Molecular epidemiology of antibiotic resistant salmonella spp. from farm to fork in an intensive pig production system in KwaZulu-Natal South Africa.

Abstract

Antibiotic resistance (ABR) is a worldwide challenge, and, if not resolved, can be a danger to humans, animals and the ecosystem. The inappropriate use and misuse of antibiotics in food animal production creates selection pressure for the development of bacterial resistance. We investigated the molecular epidemiology, antibiotic resistance and virulence of Salmonella spp. from farm-to-fork in an intensive pig production system in KwaZulu-Natal. A herd of pigs was followed from birth to slaughter over a period of 4 months. Following ethical approval, a total of 408 samples were collected, which consisted of feces, litter, slurry, hand and nasal swabs from occupationally exposed workers, carcass swabs and rinsate, caecal samples and pork for retail purposes. Salmonella was putatively identified using selective media, i.e., Brilliance Salmonella Agar and Salmonella Shigella Agar (SS agar). Identification to species and sub-species level was confirmed by polymerase chain reaction (PCR), where the invA gene was used to confirm Salmonella spp. and the iroB gene for Salmonella enterica. Isolates were subjected to antibiotic susceptibility testing using the Kirby-Bauer disk diffusion method against a panel of 14 antibiotics. Isolates were screened for selected virulence genes, misL, spiC, orfL, sopB, pipD, hilA and stn, conferring intracellular survival (misL), type III secretion system (spiC), adhesion and autotransporter (orfL), type III secreted effector protein (sopB), type III secreted effector associated with SPI-1 system (pipD), host cell invasion (hilA), and enterotoxin production (stn) by PCR. Genetic relatedness of the isolates was determined by ERIC-PCR. A total of 399 putative Salmonella spp. were detected by selective media, of which 49% (n= 197) were confirmed by the presence of the invA gene and 45% (n=179) were identified as Salmonella enterica by the presence of the iroB gene. The largest number of Salmonella were isolated from retail meat samples. Antibiotic susceptibility testing showed 10% (n=19) resistance to cefoxitin, 8% (n=16) to amoxicillin and 0.5% (n=1) to gentamicin and chloramphenicol. The isolates carried the hilA (91%), stn (91%), misL (89%), pipD (88%), spiC (87%), orfL (85%) and sopB (72%) virulence genes. The isolates were clonally diverse with 26 ERIC-types and four major ERIC-type groups. The large number of isolates in retail meat samples, their virulence, and, to a lesser extent their antibiotic resistance profiles poses a challenge to the food safety system and requires a comprehensive understanding of molecular epidemiology of the organism so that it’s incidence spread can be reduced and better controlled from the primary source within the food chain.