2847. Comparative Genomics and Clonal Tracking of Multi-drug-Resistant Uropathogens Implicates the Fecal Microbiome as a Potential Reservoir for Recurrent Urinary Tract Infections

Abstract

BackgroundMulti-drug-resistant organisms (MDRO) have complicated the treatment of urinary tract infections (UTIs), especially in patients with recurrent UTIs (rUTI). The objective of this pilot prospective cohort study is to determine the role of the fecal microbiome in rUTIs.MethodsStool and urine specimens were prospectively collected from patients with MDRO UTIs at 6 time points during and after the UTI, and with any rUTI. Specimens underwent semi-quantitative culture on differential and selective media for MDROs, and isolates underwent phenotypic susceptibility testing and whole-genome sequencing. Comparative genomics and clonal tracking were used to detect clonal uropathogen strains in the urinary and gastrointestinal tracts. Resistance genes, resistance-plasmids, and virulence genes of MDROs were characterized in silico.ResultsA total of 110 isolates (95 Escherichia coli, 2 Klebsiella pneumoniae, 13 Proteus mirabilis) were cultured from the urine and stool of 15 patients (7 non-rUTI, 8 rUTI). Clonal uropathogens were isolated between the urinary tract and their intestinal reservoir (Figure 1). Integration of clonality information with semiquantitative culturing implicated three potential routes for recurrence of UTIs: (i) bladder colonization following an intestinal bloom of uropathogens, (ii) reinfection from an external source, and (III) bacterial persistence within the urinary tract (Figures 2 and 3). Antibiotic susceptibility testing and genomic profiling indicated that antibiotic-resistant uropathogen populations colonizing the urinary tract and intestinal reservoir at symptomatic and asymptomatic timepoints have similar resistance profiles that are largely determined via a pool of shared resistance plasmids (Figure 3).ConclusionThis study provides the first time-resolved analysis of uropathogen persistence following UTIs, showing that clonal antibiotic-resistant uropathogens can be detected in both the urine and stool at varying time points post-initial infection. The study implicates 3 potential routes of rUTI, including uropathogen persistence within the gut microbiota, reinfection from an external source, and persistent bacteriuria. Study findings could be utilized to inform future diagnostics and therapies for treatment of rUTIs. DisclosuresCarey-Ann Burnham, PhD, BioFire: Research Grant; bioMerieux: Research Grant; Cepheid: Research Grant; Luminex: Research Grant.