Microbial Food Safety in Small-Scale and Commercial Integrated Crop and Pig Production Environments in South Africa

Integrated farming systems (IFSs) combining crop and livestock production are globally promoted for enhancing resource recycling and food security. However, the interconnectedness of these food production systems may create pathways for transmission of bacterial pathogens and antimicrobial resistance (AMR) between animals, crops, and the surrounding environment, potentially compromising food safety. This study determined the level of microbial contamination using indicator microorganisms (total coliforms and Escherichia coli). In addition, the presence and prevalence of foodborne pathogens (Shiga toxin-producing Escherichia coli (STEC), Salmonella spp., Listeria monocytogenes) and antibiotic-resistant Enterobacterales (extended-spectrum and AmpC-type β-lactamase-producing) were evaluated across three representative small-scale and three commercial crop and pig production systems in South Africa. Replicate samples (n = 5) of soil, irrigation water, animal feed, drinking water, animal waste (fertilizer), and spinach or maize crops were randomly collected at each site. The water samples and solid farm materials analyzed from both farming scales contained ≤3 log MPN/100 mL and 2-7 log CFU/g total coliforms. E. coli counts were higher in animal feed and fresh produce from small-scale farms, and in soil and irrigation water of commercial farms. In total, 95 isolates of generic E. coli, 70 presumptive STEC isolates, three PCR-confirmed STEC, 74 presumptive extended-spectrum [ESBL] and/or AmpC-type β-lactamase-producing Enterobacterales, 11 confirmed ESBL and/or AmpC-type β-lactamase-producing Enterobacterales, and four Salmonella spp. were recovered across all farms. The frequency of indicator bacteria occurrence differed between sampling sites and sample types. Thus, farm management practices, resources, and production scale collectively influence microbial food safety within the evaluated IFS, with implications for informing effective strategies to mitigate food safety risks in sustainable agricultural systems.