The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure

ABSTRACTEscherichia coliisolates (n= 658) obtained from drinking water intakes of Comox Lake (2011 to 2013) were screened for the following virulence genes (VGs):stx1andstx2(Shiga toxin-producingE. coli[STEC]),eaeand the adherence factor (EAF) gene (enteropathogenicE. coli[EPEC]), heat-stable (ST) enterotoxin (variants STh and STp) and heat-labile enterotoxin (LT) genes (enterotoxigenicE. coli[ETEC]), andipaH(enteroinvasiveE. coli[EIEC]). The only genes detected wereeaeandstx2, which were carried by 37.69% (n= 248) of the isolates. Onlyeaewas harbored by 26.74% (n= 176) of the isolates, representing potential atypical EPEC strains, while onlystx2was detected in 10.33% (n= 68) of the isolates, indicating potential STEC strains. Moreover, four isolates were positive for both thestx2andeaegenes, representing potential EHEC strains. The prevalence of VGs (eaeorstx2) was significantly (P< 0.0001) higher in the fall season, and multiple genes (eaeplusstx2) were detected only in fall. Repetitive element palindromic PCR (rep-PCR) fingerprint analysis of 658E. coliisolates identified 335 unique fingerprints, with an overall Shannon diversity (H′) index of 3.653. Diversity varied among seasons over the years, with relatively higher diversity during fall. Multivariate analysis of variance (MANOVA) revealed that the majority of the fingerprints showed a tendency to cluster according to year, season, and month. Taken together, the results indicated that the diversity and population structure ofE. colifluctuate on a temporal scale, reflecting the presence of diverse host sources and their behavior over time in the watershed. Furthermore, the occurrence of potentially pathogenicE. colistrains in the drinking water intakes highlights the risk to human health associated with direct and indirect consumption of untreated surface water.

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Temporal Dynamics and Impact of Manure Storage on Antibiotic Resistance Patterns and Population Structure of Escherichia coli Isolates from a Commercial Swine Farm

Applied and Environmental Microbiology ◽

10.1128/aem.00218-07 ◽

2007 ◽

Vol 73 (17) ◽

pp. 5486-5493 ◽

Cited By ~ 35

Author(s):

Patrick Duriez ◽

Edward Topp

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Population Structure ◽

Temporal Dynamics ◽

Swine Farm ◽

Bacterial Populations ◽

E Coli ◽

Resistance Patterns ◽

Fresh Feces ◽

Antibiotic Resistance Patterns

ABSTRACT Many confined-livestock farms store their wastes for several months prior to use as a fertilizer. Storing manure for extended periods could significantly bias the composition of enteric bacterial populations subsequently released into the environment. Here, we compared populations of Escherichia coli isolated from fresh feces and from the manure-holding tank (stored manure) of a commercial swine farm, each sampled monthly for 6 months. The 4,668 confirmed E. coli isolates were evaluated for resistance to amikacin, ampicillin, cephalothin, chloramphenicol, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline, trimethoprim, and trimethoprim plus sulfamethoxazole. A subset of 1,687 isolates was fingerprinted by repetitive extragenic palindromic PCR (rep-PCR) with the BOXA1R primer to evaluate the diversity and the population structure of the collection. The population in the stored manure was generally more diverse than that in the fresh feces. Half of the genotypes detected in the stored manure were never detected in the fresh fecal material, and only 16% were detected only in the fresh feces. But the majority of the isolates (84%) were assigned to the 34% of genotypes shared between the two environments. The structure of the E. coli population showed important monthly variations both in the extent and distribution of the diversity of the observed genotypes. The frequency of detection of resistance to specific antibiotics was not significantly different between the two collections and varied importantly between monthly samples. Resistance to multiple antibiotics was much more temporally dynamic in the fresh feces than in the stored manure. There was no relationship between the distribution of rep-PCR fingerprints and the distribution of antibiotic resistance profiles, suggesting that specific antibiotic resistance determinants were dynamically distributed within the population.

