Genetic Diversity and Virulence Factor Characterisation of Carbapenem-Resistant Klebsiella pneumoniae Isolates from Tertiary Hospitals in South East Nigeria

Carbapenem-resistant Klebsiella pneumoniae is an emerging nosocomial pathogen of critical concern, with virulence factor diversity influencing clinical outcomes and complicating therapeutic management in resource-limited settings. This study characterised the genetic diversity and virulence determinants of carbapenem-resistant K. pneumoniae isolates from tertiary hospitals in Anambra and Enugu States, South East Nigeria. Clinical isolates from blood, urine, wound swabs, and respiratory samples submitted between 2022 and 2024 were screened for carbapenem resistance by modified carbapenem inactivation method. Confirmed isolates were subjected to carbapenemase gene detection by multiplex PCR for blaKPC, blaNDM, blaOXA-48, and blaVIM. Virulence genes including wzi, rmpA, mrkD, and uge were amplified. Molecular typing was performed by multi-locus sequence typing. A total of 68 carbapenem-resistant K. pneumoniae isolates were recovered. NDM-1 was the most prevalent carbapenemase at 55.9%, followed by OXA-48 at 29.4%. Virulence gene carriage was high, with mrkD in 85.3% and uge in 72.1% of isolates. Hypervirulent sequence types ST23 and ST86 were identified, raising concern for invasive infection potential. Co-occurrence of multiple carbapenemase genes was found in 14.7% of isolates. Phylogenetic analysis revealed limited inter-hospital clonal spread. The study provides critical molecular epidemiological data for infection prevention planning and recommends implementation of carbapenem-resistant K. pneumoniae surveillance networks, contact precautions for colonised patients, and development of national guidelines for carbapenem-sparing treatment strategies in South East Nigeria. Keywords: Klebsiella pneumoniae, carbapenem resistance, NDM-1, virulence factors, molecular typing