Interrogating genomic diversity of E. coli O157:H7 using DNA tiling arrays

AbstractAquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

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Applications of DNA tiling arrays for whole-genome analysis

Genomics ◽

10.1016/j.ygeno.2004.10.005 ◽

2005 ◽

Vol 85 (1) ◽

pp. 1-15 ◽

Cited By ~ 250

Author(s):

Todd C. Mockler ◽

Joseph R. Ecker

Keyword(s):

Genome Analysis ◽

Whole Genome ◽

Whole Genome Analysis ◽

Tiling Arrays ◽

Dna Tiling

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Species-Wide Collection of Escherichia coli Isolates for Examination of Genomic Diversity

Genome Announcements ◽

10.1128/genomea.01321-17 ◽

2017 ◽

Vol 5 (50) ◽

Cited By ~ 6

Author(s):

Jayanthi Gangiredla ◽

Mark K. Mammel ◽

Tammy J. Barnaba ◽

Carmen Tartera ◽

Solomon T. Gebru ◽

...

Keyword(s):

Escherichia Coli ◽

Human Health ◽

Potential Risk ◽

Phylogenetic Relationships ◽

Genomic Diversity ◽

Genome Sequences ◽

Content Type ◽

E Coli

ABSTRACT Pathogenic and nonpathogenic Escherichia coli strains present a vast genomic diversity. We report the genome sequences of 2,244 E. coli isolates from multiple animal and environmental sources. Their phylogenetic relationships and potential risk to human health were examined.

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Comparison of the Microbial Quality of Lamb and Goat Meat Acquired from Internet and Local Retail Markets†

Journal of Food Protection ◽

10.4315/0362-028x.jfp-15-026 ◽

2015 ◽

Vol 78 (11) ◽

pp. 1980-1987 ◽

Cited By ~ 3

Author(s):

CHYER KIM ◽

ROSLYN A. STEIN ◽

STEVEN PAO

Keyword(s):

Meat Products ◽

Genomic Diversity ◽

Microbial Quality ◽

Ground Meat ◽

Retail Markets ◽

Goat Meat ◽

E Coli ◽

High Prevalence ◽

Pfge Profiles

This study was conducted to evaluate the microbial quality of lamb and goat meat sold through local (Virginia) and Internet (U.S.) retail markets. A total of 134 frozen meat products consisting of locally purchased lamb ground (LLG) and lamb chops and Internet-procured lamb ground, goat ground, lamb chops (ILC), goat chops (IGC), lamb stew, and goat stew were tested. Significantly higher levels of aerobic mesophiles, psychrotrophs, and coliforms were found in the meat locally acquired than in the meat procured from the Internet. Similar average prevalence (27%) of Escherichia coli was observed regardless of market source. Ground meat had significantly high levels and prevalence of mesophiles, psychrotrophs, coliforms, and Listeria spp. One sample of LLG contained Campylobacter, and one sample of IGC contained Salmonella. Listeria spp. were present in 23 to 40% and 17 to 80% of samples from local and Internet markets, respectively. Pulsed-field gel electrophoresis (PFGE) of isolated E. coli strains revealed brand specificity and genomic diversity. No isolate from different brands and market sources had matching PFGE profiles. The average price of Internet meat ($23.4/kg) was about 1.2 times higher than the price of local meat, except for ILC, whose price was 2.7 times higher. This study revealed differences in microbial quality of lamb and goat meat based on market source; thus, meat products should be handled carefully regardless of market source because of the presence of high microbial levels and the high prevalence of pathogens.

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Genomic Diversity and Virulence Profiles of Historical Escherichia coli O157 Strains Isolated from Clinical and Environmental Sources

Applied and Environmental Microbiology ◽

10.1128/aem.02616-14 ◽

2014 ◽

Vol 81 (2) ◽

pp. 569-577 ◽

Cited By ~ 8

Author(s):

Lydia V. Rump ◽

Narjol Gonzalez-Escalona ◽

Wenting Ju ◽

Fei Wang ◽

Guojie Cao ◽

...

