Abstract:
Antimicrobial resistance (AMR) poses a significant global One Health challenge
that causes increased mortality and a high financial burden. Animal production
contributes to AMR, as more than half of antimicrobials are used in food-producing
animals globally. There is a growing body of literature on AMR in food-producing
animals in African countries, but the surveillance practices across countries vary
considerably. This pilot study aims to explore the potential of wastewater and
environmental surveillance (WES) of AMR and its extension to the veterinary field.
Floor drainage swab (n = 18, 3/abattoir) and wastewater (n = 16, 2-3/abattoir)
samples were collected from six South African abattoirs that handle various animal
species, including cattle, sheep, pig, and poultry. The samples were tested for
Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase-producing
Enterobacterales, Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycinresistant Enterococci (VRE), and Candida auris by using selective culturing and
MALDI-TOF MS identification. The phenotype of all presumptive ESBL-producing
Escherichia coli (n = 60) and Klebsiella pneumoniae (n = 24) isolates was confirmed
with a disk diffusion test, and a subset (15 and 6 isolates, respectively), were
further characterized by whole-genome sequencing. In total, 314 isolates (0–12
isolates/sample) withstood MALDI-TOF MS, from which 37 species were identified,
E. coli and K. pneumoniae among the most abundant. Most E. coli (n = 48/60;
80%) and all K. pneumoniae isolates were recovered from the floor drainage
samples, while 21 presumptive carbapenem-resistant Acinetobacter spp. isolates
were isolated equally from floor drainage and wastewater samples. MRSA, VRE,
or C. auris were not found. All characterized E. coli and K. pneumoniae isolates
represented ESBL-phenotype. Genomic analyses revealed multiple sequence
types (ST) of E. coli (n = 10) 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-55 and blaCTX-M-15, were detected. The presence of food-production animal-associated ESBL-gene-carrying E. coli and K. pneumoniae in an abattoir
environment and wastewater indicates the potential of WES in the surveillance of AMR in food-producing animals. Furthermore, the results of this pilot study
encourage studying the topic further with refined methodologies.
