Antimicrobial resistance and virulence characteristics of Klebsiella pneumoniae isolates in Kenya

• Published in: bioRxiv
• Main Authors: Muraya, Angela W, Kyany'a, Cecilia, Kiyaga, Shahiid, Smith, Hunter J, Kibet, Caleb, Martin, Melissa J, Kimani, Josephine, Musila, Lillian
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 02.02.2022
• Subjects: Aerobactin; Antimicrobial resistance; Bioinformatics; Carbapenemase; Cloning; Colistin; DNA topoisomerase IV; Epidemiology; Genetic analysis; Genomes; Health care; Klebsiella pneumoniae; Morbidity; Multidrug resistance; Opportunist infection; Outbreaks; Virulence; Virulence factors; Whole genome sequencing; β Lactamase; Kenya
• DOI: 10.1101/2022.02.01.478614

Klebsiella pneumoniae is a globally significant opportunistic pathogen causing healthcare-associated and community-acquired infections. This study examined the epidemiology and the distribution of resistance and virulence genes in clinical K. pneumoniae strains in Kenya. Eighty-nine K. pneumoniae isolates were collected over six years from five counties in Kenya and were analyzed using whole genome sequencing and bioinformatics. These isolates were obtained from community-acquired (62/89) and healthcare-associated infections (21/89), and the hospital environment (6/89). Genetic analysis revealed the presence of bla NDM-1 and bla OXA-181 carbapenemase genes and the armA and rmtF genes known to confer pan-aminoglycoside resistance. The most abundant extended-spectrum beta-lactamase genes identified were bla CTX-M-15 (36/89), bla TEM (35/89), and bla OXA (18/89) . In addition, one isolate had a mobile colistin resistance gene ( mcr-8 ). Fluoroquinolone resistance-conferring mutations in gyrA and parC genes were also observed. The most notable virulence factors were those associated with hyper-virulence ( rmpA/A2 and magA ), yersiniabactin ( ybt ), salmochelin ( iro ), and aerobactin ( iuc and iutA ). Thirty-eight distinct sequence types were identified, including known global lineages ST14, ST15, ST147, and ST307, and a regional clone ST17 implicated in regional outbreaks. In addition, this study genetically characterized two potential hypervirulent isolates and two community-acquired ST147 high-risk clones that contained carbapenemase genes, yersiniabactin, and other multidrug resistance genes. These results demonstrate that the resistome and virulome of Kenyan clinical and hospital environmental K. pneumoniae isolates are diverse. The reservoir of high risk-clones capable of spreading resistance and virulence factors have the potential to cause unmanageable infection outbreaks with high morbidity and mortality. Competing Interest Statement The authors have declared no competing interest.