3389/fmicb.2017.02512

Cited by 97 publications

(79 citation statements)

References 91 publications

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“…For the rest, the analysis showed a good correspondence between the assignment into the known phylogroups - A, B1, B2, D, E, F, and G – and the different clades of this tree. In line with the literature 40 , four major phylogroups were very abundant - A (24% of the dataset), B1 (24%), B2 (25%) and D (14%) – whereas the others were rarer. The nucleotide diversity of the phylogroups is very dependent on their phylogenetic structure, since some clades have more closely related clusters of strains than others (Supplementary Fig.…”

Section: Resultssupporting

confidence: 88%

“…This allowed us to study the joint effect of population structure and habitat on the variation of gene repertoires. Our study focused on E. coli isolates from Australia, but its genetic diversity was higher or comparable to other worldwide genome datasets, and its population structure was consistent with previous works 16, 40, 74 . This indicates that what we have observed is likely to be representative of the species as a whole.…”

Section: Discussionsupporting

confidence: 85%

“…Genome size also differs among phylogroups, with A and B1 strains having smaller genomes than B2 or D strains 23 . The phylogenetic vicinity of geographically remote E. coli isolates, and the co-isolation of phylogenetically distant strains, supports the hypothesis that strains circulate rapidly 39, 40 . The genome of the species is also remarkably plastic, since only about half of the average genome is present across most strains of the species (core or persistent genome) and the pan-genome vastly exceeds the size of the typical genome 41–44 .…”

Section: Introductionsupporting

confidence: 66%

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Phylogenetic background and habitat drive the genetic diversification ofEscherichia coli

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Amandine

Sousa

et al. 2020

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23Escherichia coli is a commensal of birds and mammals, including humans. It can act as an 24 opportunistic pathogen and is also found in water and sediments. Since most population 25 studies have focused on clinical isolates, we studied the phylogeny, genetic diversification, 26 and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more 27 than 5,000, mostly non-clinical, isolates originating from humans, poultry, wild animals and 28 water sampled from the Australian continent. These strains represent the species diversity 29 and show large variations in gene repertoires within sequence types. Recent gene transfer is 30 driven by mobile elements and determined by habitat sharing and by phylogroup 31 membership, suggesting that gene flow reinforces the association of certain genetic 32 backgrounds with specific habitats. The phylogroups with smallest genomes had the highest 33 rates of gene repertoire diversification and fewer but more diverse mobile genetic elements, 34 suggesting that smaller genomes are associated with higher, not lower, turnover of genetic 35 information. Many of these small genomes were in freshwater isolates suggesting that some 36 lineages are specifically adapted to this environment. Altogether, these data contribute to 37 explain why epidemiological clones tend to emerge from specific phylogenetic groups in the 38 presence of pervasive horizontal gene transfer across the species. 39 40 circulation of strains and the high plasticity of their genomes have not erased the 68 associations of certain clades with certain isolation sources. In consequence, such 69 associations might reflect local adaptation 16,45 , which would suggest frequent genetic 70 interactions between the novel adaptive changes and the strains' genomic background. 71Understanding how the evolution of gene repertoires is shaped by population structure and 72 habitats requires large-scale comparative genomics of samples with diverse sources of 73 isolation representative of natural populations of E. coli. Most of the efforts of genome 74 sequencing have been devoted to study pathogenic lineages and very few genomic data are 75 available for commensal strains, especially in wild animals, and environmental strains. Here, 76we analysed the genomes of a large collection of E. coli strains collected across many 77 human, domestic and wild animal and environmental sources in different geographic 78 locations from the Australian continent. This collection is dominated by non-clinical isolates, 79 corresponding to the main habitats of the species. We sought to understand the dynamics of 80 the evolution of gene repertoires and how it was driven by mobile genetic elements. The 81 analysis of the isolation sources in the light of phylogenetic structure and genome variation 82 suggests that adaptation varies with the habitat and the phylogenomic background. This 83 contributes to explain why known epidemiological clones of the species emerge from specific 84 phylogenetic groups, even though virulen...

