Research Project: Monitoring and Molecular Characterization of Antimicrobial Resistance in Foodborne Bacteria

Location:

2021 Annual Report

Objectives
1. Provide data and characterize pathogen prevalence, unique characteristics and trends on antibiotic resistance, subtyping and molecular characterization of foodborne pathogens in food animals. 2. Identify and characterize potential genetic markers within and across serotypes for Salmonella isolated from poultry for rapid identification and diagnosis. 3. Evaluate the role of innovative chemical and/or biological treatments including arsenicals, prebiotics, or ammonium compounds and how they impact the prevalence and type of antimicrobial resistant pathogens or resistance genes. 4. Develop, evaluate and optimize processing treatments to reduce, control and potentially eliminate foodborne pathogens in poultry processing. 5. Evaluate and define the potential role of protozoa in shaping the ecology of bacterial pathogens in controlling foodborne pathogens in poultry processing environments. 6. Develop algorithms for interpreting and handling sequencing data to aid in epidemiological tracking, defining differences in isolates of foodborne pathogens, including antibiotic resistance patterns, and predicting and determining the source of the isolate.

Approach
The goals of this project fit into four major approaches: 1) analysis of antimicrobial resistance mechanisms and genetic elements in foodborne bacteria from poultry, 2) analysis of innovative chemical and/or biological treatments used for poultry processing on resistance in foodborne bacteria, 3) development of alternative methods for processing poultry products, and 4) development of methods that accurately monitor the microbial quality of poultry products processed by alternative methods. Studies will focus on the molecular aspects of antimicrobial resistance to identify and characterize new and emerging resistance phenotypes and genotypes of high priority type bacteria from poultry [categorized as urgent and serious threat level antimicrobial-resistant pathogens by the Centers for Disease Control and Prevention (CDC)]. Those high priority bacteria will be evaluated for resistance to biocides. This project will target foodborne pathogens including Salmonella, Campylobacter, and Listeria and commensals including Escherichia coli and Enterococcus, for their role as reservoirs of resistance. The alternative processing methods in this project include testing several novel chemical and physical decontamination procedures. The approach for most of this work is to apply the intervention strategy and compare the microbial quality of the treated poultry product with control product treated by standard methods. Intervention strategies will include studies on the microbial ecology in and around poultry processing and further processing plants, such as floor drains, to determine a particular ecological niche or reservoir for a specific pathogen in the processing environment. These studies will improve understanding of sources and harborage points for human pathogens and how best to combat colonization of a processing plant with those pathogens. A long term objective is to develop systems using protozoa as natural controllers of foodborne pathogens. This will involve studying the ecology of protozoa that feed on the pathogens and determining methods to enrich the processing environment with effective protozoa. Approaches for monitoring microbial quality will include enhancing the sensitivity and specificity of microbial detection. The project will also use genetic typing methods including whole genome sequencing and metagenomics sequencing to characterize antimicrobial and biocide resistance and track specific clones of pathogens in and around poultry processing environments. Data from this research will be used to assist other Federal agencies in assessing antimicrobial resistance in food animal populations as well as to address a direct need outlined by the National Action Plan for Combating Antibiotic-Resistant Bacteria (CARB) in evaluating potential alternatives to antimicrobials. Data generated on biocide resistance and resistance genes active against chemicals specific to poultry production and processing is a specific concern to USDA-FSIS. Development of technologies for detection of microbial contaminants is a critical need for Federal regulatory agencies.

