High proportion of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae among extended-spectrum β-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 β-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.