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Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.737720 ◽

2021 ◽

Vol 8 ◽

Author(s):

Ilias Apostolakos ◽

Andrea Laconi ◽

Lapo Mughini-Gras ◽

Özlem Şahan Yapicier ◽

Alessandra Piccirillo

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Virulence Gene ◽

Genotypic Diversity ◽

Economic Loss ◽

Molecular Characteristics ◽

E Coli ◽

Broiler Production ◽

Pathogenic Escherichia Coli ◽

Production Stages

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal E. coli (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0%) and high (53.3%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.

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Genomic epidemiology and evolution of Escherichia coli in wild animals

10.1101/2020.07.23.216937 ◽

2020 ◽

Author(s):

Robert Murphy ◽

Martin Palm ◽

Ville Mustonen ◽

Jonas Warringer ◽

Anne Farewell ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Host Species ◽

Bacterial Species ◽

Clinical Importance ◽

Wild Animal ◽

Whole Genome ◽

Wild Animals ◽

E Coli ◽

Wild Hosts

AbstractEscherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenic and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in non-human hosts and E. coli in humans is still scarce. In this study, we analysed the whole genome sequencing data of a collection of 119 commensal E. coli recovered from the guts of 68 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli colonizing wild animals and the phylogeny, taxonomy and ecological and physiological attributes of the host species, with distantly related E. coli often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic for Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harboured the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli in wild animal hosts often harboured known antibiotic resistance determinants, including against ciprofloxacin, aminoglycosides, tetracyclines and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that although the genome pools of E. coli colonizing wild animal and human gut are well separated, they share virulence and antibiotic resistance genes and E. coli underscoring that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections.ImportanceEscherichia coli is a clinically importance bacterial species implicated in human and livestock associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock and wild animals. Although wild animals are recognized to serve as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study we used the fine resolution of whole genome sequencing to provide novel insights into the evolution of E. coli genomes within a broad range of wild animal species (including mammals and birds), the co-evolution of E. coli strains with their hosts and the genetics of pathogenicity of E. coli strains in wild hosts. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and necessitate the inclusion of non-human hosts in the surveillance programs for E. coli infections.

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Inhibitor-Resistant TEM- and OXA-1-Producing Escherichia coli Isolates Resistant to Amoxicillin-Clavulanate Are More Clonal and Possess Lower Virulence Gene Content than Susceptible Clinical Isolates

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02738-13 ◽

2014 ◽

Vol 58 (7) ◽

pp. 3874-3881 ◽

Cited By ~ 15

Author(s):

Jesús Oteo ◽

Juan José González-López ◽

Adriana Ortega ◽

J. Natalia Quintero-Zárate ◽

Germán Bou ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Virulence Gene ◽

Control Group ◽

Susceptible Population ◽

Content Type ◽

E Coli ◽

Amoxicillin Clavulanate ◽

Susceptible Control ◽

Control Set

ABSTRACTIn a previous prospective multicenter study in Spain, we found that OXA-1 and inhibitor-resistant TEM (IRT) β-lactamases constitute the most common plasmid-borne mechanisms of genuine amoxicillin-clavulanate (AMC) resistance inEscherichia coli. In the present study, we investigated the population structure and virulence traits of clinical AMC-resistantE. colistrains expressing OXA-1 or IRT and compared these traits to those in a control group of clinical AMC-susceptibleE. coliisolates. All OXA-1-producing (n= 67) and IRT-producing (n= 45) isolates were matched by geographical and temporal origin to the AMC-susceptible control set (n= 56). We performed multilocus sequence typing and phylogenetic group characterization for each isolate and then studied the isolates for the presence of 49 virulence factors (VFs) by PCR and sequencing. The most prevalent clone detected was distinct for each group: group C isolates of sequence type (ST) 88 (C/ST88) were the most common in OXA-1 producers, B2/ST131 isolates were the most common in IRT producers, and B2/ST73 isolates were the most common in AMC-susceptible isolates. The median numbers of isolates per ST were 3.72 in OXA-1 producers, 2.04 in IRT producers, and 1.69 in AMC-susceptible isolates; the proportions of STs represented by one unique isolate in each group were 19.4%, 31.1%, and 48.2%, respectively. The sum of all VFs detected, calculated as a virulence score, was significantly higher in AMC-susceptible isolates than OXA-1 and IRT producers (means, 12.5 versus 8.3 and 8.2, respectively). Our findings suggest that IRT- and OXA-1-producingE. coliisolates resistant to AMC have a different and less diverse population structure than AMC-susceptible clinicalE. coliisolates. The AMC-susceptible population also contains more VFs than AMC-resistant isolates.

