Genomic characterization of multidrug-resistant ESBL-producing Klebsiella pneumoniae isolated from a Ghanaian teaching hospital

Abstract Objectives This study delineated the clonal lineages, antibiotic resistome and plasmid replicon types in multidrug-resistant K. pneumoniae isolates from a teaching hospital in Ghana. Methods Identification and antibiotic susceptibility testing were done using the MALDI-TOF MS and Vitek‑2 automated system. Genomic DNA extraction was carried out using the NucliSens easyMAG® (BioMerieux) kits and the DNA was subjected to whole genome sequencing (WGS) using the Illumina MiSeq platform. Results Of the 200 isolates obtained, 37 were identified as K. pneumoniae of which 9 were resistant to all second and third-generation cephalosporins. These 9 isolates selected for further genomic analysis were characterized by the presence of 8 diverse sequence types (STs), capsular polysaccharide serotypes ( K types and wzi allelic types) and multiple genes encoding resistance to β-lactams ( bla CTX-M-15 , bla SHV-11, bla TEM-1B, bla OXA-1 ), aminoglycosides ( aac(3)-IIa, strB, strA, aadA16 ), fluoroquinolones/quinolones ( qnrB66, oqxA, oqxB ) and other antibiotic classes. Resistance genes were associated with plasmids, predominantly IncFIB(K) and ColRNAI. Multiple and diverse mutations in quinolone resistance-determining regions of gyrA (S83Y, D87A) and parC (S80I, N304S) in isolates resistant to ciprofloxacin (MIC ≥4mg/mL) were found. Global phylogenomic analysis affirmed the diverse clonal clustering and origin of these isolates. Conclusions The varied clonal clusters and resistome identified in the multidrug-resistant K. pneumoniae isolates is a major threat to the management of infections in Ghana. The molecular characterization of antibiotic resistance is thus imperative to inform strategies for containment.