South African abattoir wastewater
Abstract Antimicrobial resistance (AMR) poses a significant global One Health challenge, leading to hard-to-treat infections and increased mortality. Animal production contributes to the progression??  of AMR, as over half of all antibiotics globally are used in food-producing animals. There is a growing number of publications about AMR in food-producing animals in African countries, but the surveillance practices vary considerably. This pilot study explores the potential of wastewater-based surveillance in abattoirs as a swift and effective method for assessing AMR in food-producing animals.  Wastewater samples (n=16) and swab samples from floor drainages (n=18) were collected from six South African abattoirs handling various animal species. The samples were analyzed for extended-spectrum beta-lactamase-producing bacteria (ESBL), carbapenemase-producing Enterobacteriaceae, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci, and Candida auris. Samples were cultured on selective agar plates (CHROMagar™, Paris, France), and species were identified using MALDI-TOF MS. A subset of isolates was further characterized by disk diffusion test (n=84) and by whole genome sequencing (n=21).  The most prevalent species from plates selective for ESBL-producing bacteria included Escherichia coli (n=60) and Klebsiella pneumoniae (n=24), all phenotypically ESBL-producers. One E. coli isolate exhibited phenotypical resistance against meropenem. Acinetobacter baumannii (n=16), A. pittii (n=3), and A. nosocomialis (n=2) were isolated from plates selective for carbapenem-resistant Enterobacteriaceae. S. aureus, vancomycin-resistant Enterococcus faecalis/E.faecium, or C. auris were not found. Genomic analyses revealed multiple sequence types (ST) of E. coli (n=9) and K. pneumoniae (n=5), including STs associated with food-producing animals globally such as E. coli ST48 and ST10 and K. pneumoniae ST101. Common beta-lactamases linked to food-producing animals, such as blaCTX-M-15, blaCTX-M-14, and blaCTX-M-55, were detected.  In this study, we detected ESBL-producing E. coli with STs associated previously with food-producing animals. We also found E. coli and K. pneumoniae isolates harboring beta-lactamases commonly linked to food-producing animals. The results underscore the potential of abattoir environment and wastewater sampling for AMR surveillance in food-producing animals. However, refinement of methodologies and concurrent sampling of animals entering abattoirs or comparison of data from countries whit regular surveillance would enhance whether wastewater-based surveillance accurately reflects the AMR situation in food-producing animals.