Molecular characterization of multidrug-resistant Klebsiella pneumoniae and Escherichia coli harbouring extended spectrum beta-lactamases and carbapenemases genes at a tertiary hospital, Kenya

Background. Multidrug-resistant (MDR) Gram negative rods are increasingly being reported in sub-Saharan Africa. Molecular investigations play an important role, alongside other measures, in controlling nosocomial infections attributed to these organisms. This study aimed to determine the common extended spectrum beta-lactamases (ESBL) and carbapenemases genes, and clonal relationship in MDR Klebsiella pneumoniae and Escherichia coli. Methods. Fifty-four MDR isolates collected at the Aga Khan University hospital, Nairobi in the month of August 2012 formed the study. These were picked after an increase in the number of resistant strains during the said period was experienced. Results. bla_CTXM was present in 41 (74%) of the isolates, while bla_SHV was detected in 18 (33%) and bla_TEM in 13 (24%) of the isolates. Nine (16.7%) of the isolates harboured all three ESBL genes and 8 (14.8%) harboured two. Eight of the isolates (all E. coli) had none of the ESBL genes tested. Two isolates harboured carbapenemases genotypes: one had bla_NDM-1 and the other bla_SPM. Sequencing matched CTXM-15 and TEM-1 genes in all the isolates harbouring bla_CXTM and bla_TEM respectively. However, there was diversity in bla_SHV with SHV-11 and SHV-12 genes predominant. The isolates were non-clonal. Conclusions. The isolates mostly harboured bla_CTX-M-15 while only a few had carbapenemases genes. Lack of clonality suggests these were the stable circulating strains at the time of the study.