The sample types included skin-on/bone-in chicken, ground beef, ground turkey, and pork chops . Meat samples in different packages , vacuum packing, and paper wrapping were placed on ice immediately after purchasing, transported to the lab in refrigerated conditions, and processed within 72 hours after collection. Samples were processed according to the NARMS Retail Meat Surveillance protocol . Briefly, 50 g of each sample was placed into 250 ml buffered peptone water in whirl-pak bags and massaged by hand for 3 minutes. After massaging, the homogenates were incubated at 35°C for 18–24 h. Then, 0.1 ml overnight enrichment was transferred to 10 ml RVR10 and incubated at 42°C for 20-24 hours. The RVR10 enrichments were streaked onto XLT-4 . Two colonies of presumptive Salmonella based on colony morphology were then streaked onto blood agar plates and incubated at 35°C for 20-24 hours. Presumptive Salmonella isolates were banked in Brucella broth with 15% glycerol tubes and shipped to the FDA’s Center for Veterinary Medicine for antimicrobial susceptibility test, whole genome sequencing , and other analysis.R statistical software Statistical Computing, Vienna, Austria was used to do all the analysis. The statistical significance is defined at an alpha level of 0.05. Descriptive statistics for the prevalence of Salmonella and distribution of antimicrobial susceptibility test results were conducted in R. Data analysis was conducted on a total of 132 Salmonella isolates from 130 different meat samples due to two Salmonella isolates of different serotypes recovered from 2 pork samples. The reduced antibiotic use category is composed of samples with label claims of no antibiotic ever and/or organic in packages. The association between Salmonella prevalence in retail meat samples and sampling region, season, meat type, pots for cannabis plants package type, label claim, and store types based on their size were assessed using Fisher’s exact test.
Post-hoc analysis was performed using the cldList function of the R package companion . The correlation between phenotypical and genotypical AMR was calculated by dividing the number of phenotypical antimicrobial-resistant Salmonella isolates by the number of Salmonella isolates with corresponding resistant genes. A heatmap of hierarchical clustering was generated utilizing the heatmap3. package in R .The occurrence of Salmonella in retail meat in California in this study was higher than both the national average and that from the previous year in California . This overall higher prevalence was likely due to higher recovery rate by 1) changes in the NARMS protocol the high number of whole chicken carcasses samples collected in Southern California than Northern California in 2019 . Previous research has also reported a higher prevalence of Salmonella in whole chicken carcasses compared to cut samples of chicken . In addition to the higher number and higher prevalence of Salmonella in whole chicken carcasses from Southern California, other chicken parts such as breasts, wings, and legs from Southern California also had a higher prevalence of Salmonella compared to those from Northern California, which collectively contributed to the significant higher Salmonella prevalence in chicken in Southern California in contrast to that in Northern California . Meat types in this study were not collected in identical proportions: chicken samples – 479 , ground turkey samples – 240 , ground beef samples – 65 , and pork samples – 65 . The disproportionate distribution of samples among the meat types might affect the Salmonella recovery rate from different types of meat. For instance, a larger variety of chicken samples were purchased as compared to turkey and beef, where only ground samples were collected. Our data indicated the highest recovery of Salmonella was in chicken samples , followed by ground turkey and pork samples , and zero recovery from ground beef samples. The cause of the higher prevalence of Salmonella in chicken was aforementioned.
With respect to prevalence in other types of meat, ground turkey samples were lower compared to the national average , pork and ground beef samples were close to the national averages of 4.00% in pork and ~1% in ground beef . The high prevalence of Salmonella in chicken compared to other types of retail meat has been well-documented in previous studies . In general, chicken is a significant source of Salmonella, as contamination can potentially occur throughout the entire production chain, from farm to transportation, during processing in slaughterhouses, and on retail shelves . The prevalence of Salmonella in chicken also varied by U.S. states . For example, Zhao et al. reported that higher prevalence in chicken might be caused by sample type , while Nyirabahizi et al. found that regional factors may impact the prevalence of Salmonella. The current study revealed a notably greater prevalence of Salmonella in samples with reduced antibiotics claim compared to those from conventional production . These findings differ from previous NARMS data, which reported a slightly higher prevalence of Salmonella in samples with conventional production compared to those with reduced antibiotics claims. . One possible explanation might be attributed, at least in part, to the survival and propagation of Salmonella on these farms, which may be favored by conditions associated with reduced antibiotic use. For example, reduced antimicrobial use might result in fewer interventions to control bacterial infections on farms, and lack of routine antimicrobial treatments might increase the prevalence of Salmonella. Moreover, lack of antimicrobial use can affect the competitive balance between beneficial and harmful bacteria in the gut of animals, leading to an increased Salmonella prevalence .
