Mobilized colistin-resistant gene (MCR-1) in extended-spectrum beta-lactamase-producing clinical isolates of Escherichia coli in Abuja, Nigeria

Introduction: The global increase in reports of transferable colistin resistance has become a significant public health concern. In Nigeria, only a limited number of studies have documented the presence of mobilized colistin resistance genes (MCR) in isolates derived from both human and animal sources. Aim: This investigation aimed to detect the presence of the mobilized colistin-resistant gene (MCR-1) in multiple drug-resistant, extended-spectrum beta-lactamase-producing clinical isolates of Escherichia (E.) coli and Klebsiella (K.) pneumoniae obtained from selected hospitals in Abuja, Nigeria. Materials and method: A total of 115 consecutive, non-duplicate presumptive clinical isolates of E. coli and K. pneumoniae were collected over three months from two hospitals in Abuja: Garki Hospital Abuja and Nisa Hospital Abuja. These isolates were identified employing rapid identification kits. Antimicrobial susceptibility testing was conducted using the agar disc diffusion method, while phenotypic detection of ESBLs was performed via double-disc synergy tests. The MIC of colistin was determined using the broth microdilution method. Molecular characterization of the ESBL and MCR-1 genes was achieved through PCR analysis. Results: Out of 115 clinical isolates, 49 (42.6%) were identified as E. coli and K. pneumoniae, with 36 (73.5%) of these being multidrug-resistant (MDR). Among the MDR isolates, 15 demonstrated phenotypic resistance to third-generation cephalosporins (primary indicators for TEM and SHV-derived ESBLs), e.g., cefpodoxime. These 15 isolates were selected for ESBL screening. Seven isolates tested positive and were subsequently subjected to double-disc synergy testing. Notably, five out of these seven isolates were confirmed as phenotypic ESBL producers. The result of PCR analysis revealed that 3/5 harbored multiple ESBL genes; E. coli harbored blaSHV and blaCTX-M or blaSHV and blaTEM, K. penumoniae harbored blaSHV, blaTEM, and blaCTX-M. None of the investigated isolates harbored the blaOXA gene. A total of 8 isolates comprising the 3 genotypic ESBL-positive isolates, the 2 phenotypic colistin-resistant isolates, and 3 borderline phenotypic colistin-resistant isolates were molecularly analyzed to detect MCR-1 genes. One out of /8 isolates of E. coli isolated from a patient’s urine sample harbored the MCR-1 gene. Conclusion: This study is, to the best of our knowledge, the first report of MCR-1 gene detection from a human clinical sample in Abuja, the capital city of Nigeria. The increasing emergence of mobilized colistin resistance genes in isolates of clinical significance as such, calls for an urgent need to preserve the efficacy of our last resort antibiotics through the institutionalization and adequate implementation of antibiotic stewardship.