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Livestock, farms, abattoirs, and food supply systems can become the source of foodborne pathogens, including S. aureus, in the absence of monitoring, general hygienic practices, and control. Studies are scarce on reservoirs (hiding places) and routes of entry of S. aureus into the food supply chain in Ethiopia. To fill these gaps, we evaluated the role of cows (milk), meat, equipment, and food handlers on the abundance and AMR of S. aureus in five geographical areas in central Oromia, Ethiopia. We isolated S. aureus from 10 different ecologies per area in 5 areas and tested their sensitivity to 14 antimicrobials of 9 different classes. We ranked the 5 areas and 10 ecologies by computing their multiple AMR index (MARI) at a cut-off value of 0.2 to determine ‘high-risk’ ecologies for AMR. We recorded as MDR if an isolate had resistance to ≥3 antimicrobial classes. We used a circos diagram to analyze if isolates with identical AMR patterns were shared between different ecologies. S. aureus is prevalent in central Oromia (16.1–18.3%), higher in dairy farms than in abattoirs, and varied among 10 ecologies (p < 0.001) but not among 5 areas (p > 0.05). Of the 92 isolates, 94.6% were penicillin-resistant. Their AMR prevalence was above 40% for 9 of 14 antimicrobials. All isolates (100%) had AMR in at least one antimicrobial class (range = 1–9; median = 5), indicating MDR was prevalent. The prevalence of MDR S. aureus varied (p < 0.05) among areas and 10 ecologies; the highest was in slaughter lines. All isolates had a MARI of >0.2, indicating drug overuse, and S. aureus’s AMR burden is high in central Oromia. Dairy farms had higher MARI values (0.44) than abattoirs (0.39). Of 10 ecologies, the highest and lowest MARI values were in the beef supply chain, i.e., slaughter line (0.67) and butcher’s hand (0.25). Of the 68 different AMR patterns by 92 isolates against 14 antimicrobials, 53 patterns (77.9%) were unique to individual isolates, indicating they were phenotypically dissimilar. MDR S. aureus was widespread in central Oromia in dairy and meat supply chains, contaminating milk, meat, equipment, and workers in farm and abattoir settings. In the absence of strict regulations and interventions, MDR S. aureus can be disseminated from these epicenters to the public.

Background: Safe food is central to social wellbeing. Coagulase-negative staphylococci (CNS) are a threat to food safety because they may harbor multiple enterotoxins and antimicrobial resistance (AMR) genes. CNS bacteria are an emerging nosocomial pathogen in public health. CNS also cause bovine mastitis with a significant economic loss in the dairy industry and may introduce toxins to the food supply chain resulting in foodborne illnesses. However, information on CNS and their AMR status are scarce in food animal production and processing lines in Ethiopia. Methodology: This cross-sectional study evaluated the prevalence and AMR patterns of CNS in dairy farms and abattoirs using samples (n = 1001) from udder milk, beef carcass, personnel, and different abattoir and dairy equipment across five locations of central Oromia. The CNS isolates were identified via standard microbiological protocols and evaluated using disc diffusion test against 14 antimicrobials belonging to nine different broad classes. Uni-and-multivariable logistic regressions were used to analyze the association between potential risk factors (location, sample source, and sample type) and positivity to CNS. Results: The overall prevalence of CNS in the five different geographic locations studied was 9.6% (range: 6.7–12.4%) and varied between abattoirs (11.3%) and dairy farms (8.0%). CNS were prevalent on the carcass, milk, equipment, personnel hands, and nasal samples. Of all CNS isolates, 7.1, 10.7, 7.1, 12.5, 17.9, 10.7, 12.5, 7.1, 1.8, 5.4, 1.8, and 5.4% exhibited AMR simultaneously to single, double, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, and 13 antimicrobials, respectively. Overall, the isolates displayed 51 different AMR phenotypic patterns in which 50% of the isolates exhibited quadruple-resistance simultaneously based on the nine broad antimicrobial classes tested using 14 representative antimicrobials. The prevalence of multidrug-resistant (MDR) CNS (i.e. ≥ 3 classes of antimicrobials) was significantly (p = 0.037) different between locations with 100, 57.1, 50, 86.7, and 76.9% in Addis Ababa, Adama, Assela, Bishoftu, and Holeta, respectively. However, the prevalence of MDR CNS was not significantly (p = 0.20) different between dairy farms (87.5%) and abattoirs (71.9%). We evaluated the effect of acquiring cefoxitin-resistance of the isolates on the efficacy (i.e. inhibition zone) of the rest antimicrobials using General Linear Model after adjusting geographical locations as a random effect. Isolates with cefoxitin-resistance significantly displayed resistance to eight antimicrobials of 14 tested including amoxicillin, penicillin, cloxacillin, chloramphenicol, nalidixic acid, nitrofurantoin, and tetracycline (p = 0.000), and erythromycin (p = 0.02). On the other hand, cefoxitin-resistant isolates were susceptible to gentamicin, ciprofloxacin, kanamycin, streptomycin, and sulphamethoxazone trimethoprim (p = 0.000). Thus, antimicrobials such as gentamicin and ciprofloxacin may be an alternative therapy to treat cefoxitin-resistant CNS, as 96.4% of CNS isolates were susceptible to these antimicrobials. Overall, 94.1 and 54.5% of the CNS isolates among cefoxitin-resistant and cefoxitin-susceptible, respectively, harbored resistance to 3 or more classes of antimicrobials i.e. MDR. Conclusion: The overall prevalence of CNS in milk, meat, equipment, and food handlers in central Oromia was 9.6% but varied by location and sample source. Some specific niches such as equipment, hands, and nasal cavities of personnel are significant sites for the source of CNS. Most, but not all, MDR CNS isolates were cefoxitin-resistant. Overall, 78.6% of the CNS tested were MDR and 50% had resistance to four or more broad classes of antimicrobials. CNS in food animals (raw milk and meat), equipment, and food handlers can be the source of MDR to the public. Personnel safety and hygienic food handling practices are needed. In addition, further investigation into the risk factors for the transmission and mechanisms of resistance of the CNS is required for intervention.