It is also worth noting that larger numbers of pork, ground beef, and ground turkey samples from conventional production had low or zero recoveries of Salmonella, which contributed to the overall low prevalence of Salmonella in meat samples from conventional raise in our study. More than 2,600 Salmonella serotypes have been identified, with specific serotypes frequently associated with severe illnesses . The present study classified the 132 Salmonella isolates into 25 serotypes. Among these serotypes, those frequently implicated in foodborne illness are S. Typhimurium and S. Enteritidis. In the present study, both S. Typhimurium and S. Enteritidis were found in chicken samples. Salmonella Infantis accounted for 64.29% of MDR isolates and was the most prevalent MDR serotype in retail meat in California in 2019, which was different than the national NARMS data. In 2019, the most common MDR Salmonella serotype was I 4,[5],12:i: which comprised 26% of nationwide MDR isolates . However, the rise of MDR S. Infantis caused the national average of MDR Salmonella strains in retail chicken to increase from 20% in2018 to 32% in 2019 . In our study, all the S. Infantis isolates were from chicken samples, which was consistent with the national trend. Finally, the prevalence of MDR Salmonella isolates in our study in California was at the same level as the national average from the NARMS 2019 surveillance data . In the present study, a high prevalence of resistance to tetracycline and streptomycin in Salmonella isolates from poultry samples was observed. This is consistent with the results of the NARMS retail meat surveillance in California in 2018 and the NARMS national AMR data of Salmonella from retail poultry in 2008-2017 . Tetracycline has been commonly used in poultry farming to prevent and cure different poultry illnesses, such as respiratory problems, gut inflammation, and joint infection . Streptomycin, as one of the earliest aminoglycosides developed for combating bacterial infections in the poultry industry, has been utilized against various pathogens including E. coli, Salmonella, Mycoplasma, and Staphylococcus . A notable observation in the current study is that the majority of S. Infantis isolates were resistant to ciprofloxacin and nalidixic acid despite restrictions in fluoroquinolone use in food animal production in the U.S. We attempted to determine the relationships between the occurrence of Salmonella resistance and the claims of antibiotics use. However, indoor cannabis grow system no significant difference was found between isolates with reduced antibiotic claims and conventional in single and multidrug resistance despite the fact that resistance to two drugs was higher in isolates with claims of reduced antibiotics than in isolates with claims of conventional production. Whole genome sequencing has been an essential tool for the characterization and confirmation of AMR in bacteria, especially in the identification of resistance mechanisms where AST has limitations . Our results showed that genotypic resistance was highly corellated with phenotypic resistance, with a sensitivity of 96.85%. Only one of the three Salmonella isolates that exhibited resistance to gentamicin by AST lacked the corresponding resistance gene by WGS analysis. This discordance might be due to the presence of undetected AMR genetic determinants or misclassification of the isolate from AST . On the other hand, the ability of WGS to detect only known AMR genetic determinants highlights the importance of continuous traditional AST for comprehensive AMR assessment .
Consequently, it remains valuable to incorporate both WGS and AST to assess AMR patterns in pathogens, particularly given the potential of new resistance genes continuing to emerge. Plasmid replicons are essential genetic elements that play a crucial role in the dissemination of antimicrobial resistant genes within and between bacterial species . Therefore, the identification and characterization of plasmids can provide insight into the transmission potential of AMR genes between or within bacteria species . In the present study, we discovered various plasmid replicons among various Salmonella serovars. Many of these plasmid replicons have previously been associated with AMR genes. Seventy-six of these isolates were from chicken samples, and one isolate was from the ground turkey sample. Previous studies reported plasmid replicon IncX1 being associated with beta-lactam, quinolones, and tetracycline resistance genes . Additionally, in the present study, plasmid replicon IncFIB was found in 7 MDR, ESBLproducing S. Infantis isolates, and all these isolates came from poultry samples. This is worrisome because previously, plasmid replicon IncFIB has been linked to S. Infantis clone with large megaplasmid, which has been disseminating quickly in the U.S. and worldwide during the last nine years . In the present research, all the MDR S. Infantis genes harbored a gyrA mutation that confers resistance to fluoroquinolone, and four MDR S.Infantis had the extended-spectrum beta-lactamase gene blaCTX-M-65. The fast spread of this MDR S. Infantis clone is concerning as it might undermine the existing treatment options to treat infections.Antimicrobial resistance has become a serious issue worldwide, challenging existing treatment options in human and veterinary medicine. Identifying the transmission routes of antimicrobial-resistant bacteria and the characterization of resistance patterns in antimicrobial resistant bacteria is crucial in combatting the antimicrobial resistance problem. The first study tried to identify probable transmission routes of bacteria from poultry farm environments to farm workers. According to previous studies, farm workers were exposed to antimicrobial resistance via direct contact with farm animals or indirectly through farm environments such as urine or feces, water, and soil. We isolated E. coli from environmental samples and worker’s outwear and footwear samples. Then, antimicrobial patterns in E. coli isolates were characterized. The results showed that E. coli isolates from environmental and worker’s samples shared similar resistant patterns, implying that antimicrobial-resistant bacteria might be transmitted to workers. The results also indicated that the door handles of the facilities pose a serious risk to worker’s health, and worker’s outwear and footwear an important defense to limit the transmission of ARB or ARG. Occupational exposure of farm workers to antimicrobial resistance has been long neglected, and further studies are needed to raise awareness among policymakers and farm workers. The objective of the second study was to characterize antimicrobial resistance patterns in Salmonella from the collected retail meat samples in California. The study found that whole chicken samples had a higher prevalence of Salmonella compared to other chicken parts. Overall, Salmonella isolates from chicken samples were resistant to most of the tested antimicrobial drugs. Resistance to streptomycin and tetracycline was very high in Salmonella isolates. The multi-resistance pattern was most prevalent in S. Infantis isolates.Phenotypical resistance in Salmonella was confirmed by using Whole Genome Sequencing , and WGS accurately found resistance in bacteria with a sensitivity of 96.85 %. Additionally, WGS allowed us to find plasmid replicons that play a crucial role in the transmission of antimicrobial resistance. The study identified resistance genes mutation and plasmid replicons which were associated with the previous outbreaks in North America. The study characterized antimicrobial resistance patterns in Salmonella and identified resistant genes and plasmid replicons that play crucial roles in the dissemination of AMR. Additionally, this comprehensive study helped to identify regional patterns of antimicrobial resistance in Salmonella and established a baseline understanding of the current resistance patterns.