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

Abstract

<p><i>Objectives - </i>This study delineated the clonal lineages, antibiotic resistome and plasmid replicon types in multidrug-resistant <i>K. pneumoniae</i> isolates from a teaching hospital in Ghana. <p><i>Methods - </i>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® (BioMérieux) kits and the DNA was subjected to whole genome sequencing (WGS) using the Illumina MiSeq platform. <p><i>Results - </i>Of the 200 isolates obtained, 37 were identified as <i>K. pneumoniae</i> 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 (<i>K</i> types and <i>wzi</i> allelic types) and multiple genes encoding resistance to β-lactams (<i>bla</i>_CTX-M-15, <i>bla</i>_SHV-11, <i>bla</i>_TEM-1B, <i>bla</i>_OXA-1), aminoglycosides (<i>aac(3)-IIa, strB, strA, aadA16</i>), fluoroquinolones/quinolones (<i>qnrB66, oqxA, oqxB</i>) 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 <i>gyrA</i> (S83Y, D87A) and <i>parC</i> (S80I, N304S) in isolates resistant to ciprofloxacin (MIC ≥ 4 mg/mL) were found. Global phylogenomic analysis affirmed the diverse clonal clustering and origin of these isolates. <p><i>Conclusions - </i>The varied clonal clusters and resistome identified in the multidrug-resistant <i>K. pneumoniae</i> 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.