Detection of diverse carbapenem and multidrug resistance genes and high-risk strain types among carbapenem non-susceptible clinical isolates of target gram-negative bacteria in Kenya

Carbapenem-resistant gram-negative bacteria are an increasingly significant clinical threat globally. This risk may be underestimated in Kenya as only four carbapenemase genes in three bacterial species have been described. The study aimed to understand the antibiotic resistance profiles, genes, sequence types, and distribution of carbapenem-resistant gram-negative bacteria from patients in six hospitals across five Kenyan counties by bacterial culture, antibiotic susceptibility testing, and whole-genome sequence analysis. Forty-eight, non-duplicate, carbapenem non-susceptible, clinical isolates were identified across the five counties (predominantly in Nairobi and Kisii): twenty-seven Acinetobacter baumannii, fourteen Pseudomonas aeruginosa, three Escherichia coli, two Enterobacter cloacae, and two Klebsiella pneumoniae. All isolates were non-susceptible to β-lactam drugs with variable susceptibility to tigecycline (66%), minocycline (52.9%), tetracycline (29.4%), and levofloxacin (22.9%). Thirteen P. aeruginosa isolates were resistant to all antibiotics tested. Eleven carbapenemase genes were identified: bla(NDM-1,) bla(OXA-23, -58, -66, -69, and -91) in A. baumannii (STs 1, 2, 164 and a novel ST1475), bla(NDM-1) in E. cloacae (STs 25,182), bla(NDM-1), bla(VIM-1and -6), bla(OXA-50) in P. aeruginosa (STs 316, 357, 654, and1203), bla(OXA-181,) bla(NDM-1) in K. pneumoniae (STs 147 and 219), and bla(NDM-5) in E. coli (ST164). Five A. baumannii isolates had two carbapenemases, bla(NDM-1,) and either bla(OXA-23) (4) or bla(OXA-58) (1). AmpC genes were detected in A. baumannii (bla(ADC-25)), E. cloacae (bla(DHA-1 and) bla(ACT-6, 16)), and K. pneumoniae (bla(CMY)). Significant multiple-drug resistant genes were the pan-aminoglycoside resistance16srRNA methyltransferase armA, rmtB, rmtC, and rmtF genes. This study is the first to report bla(OXA-420, -58, -181, VIM-6,) and bla(NDM-5) in Kenyan isolates. High-risk STs of A. baumannii (ST1475, ST2), E. cloacae ST182, K. pneumoniae ST147, P. aeruginosa (ST357, 654), and E. coli ST167, ST648 were identified which present considerable therapeutic danger. The study recommends urgent carbapenem use regulation and containment of high-risk carbapenem-resistant bacteria.