The use of antibiotics in food animals results to antimicrobial resistant bacteria that complicates the ability to treat infections. The purpose of this study was to investigate the prevalence of pathogenic and commensal bacteria in soil, water, manure, and milk from cattle and goat farms. A total of 285 environmental and 81 milk samples were analyzed for Enterobacteriaceae by using biochemical and PCR techniques. Susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion technique. A total of 15 different Enterobacteriaceae species were identified from goat and cattle farms. Manure had significantly higher (p < 0.05) Enterobacteriaceae (52.0%) than soil (37.2%), trough water (5.4%), and runoff water (5.4%). There was a significant difference (p < 0.05) in Enterobacteriaceae in goat milk (53.9%) and cow milk (46.2%). Enterobacteriaceae from environment showed 100% resistance to novobiocin, erythromycin, and vancomycin E. coli O157:H7, Salmonella spp., Enterococcus spp., and Listeria monocytogenes displayed three, five, six, and ten. AMR patterns, respectively. NOV-TET-ERY-VAN was the most common phenotype observed in all isolates. Our study suggest that cattle and goat farms are reservoirs of multidrug-resistant bacteria. Food animal producers should be informed on the prudent use of antimicrobials, good agricultural practices, and biosecurity measures.

Access to safe and nutritious food is critical for maintaining life and supporting good health. Eating food that is contaminated with pathogens leads to serious diseases ranging from diarrhea to cancer. Many foodborne infections can cause long-term impairment or even death. Hence, early detection of foodborne pathogens such as pathogenic Escherichia coli strains is essential for public safety. Conventional methods for detecting these bacteria are based on culturing on selective media and following standard biochemical identification. Despite their accuracy, these methods are time-consuming. PCR-based detection of pathogens relies on sophisticated equipment and specialized technicians which are difficult to find in areas with limited resources. Whereas CRISPR technology is more specific and sensitive for identifying pathogenic bacteria because it employs programmable CRISPR-Cas systems that target particular DNA sequences, minimizing non-specific binding and cross-reactivity. In this project, a robust detection method based on CRISPR-Cas12a sensing was developed, which is rapid, sensitive and specific for detection of pathogenic E. coli isolates that were collected from the fecal samples from adult goats from 17 farms in Tennessee. Detection reaction contained amplified PCR products for the pathogenic regions, reporter probe, Cas12a enzyme, and crRNA specific to three pathogenic genes—stx1, stx2, and hlyA. The CRISPR reaction with the pathogenic bacteria emitted fluorescence when excited under UV light. To evaluate the detection sensitivity and specificity of this assay, its results were compared with PCR based detection assay. Both methods resulted in similar results for the same samples. This technique is very precise, highly sensitive, quick, cost effective, and easy to use, and can easily overcome the limitations of the present detection methods. This project can result in a versatile detection method that is easily adaptable for rapid response in the detection and surveillance of diseases that pose large-scale biosecurity threats to human health, and plant and animal production.

Introduction: The increase of antimicrobial resistance (AMR) in zoonotic pathogens poses a substantial threat to both animal production and human health. Although large-scale animal farms are acknowledged as major reservoirs for AMR, there is a notable knowledge gap concerning AMR in small-scale farms. This study seeks to address this gap by collecting and analyzing 137 fecal samples from goat and sheep farms in Tennessee and Georgia.Method: Bacteria were identified using culture-dependent methods and polymerase chain reaction (PCR), and antimicrobial susceptibility testing (AST) was performed using the Kirby-Bauer Disk Diffusion method.Results and discussion: The prevalence of E. coli (94.9%) in goats and sheep significantly exceeded (p < 0.05) that of S. aureus (81.0%), Shigella (35.0%), S. saprophyticus, and Salmonella (3.0%). Salmonella occurrence in goat feces (2.2%) was higher than in sheep (0.8%). Notably, 27% of goats and 8% of sheep tested positive for Shigella spp., while 60% of goats and 21% of sheep tested positive for S. aureus. Antibiotic resistance was observed primarily against ampicillin (79.4%), vancomycin (65.1%), and gentamycin (63.6%), significantly surpassing (p < 0.05) resistance to tetracycline (41.6%) and imipenem (21.8%). The penicillin (79.4%), glycopeptide (65.1%), and aminoglycoside (63.6%) antibiotic classes displayed significantly higher (p < 0.05) resistance compared to tetracyclines (45.7%) and carbapenem (21.8%). Our findings suggest that goats and sheep feces may serve as source for multidrug-resistant bacteria, raising concerns about the potential introduction of their fecal matter into soil, water, and eventually to the food chain. This highlights the need for proactive measures to address and mitigate AMR in goats and sheep within small-scale farms.

This study explores into the levels of coliform contamination, prevalence of antibiotic-resistant bacteria, and the hygienic practices in goat meat retail stores. Goat meat from 10 retail stores was analyzed for E. coli, Salmonella, and S. aureus using serological and PCR methods. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Data on hygienic practices were collected through a structured observational questionnaire. Pearson’s correlation analysis was also employed to establish the relationship between hygienic practices and coliform loads. The average coliform loads on goat meat ranged between 0.88–5.04 log10 cfu/g. Our results revealed that 52% of examined goat meat was deemed unacceptable (>3.30 log10 CFU/g). The overall level of good meat handling practices among meat handlers in our study was 45.75%. Further, the study establishes a significant correlation between the level of food safety practices and coliform load. Hence, stores with higher hygienic practice scores exhibited lower coliform loads. The prevalence of S. aureus (44%) in goat meat was significantly higher (p < 0.05) as compared to E. coli (29%), and Salmonella spp. (20%). E. coli isolates displayed the highest resistance to penicillin (31.2%), Salmonella spp. to oxytetracycline (13.9%), and S. aureus to ampicillin (29.0%). Resistance was observed across selected antibiotic classes, particularly in beta-lactams and tetracyclines, with penicillin (78.5%) and oxytetracycline (64.5%) exhibiting notable resistance. Cephalosporin resistance was noted, with 48.4 and 33.3% of isolates showing resistance to cephalothin and cefpodoxime, respectively. Bacterial isolates also demonstrated resistance to phenicol antibiotics, including chloramphenicol (9.7%) and florfenicol (16.1%), respectively. Approximately 44.1% of bacterial isolates displayed multidrug resistance and MAR index ranged from 0.25 to 0.75. The study’s findings reveal heightened levels of coliform contamination, the presence of pathogenic and multidrug-resistant bacteria in goat meat, and suboptimal meat handling practices in retail stores. The significance of improving food safety practices in retail settings is emphasized to ensure the safety of goat meat, a matter of increasing importance due to its growing demand globally.