Genomic and prophages analysis of a ST16 Klebsiella pneumoniae carrying blaOXA-181 from Botswana, 2023

Abstract

Introduction: Carbapenemase-producing Enterobacterales (CPE) pose a serious threat to public health worldwide and are a challenge for clinicians due to the limited antimicrobial options available. Here, we characterize the genome of a Klebsiella pneumoniae (named Kp51) producing OXA-181 carbapenemase isolated from a rectal swab of a hospitalized patient in Botswana in 2023. We also investigate the genomic epidemiology of carbapenemase gene and prophage regions among bla_OXA-181-harboring K. pneumoniae strains collected worldwide.

Methodology: Whole-genome sequencing was performed on the Illumina MiSeq system, and assembly was executed with SPAdes. Phylogenetic analysis was performed on core genome SNPs among OXA-181-producing K. pneumoniae genomes. Analysis of prophage regions was performed among closely related genomes by pairwise comparison.

Results: Resistome analysis results showed that Kp51 harbored qnrS1, bla_TEM-1, and bla_OXA-181 carbapenemase gene. Also, Kp51 strain belonged to ST16 and carried an IncX3 plasmid harboring the bla_OXA-181 carbapenemase gene. Phylogenetic analysis showed that the Kp51 genome was closely related to an OXA-181-producing strain isolated from a dog in China, and the IncX3 plasmid exhibited high sequence homology with bla_OXA-181-carrying plasmids collected worldwide. Prophage analysis revealed that high variability was observed in ST16 K. pneumoniae strains harboring bla_OXA-181.

Conclusions: Here we demonstrate the genomic spread of OXA-181-producing ST16 K. pneumoniae worldwide and that the major source of variability is located within prophage regions. Our work emphasizes the need for constant monitoring of the OXA-181 carbapenemase producers diffusion with special emphasis on low and middle-income countries in order to trace the spread of CPE pathogens globally.