Dataset Information

Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada.

ABSTRACT: Background:A few extraintestinal pathogenic Escherichia coli (ExPEC) multilocus sequence types (STs) cause the majority of community-acquired urinary tract infections (UTIs). We examine the genomic epidemiology of major ExPEC lineages, specifically factors associated with intestinal acquisition. Methods:A total of 385 women with UTI caused by E. coli across Canada were asked about their diet, travel, and other exposures. Genome sequencing was used to determine both ST and genomic similarity. Logistic regression was used to identify factors associated with the acquisition of and infection with major ExPEC STs relative to minor ExPEC STs. Results:ST131, ST69, ST73, ST127, and ST95 were responsible for 54% of all UTIs. Seven UTI clusters were identified, but genomes from the ST95, ST127, and ST420 clusters exhibited as few as 3 single nucleotide variations across the entire genome, suggesting recent acquisition. Furthermore, we identified a cluster of UTIs caused by 6 genetically-related ST1193 isolates carrying mutations in gyrA and parC. The acquisition of and infection with ST69, ST95, ST127, and ST131 were all associated with increased travel. The consumption of high-risk foods such as raw meat or vegetables, undercooked eggs, and seafood was associated with acquisition of and infection with ST69, ST127, and ST131, respectively. Conclusions:Reservoirs may aid in the dissemination of pandemic ExPEC lineages in the community. Identifying ExPEC reservoirs may help prevent future emergence and dissemination of high-risk lineages within the community setting.

SUBMITTER: Fibke CD

PROVIDER: S-EPMC6824535 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Genomic Epidemiology of Major Extraintestinal Pathogenic <i>Escherichia coli</i> Lineages Causing Urinary Tract Infections in Young Women Across Canada.

Fibke Chad D CD Croxen Matthew A MA Geum Hyun Min HM Glass Magdalena M Wong Eugenia E Avery Brent P BP Daignault Danielle D Mulvey Michael R MR Reid-Smith Richard J RJ Parmley E Jane EJ Portt Andrea A Boerlin Patrick P Manges Amee R AR

Open forum infectious diseases 20191009 11

<h4>Background</h4>A few extraintestinal pathogenic <i>Escherichia coli</i> (ExPEC) multilocus sequence types (STs) cause the majority of community-acquired urinary tract infections (UTIs). We examine the genomic epidemiology of major ExPEC lineages, specifically factors associated with intestinal acquisition.<h4>Methods</h4>A total of 385 women with UTI caused by <i>E. coli</i> across Canada were asked about their diet, travel, and other exposures. Genome sequencing was used to determine both S ...[more]

PMID: 31696141

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Project description:Urinary tract infections (UTIs) are the most common bacterial infections requiring medical attention and a leading justification for antibiotic prescription. Trimethoprim is prescribed empirically for uncomplicated cases. UTIs are primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) and ExPEC strains play a central role in disseminating antimicrobial-resistance genes worldwide. Here, we describe the whole-genome sequences of trimethoprim-resistant ExPEC and/or ExPEC from recurrent UTIs (67 in total) from patients attending a regional Australian hospital from 2006 to 2008. Twenty-three sequence types (STs) were observed, with ST131 predominating (28 %), then ST69 and ST73 (both 7 %). Co-occurrence of trimethoprim-resistance genes with genes conferring resistance to extended-spectrum β-lactams, heavy metals and quaternary ammonium ions was a feature of the ExPEC described here. Seven trimethoprim-resistance genes were identified, most commonly dfrA17 (38 %) and dfrA12 (18 %). An uncommon dfrB4 variant was also observed. Two blaCTX-M variants were identified - blaCTX-M-15 (16 %) and blaCTX-M-14 (10 %). The former was always associated with dfrA12, the latter with dfrA17, and all blaCTX-M genes co-occurred with chromate-resistance gene chrA. Eighteen class 1 integron structures were characterized, and chrA featured in eight structures; dfrA genes featured in seventeen. ST131 H30Rx isolates possessed distinct antimicrobial gene profiles comprising aac(3)-IIa, aac(6)-Ib-cr, aph(3')-Ia, aadA2, blaCTX-M-15, blaOXA-1 and dfrA12. The most common virulence-associated genes (VAGs) were fimH, fyuA, irp2 and sitA (all 91 %). Virulence profile clustering showed ST131 H30 isolates carried similar VAGs to ST73, ST405, ST550 and ST1193 isolates. The sole ST131 H27 isolate carried molecular predictors of enteroaggregative E. coli/ExPEC hybrid strains (aatA, aggR, fyuA). Seven isolates (10 %) carried VAGs suggesting ColV plasmid carriage. Finally, SNP analysis of serial UTI patients experiencing worsening sequelae demonstrated a high proportion of point mutations in virulence factors.

