Comparative Genomics of Antibiotic-Resistant Uropathogens Implicates Three Routes for Recurrence of Urinary Tract Infections

Abstract

The rise of antimicrobial resistance in uropathogens has complicated the management of urinary tract infections (UTIs), particularly in patients who are afflicted by recurrent episodes of UTIs. Antimicrobial-resistant (AR) uropathogens persistently colonizing individuals at asymptomatic time points have been implicated in the pathophysiology of UTIs. The dynamics of uropathogen persistence following the resolution of symptomatic disease are, however, mostly unclear. To further our understanding, we determined longitudinal AR uropathogen carriage and clonal persistence of uropathogenic Escherichia coli, Proteus mirabilis, and Klebsiella pneumoniae isolates in the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Clonal tracking of isolates in consecutively collected urine and fecal specimens indicated repeated transmission of uropathogens between the urinary tract and their intestinal reservoir. Our results further implicate three independent routes of recurrence of UTIs: (i) following an intestinal bloom of uropathogenic bacteria and subsequent bladder colonization, (ii) reinfection of the urinary tract from an external source, and (iii) bacterial persistence within the urinary tract. Taken together, our observation of clonal persistence following UTIs and uropathogen transmission between the intestinal and urinary tracts warrants further investigations into the connection between the intestinal microbiome and recurrent UTIs.IMPORTANCE The increasing antimicrobial resistance of uropathogens is challenging the continued efficacy of empiric antibiotic therapy for UTIs, which are among the most frequent bacterial infections worldwide. It has been suggested that drug-resistant uropathogens could persist in the intestine after the resolution of UTI and cause recurrences following periurethral contamination. A better understanding of the transmission dynamics between the intestinal and urinary tracts, combined with phenotypic characterization of the uropathogen populations in both habitats, could inform prudent therapies designed to overcome the rising resistance of uropathogens. Here, we integrate genomic surveillance with clinical microbiology to show that drug-resistant clones persist within and are readily transmitted between the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Thus, our results advocate for understanding persistent intestinal uropathogen colonization as part of the pathophysiology of UTIs, particularly in patients affected by recurrent episodes of symptomatic disease.

Keywords: antibiotic resistance; clonal tracking; comparative genomics; recurrence; urinary tract infection.

FIG 1

The clonal diversity of the uropathogen population varies between individual patients. (a) UTI-associated E. coli strains belong to the major phylogroups D and B2. The maximum likelihood phylogenetic tree includes all available E. coli isolates cultured from diagnostic urine samples and publicly available reference strains. Diagnostic isolates are depicted in red; publicly available reference genomes are indicated in black. Escherichia marmotae strain HT073016 was added as an outgroup (italics). (b) Phylogenetic reconstruction indicates that the E. coli isolates clustered by patient. The maximum likelihood phylogenetic tree includes all available E. coli isolates cultured from urine and stool samples. Isolates are colored according to patient. E. coli strain UTI89 was added as a reference. (c) Isolates from the same patient generally differed by <50 SNPs. The histogram shows the number of SNPs identified for all within-patient pairwise comparisons of E. coli isolates. (d) The average number of SNPs identified in all pairwise comparisons of E. coli isolates collected from each patient. Error bars depict standard deviations.

FIG 2

Recurrent urinary tract infections are associated with differences in stool and urine uropathogen density. (Top) Non-rUTI patients; (bottom) patients with rUTIs. Subsequent episodes for rUTI patients are depicted from bottom to top in the bottom panel. Different colonization patterns are indicated by header background colors: red, persistent urinary tract colonization; turquoise, nonpersistent colonization; blue, intestinal blooms. Patient identifiers are given on the top of each panel. The bubble size corresponds to the number of CFU that grew on species-specific selective agar plates (see Materials and Methods). Yellow bubbles correspond to the culture results for urine samples; brown bubbles correspond to the culture results for stool samples. Missing culture data are indicated by gray fields. A red line indicates the time frame in which an rUTI patient experienced a recurrence.

FIG 3

Isolate antibiotic susceptibility profile clusters by patient. A heat map of the results of antibiotic susceptibility testing of all isolates is shown. Profiles of susceptibility to specific antibiotics and individual isolates are hierarchically clustered on the y axis and the x axis, respectively. Black squares, resistance; dark gray squares, intermediate phenotype; white squares, susceptibility; light gray squares, missing data. The patient and episode of isolation, and the isolate species identity are given as colored annotations on top of the heat map.

FIG 4

Isolate antibiotic gene repertoire clusters by patient. A heat map of all resistance genes identified by use of the RGI software and the ResFinder database in the genomes of all isolates is shown. Resistance genes and individual isolates are hierarchically clustered on the y axis and x axis, respectively. Black squares, the presence of a specific resistance gene. The patient and episode of isolation, and the isolate species identity are given as colored annotations on top of the heat map.