Whole-Genome Sequencing and Bioinformatics Analysis of ESBL- producing Klebsiella pneumoniae in a Ghanaian teaching hospital

Abstract

Background Multidrug-resistant (MDR) ESBL-producing K. pneumoniae is widely implicated in community and hospital-acquired infections. Thus, the current study determined the prevalence and clonal relatedness of MDR K. pneumoniae from hospital environments, patients and healthcare workers in a Ghanaian hospital. Methods Patients (rectal and hand, collected on admission and 48 h post admission), healthcare workers (hands) and hospital environment samples were sampled for three months. Antimicrobial susceptibility was determined using VITEK-2. Ten MDR ESBL-producing K. pneumoniae isolates were further analysed by whole-genome sequencing. Results All the isolates were ceftazidime-resistant; 90% were resistant to cefepime, amoxicillin/clavulanic, acid piperacillin/tazobactam, and sulphamethoxazole/trimethoprim. The isolates showed varying resistance to the cephalosporins and were susceptible to tigecycline. One environmental isolate isolate was resistant to meropenem but harboured no carbapenemase gene. The β-lactamase gene, blaSHV, was dominant and harboured by three environmental and five carriage isolates. Furthermore, three environmental and three carriage isolates harboured blaCTX-M-15. All isolates showed ompK36 and ompK37 mutations. Fluoroquinolone (qnrB), aminoglycosides (aadA1, aadA2, aac(3)-IIa, aac(6')-Ib-cr,aph(3'')-Ib, aph(6)-Id) and sulphamethoxazole/trimethoprim (sul1, sul2, dfrA14, dfrA15) resistance-encoding genes were also detected. A diverse range of sequence types were identified, including ST39, ST307, ST815, ST1552, ST636, ST464, and ST1996, with ST39 being the most frequently observed (environmental = 3; carriage = 1). Three environmental and three carriage isolates harboured the Int1l integron. Many virulence genes, including irp1, irp2, iutA, gndA, ompA, fes, fep, mrkD and fimH, were detected in environmental and carriage isolates. IncFIB was the most abundant plasmid replicon in five environmental and four carriage isolates. A clonal relationship was identified between a carriage isolate (ST39) and three environmental isolates (ST39) with shared genetic elements, suggesting that environmental reservoirs may play a role in the transmission and persistence of resistant K. pneumoniae. Conclusion This study highlights the prevalence of MDR ESBL-producing K. pneumoniae in both hospital environments and patients, emphasizing the potential for cross-transmission within healthcare settings. These findings reinforce the urgent need for strengthened infection prevention and control measures, enhanced antimicrobial stewardship, and continuous genomic surveillance to mitigate the spread of resistant K. pneumoniae in healthcare settings.