Prevalence of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolates from healthcare facilities in Abuja, Nigeria

Carbapenem-resistant Enterobacteriaceae (CRE) pose a severe worldwide health crisis. However, there are limited data on the prevalence of CRE in Nigeria. This study investigated the prevalence of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolates from three primary healthcare facilities in Abuja, Nigeria. Urine specimens ( n = 400) were cultured using conventional microbiological techniques. Isolated E. coli and K. pneumoniae were further characterized by antibiotics susceptibility testing and a PCR assay to screen for bla KPC , bla NDM , and bla IMP genes. Out of the 400 samples, 181 (45.25%) yielded positive cultures: 156 (39%) E. coli and 25 (6.25%) K. pneumoniae. The PCR assay revealed that the bla NDM gene was the most predominant carbapenemase (41.67%), followed by bla KPC and bla IMP (33.33% each). Co-occurrence of all three genes was detected in some isolates, which will significantly compromise therapeutic efficacy. A critical finding was the significantly higher prevalence and co-carriage of these carbapenemase genes in K. pneumoniae compared to E. coli , identifying it as a high-risk reservoir in this setting. This study provides novel insights into the species-specific dynamics of carbapenem resistance in Nigeria, underscoring the urgent need for targeted surveillance and strengthened infection control measures.