Genomic characterization of NDM-1 and 5, and OXA-181 carbapenemases in uropathogenic Escherichia coli isolates from Riyadh, Saudi Arabia

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.

Fig 1. The distribution of plasmid genes associated with antimicrobial resistance among UPEC isolates from KSA.

Heat map showing the antimicrobial resistance genotypes identified in the plasmids contained in the UPEC isolates from Riyadh, KSA. The resistance genes were identified by ResFinder 1.5 using BLAST analysis against the acquired resistance sequences of ResFinder 1.5 database. Black: no sequence matching, dark green: perfect match (100% of sequence identity and 100% of sequence length), pale green: match (<100% of sequence identity and 100% of sequence length), grey: weak match (90–100% of sequence identity and 80–90%of sequence length). No plasmid sequencing data was generated for UPEC-RIY-9.

Fig 2. Phylogenomic distribution of publicly available UPEC isolates with KSA isolates from this study.

A mid-point rooted SNP-based maximum likelihood phylogenomic tree of the MDR UPEC isolates from KSA, UPEC reference genomes and publicly available E coli genomes associated with UTI from Petty et al. [15] and Salipante et al. [18] (accession numbers are given in S1 Table). The major phylogenomic clades were colored according to MLST Cplx with the positions of UPEC reference genomes indicated.

Fig 3. Comparative genomic analysis of UPEC isolates from Riyadh, KSA.

The ORFs of the UPEC genomes sequenced in this study and the available reference genomes representing distinct UPEC phylogenetic lineages were compared against the reference genome of E. coli CFT073 (accession number AE014075). The genomes are displayed in the order of the legend on the right (going from innermost to outermost). The structural variations identified, particularly those associated with key UPEC virulence factors, are displayed on the outermost ring and were coded according to the associated function/origin (red, iron acquisition; blue, colonization factors [fimbriae, pilli]; black, capsule synthesis; purple, toxin and green, phage-related).