Keyword(s):

Escherichia Coli ◽

The United States ◽

Genomic Diversity ◽

Severe Illness ◽

Pathogenic Potential ◽

Content Type ◽

E Coli ◽

Virulence Markers ◽

Virulence Potential ◽

Food Borne

ABSTRACTEscherichia coliO157:H7 is, to date, the majorE. coliserotype causing food-borne human disease worldwide. Strains of O157 with other H antigens also have been recovered. We analyzed a collection of historic O157 strains (n= 400) isolated in the late 1980s to early 1990s in the United States. Strains were predominantly serotype O157:H7 (55%), and various O157:non-H7 (41%) serotypes were not previously reported regarding their pathogenic potential. Although lacking Shiga toxin (stx) andeaegenes, serotypes O157:H1, O157:H2, O157:H11, O157:H42, and O157:H43 carried several virulence factors (iha,terD, andhlyA) also found in virulent serotypeE. coliO157:H7. Pulsed-field gel electrophoresis (PFGE) showed the O157 serogroup was diverse, with strains with the same H type clustering together closely. Among non-H7 isolates, serotype O157:H43 was highly prevalent (65%) and carried important enterohemorrhagicE. coli(EHEC) virulence markers (iha,terD,hlyA, andespP). Isolates from two particular H types, H2 and H11, among the most commonly found non-O157 EHEC serotypes (O26:H11, O111:H11, O103:H2/H11, and O45:H2), unexpectedly clustered more closely with O157:H7 than other H types and carried several virulence genes. This suggests an early divergence of the O157 serogroup to clades with different pathogenic potentials. The appearance of important EHEC virulence markers in closely related H types suggests their virulence potential and suggests further monitoring of those serotypes not implicated in severe illness thus far.

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Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.636715 ◽

2021 ◽

Vol 8 ◽

Author(s):

Joshua Mbanga ◽

Daniel G. Amoako ◽

Akebe L. K. Abia ◽

Mushal Allam ◽

Arshad Ismail ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Treatment Plant ◽

Multidrug Resistant ◽

Genomic Diversity ◽

Health Concern ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

E Coli ◽

Wwtp Effluent

There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the blaTEM1B gene and a single isolate the blaCTX−M−14 and blaCTX−M−55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.

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Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli

Frontiers in Microbiology ◽

10.3389/fmicb.2021.642125 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ama Szmolka ◽

Haleluya Wami ◽

Ulrich Dobrindt

Keyword(s):

Resistance Genes ◽

Genetic Interaction ◽

Bacterial Species ◽

Enteric Bacteria ◽

Genomic Diversity ◽

Comparative Genomic ◽

Broiler Chicks ◽

Simultaneous Presence ◽

E Coli ◽

Insight Into

IntroductionCommensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants.ObjectivesIn order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources.ResultsThe core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers.ConclusionThis is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.

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Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar

Frontiers in Microbiology ◽

10.3389/fmicb.2021.786146 ◽

2021 ◽

Vol 12 ◽

Author(s):

Milen Milenkov ◽

Saida Rasoanandrasana ◽

Lalaina Vonintsoa Rahajamanana ◽

Rivo Solo Rakotomalala ◽

Catherine Ainamalala Razafindrakoto ◽

...

Keyword(s):

Public Health ◽

Risk Factors ◽

Pregnant Women ◽

Large Scale ◽

Genomic Diversity ◽

World Health ◽

Health Concern ◽

Snp Analysis ◽

Phylogenetic Groups ◽

E Coli

Antimicrobial resistance is a major public health concern worldwide affecting humans, animals and the environment. However, data is lacking especially in developing countries. Thus, the World Health Organization developed a One-Health surveillance project called Tricycle focusing on the prevalence of ESBL-producing Escherichia coli in humans, animals, and the environment. Here we present the first results of the human community component of Tricycle in Madagascar. From July 2018 to April 2019, rectal swabs from 492 pregnant women from Antananarivo, Mahajanga, Ambatondrazaka, and Toamasina were tested for ESBL-E. coli carriage. Demographic, sociological and environmental risk factors were investigated, and E. coli isolates were characterized (antibiotic susceptibility, resistance and virulence genes, plasmids, and genomic diversity). ESBL-E. coli prevalence carriage in pregnant women was 34% varying from 12% (Toamasina) to 65% (Ambatondrazaka). The main risk factor associated with ESBL-E. coli carriage was the rainy season (OR = 2.9, 95% CI 1.3–5.6, p = 0.009). Whole genome sequencing was performed on 168 isolates from 144 participants. blaCTX–M–15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the blaNDM–5 gene. Most isolates belonged to commensalism associated phylogenetic groups A, B1, and C (90%) and marginally to extra-intestinal virulence associated phylogenetic groups B2, D and F (10%). Multi locus sequence typing showed 67 different sequence types gathered in 17 clonal complexes (STc), the most frequent being STc10/phylogroup A (35%), followed distantly by the emerging STc155/phylogroup B1 (7%), STc38/phylogroup D (4%) and STc131/phylogroup B2 (3%). While a wide diversity of clones has been observed, SNP analysis revealed several genetically close isolates (n = 34/168) which suggests human-to-human transmissions. IncY plasmids were found with an unusual prevalence (23%), all carrying a blaCTX–M–15. Most of them (85%) showed substantial homology (≥85%) suggesting a dissemination of IncY ESBL plasmids in Madagascar. This large-scale study reveals a high prevalence of ESBL-E. coli among pregnant women in four cities in Madagascar associated with warmth and rainfall. It shows the great diversity of E. coli disseminating throughout the country but also transmission of specific clones and spread of plasmids. This highlights the urgent need of public-health interventions to control antibiotic resistance in the country.

