Novel Carbapenem-Resistant Klebsiella pneumoniae ST147 Coharboring bla(NDM-1), bla(OXA-48) and Extended-Spectrum β-Lactamases from Pakistan

PURPOSE: The emergence of multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) is associated with the acquisition of multiple carbapenemases. Their clonal spread is a worldwide concern due to their critical role in nosocomial infections. Therefore, the identification of high-risk clones with antibiotic resistance genes is very crucial for controlling its global spread. MATERIALS AND METHODS: A total of 227 K. pneumoniae strains collected during April 2018 to November 2019 were confirmed by PCR. Carbapenemases and extended-spectrum β-lactamases (ESBL) were detected phenotypically. Confirmation of carbapenemases was carried out by PCR and Sanger sequencing. The clonal lineages were assigned to selected isolates by multilocus sequence typing (MLST), and the plasmid analysis was done by PCR-based detection of the plasmid replicon typing. RESULTS: Of the total K. pneumoniae, 117 (51.5%) were carbapenem resistant (CRKP) and 140 (61.7%) were identified as ESBL producers. Intermediate to high resistance was detected in the tested β-lactam drugs while polymyxin-B and tigecycline were found to be susceptible. Among CRKP, 91 (77.8%) isolates were detected as carbapenemase producing, while 55 (47%) were positive for bla(NDM-1) 23.9% (n=28), bla(OXA-48) 22.2% (n=26) and bla(VIM) 0.85% (n=1) while 12.7% (n=7) carried both bla(NDM-1) and bla(OXA-48) genes. The CRKP coharboring bla(NDM-1) and bla(OXA-48) genes (n=7) were positive for bla(CTX-M) bla(SHV) (n=3), bla(SHV) (n=1) and bla(CTX-M) (n=3). The novel CRKP with the coexistence of bla(NDM-1), bla(OXA-48), bla(CTX-M) and bla(SHV) genes were associated with the high-risk clone ST147 (n=5) and ST11 (n=2). The assigned replicon types were IncL/M, IncFII, IncA/C and IncH1. CONCLUSION: This is the first report of the coexistence of bla(NDM-1), bla(OXA-48), bla(CTX-M) and bla(SHV) genes on a high-risk lineage ST147 from Pakistan. This study highlights the successful dissemination of carbapenemase resistance genes in the high-risk clones that emphasizes the importance of monitoring and controlling the spread of these diverse clones globally.