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A 21-year survey of Escherichia coli from bloodstream infections (BSIs) in a tertiary hospital reveals how community-hospital dynamics, influence local BSI rates, the trends of the B2 phylogroup and the STc131 pandemic clone

10.1101/2020.04.10.034777 ◽

2020 ◽

Author(s):

Irene Rodríguez ◽

Ana Sofia Figueiredo ◽

Melissa Sousa ◽

Val F. Lanza ◽

Concepción Rodríguez ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Gut Microbiota ◽

Bloodstream Infections ◽

Tertiary Hospital ◽

Multidrug Resistant ◽

Laboratory System ◽

Phylogenetic Groups ◽

E Coli ◽

Hospital Acquired

ABSTRACTEscherichia coli is overrepresented in all bloodstream infections (BSIs) series, mostly associated with a few clonal lineages. Its population structure has been analyzed but the dynamics remains to be fully understood. We analyze the dynamics of E. coli-BSIs in a sample of 649 isolates, representing all 7165 E. coli BSI episodes recorded in a tertiary hospital (1996-2016) according to clonal identification (phylogenetic groups/subgroups, STc131 subclades), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs, 29 genes). Patient data were obtained from the laboratory system and clinical charts. The incidence of BSI-EC doubled from 1996 to 2016 (5.5 to 10.8 BSI episodes/1000 hospitalizations). Intertwined waves of community-acquired (CA) and hospital-acquired isolates (HA) episodes of both B2 and non-B2 phylogroups, occurred until B2 overtook non-B2 BSI episodes. ST131 contributed to increasing the B2 rates, but only transiently altered the population structure. B2 isolates predominates (53%), overrepresented by subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI (25%, 25%, 14%, and 9%). We observed a remarkable increase only for B2-I-STc131 (C1/C2 subclades), a decreasing trend for phylogroup D, and oscillations for other B2 subgroups throughout the years. According to VAG patterns, B2 strains exhibit a population structure compatible with the niche specialization theory. A reservoir of B2 and non-B2 strains represented in human microbiota, flows from the community to the hospital and vice-versa, where they can either be selected or coexist. The increase of BSI is determined by waves of CA that predate the amplification of HA episodes of both B2 and non-B2 phylogroups in various time periods, influenced by FQR and microbiota composition.IMPORTANCEThe gut microbiota is an important reservoir for bacteria that cause extraintestinal infections including sepsis, which is the third cause of mortality in Western countries and one of the Global Health threads recognized by the WHO since 2017. Most of the bloodstream infections (BSI) and UTIs due to Escherichia coli strains originate in the gut microbiota and belong to the phylogenetic group B2. Most B2 strains recovered from BSI infections are clonal lineages predominant in fecal isolates, often associated with outbreaks. Our study analyzes the long-term dynamics of B2 E. coli subtypes and reveals waves of different E.coli lineages including pandemic clones that emerge periodically and are established in the intestinal microbiota afterward. It also reflects that clonal amplifications in the community predates the clonal increases in hospitals which may favor the acquisition of antibiotic resistance in health centers and further dissemination of well adapted clones that become multidrug resistant.

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Niche preference of Escherichia coli in a peri-urban pond ecosystem

10.1101/2020.01.30.926667 ◽

2020 ◽

Cited By ~ 1

Author(s):

Gitanjali NandaKafle ◽

Taylor Huegen ◽

Sarah C. Potgieter ◽

Emma Steenkamp ◽

Stephanus N. Venter ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Flow Analysis ◽

Virulence Gene ◽

Phenotypic Traits ◽

E Coli ◽

Population Structure Analysis ◽

Pond Ecosystem ◽

Disk Diffusion Assay ◽

Urban Pond

AbstractEscherichia coli comprises of diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity / virulence genes (stxI, stxII, eaeA, hlyA, ST and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azitrhomycin. Our results showed that isolates from water, sediment and water plants were similar by phylogroup distribution, virulence gene distribution and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.

