scholarly journals Bacterial “Virulence” Traits and Host Demographics Predict Escherichia coli Colonization Behaviors Within Households

2020 ◽  
Vol 7 (11) ◽  
Author(s):  
Teresa C Fox ◽  
Connie Clabots ◽  
Stephen B Porter ◽  
Tricia Bender ◽  
Paul Thuras ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Clinical Isolate ◽  
Virulence Genes ◽  
Bacterial Virulence ◽  
E Coli ◽  
Alpha Hemolysin ◽  
Virulence Traits ◽  
Colonization Patterns ◽  
Colonization Behavior ◽  
Fecal Sampling

Abstract Background Although intestinal colonization precedes most extraintestinal Escherichia coli infections, colonization-promoting factors are incompletely understood. We compared within-household E. coli colonization patterns with host and bacterial traits. Methods Twenty-two veterans with a clinical E. coli isolate and their 46 human and animal household members underwent longitudinal fecal sampling. Distinct E. coli strains were characterized for phylogenetic background, virulence genes, antibiotic resistance, and colonization behaviors. Host and bacterial traits were assessed statistically as predictors of colonization behaviors. Results Among the 139 unique-by-household fecal E. coli strains, univariable predictors of colonization behavior included (i) host demographics, (ii) matching the index clinical isolate, and (iii) bacterial characteristics (2 phylogroups, 5 clonal lineages, 18 virulence genes, and molecular extraintestinal pathogenic E. coli status). Multivariable predictors of colonization behavior included veteran host, spouse host, matching the index clinical isolate, phylogroup F, ST73, hlyD (alpha hemolysin), hlyF (variant hemolysin), H7 fliC (flagellar variant), vat (vacuolating toxin), and iha (adhesin-siderophore). Conclusions Host demographics, multiple bacterial “virulence” traits, and matching the index clinical isolate predicted E. coli fecal colonization behaviors. Thus, certain bacterial characteristics may promote both colonization and pathogenicity. Future interventions directed toward such traits might prevent E. coli infections both directly and by disrupting antecedent colonization.

scholarly journals 2609. Escherichia coli Clonal Lineages and Virulence Factors Predict Fecal Colonization within Households

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S907-S907
Author(s):  
Teresa C Fox ◽  
Paul Thuras ◽  
Connie Clabots ◽  
Stephen Porter ◽  
James R Johnson
Keyword(s):  
Escherichia Coli ◽  
Clinical Isolate ◽  
Virulence Factors ◽  
Outcome Variable ◽  
E Coli ◽  
Wilcoxon Rank Sum Test ◽  
Colonization Patterns ◽  
Stool Samples ◽  
Colonization Factors ◽  
Colonization Behavior

Abstract Background Extraintestinal Escherichia coli infections are an ever-growing threat, to which specific clonal lineages and virulence factors contribute disproportionately. Despite the gut being the main reservoir for such E. coli strains, relationships between clonal lineages, virulence factors, and fecal colonization patterns are poorly understood. Accordingly, we defined E. coli fecal colonization patterns within households (HHs) and assessed specific lineages and virulence genes (VGs) as predictors of colonization behaviors. Methods Veterans with an E. coli clinical isolate (n = 22: 11 fluoroquinoline [FQ]-resistant, 11 FQ-susceptible) and their HH members provided stool samples on 2–6 occasions each. Stools were screened for total and FQ-resistant E. coli. Distinct E. coli strains were resolved by genomic profiling of 10 colonies/sample. Strains underwent molecular lineage identification, VG detection, and comparison with the veteran’s clinical isolate. Clonal lineages and VGs were assessed (Wilcoxon rank-sum test) as predictors of strains’ (i) predominance within the fecal sample, (ii) persistence across serial fecal samples, (iii) within-HH strain sharing, and (iv) overall within-HH colonization prevalence. Results From the 22 veterans and 46 HH members (27 humans, 19 pets) we recovered 139 unique-by-household fecal E. coli strains. Sixty-four traits were evaluated (16 clonal lineages, 48 VGs). Of these, 44 exhibited n ≥ 5, so could be analyzed statistically. Among these 44 traits, the proportion significantly associated with ≥ 1 outcome variable was 5/6 (83%) for clonal lineages and 18/38 (47%) for VGs. Additionally, fecal strains that matched the veteran’s clinical isolate exhibited significantly greater sharing, persistence, and overall colonization. Conclusion The studied E. coli traits – known for their associations with clinical infections –here were significantly associated with within-HH colonization behavior. These findings support that “virulence factors” may be regarded also (or perhaps best) as “colonization factors,” and “virulent lineages” as “colonizing lineages.” This suggests the possibility that future interventions that disrupt colonization behavior also could prevent E. coli infections. Disclosures All authors: No reported disclosures.

