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

Victor Dinda; Andrew Nyerere Kimang'a; Daniel Kariuki; Anthony Wawire Sifuna; Thomas James O'Brien; Martin Welch; Oleg N Reva

doi:10.1099/acmi.0.000667.v4

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

Access Microbiol. 2024 Jan 22;6(1):000667.v4. doi: 10.1099/acmi.0.000667.v4. eCollection 2024.

Authors

Victor Dinda¹, Andrew Nyerere Kimang'a², Daniel Kariuki³, Anthony Wawire Sifuna⁴, Thomas James O'Brien⁵, Martin Welch⁵, Oleg N Reva⁶

Affiliations

¹ Department of Medical Laboratory Science, Masinde Muliro University of Science and Technology, Kakamega, Kenya.
² Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
³ Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
⁴ Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya.
⁵ Department of Biochemistry, University of Cambridge, Hopkins Building, Cambridge, UK.
⁶ Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.

Abstract

Objectives: Klebsiella pneumoniae are a frequent cause 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. However, the distribution of this pathogen in Western African hospitals has been scarcely studied. The main objective of this work was to perform whole genome sequencing of K. pneumoniae 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: ST147 was the dominant lineage among the highly-resistant K. pneumoniae isolates that we sequenced. ST147 was associated with both community- and the hospital-acquired infections, and with different infection sites, whereas other STs were predominantly uropathogens. Multiple antibiotic resistance and virulence determinants were detected in the genomes including extended-spectrum β-lactamases (ESBL) and carbapenemases. Many of these genes were plasmid-borne.

Conclusions: Our data suggest that the evolutionary success of ST147 may be linked with the acquisition of broad host-range plasmids, and their propensity to accrue AMR and virulence determinants. Although ST147 is a dominant lineage in many countries worldwide, it has not been previously reported as prevalent in Africa. Our data suggest an influx of new nosocomial pathogens with new virulence genes into African hospitals from other continents.

Keywords: Klebsiella pneumoniae; MLST; antibiotic resistance; environmental isolate; whole genome sequence.