Genetic diversity of ESBL-producing Enterobacteriaceae isolated from pit latrines in urban and suburban communities in Lagos, Nigeria.

The burden of antimicrobial resistant bacteria and resistance genes exists in diverse niches, where they can be disseminated to other ecosystems, including the food chain. This study was conducted to investigate the distribution of antibiotic resistant and extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae in pit latrines in urban and suburban communities in Lagos State, Nigeria. Using standard microbiological methods, bacteria strains were isolated from twenty sludge samples obtained from three sites. Isolates were molecularly identified by 16S rRNA gene amplicon sequencing and bioinformatics analysis. Antibiotic susceptibility testing and screening for ESBL production was done by the disc diffusion and double-disc synergy test. Genetic determinants that encode ESBL were detected by PCR. Forty-five bacterial strains belonging to Aeromonadaceae (5), Enterobacteriaceae (35), Erwiniaceae (1), and Vibrionaceae (4) were isolated from the sludge samples. Escherichia fergusonii, Klebsiella pneumoniae, and Shigella spp. comprised Enterobacteriaceae that were isolated. All (100%) the isolates were sensitive to cefixime and ceftriaxone, while 23% and 46% were resistant to aztreonam and ampicillin respectively. Multidrug resistance was prevalent among E. fergusonii compared to the other two bacterial species. Twenty six percent of the isolates phenotypically displayed ESBL production. blaTEM gene was detected across all three bacterial species and blaSHV was the dominant (49%) among ESBL encoding genes detected. Six percent of E. fergusonii isolates harboured all four ESBL encoding genes. Pit latrines are potential reservoir of antibiotic resistance bacteria and resistance genes that mediate ESBL production. Improved hygiene and sanitation should be implemented to forestall the spread of these pathogens.