From the Farms to the Dining Table: The Distribution and Molecular Characteristics of Antibiotic-Resistant <i>Enterococcus</i> spp. in Intensive Pig Farming in South Africa

• Main Authors: Sasha Badul, Akebe L. K. Abia, Daniel G. Amoako, Keith Perrett, Linda A. Bester, Sabiha Y. Essack
• Format: Article
• Language: English
• Published: MDPI AG 2021-04-01
• Series: Microorganisms
• Subjects: antibiotic resistance; <i>Enterococcus</i> spp.; multidrug resistance; farm-to-fork; intensive pig farming; public health
• Online Access: https://www.mdpi.com/2076-2607/9/5/882

Foodborne pathogens, including antibiotic-resistant species, constitute a severe menace to food safety globally, especially food animals. Identifying points of concern that need immediate mitigation measures to prevent these bacteria from reaching households requires a broad understanding of these pathogens’ spread along the food production chain. We investigated the distribution, antibiotic susceptibility, molecular characterization and clonality of <i>Enterococcus</i> spp. in an intensive pig production continuum in South Africa, using the farm-to-fork approach. <i>Enterococcus</i> spp. were isolated from 452 samples obtained along the pig farm-to-fork continuum (farm, transport, abattoir, and retail meat) using the IDEXX Enterolert^®/Quanti-Tray^® 2000 system. Pure colonies were obtained on selective media and confirmed by real-time PCR, targeting genus- and species-specific genes. The susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion method against 16 antibiotics recommended by the WHO-AGISAR using EUCAST guidelines. Selected antibiotic resistance and virulence genes were detected by real-time PCR. Clonal relatedness between isolates across the continuum was evaluated by REP-PCR. A total of 284 isolates, consisting of 79.2% <i>E. faecalis</i>, 6.7% <i>E. faecium</i>, 2.5% <i>E. casseliflavus</i>, 0.4% <i>E. gallinarum</i>, and 11.2% other <i>Enterococcus</i> spp., were collected along the farm-to-fork continuum. The isolates were most resistant to sulfamethoxazole-trimethoprim (78.8%) and least resistant to levofloxacin (5.6%). No resistance was observed to vancomycin, teicoplanin, tigecycline and linezolid. <i>E. faecium</i> displayed 44.4% resistance to quinupristin-dalfopristin. Also, 78% of the isolates were multidrug-resistant. Phenotypic resistance to tetracycline, aminoglycosides, and macrolides was corroborated by the presence of the <i>tet</i>M, <i>aph(3′)-IIIa</i>, and <i>erm</i>B genes in 99.1%, 96.1%, and 88.3% of the isolates, respectively. The most detected virulence gene was <i>gel</i>E. Clonality revealed that <i>E</i>. <i>faecalis</i> isolates belonged to diverse clones along the continuum with major REP-types, mainly isolates from the same sampling source but different sampling rounds (on the farm). <i>E. faecium</i> isolates revealed a less diverse profile. The results suggest that intensive pig farming could serve as a reservoir of antibiotic-resistant bacteria that could be transmitted to occupationally exposed workers via direct contact with animals or consumers through animal products/food. This highlights the need for more robust guidelines for antibiotic use in intensive farming practices and the necessity of including <i>Enterococcus</i> spp. as an indicator in antibiotic resistance surveillance systems in food animals.