Progress Report
This is the final report for this project. See project 6040-32000-079-000D, Alternatives to Antibiotics and Genomics of Antimicrobial Resistance to Control Foodborne Pathogens in Poultry" for additional information. Whole-genome sequencing (WGS) of drug-resistant Salmonella, Escherichia coli, and Enterococcus (100 isolates each) was completed. A database of antimicrobial resistance (AMR) phenotypes, genes, and mobile genetic elements (MGEs) in those bacteria is under construction for rapid searches of unique genes, co-linkage of AMR genes and associations with mobile and extra-chromosomal elements. Prevalence of multidrug resistant (MDR) Salmonella serotype Infantis plasmid pESI (plasmid for Emerging Salmonella Infantis) in U.S. isolates was determined and compared to other countries. Approximately 90 percent of genes in pESI were conserved across all isolates, indicating that conserved regions (virulence, iron acquisition, and metal resistance genes) may be required for Infantis persistence in U.S. poultry. Infantis with the plasmid was found in almost 30% of U.S. chicken isolates in 2020. In late 2020, pESI was also detected in two new serotypes of Salmonella from turkeys. “No Antibiotic Ever” poultry was assessed to determine if products contained resistant foodborne bacteria posing a risk to consumers. Salmonella, E. coli, Enterococcus, and Staphylococcus were isolated and tested for AMR. Enterococcus faecalis was resistant to ten of the 16 drugs tested including tigecycline and linezolid, two of the newer antibiotics used in human medicine. Five different incubation methods using different media were tested for isolation of Salmonella. Up to six Salmonella serotypes were isolated including multiple serotypes from the same product. Salmonella Infantis was isolated regardless of the method used. Research on products will continue in the next project plan. The sixth year of seasonal monitoring of surface water as a reservoir and potential vehicle for development of resistant bacteria was completed. The Upper Oconee Watershed was contaminated with antimicrobial resistant E. coli and Enterococcus. Pathogenic strains of E. coli were detected including globally spread ST131 strains. Meetings with the National Antimicrobial Resistance Monitoring System (NARMS) Environmental Working Group (EWG) discussed development of a monitoring system for AMR in U.S. surface waters. Protocols and testing procedures were developed by the NARMS EWG. International collaborations progressed. E. coli from food and companion animals and clinical sources from Nigeria and Egypt were MDR or resistant to drugs of significant use in humans. E. coli ST131 from these studies were shared with other ARS researchers for WGS and further analyses. With Japan, carbapenem-resistant Enterobacteriaceae were analyzed for the presence of carbapenem resistance genes and MGEs. Transfer of colistin resistance on plasmid replicons was shown. A visiting Fulbright Scholar from Burkina Faso compared typing techniques for Salmonella and WGS. The computer program SeqSero2 gave the best results. Studies on AMR in staphylococci from eggs and chickens from Pakistan showed Staphylococcus aureus from table eggs were the same genotype of methicillin-resistant S. aureus that causes human infections. MDR Staphylococcus xylosus from domesticated chicken eggs produced bacteriocins that killed Salmonella, E. coli, and drug-resistant S. aureus. The bacteriocins will be used in the next project plan on alternatives to antibiotics research. Comparative genomic analysis of Enterococcus cecorum associated with outbreaks of enterococcal spondylitis in broilers showed that non-clinical E. cecorum genomes were comparatively diverse; genome reduction in the conserved clinical genomes suggested better host adaptability. Data will be used in prediction of AMR using machine learning. A biocide panel of 17 chemicals was developed. The panel was used to assay Salmonella Infantis isolates to determine if the pESI plasmid conferred resistance to biocides to explain the persistence of S. Infantis in U.S. poultry. Precipitation of solutions when bacterial growth media was added to the metal plate assay was addressed with the use of minimal media. Development of the biocide and metal resistance plate will continue in the next project plan. A new medium, neutralizing-BPW (n-BPW) was developed for sampling processed broiler carcasses to detect Salmonella in the presence of residual antimicrobial carcass washing chemicals. n-BPW was effective in counteracting the most common antimicrobial treatments currently used in broiler processing for detection of Salmonella, decreasing false negatives. n-BPW was adopted by the Food Safety and Inspection Service for regulatory sampling of broiler carcasses. n-BPW outperformed traditional carcass rinse medium significantly improving recovery of Campylobacter and represents a significant improvement in the broiler carcass rinse method for Campylobacter detection. Campylobacter prevalence in chicken livers at retail and subtypes detected on the surface versus internal tissues of livers was done. Campylobacter was found from the surface of livers (64%), internal tissue (31%), and blended whole liver (67%). Various subtypes of Campylobacter were isolated from fresh retail chicken livers confirming the food safety risk to consumers associated with undercooked chicken livers. Shredded absorbent sponge material to plug the broiler carcass cloaca prior to scalding was developed to control contamination of poultry carcasses during processing. The high surface area and high friction shredded sponge material was placed in the cloaca and much stayed in place while plugged carcasses were in the feather-picking machinery. Significantly fewer Campylobacter cells were detected on the breast skin of post-pick carcasses plugged with 50 mL of shredded sponge than on post-pick, unplugged control carcasses. This system may prevent Campylobacter escape from the cloaca during defeathering. A pilot scale method to treat inoculated chicken skin and meat with antimicrobial chemicals prior to grinding was developed to determine the efficacy of chlorine and peracetic acid to lower numbers of skin borne Campylobacter, Salmonella and Listeria monocytogenes in ground chicken meat product. A 1200 ppm peracetic acid dip was effective to decrease numbers of pathogens on chicken meat and skin and the ground chicken meat product made from it. Steam to decontaminate transport cage flooring resulted in an approximately 99% reduction in Campylobacter numbers. Steam treatment preceded by a 15 second water spray reduced Campylobacter to 99.99% compared to untreated controls. Campylobacter was not eliminated, but steam is potentially effective in broiler transport cage sanitation and to control transfer to previously negative broilers. A field-ready drain heater to decontaminate Listeria-positive floor drains in commercial food processing plants was developed and tested. Data suggested that the field heater treatment will scale well to floor drains in food processing plants; field testing is planned. A self-contained chlorine dioxide generating pod for decontamination of floor drains worked well to greatly lower natural bacterial numbers in floor drains. The easy to use and safe to deploy pods were extremely effective at decreasing L. monocytogenes in inoculated model floor drain water and as drainpipe biofilm by more than 99.9999%. A 0.45- or 0.65-micron pore size nitrocellulose filter, placed on top of solid plating medium, eliminated non-Campylobacter contamination from samples with high numbers of both Campylobacter and background bacteria such as broiler feces or gut contents. The filter method improved Campylobacter detection and can quantitatively estimate the cellular density in a complex, highly contaminated sample. A bacteria-eating protozoan, Tetrahymena pyriformis, killed Listeria when cultured together. The protozoa ingested a share of the bacteria; residual bacteria outside of the protozoa were killed with antibiotic. Almost all ingested Listeria were killed within 24 hours. Nineteen different tested strains of Listeria were equally killed. Tetrahymena killed adherent and culture suspension Listeria and may be a useful candidate for controlling Listeria in food processing plants. L. monocytogenes contamination in the processed food factory environment is difficult to remove by sanitation. To identify traits for resistance to sanitation, WGS of persistent and transient isolates in two poultry further-processing plants were compared. Genes linked to persistent or transient isolates were identified including genes related to metabolism, membrane transport, oxidative stress, and chemotaxic functions. Chemotaxis is important for niche localization for bacteria to set up persistent colonization. Retail chicken microbiomes were characterized by metagenomic DNA sequencing of chicken breast samples. Character of the microbiomes correlated with the processing establishment and even more with vacuum packaging of the product. Birds from three establishments were raised "No Antibiotic Ever"; one of those establishments had a substantially elevated presence of AMR genes compared to all other establishments. The chicken microbiome is a robust and multifaceted food microbiology attribute providing a variety of safety and quality information. Genome analyses by core gene multilocus sequence analysis (cgMLST) of a panel of strains of Campylobacter jejuni from chickens and river water was done. Four very distinct populations, two from chickens and two from water were found. Further analysis on a gene-by-gene basis showed only one gene clearly separated water isolates from poultry isolates. That gene was involved in producing cell surface structures and needs to be further investigated for its role in poultry colonization.

