Genomic Epidemiology of Clinical Klebsiella pneumoniae in the Middle East and North Africa

Background: Klebsiella pneumoniae is a Gram-negative bacterium that is found in human microbiota and in diverse environments. This opportunistic pathogen exhibits a highly variable genetic background and is responsible for a broad range of hospital- and community-acquired, multidrug-resistant infections worldwide. To track transmission pathways and understand genetic diversity, single-nucleotide polymorphism (SNP) clustering has become an essential tool. Methods: This study examines data from 2018 to 2024 in the NCBI Pathogen Detection database to determine the temporal and spatial distribution of SNP clusters in clinical K. pneumoniae across Middle East and North Africa (MENA) countries. Results: Among 1858 isolates, a heterogeneous population structure was observed. Of the 478 identified SNP clusters, a few dominant clusters accounted for 37% of the isolates, and numerous low-frequency lineages were detected. The descriptive yearly snapshot revealed a diverse representation of top clusters. Geographical analysis showed the presence of both localized and limited cross-border distribution patterns. Countries with diverse clusters also exhibit higher diversity of carbapenem- and ESBL-resistant genes. Conclusions: These findings provide valuable insights into the dominant, regionally concentrated K. pneumoniae lineage across MENA countries, assisting future genomic surveillance and efforts to combat clinical K. pneumoniae infections in this region.