Phenotypic and genotypic characterization of clinical carbapenem-resistant Enterobacteriaceae isolates from Sokoto, northwest Nigeria

Abstract

Emergence and spread of carbapenemase-producing Enterobacteriaceae (CPE) are two of the major problems currently threatening global public health. In Nigeria, interest in CPE is recent. In Sokoto, northwest Nigeria, there are no data on the prevalence and mechanism underlying carbapenem resistance. In this study, we aimed to investigate the presence of clinical carbapenems-resistant Enterobacteriaceae isolates in two leading hospitals in Sokoto, northwest Nigeria. A total of 292 non-duplicate Enterobacteriaceae isolated from clinical specimens processed in the diagnostic laboratories of two hospitals between January and June 2019 were collected. Of these, 129 (44.2 %) and 19 (6.5%) were resistant to third-generation cephalosporin and carbapenems, respectively. RT-PCR revealed that 10 (7.8%), 19 (14.7%) and 46 (35.7%) of the third-generation cephalosporin-resistant isolates harboured bla SHV , bla TEM and bla CTX-M genes, respectively. The modified Carba NP test result showed that only 7 (36.8 %) of the 19 carbapenem-resistant isolates were carbapenemase producing; among them, bla NDM-5 and bla OXA-181 genes were identified in five and two isolates, respectively. However, none of the carbapenemase genes investigated, including bla VIM , bla KPC and bla IMP , was detected in the remaining carbapenem-resistant isolates, suggesting a non-enzymatic mechanism. This study reports for the first time, the emergence of CPE in Sokoto state and the detection of NDM-producing Citrobacter freundii in Nigeria. The observed CPE in this study is a concern in a country where alternative antibiotics are rarely available.

Concurrent Resistance to Carbapenem and Colistin Among Enterobacteriaceae Recovered From Human and Animal Sources in Nigeria Is Associated With Multiple Genetic Mechanisms

“…Surprisingly, we found no evidence for carbapenemase producing genes in both our phenotypic and genomic investigations (WGS). This is in contrast to some studies on resistance in the region that reported carbapenemase genes such as bla NDM and bla OXA−181 are widespread (Jesumirhewe et al, 2017;Olalekan et al, 2020;Olowo-Okere et al, 2020;Shettima et al, 2020).…”

“…The high resistance rates we recorded are in accordance with data in other reports on human and animal isolates from Nigeria and Sub-Saharan Africa (Ojo et al, 2016;Chah et al, 2018;Aworh et al, 2019;Olalekan et al, 2020;Shettima et al, 2020). Most of our isolates also carried the bla CTX−M−15 which is consistent with the increasing reports of this genotype from animal and human sources in Nigeria (Chah et al, 2018;Okpara et al, 2018;Olowo-Okere et al, 2020). There is thus growing evidence that this genotype is expanding rapidly and might become the dominant mechanism mediating resistance to the β-lactams.…”

“…We recently reported the occurrence of mcr-mediated colistin resistance among 99 colistin resistant isolates; Escherichia coli (67/99), Klebsiella pneumoniae (30/99), Citrobacter werkmanii (1/99), and Alcaligenes faecalis (1/99) from humans and animals in Nigeria (Ngbede et al, 2020). Studies have also reported a high prevalence, up to 52%, of carbapenem resistance mediated by carbapenemase producing genes in samples from humans in Nigeria (Ogbolu and Webber, 2014;Jesumirhewe et al, 2017;Olowo-okere et al, 2019;Otokunefor et al, 2019;Ogbolu et al, 2020;Olalekan et al, 2020;Olowo-Okere et al, 2020;Shettima et al, 2020). These findings suggest that resistance to the last resort drugs carbapenem and colistin is a significant problem in Nigeria.…”

Escalating antimicrobial resistance among Enterobacteriaceae: focus on carbapenemases

“…In one study, surveillance in 31 of 47 (66%) countries identified low rates of CP resistance among E. coli ( > 5% in only one country); for Klebsiella spp., rates of CP resistance exceeded 5% in only 2 nations (13%) 137 . In a study of 292 clinical isolates of Enterobacteriaceae from two hospitals in Nigeria between January and June 2019, 129 (44.2%) were resistant to 3 rd -generation cephalosporins but only 19 (6.5%) were CRE 138 . Only 7 of 19 (36.8 %) CRE isolates produced CPases; genotypes included NDM-5 (n=5) and OXA-181 (n=2), respectively.…”

Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens

“…com) [19]. Codon-code aligner version 9.0.1 was used to obtain contig sequences [20]. The contig sequences were compared to the reference 16S rRNA sequences at National Center for Biotechnology Information (NCBI) database by using Basic Local Alignment Search Tool (BLAST) algorithm.…”