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.

Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls

“…The presence of these insertion elements serves as a hotspot for capture of ARGs flanked by IS 26 [ 73 ]. IS 26 also plays an important role in altering the structure of class 1 integrons by truncating the 3’-CS and the 3´ end of intI1 [ 77 , 78 , 79 ]. IS 26 has played a role in shaping the resistance regions in HI2 ST1 and ST3 and F plasmids that are carried by E. coli ST216 from silver gulls described in this study.…”

Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

“…Several studies have investigated the virulence of recurrent E. coli without identification of any traits associated to recurrent uropathogenic E. coli [ 4 , 7 , 8 , 9 , 10 ]. It has been shown that specific virulence factors and clonal groups of E. coli were over-represented in either rUTI or cure based on PCR studies of specific genetic traits [ 11 ].…”

“…It has been shown that specific virulence factors and clonal groups of E. coli were over-represented in either rUTI or cure based on PCR studies of specific genetic traits [ 11 ]. Recurrence has been associated with specific antibiotic resistance traits and sequence types [ 7 , 9 ] or significantly related to genes associated with biofilm production [ 12 ]. Today, whole-genome sequencing (WGS) enables an unbiased search for differences in genetic traits and includes not only known virulence traits but rather a whole-genome scale, i.e., gene content, single nucleotide polymorphisms (SNPs) and k-mers.…”

L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli

“…This demonstrated that E. coli L-forms are less metabolically active than parent cell-walled bacteria (CWB). Plotting the growth of the two L-forms, J53 (a well-characterised K12 derivate) (14) and WH62 (an uropathogenic clinical isolate) (15) by measuring optical density at 540nm (OD540), revealed a characteristic lag phase followed by a slow density increase (Fig. 1D).…”

“…L-form growth for E. coli WH62 strain (ST127, a virulent subtype of uropathogenic E. coli ) (15) was imaged using time-lapse differential interference contrast (DIC) microscopy. The addition of meropenem to exponential phase cell-walled bacteria in osmoprotective semisolid LFA led to the emergence of L-forms that differed in morphology and size (Fig.…”