High proportion of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae among extended-spectrum ß-lactamase-producers in Nigerian hospitals.

OBJECTIVES: Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria. METHODS: ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK®2 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for blaKPC, blaCTX-M, blaCMY-2, blaNDM, blaVIM, blaIMP, blaOXA-181 and blaOXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing. RESULTS: The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried blaNDM (n = 30; 62.5%), blaNDM + blaOXA-181 (n = 10; 20.8%), blaOXA-181 (n = 2; 4.2%) and blaNDM + blaOXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae. CONCLUSION: Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with blaNDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.