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Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections.

ABSTRACT: 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.

SUBMITTER: Li D

PROVIDER: S-EPMC8116683 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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:BackgroundThe AnTIC trial linked continuous low-dose antibiotic prophylaxis treatments to a lower incidence of symptomatic urinary tract infections (UTIs) among individuals performing clean intermittent self-catheterisation (CISC).ObjectiveTo explore potential mechanisms underlying the protective effects of low-dose antibiotic prophylaxis treatments, blood and urine samples and uro-associated Escherichia coli isolates from AnTIC participants were analysed.Design setting and participantsBlood samples (n = 204) were analysed for TLR gene polymorphisms associated with UTI susceptibility and multiple urine samples (n = 558) were analysed for host urogenital responses. E.coli sequence data for 45 temporal isolates recovered from the urine samples of 16 trial participants in the prophylaxis (n = 9) and no-prophylaxis (n = 7) study arms, and characterised by multidrug resistance (MDR), were used to classify individual strains.Outcome measurements and statistical analysisTLR polymorphism data were analysed using Poisson regression. Concentrations of urine host defence markers were analysed using linear mixed-effects models, which accounted for repeated urine samples.Results and limitationsUrine samples from CISC users, irrespective of antibiotic treatment regimens, were associated with robust urothelial innate responses. No links were identified between TLR genotype and CISC user susceptibility to recurrent UTIs. Microbiological study data were limited to the predominant MDR E. coli population; participants prescribed low-dose prophylactic antibiotics were predominantly colonised by a single uro-associated E. coli strain, while participants given acute antibiotic treatments were each colonised by more than one E. coli strain.ConclusionsAntibiotic treatments did not impact urogenital responses to infection in CISC users. Host genetics in terms of TLR polymorphisms played no role in determining CISC user susceptibility to or protection from recurrent UTIs. Prophylactic antibiotic treatments associated with MDR E. coli were associated with colonisation by stable uro-associated E. coli genotypes.Patient summaryOur findings show that the natural urogenital defences of clean intermittent self-catheterisation (CISC) users were not impacted by antibiotic treatments. For some CISC users, prophylaxis with low-dose antibiotics selected for a stable, predominantly, Esherichia coli rich uromicrobiota.

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Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections.

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