scholarly journals Diversity of P1 phage-like elements in multidrug resistant Escherichia coli

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Carola Venturini ◽  
Tiziana Zingali ◽  
Ethan R. Wyrsch ◽  
Bethany Bowring ◽  
Jonathan Iredell ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Clinical Isolate ◽  
Insertion Sequence ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Resistance Markers

AbstractThe spread of multidrug resistance via mobile genetic elements is a major clinical and veterinary concern. Pathogenic Escherichia coli harbour antibiotic resistance and virulence genes mainly on plasmids, but also bacteriophages and hybrid phage-like plasmids. In this study, the genomes of three E. coli phage-like plasmids, pJIE250-3 from a human E. coli clinical isolate, pSvP1 from a porcine ETEC O157 isolate, and pTZ20_1P from a porcine commensal E. coli, were sequenced (PacBio RSII), annotated and compared. All three elements are coliphage P1 variants, each with unique adaptations. pJIE250-3 is a P1-derivative that has lost lytic functions and contains no accessory genes. In pTZ20_1P and pSvP1, a core P1-like genome is associated with insertion sequence-mediated acquisition of plasmid modules encoding multidrug resistance and virulence, respectively. The transfer ability of pTZ20_1P, carrying antibiotic resistance markers, was also tested and, although this element was not able to transfer by conjugation, it was able to lysogenize a commensal E. coli strain with consequent transfer of resistance. The incidence of P1-like plasmids (~7%) in our E. coli collections correlated well with that in public databases. This study highlights the need to investigate the contribution of phage-like plasmids to the successful spread of antibiotic resistant pathotypes.

scholarly journals DNA Sequence of a ColV Plasmid and Prevalence of Selected Plasmid-Encoded Virulence Genes among Avian Escherichia coli Strains

2006 ◽  
Vol 188 (2) ◽  
pp. 745-758 ◽  
Author(s):  
Timothy J. Johnson ◽  
Kylie E. Siek ◽  
Sara J. Johnson ◽  
Lisa K. Nolan
Keyword(s):  
Escherichia Coli ◽  
Dna Sequence ◽  
Transport System ◽  
Iron Transport ◽  
Virulence Genes ◽  
Iron Acquisition ◽  
Transport Systems ◽  
E Coli ◽  
Virulence Traits ◽  
Associated Sequences

ABSTRACT ColV plasmids have long been associated with the virulence of Escherichia coli, despite the fact that their namesake trait, ColV production, does not appear to contribute to virulence. Such plasmids or their associated sequences appear to be quite common among avian pathogenic E. coli (APEC) and are strongly linked to the virulence of these organisms. In the present study, a 180-kb ColV plasmid was sequenced and analyzed. This plasmid, pAPEC-O2-ColV, possesses a 93-kb region containing several putative virulence traits, including iss, tsh, and four putative iron acquisition and transport systems. The iron acquisition and transport systems include those encoding aerobactin and salmochelin, the sit ABC iron transport system, and a putative iron transport system novel to APEC, eit. In order to determine the prevalence of the virulence-associated genes within this region among avian E. coli strains, 595 APEC and 199 avian commensal E. coli isolates were examined for genes of this region using PCR. Results indicate that genes contained within a portion of this putative virulence region are highly conserved among APEC and that the genes of this region occur significantly more often in APEC than in avian commensal E. coli. The region of pAPEC-O2-ColV containing genes that are highly prevalent among APEC appears to be a distinguishing trait of APEC strains.