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Niche Preference of Escherichia coli in a Peri-Urban Pond Ecosystem

Life ◽

10.3390/life11101020 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1020

Author(s):

Gitanjali NandaKafle ◽

Taylor Huegen ◽

Sarah C. Potgieter ◽

Emma Steenkamp ◽

Stephanus N. Venter ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Flow Analysis ◽

Virulence Gene ◽

Phenotypic Traits ◽

E Coli ◽

Population Structure Analysis ◽

Pond Ecosystem ◽

Disk Diffusion Assay ◽

Urban Pond

Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond, as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity/virulence genes (stxI, stxII, eaeA, hlyA, ST, and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azithromycin. Our results showed that isolates from water, sediment, and water plants were similar by phylogroup distribution, virulence gene distribution, and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail, and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.

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Impermanence of bacterial clones

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1501724112 ◽

2015 ◽

Vol 112 (29) ◽

pp. 8893-8900 ◽

Cited By ~ 20

Author(s):

Louis-Marie Bobay ◽

Charles C. Traverse ◽

Howard Ochman

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

Homologous Recombination ◽

Bacterial Species ◽

Reproductive Mode ◽

Unique Sequence ◽

Gene Exchange ◽

E Coli ◽

Large Samples ◽

Single Genome

Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied inEscherichia colifor over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on theE. coligenome.

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Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkz366 ◽

2019 ◽

Vol 74 (12) ◽

pp. 3489-3496 ◽

Cited By ~ 10

Author(s):

María Pérez-Vázquez ◽

Pedro J Sola Campoy ◽

Adriana Ortega ◽

Verónica Bautista ◽

Sara Monzón ◽

...

Keyword(s):

Escherichia Coli ◽

Population Structure ◽

High Risk ◽

High Resolution ◽

Klebsiella Pneumoniae ◽

Core Genome ◽

Acquired Resistance ◽

Variable Region ◽

E Coli ◽

The Impact

Abstract Objectives NDM carbapenemases have spread worldwide. However, little information exists about the impact of NDM-producing Enterobacteriaceae in Spain. By WGS, we sought to elucidate the population structure of NDM-like-producing Klebsiella pneumoniae and Escherichia coli in Spain and to determine the plasmids harbouring blaNDM-like genes. Methods High-resolution SNP typing, core-genome MLST and plasmid reconstruction (PlasmidID) were performed on 59 NDM-like-producing K. pneumoniae and 8 NDM-like-producing E. coli isolated over an 8 year period in Spain. Results Five major epidemic clones of NDM-producing K. pneumoniae caused five important nationwide outbreaks: ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1; in contrast, the spread of NDM-producing E. coli was polyclonal. Three blaNDM types were identified: blaNDM-1, 61.2%; blaNDM-7, 32.8%; and blaNDM-5, 6%. Five K. pneumoniae isolates co-produced other carbapenemases (three blaOXA-48 and two blaVIM-1). The average number of acquired resistance genes was higher in K. pneumoniae than in E. coli. The plasmids encoding blaNDM-like genes belonged to IncFII, IncFIB, IncX3, IncR, IncN and IncC types, of which IncF, IncR and IncC were associated with MDR. The genetic surroundings of blaNDM-like genes showed a highly variable region upstream of ISAba125. Conclusions In recent years NDM-producing K. pneumoniae and E. coli have emerged in Spain; the spread of a few high-risk K. pneumoniae clones such as ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1 have caused several interregional outbreaks. In contrast, the spread of NDM-producing E. coli has been polyclonal. Plasmid types IncFII, IncFIB, IncX3, IncR, IncN and IncC carried blaNDM, and the same IncX3 plasmid was detected in K. pneumoniae and E. coli.

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