Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

Abstract

<i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i> strains in Kenya. A total of 89 <i>K. pneumoniae</i> 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 from the hospital environment (6/89). Genetic analysis revealed the presence of <i>bla_NDM-1</i> and <i>bla_OXA-181</i> carbapenemase genes and the <i>armA</i> and <i>rmtF</i> genes known to confer pan-aminoglycoside resistance. The most abundant extended-spectrum beta-lactamase genes identified were <i>bla_CTX-M-15</i> (36/89), <i>bla_TEM</i> (35/89), and <i>bla_OXA</i> (18/89)_. In addition, one isolate had a mobile colistin resistance gene (<i>mcr-8</i>). Fluoroquinolone resistance-conferring mutations in <i>gyrA</i> and <i>parC</i> genes were also observed. The most notable virulence factors were those associated with hyper-virulence (<i>rmpA/A2</i> and <i>magA</i>), yersiniabactin (<i>ybt</i>), salmochelin (<i>iro</i>), and aerobactin (<i>iuc</i> and <i>iutA</i>). A total of 38 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 <i>K. pneumoniae</i> 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.