Project description:Extraintestinal pathogenic Escherichia coli (ExPEC) have a capacity to cause serious infections of blood, the central nervous system and particularly the urinary tract. Relatively little is known about how ExPEC adapt their cell-wide protein expression to environments with different carbon sources and other required nutrients. We used label-free quantitative (LFQ) proteomic analysis to determine proteomes of five ExPEC strains purified from clinical blood cultures, and compared them with proteomes of reference uropathogenic E. coli strain 536 derived from blood culture and two chemically different solid media. We identified 2,883 proteins in total, and for 90% of the detected proteins described their relative quantitative levels based on LFQ intensity scores. Comparison of anaerobic and aerobic blood cultures revealed significant differences in the levels of 32 proteins out of 1854 shared proteins. A majority of these proteins was associated with acquisition and utilization of metal ions, which are critical either for anaerobic (nickel) or aerobic (iron) respiration. ANOVA analysis of the relative quantitative levels of 1758 proteins shared between the strains identified 47 differentially expressed proteins, including proteins involved in vitamin B6 metabolism, cell motility and virulence. Comparison of strain 536 proteomes derived from blood cultures and solid media showed substantial variation in the relative quantitative levels of 200 proteins, which represented 11% of the common proteins between the conditions. Blood culture condition was characteristic by upregulation of anaerobic fermentative metabolism, cell motility and iron utilization. In a response to the growth on solid media increased levels of proteins functional in aerobic respiration, catabolism of various biochemicals obtained from the media and protection against environmental stresses. The study presents the largest coverage of ExPEC/UPEC proteome to date,with a detail account of ExPEC metabolism under three chemically different environments.

Project description:The molecular epidemiology and biological characteristics of Escherichia coli associated with hemorrhagic pneumonia (HP) mink from five Chinese Provinces were determined. From 2017 to 2019, 85 E. coli strains were identified from 115 lung samples of mink suffering from HP. These samples were subjected to serotyping, antimicrobial susceptibility, detection of virulence genes, phylogenetic grouping, whole-genome sequencing, drug resistant gene, multilocus sequence typing (MLST) and biofilm-forming assays. E. coli strains were divided into 18 serotypes. Thirty-nine E. coli strains belonged to the O11 serotype. Eighty-five E. coli strains were classified into seven phylogenetic groups: E (45.9%, 39/85), A (27.1%, 23/85), B1 (14.1%, 12/85), B2 (3.7%, 3/85), D (3.7%, 3/85), F (2.4%, 2/85) and clade I (1.2%, 1/85). MLST showed that the main sequence types (STs) were ST457 (27/66), All E. coli strains had ≥4 virulence genes. The prevalence of virulence was 98.8% for yijp and fimC, 96.5% for iucD, 95.3% for ompA, 91.8% for cnf-Ⅰ, 89.4% for mat, 82.3% for hlyF, and 81.2% for ibeB. The prevalence of virulence genes iss, cva/cvi, aatA, ibeA, vat, hlyF, and STa was 3.5-57.6%. All E. coli strains were sensitive to sulfamethoxazole, but high resistance was shown to tetracycline (76.5%), chloramphenicol (71.8%), ciprofloxacin (63.5%) and florfenicol (52.9%), resistance to other antibiotics was 35.3-16.5%. The types and ratios of drug-resistance genes were tet(A), strA, strB, sul2, oqxA, blaTEM-1B, floR, and catA1 had the highest frequency from 34%-65%, which were consistent with our drug resistance phenotype tetracycline, florfenicol, quinolones, chloramphenicol, the bla-NDM-I and mcr-I were presented in ST457 strains. Out of 85 E. coli strains, six (7.1%) possessed a strong ability, 12 (14.1%) possessed a moderate ability, and 64 (75.3%) showed a weak ability to form biofilm. Our data will aid understanding of the epidemiological background and provide a clinical basis for HP treatment in mink caused by E. coli.

Dataset Information

Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada.

Publications

Genomic Epidemiology of Major Extraintestinal Pathogenic <i>Escherichia coli</i> Lineages Causing Urinary Tract Infections in Young Women Across Canada.

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