UC Davis

Antimicrobial resistance (AMR) in bacteria is a natural phenomenon that has been developing for thousands of years. However, intensive use of antibiotics in humans and animals starting in the middle of the last century has resulted in increased AMR, which has become a global threat to public health. Excessive use and misuse of antibiotics in food animals are blamed for the emergence of AMR. In recent years, multidrug resistance (MDR) in bacteria has become a serious issue by limiting the treatment options, making hospital stays longer and healthcare costs more expensive. In some cases, infectious diseases caused by AMR are impossible to treat. Antimicrobial-resistant bacteria (ARB) and their genetic determinants can be transferred from animals to the environment, workers, and animal products such as meat. Governments and various global organizations have taken the AMR issue seriously and have started to implement measures to limit the spread of AMR. In the U.S., the National Antimicrobial Resistance Monitoring System (NARMS) was founded in 1996 to track Antimicrobial-resistant bacteria (ARB )in humans, animals, and retail food and identify resistance trends, patterns, and mechanisms to make efficient interventions and drug development. However, the exposure of farm workers has been largely neglected by government agencies, industries, and researchers. Among the ARB, antimicrobial-resistant Salmonella poses a serious threat to public health. California is the most populated state in the U.S. However, antimicrobial resistance patterns of Salmonella in various retail meats have not been examined adequately. Therefore, two studies were conducted: 1) characterize AMR patterns in a farm environment and identify possible transmission routes of ARB from the farm environment to the farm workers; 2) characterize AMR patterns of antimicrobial-resistant Salmonella in retail meat from California. In the first study, environmental and worker samples were collected from the Hopkins Avian facility of the University of California, Davis.Overall, 5 types of environmental (fecal samples, cage and eggs swab from layer house (LH) and fecal samples and door handle swabs from floor house (FH)) and 2 types of worker's samples (outwear and boots swabs). Samples were processed to isolate Salmonella and Generic Escherichia coli (E. coli) to assess their prevalence and test for antimicrobial resistance using the microbroth dilution method. Additionally, E. coli and aerobic bacteria were counted to evaluate the overall bacterial load in the facilities and on worker's personal protective equipment (PPE). Salmonella was not detected in any of the collected samples. Generic E. coli was present in all the samples except LH cage and egg swab samples. Counts of E. coli and aerobic bacteria were higher in fecal samples from both houses compared to other samples. Thirty-five isolates out of one hundred tested isolates were resistant to one drug, 9 isolates were resistant to two drugs and 6 isolates were multidrug-resistant (MDR) (resistant to at least three or more drugs). Higher resistance in E. coli isolates was observed to ampicillin (15 %) and nitrofurantoin (13 %), among other tested drugs. Antimicrobial-resistant E. coli isolates from LH fecal samples, FH fecal and door handle swab samples shared similar antimicrobial resistance patterns with worker's outwear and boots swab samples. The study results showed that door handles of FH pose a high risk of exposure as the prevalence of ARB was high in isolates of E. coli from the door handle swabs. Moreover, our results demonstrated that workers' PPE can serve as a protective measure against the transmission of ARB to workers. In the second study, a total of 849 meat samples (chicken, pork, ground turkey and beef) were collected from Northern and Southern California. One hundred thirty-two Salmonella isolates were recovered from the meat sample. Antimicrobial susceptibility test (AST) and whole genome sequencing were conducted to identify antimicrobial resistance patterns of Salmonella isolates. The recovery rate of Salmonella was high in chicken samples (24.01%) compared to ground turkey (5.42%) and pork samples (3.08%) (P < 0.001). Ground beef samples were not contaminated with Salmonella. Prevalence of Salmonella was higher in meat samples with reduced antibiotic claim (20.35%) compared to conventional (11.96%) ((P < 0.001). Out of 132 isolates, 32 isolates (24.24%) were susceptible to all the tested drugs, while 17 isolates (12.88%) were resistant to one drug, 69 isolates (52.27%) to two drugs and 14 isolates (10.61%) to three or more drugs. Salmonella isolates were more resistant to tetracycline and streptomycin compared to other drugs. Whole Genome Sequencing (WGS) identified a total of 24 antimicrobial resistance genes, including the gyrA mutation as a notable resistance mechanism, along with the identification of 23 plasmid replicons in Salmonella isolates. Among the plasmid replicons, IncFIB (pN55391) was detected in 7 MDR S. Infantis isolates. IncFIB (pN55391) has been linked to the worldwide dissemination of pESI-like mega plasmid carriage in an emerging S. Infantis clone in previous studies. WGS results showed that the correlation between phenotypic and genotypic resistance was very high (96.85%). Overall, this study characterized AMR patterns and trends in Salmonella from retail meat in California, which might be helpful for public health protection, infection control, and clinical decision-making.