scholarly journals The Ferric Citrate Uptake System Encoded in a Novel blaCTX–M–3- and blaTEM–1-Harboring Conjugative Plasmid Contributes to the Virulence of Escherichia coli

2021 ◽  
Vol 12 ◽  
Author(s):  
Wen-Chun Huang ◽  
Min-Yi Wong ◽  
Ssu-Han Wang ◽  
Masayuki Hashimoto ◽  
Meng-He Lin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Clinical Isolate ◽  
Iron Uptake ◽  
Virulence Genes ◽  
Ferric Citrate ◽  
Conjugative Plasmid ◽  
E Coli ◽  
Conjugative Plasmids ◽  
Tract Infections

Escherichia coli is one major cause of bacterial infections and can horizontally acquire antimicrobial resistance and virulence genes through conjugation. Because conjugative plasmids can rapidly spread among bacteria of different species, the plasmids carrying both antimicrobial resistance and virulence genes may pose a significant threat to public health. Therefore, the identification and characterization of these plasmids may facilitate a better understanding of E. coli pathogenesis and the development of new strategies against E. coli infections. Because iron uptake ability is a potential virulence trait of bacteria, we screened for E. coli conjugative plasmids able to confer both iron uptake ability and ampicillin resistance. The plasmid pEC41, which was derived from the bacteremia clinical isolate EC41, was identified. EC41, which carried the fimH27 allele, belonged to sequence type (ST) 405 and phylogroup D. According to the sequencing analyses, pEC41 was 86 kb in size, and its backbone structure was almost identical to that of another highly conjugative plasmid, pCTX-M3, in which the extended-spectrum β-lactamase gene blaCTX–M–3 was originally identified. pEC41 carried blaCTX–M–3 and blaTEM–1. The ferric citrate uptake (fec) system was identified in pEC41 and was responsible for conferring iron uptake ability. The fec system contributes to the pathogenesis of EC41 in systemic infections but not in urinary tract infections (UTIs). However, this system promoted competitive fitness of a cystitis-associated clinical isolate to colonize urinary tracts. Additionally, the distribution of the fec system was related to E. coli isolates associated with human bacteremia and UTIs. In summary, the present study identified a novel conjugative plasmid, pEC41, which conferred both antimicrobial resistance and an extra iron uptake ability to E. coli. The iron uptake ability was encoded in the fec system and contributed to E. coli pathogenesis. This study is the first to show that the fec system is a virulence factor in E. coli.

scholarly journals Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

2021 ◽  
Vol 22 (11) ◽  
pp. 5905
Author(s):  
Olivia M. Grünzweil ◽  
Lauren Palmer ◽  
Adriana Cabal ◽  
Michael P. Szostak ◽  
Werner Ruppitsch ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Marine Mammals ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Healthcare Sector ◽  
Whole Genome ◽  
E Coli ◽  
High Prevalence ◽  
Lactamase Gene ◽  
Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals Assessing the population dynamics of Escherichia coli in a metropolitan river after an extreme flood event

2016 ◽  
Vol 15 (2) ◽  
pp. 196-208 ◽  
Author(s):  
Nicole M. Masters ◽  
Aaron Wiegand ◽  
Jasmin M. Thompson ◽  
Tara L. Vollmerhausen ◽  
Eva Hatje ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Dynamics ◽  
Antibiotic Resistance ◽  
Virulence Genes ◽  
Wastewater Treatment Plants ◽  
Vero Cells ◽  
Flood Event ◽  
Typing Method ◽  
E Coli ◽  
Extreme Flood

