Prevalence, Antimicrobial Resistance Patterns, and Emerging Carbapenemase-Producing Enterococcus Species from Different Sources in Lagos, Nigeria

<b>Background</b>: <i>Enterococcus</i> species present significant health risks due to their widespread presence in humans, animals, and the environment. This study examined the patterns of antimicrobial resistance (AMR) and the presence of carbapenemase-producing <i>Enterococcus</i> species from various sources. <b>Methods</b>: Between November 2023 and February 2024, 500 samples were collected in Lagos State, including 350 clinical human samples, 50 environmental samples, and 100 animal samples. The samples were processed, and <i>Enterococcus</i> isolates were identified and subjected to antimicrobial susceptibility tests (AST) by standard methods. Furthermore, carbapenemase (<i>bla</i>_KPC and <i>oxa-48</i>) and virulence genes (<i>gelE</i>) were detected by real-time polymerase chain reaction (RT-PCR) methods using specific primers. <b>Results</b>: The overall prevalence of <i>Enterococcus</i> isolates was 4.6% (23/500), including 18 <i>E. faecalis</i> and 5 <i>E. faecium</i>. The source prevalence was 24% (12/50) from the environmental samples, 5% (5/100) from animal sources, and 1.7% (6/350) from the clinical samples. All <i>Enterococcus</i> isolates were 100% resistant to ciprofloxacin, erythromycin, imipenem, vancomycin, and ampicillin. However, 91% were susceptible to gentamicin. Six (6) distinct resistance profiles were observed, with the pattern AMP-ERY-TGC-CIP-TS-VA-CHL-AUG-MEM-IMI being the most frequent in 12 <i>E. faecalis</i> (4 isolates from humans, 2 from animals, and 6 from the environment). Notably, 39.1% (9/23) of multiple-drug resistant <i>Enterococcus</i> isolates harbored the <i>gelE</i> virulence gene, including seven <i>E. faecalis</i> (five environmental and two human) and two <i>E. faecium</i> from animal sources. The <i>E. faecalis</i> strains HB003 and HB050, from human bacteremia cases carrying <i>gelE</i>, were the first in Nigeria to produce <i>bla</i>_KPC and <i>oxa-48</i> carbapenemase genes. <b>Conclusions</b>: This study revealed the emergence of carbapenemase-producing <i>Enterococcus</i> species in our environment. A one-health approach and further molecular studies are essential to mitigate the spread and understand the transmission dynamics.