Prevalence, antibiogram and whole genome sequence of multidrug-resistant Klebsiella pneumoniae isolated from community-onset urinary tract infections in Calabar, Southern Nigeria.

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Purpose: To carry out genome characterization of clinical multidrug-resistant Klebsiella pneumoniae strains isolated from urine samples and determine the clones implicated in community onset urinary tract infection (UTI), with a focus on antimicrobial resistance genes, multi-locus sequence typing (MLST), plasmid content, virulence gene and capsule typing. Methods: Three hundred and eighty-four urine samples were collected from outpatients in General Hospital, Calabar and the General Hospitals in Calabar Municipal and Akampka Local Government Area of Cross River State, Nigeria. Isolates were confirmed using 16S rRNA sequencing and were evaluated for antibiotic susceptibility using CLSI protocols. Whole-genome sequencing (WGS) was performed using Illumina technique. Results: The prevalence of ESBL and carbapenemase-producing K. pneumoniae strains was predominant in Calabar (21.87 %) and Akampka (22.00 %). Fourteen K. pneumoniae strains isolated showed acquired resistance genes including; tet(A); aph(3')-Ia, aadA1, acc(6')-Ib, aph(6)-Id, rmtF, armA, aph(3')-VIb; fosA, fosA6, fosA3; blaSHV-11, blsSHV-26, blaSHV-98, blaTEM-1C, blaCTX-M-14b, blaCTX-M-15, blaOXA-9, blaOXA-48, blaNDM-1, blaNDM-5, and blaKPC-2 which were responsible for multi-drug resistance mechanisms. The K and O-typing revealed that the 14 isolates were K15, K30, K35, K47, K51, K64, K74, variant type KL114 and O1ab, O2afg, O4, O5, O13, variant type OL104, respectively. The following plasmid and virulence genes were found in all K. pneumoniae clones: Col44OI, ColRNAI, IncFIB (Mar) types and fimH, iutA, fyuA, irp2, nlpl, terC, iucC, respectively. Conclusion: Genotyping of clinical MDR-K. pneumoniae using WGS has revealed diverse beta-lactamase genes and identified genomic variations between local isolates. The data provide insights into transmission patterns and clonal dissemination within the community.

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