We investigated Escherichia coli populations in a metropolitan river after an extreme flood event. Between nine and 15 of the 23 selected sites along the river were sampled fortnightly over three rounds. In all, 307 E. coli were typed using the PhP typing method and were grouped into common (C) or single (S) biochemical phenotypes (BPTs). A representative from each of the 31 identified C-BPTs was tested for 58 virulence genes (VGs) associated with intestinal and extra-intestinal E. coli, resistance to 22 antibiotics, production of biofilm and cytotoxicity to Vero cells. The number of E. coli in the first sampling round was significantly (P < 0.01) higher than subsequent rounds, whereas the number of VGs was significantly (P < 0.05) higher in isolates from the last sampling round when compared to previous rounds. Comparison of the C-BPTs with an existing database from wastewater treatment plants (WWTPs) in the same catchment showed that 40.6% of the river isolates were identical to the WWTP isolates. The relatively high number of VGs and antibiotic resistance among the C-BPTs suggests possessing and retaining these genes may provide niche advantages for those naturalised and/or persistent E. coli populations which may pose a health risk to the community.

Multiplex Quantitative PCR Assays for the Detection and Quantification of the Six Major Non-O157 Escherichia coli Serogroups in Cattle Feces†

2016 ◽  
Vol 79 (1) ◽  
pp. 66-74 ◽  
Author(s):  
P. B. SHRIDHAR ◽  
L. W. NOLL ◽  
X. SHI ◽  
B. AN ◽  
N. CERNICCHIARO ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Quantitative Pcr ◽  
Foodborne Pathogens ◽  
Virulence Genes ◽  
Target Genes ◽  
Culture Methods ◽  
Fecal Samples ◽  
E Coli ◽  
Cattle Feces ◽  
Before And After

ABSTRACT Shiga toxin–producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, and O145, called non-O157 STEC, are important foodborne pathogens. Cattle, a major reservoir, harbor the organisms in the hindgut and shed them in the feces. Although limited data exist on fecal shedding, concentrations of non-O157 STEC in feces have not been reported. The objectives of our study were (i) to develop and validate two multiplex quantitative PCR (mqPCR) assays, targeting O-antigen genes of O26, O103, and O111 (mqPCR-1) and O45, O121, and O145 (mqPCR-2); (ii) to utilize the two assays, together with a previously developed four-plex qPCR assay (mqPCR-3) targeting the O157 antigen and three virulence genes (stx1, stx2, and eae), to quantify seven serogroups and three virulence genes in cattle feces; and (iii) to compare the three mqPCR assays to a 10-plex conventional PCR (cPCR) targeting seven serogroups and three virulence genes and culture methods to detect seven E. coli serogroups in cattle feces. The two mqPCR assays (1 and 2) were shown to be specific to the target genes, and the detection limits were 4 and 2 log CFU/g of pure culture–spiked fecal samples, before and after enrichment, respectively. A total of 576 fecal samples collected from a feedlot were enriched in E. coli broth and were subjected to quantification (before enrichment) and detection (after enrichment). Of the 576 fecal samples subjected, before enrichment, to three mqPCR assays for quantification, 175 (30.4%) were quantifiable (≥4 log CFU/g) for at least one of the seven serogroups, with O157 being the most common serogroup. The three mqPCR assays detected higher proportions of postenriched fecal samples (P < 0.01) as positive for one or more serogroups compared with cPCR and culture methods. This is the first study to assess the applicability of qPCR assays to detect and quantify six non-O157 serogroups in cattle feces and to generate data on fecal concentration of the six serogroups.

scholarly journals The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France

2021 ◽  
Author(s):  
Julie Marin ◽  
Olivier Clermont ◽  
Guilhem Royer ◽  
Melanie Mercier-Darty ◽  
Jean-Winoc Decousser ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
High Risk ◽  
Virulence Genes ◽  
Population Genomics ◽  
E Coli ◽  
O Antigen ◽  
Similar Region ◽  
Intestinal Infections ◽  
Evolution Of Virulence