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The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

Journal of Bacteriology ◽

10.1128/jb.00619-08 ◽

2008 ◽

Vol 190 (20) ◽

pp. 6881-6893 ◽

Cited By ~ 499

Author(s):

David A. Rasko ◽

M. J. Rosovitz ◽

Garry S. A. Myers ◽

Emmanuel F. Mongodin ◽

W. Florian Fricke ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequencing ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Genomic Diversity ◽

Comparative Genomic ◽

Whole Genome ◽

E Coli ◽

Important Group ◽

Commensal Species

ABSTRACT Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

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625. Genomic Epidemiology of Carbapenem-Resistant Enterobacteriaceae from Colombia: A Prospective Multicenter Study

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.693 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S290-S290 ◽

Cited By ~ 1

Author(s):

Jinnethe Reyes ◽

Lorena Diaz ◽

Lina P Carvajal ◽

Rafael Rios ◽

Lina V Millan ◽

...

Keyword(s):

High Risk ◽

Genomic Diversity ◽

Common Mechanism ◽

Genetic Lineage ◽

Genetic Lineages ◽

E Coli ◽

Genomic Epidemiology ◽

Carbapenem Resistant ◽

Number Of Patients ◽

Carbapenem Resistant Enterobacteriaceae

Abstract Background Carbapenem-resistant Enterobacteriaceae (CRE) is a serious public health threat. A major epidemic of carbapenemase-producing Klebsiella pneumoniae has occurred in Colombia through complex mechanisms of blaKPC dissemination. In the framework of a prospective, observational cohort study (CRACKLE-2), we aimed to characterize the genomic epidemiology of CRE circulating in Colombia. Methods We performed whole-genome sequencing of 52 isolates collected from the same number of patients (July 2017–April 2018) in 5 Colombian hospitals. Species confirmation and sequence type were determined using Strain Seeker and MLST database. Resistance genes were detected using ResFinder and CARD databases. Phylogenetic reconstruction included additional 108 isolates of carbapenem-resistant K. pneumoniae from a previous study. Results K. pneumoniae (36%), Escherichia coli (17%), and Enterobacter cloacae complex(17%) were the most frequent species. Genes conferring resistance to carbapenems were detected in 93% of isolates. blaKPC-2/3,blaNDM-1 andblaVIM-2/24 were identified in 81%, 15%, and 5% of isolates, respectively. Phylogenetic reconstructions of K. pneumoniae showed that clonal group 258 (CG258) were the predominant genetic lineage (Figure 1). Among CG258, ST11 was the most common comprising ca. 26% of isolates. Of note, ST11 had been extremely rare in previous surveillance studies in Colombia. The non-CG258 were from 9 different STs and exhibited high genomic diversity. Among E. coli isolates 33% belonged to the high-risk clone ST131 harboring blaKPC-2 and we detected both blaKPC-2 and blaVIM-24 in 1 E. coli ST131 isolate. ST510 E. cloacae complex harboring blaKPC-2 was the most common (44%) lineage. Conclusion K. pneumoniae and E. coli are the most frequent CRE isolated from patients in Colombian hospitals. Dissemination of blaKPC through horizontal gene transfer to several species of Enterobacteriaceae continues to be a common mechanism of spread. Although KPC continues to be the most common carbapenemase, a rise in high-risk clonal lineages harboring metallo-carbapenemases, in particular NDM-1 is worrisome. Our results indicate emergence of virulent genetic lineages of K. pneumoniae ST11 and E. coli ST131 carrying carbapenemases in Colombia. Disclosures All authors: No reported disclosures.

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