Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya

Abstract

Multidrug resistant (MDR) Klebsiella pneumoniae is a common cause of nosocomial infections worldwide. Recent years have seen an explosion of resistance to extended-spectrum β-lactamases (ESBLs) and emergence of carbapenem resistance. Here, we examine 198 invasive K. pneumoniae isolates collected from over a decade in Kilifi County Hospital (KCH) in Kenya. We observe a significant increase in MDR K. pneumoniae isolates, particularly to third generation cephalosporins conferred by ESBLs. Using whole-genome sequences, we describe the population structure and the distribution of antimicrobial resistance genes within it. More than half of the isolates examined in this study were ESBL-positive, encoding CTX-M-15, SHV-2, SHV-12 and SHV-27, and 79% were MDR conferring resistance to at least three antimicrobial classes. Although no isolates in our dataset were found to be resistant to carbapenems we did find a plasmid with the genetic architecture of a known New Delhi metallo-β-lactamase-1 (NDM)-carrying plasmid in 25 isolates. In the absence of carbapenem use in KCH and because of the instability of the NDM-1 gene in the plasmid, the NDM-1 gene has been lost in these isolates. Our data suggests that isolates that encode NDM-1 could be present in the population; should carbapenems be introduced as treatment in public hospitals in Kenya, resistance is likely to ensue rapidly.

Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa

“…We also report a higher prevalence (87.5%) of OXA β-lactamase genes in these K. pneumoniae isolates as well as bla SHV in 83.3% of isolates, confirming that this supposedly chromosomally encoded gene, is not universally found in K. pneumoniae species 38 . Interestingly, four isolates also contained the narrow spectrum, chromosomally encoded bla LEN gene, comprising of bla LEN9 and bla LEN12 , which are rare in South Africa and Africa although it has been previously described in Kenya 39 . The bla LEN β-lactamase gene was first identified by Arakawa 30 .…”

Prevalence of CTXM, SHV, TEM AND OXA Genes among Extended-Spectrum Beta-Lactamase Producing <i>Klebsiella pneumoniae</i> from Mukuru Slum, Kenya

“…In Kenya, there are limited pediatric data on the prevalence of these ESBL variants. ESBLs were first identified in Germany in 1982 and have since spread globally, becoming a significant problem in sub-Saharan Africa including Kenya [5].…”

Description ofKlebsiella africanensissp. nov.,Klebsiella variicolasubsp.tropicalensissubsp. nov. andKlebsiella variicolasubsp.variicolasubsp. nov

“…Is not able to metabolize N-acethyl-neuraminic acid, adonitol, D-lactic acid methyl ester, L-alaninamide and 3-O-b-galactopyranosyl-D-arabinose and D-arabitol. So far, K. africanensis was recovered from asymptomatic human fecal carriage in Senegal (this study) and from human clinical samples in Kenya [13].…”

“…Strain 1266 T (internal strain bank identifier, SB5531) was chosen as reference strain for phylogroup Kp5, whereas strain 200023 T (internal strain bank identifier, SB5857) was included as reference strain of Kp7 phylogroup. The genome (Accession Number ERS214332) of the strain 38679 [13] was included for phylogenetic comparisons even though the strain was not available at the time of this study. Strains were grown in tryptocasein soy agar (TSA) (BioRad, Marnes-La-Coquette, France).…”