Escherichia coli is a commensal species of the lower intestine, but also a major pathogen causing intestinal and extra-intestinal infections. Most studies on genomic evolution of E. coli used isolates from infections, and/or focused on antibiotic resistance, but neglected the evolution of virulence. Here instead, we whole-genome sequenced a collection of 436 E. coli isolated from fecal samples of healthy adult volunteers in France between 1980 and 2010. These isolates were distributed among 159 sequence types (STs), the five most frequent being ST10 (15.6%), ST73 (5.5%) and ST95 (4.8%), ST69 (3.7%) and ST59 (3.7%), and 230 O:H serotypes. ST and serotype diversity increased over time. Comparison with 912 E. coli bacteremia isolates from similar region and time showed a greater diversity in commensal isolates. The O1, O2, O6 and O25-groups used in bioconjugate O-antigen vaccine were found in only 63% of the four main STs associated with a high risk of bacteremia (ST69, ST73, ST95 and ST131). In commensals, STs associated with a high risk of bacteremia increased in frequency. Both extra-intestinal virulence-associated genes and resistance to antibiotics increased in frequency. Evolution of virulence genes was driven by both clonal expansion of STs with more virulence genes, and increases in frequency within STs, whereas the evolution of resistance was dominated by increases in frequency within STs. This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over a 30-year period and suggests that the efficacy of O-antigen vaccines would be threatened by serotype replacement.

scholarly journals Molecular characterisation of antimicrobial resistance and virulence genes in Escherichia coli strains isolated from diarrhoeic and healthy rabbits in Tunisia

2020 ◽  
Vol 28 (2) ◽  
pp. 81
Author(s):  
Raouia Ben Rhouma ◽  
Ahlem Jouini ◽  
Amira Klibi ◽  
Safa Hamrouni ◽  
Aziza Boubaker ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Antimicrobial Agents ◽  
Antibiotic Resistance Genes ◽  
Virulence Gene ◽  
Diffusion Method ◽  
Class 1 Integron ◽  
E Coli ◽  
Class 1

The purpose of this study was to identify <em>Escherichia coli</em> isolates in diarrhoeic and healthy rabbits in Tunisia and characterise their virulence and antibiotic resistance genes. In the 2014-2015 period, 60 faecal samples from diarrhoeic and healthy rabbits were collected from different breeding farms in Tunisia. Susceptibility to 14 antimicrobial agents was tested by disc diffusion method and the mechanisms of gene resistance were evaluated using polymerase chain reaction and sequencing methods. Forty <em>E. coli</em> isolates were recovered in selective media. High frequency of resistance to tetracycline (95%) was detected, followed by different levels of resistance to sulphonamide (72.5%), streptomycin (62.5%), trimethoprim-sulfamethoxazole (60%), nalidixic acid (32.5%), ampicillin (37.5%) and ticarcillin (35%). <em>E. coli</em> strains were susceptible to cefotaxime, ceftazidime and imipenem. Different variants of bla<sub>TEM</sub>, <em>tet</em>, <em>sul</em> genes were detected in most of the strains resistant to ampicillin, tetracycline and sulphonamide, respectively. The presence of class 1 integron was studied in 29 sulphonamide-resistant <em>E. coli</em> strains from which 15 harboured class 1 integron with four different arrangements of gene cassettes, <em>dfrA17</em>+<em>aadA5</em> (n=9), <em>dfrA1</em> + <em>aadA1</em> (n=4), <em>dfrA12</em> + <em>addA2</em> (n=1), <em>dfrA12</em>+<em>orf</em>+<em>addA2</em> (n=1). The <em>qnrB</em> gene was detected in six strains out of 13 quinolone-resistant <em>E. coli</em> strains. Seventeen <em>E. coli</em> isolates from diarrhoeic rabbits harboured the enteropathogenic eae genes associated with different virulence genes tested (<em>fimA</em>, <em>cnf1</em>, <em>aer</em>), and affiliated to B2 (n=8) and D (n=9) phylogroups. Isolated <em>E. coli</em> strains from healthy rabbit were harbouring <em>fim A</em> and/or <em>cnf1</em> genes and affiliated to A and B1 phylogroups. This study showed that <em>E. coli</em> strains from the intestinal tract of rabbits are resistant to the widely prescribed antibiotics in medicine. Therefore, they constitute a reservoir of antimicrobial-resistant genes, which may play a significant role in the spread of antimicrobial resistance. In addition, the eae virulence gene seemed to be implicated in diarrhoea in breeder rabbits in Tunisia.

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