Abstract
Urinary tract infections (UTIs) associated with Escherichia coli are a growing threat with an increase in the prevalence of multidrug resistant (MDR) strains, particularly ß-lactamase producers, occurring globally. We investigated the presence of carbapenem-resistant uropathogenic E. coli clones in community-acquired UTIs in Riyadh, Kingdom of Saudi Arabia (KSA) to identify the virulence and resistance structures of the resistant clones and relate the isolates to those circulating globally. A combination of comparative genomics and phenotypic approaches were used to characterize ten MDR-uropathogenic Escherichia coli isolates recovered from UTI patients in Riyadh between November 2014 and January 2015. We report the presence of NDM-1 and 5, and OXA-181 in carbapenem-resistant UPEC strains from Riyadh, KSA. Single nucleotide polymorphism analyses demonstrated that these ten isolates fell into four phylogenetically distinct clades within the UPEC phylogeny. Comparative genomic analyses indicate that these diverse clones could be distinguished according to their multilocus sequencing type (MLST), serology, and virulence and antimicrobial gene architectures. These clones include the blaNDM-1 carrying isolates of the globally predominant MDR ST131 and ST69 types, previously identified as one of the most common UPEC strains in KSA. This is in addition to clones of ST23Cplx (ST410) and ST448Cplx (ST448) that have likely evolved from common intestinal strains, carrying copies of ß-lactamase genes including blaNDM-5, blaCTX-M-15, blaTEM-1, blaCMY-42, blaOXA-1 and blaOXA-181. These data have identified an emerging public health concern and highlight the need to use comprehensive approaches to detect the structure of MDR E. coli populations associated with community-acquired UTIs in KSA.
Highlights
Uropathogenic Escherichia coli (UPEC) is a subset of extra-intestinal pathogenic E. coli (ExPEC) that are capable of colonizing the urogenital tract and are responsible for 70–90% of community-acquired urinary tract infections (UTIs) and ~50% of nosocomial UTIs [1]
The analyses identified four UPEC clones with different evolutionary origins that are characterized by sequence type complex (ST Cplx) and distinct antimicrobial resistance and virulence architectures
Carbapenem-resistant UPEC were not identified in this study, the authors observed a high level of carbapenem prescription in the community as a consequence of the high prevalence of EBSL-producing bacteria [44]
Summary
Uropathogenic Escherichia coli (UPEC) is a subset of extra-intestinal pathogenic E. coli (ExPEC) that are capable of colonizing the urogenital tract and are responsible for 70–90% of community-acquired urinary tract infections (UTIs) and ~50% of nosocomial UTIs [1]. UPEC cause UTIs through the colonization of the human gastrointestinal tract, followed by infection of the urogenital tract, and subsequent disease establishment promoted by bacteria-specific traits (virulence factors) and host-related factors [3]. UPEC virulence factors have likely been acquired through horizontal transfer and are mainly encoded on pathogenicity islands [6]. UPEC produce several toxins including α-hemolysin (HlyA), cytotoxic necrotizing factor 1 (CNF1) and type V autotransporters that promote bacterial dissemination through the disruption of cellular integrity [10]. UPEC have the capacity to either disrupt host inflammatory signaling or mask immunogenic markers, allowing them to evade the host immune response [10]
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