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Section: Resultssupporting

confidence: 88%

Section: Discussionsupporting

confidence: 85%

Section: Introductionsupporting

confidence: 66%

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Phylogenetic background and habitat drive the genetic diversification ofEscherichia coli

Touchon

Amandine

Sousa

et al. 2020

Preprint

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“…There is a possibility, however, that some of our observations may reflect high mortality rates of certain E. coli clones. We found that all isolates belonged to phylogroups B2 and D, which have been found previously in domestic animals and the environment (Stoppe et al., ); however, the B2 phylogroup is not common in environments outside of the host, and neither B2 nor D phylogroups have been found to be common in poultry (Blyton et al., ).…”

Section: Discussionsupporting

confidence: 75%

Changes in dominant Escherichia coli and antimicrobial resistance after 24 hr in fecal matter

et al. 2018

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Intestinal bacteria carry antimicrobial resistance (AMR) genes in mobile genetic elements which have the potential to spread to bacteria in other animal hosts including humans. In fecal matter, Escherichia coli can continue to multiply for 48 hr after being excreted, and in certain environments, E. coli survive long periods of time. It is unclear the extent to which AMR in E. coli changes in the environment outside of its host. In this study, we analyzed changes in the population structure, plasmid content, and AMR patterns of 30 E. coli isolates isolated from 6 chickens (cloacal swabs), and 30 E. coli isolates from fecal samples (from the same 6 chickens) after 24 hr of incubation. Clonality of isolates was screened using the fumC gene sequence and confirmed in a subset of isolates (n = 14) by multi-locus sequence typing. Major shifts in the population structure (i.e., sequence types) and antibiotic resistance patterns were observed among the numerically dominant E. coli isolates after 24 hr. Four E. coli clones isolated from the cloaca swabs and the corresponding fecal samples (after 24 hr incubation) showed different antibiotic resistance patterns. Our study reveals that fecal matter in the environment is an intermediate habitat where rapid and striking changes occur in E. coli populations and antibiotic resistance patterns.

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“…Bacteria are paragons of adaptability and make up more biomass than all organisms other than plants 28 combined (Bar-On, Phillips, and Milo 2018). Many bacterial species have enormous population sizes, 29 disperse effectively around the globe (Stoppe et al 2017) and exhibit high rates of within-species 30 homologous recombination (Vos and Didelot 2009). Recombination acts to progressively break down 31 non-random associations between markers (linkage disequilibrium), so that in large populations a 32 natural null expectation is for there to be linkage equilibrium between sites.…”

Section: Introduction 27mentioning

confidence: 99%

Why panmictic bacteria are rare

Yang

Cui

Didelot

et al. 2018

Preprint

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15Background Bacteria typically have more structured populations than higher eukaryotes, but this 16 difference is surprising given high recombination rates, enormous population sizes and effective 17 geographical dispersal in many bacterial species. 18Results We estimated the recombination scaled effective population size in 21 bacterial species 19 and find that it does not correlate with synonymous nucleotide diversity as would be expected under 20 neutral models of evolution. Only two species have estimates substantially over 100, consistent with 21 approximate panmixia, namely Helicobacter pylori and Vibrio parahaemolyticus. Both species are far 22 from demographic equilibrium, with diversity predicted to increase more than 30 fold in V. 23 parahaemolyticus if the current value of were maintained, to values much higher than found in 24 any species. We propose that panmixia is unstable in bacteria, and that persistent environmental 25 species are likely to evolve barriers to genetic exchange, which act to prevent a continuous increase in 26 diversity by enhancing genetic drift. 27Conclusions Our results highlight the dynamic nature of bacterial population structures and imply 28 that overall diversity levels found within a species are poor indicators of its size. 29 30 Keywords 31 Panmixia, bacterial population structure, effective population size, recombination, genetic diversity 32 33 Background 34 Bacteria are paragons of adaptability and make up more biomass than all organisms other than plants 35 combined [1]. Many bacterial species have enormous population sizes, disperse effectively around the 36 globe [2-5] and exhibit high rates of within-species homologous recombination [6]. Recombination 37 progressively breaks down non-random associations between markers (linkage disequilibrium), so 38 that in large populations, where pairs of individuals distantly related, linkage equilibrium is expected 39between all pairs of genomic sites. However, in most species for which data is available, there is 40 substantial genome-wide linkage disequilibrium, indicating structuring of variation [7]. Here we 41 3 propose a resolution of this paradox, namely that large bacterial populations accumulate diversity 42 progressively until that diversity acts as an effective barrier to genetic exchange between lineages. 43 44We examine the population structure of 21 bacterial species and find that only the Asian population of 45Vibrio parahaemolyticus is close to genome-wide linkage equilibrium. We find that this population 46 has undergone a recent expansion. If the current population size was maintained over evolutionary 47

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Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates

Cited by 97 publications

References 91 publications

Phylogenetic background and habitat drive the genetic diversification ofEscherichia coli

Phylogenetic background and habitat drive the genetic diversification ofEscherichia coli

Changes in dominant Escherichia coli and antimicrobial resistance after 24 hr in fecal matter

Why panmictic bacteria are rare

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