Characterization of Antimicrobial Resistance Patterns and Resistance Genes of Enterococci from Broiler Chicken Litter

Enterococci, commonly found in the normal intestinal flora of humans and animals, have emerged as an important human pathogen. A total of 184 isolates (88 isolates in 2015 and 96 isolates in 2016) were collected from 46 flocks. Two predominant enterococcus species were identified: Enterococcus faecalis (59%) and Enterococcus faecium (~39%). Resistance to penicillin was significantly decreased in the overall enterococci community, while it remained unchanged in the multi-class drug resistant (MDR) community. We identified the emeA and efrAB genes, which encode efflux pump systems, in 93% (26/28) of the MDR isolates with (intermediate) resistance to levofloxacin. The ermB gene was present in all MDR strains with resistance to erythromycin. The lsa gene was detected in 87% (84/97) of the MDR isolates with resistance to quinupristin/dalfopristin. About 82.2% of MDR strains in 2015 and 100% of MDR strains in 2016 carried the insertion sequence IS256, which is known to be associated with AMR genes, conferring resistance to erythromycin, gentamicin and vancomycin in enterococci. These results support the need for monitoring AMR in Gram-positive bacteria in poultry production, specifically in broiler chicken farms, to complement current AMR data, and develop a timely intervention framework.