Molecular epidemiology of antibiotic-resistant enterococcus spp. from farm to food-production chain in intensive poultry production in KwaZulu-Natal, South Africa.
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Extensive antibiotic use in intensively-farmed poultry exerts selection pressure for the emergence of multidrug-resistant pathogens. The aim of this study was to determine the antibiotic resistance and virulence profiles of Enterococcus spp. along the farm to food-production chain continuum in an intensive poultry system in the uMgungundlovu District in Kwazulu-Natal, South Africa. A total of 187 samples along the poultry farm to food-production chain continuum (litter, faeces, transport, holding, abattoir and retail meat) were evaluated for the presence of Enterococcus spp. Molecular confirmation by PCR, targetting the genus- (tuf) and species-specific (sodA) genes was undertaken. Susceptibility profiles were assessed by Kirby-Bauer disk diffusion against the WHO-AGISAR recommended panel of antibiotics for Enterococcus spp. using CLSI guidelines. Antibiotic resistance and virulence genes were detected using real-time PCR. Genetic relatedness between isolates across the continuum was evaluated by REP-PCR. Of 134 isolates identified across the continuum, with a prevalence of 72%, molecular speciation confirmed the isolates as E. faecalis (36%), E. faecium (31%), E. gallinarum (2%) and other Enterococcus spp. (31%). Resistance to tetracycline (80%), erythromycin (71%), nitrofurantoin (17%), ampicillin (15%), streptomycin (15%), chloramphenicol (11%), ciprofloxacin (5%), tigecycline (4%), gentamicin (4%), teicoplanin (3%) was observed among Enterococcus spp. but no vancomycin resistance (0%). E. faecium displayed 24% resistance, and 21% were of intermediate susceptibility to quinupristin-dalfopristin. Twenty-one percent (21%) of E. faecalis and 100% of E. gallinarum, also showed intermediate susceptibility to vancomycin. Forty-three percent (43%) of E. faecium were multidrug-resistant (MDR) (resistant to 1 or more antibiotics in 3 or more antibiotic classes). The most frequently observed antibiotic resistance genes, associated with the phenotypic profiles, were tetM (76%) and ermB (67%) with a smaller percentage noted for aph(3’)-IIIa (12%) and vanC1 (1%). Virulence genes efaAFs (100%), cpd (96%) and gelE (81%) were more frequently detected in E. faecalis. The cell wall adhesin (efaAFm) was more common in E. faecium (100%) and other Enterococcus spp. (71%). Clonality evaluated by REP-PCR revealed that isolates along the continuum are highly diverse with major REP-types often consisting of isolates from the same sampling point in the continuum.