Version 1: Whole genome sequencing and genotyping Klebsiella pneumoniae multi-drug resistant hospital isolates from Western Kenya

Objectives Klebsiella pneumoniae are frequent causes of nosocomial infections worldwide. Sequence type 147 (ST147) has been reported as a major circulating high-risk lineage in many countries, and appears to be a formidable platform for the dissemination of antimicrobial resistance (AMR) determinants. Distribution of this pathogen in hospital of Western Africa is scarcely studied. An objective of this work was to perform whole genome sequencing of AMR isolates from a referral hospital in Kakamega (Kenya) for genotyping and identification of AMR and virulence determinants. 

Methods In total, 15 K. pneumoniae isolates showing a broad spectrum antimicrobial resistance were selected for whole genome sequencing by Illumina HiSeq 2500 platform. Results It was found that ST147 has become the dominant lineage among the K. pneumonia causing both the community and the hospital acquired infections from different infection sites, whereas other STs were predominantly uropathogens. Two broad range plasmids enriched in AMR determinants were found in the sequenced isolates. 

Conclusions Our data suggest that the evolutionary success of ST147 may be linked with the acquisition of these plasmids, and their propensity to accrue AMR and virulence determinants. ST147 was reported to be a dominant lineage in many countries worldwide, but it has been not frequent in Africa before. This may indicate an influx of new nosocomial pathogens with new virulence genes into African hospitals from other continents.