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

Abstract

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 bla_KPC, bla_CTX-M, bla_CMY-2, bla_NDM, bla_VIM, bla_IMP, bla_OXA-181 and bla_OXA-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 bla_NDM (n = 30; 62.5%), bla_NDM + bla_OXA-181 (n = 10; 20.8%), bla_OXA-181 (n = 2; 4.2%) and bla_NDM + bla_OXA-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 bla_NDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.

Keywords: Carbapenem-resistant Enterobacterales; Ceftazidime/avibactam; Extended-spectrum β-lactamase; Nigeria; bla(NDM); bla(OXA-181).