Accomplishments
1. Plasmid genes aid persistence of Salmonella Infantis. Salmonella is a common cause of foodborne illness in the United States with contaminated poultry implicated in transmission to humans. One particular serotype of Salmonella, Infantis, increased from 5 to 29% of the serotypes isolated from U.S. chicken samples and continues to be a problem. Most of these Infantis are resistant to antibiotics due to a specific gene that is carried by a large plasmid, known as pESI (plasmid for Emerging Salmonella Infantis). ARS researchers in Athens, Georgia, investigated the role of pESI in the expansion and persistence of Infantis in U.S. poultry by analyzing the DNA sequences of Infantis isolated from poultry and human infections. The specific gene was present in 61% of the plasmids, while over 90% of the plasmids contained genes that could help Infantis colonize chickens and persist in poultry production. This information is useful to poultry producers to modify practices to minimize the impact of the advantages that pESI gives Infantis, thus preventing the selection of antibiotic resistant Infantis and reducing its prevalence and persistence in chickens.

2. New tool to identify antimicrobial resistance genes in DNA sequences. Antimicrobial resistant bacteria are a major health issue causing 2.8 million infections and greater than 35,000 deaths each year in the U.S. A multi-agency collaboration including ARS researchers in Athens, Georgia, developed the Bacterial Antimicrobial Resistance Reference Gene Database and the AMRFinderPlus gene detection tool. The database includes 7,737 antibiotic, acid, biocide, metal, and stress resistance genes, which can be detected by AMRFinderPlus in whole genome sequences of any bacteria. AMRFinderPlus is part of the National Center for Biotechnology Information website, the world’s largest repository of DNA sequence data. AMRFinderPlus determines antimicrobial resistance (AMR) genes present in whole genome sequence data from bacterial isolates enabling linkage of antibiotic use, biocide use, and environmental conditions to the development of AMR. Reducing development of AMR without selecting for antibiotic resistance is important to eliminate pathogenic bacteria from patients, food, and hospital environments resulting in less human illnesses and fewer deaths.

3. Improving the broiler chicken microbiome. In current commercial broiler rearing practice, chicks are not exposed to grown chickens and therefore miss out on the natural transfer of gut bacteria from the mother hen. ARS researchers in Athens, Georgia, collaborated with Western University to better understand the effect of the gut microbiome on the health and development of broiler chicks. Application of gut contents from market age broilers to baby chicks was tested. Treated and control chicks were monitored for weight gain and resistance to gut colonization by human pathogens (Salmonella and Campylobacter) commonly associated with chicken. Chicks treated with gut contents had a more complex intestinal microbiome, showed some resistance to growth of human pathogens, and gained weight as well or better than controls. This work demonstrated that broiler gut microbiome can be effectively manipulated. Future work will be conducted to further understand the role that key members of the gut microbiome play as the bird matures.

4. Faster culture detection of Salmonella from poultry. Salmonella, an important human pathogen often associated with poultry meat, can be laborious to detect in poultry samples. The current culture method requires a multi-step, two-day enrichment procedure prior to plating the sample on selective agar to detect Salmonella. This is problematic if the Salmonella status of a broiler flock is needed prior to shipping meat to customers. ARS researchers in Athens, Georgia, and the University of Georgia, developed and tested a combination enrichment broth allowing a one-day enrichment period, significantly hastening the process of Salmonella detection. The secondary enrichment step where selective chemicals are usually applied was eliminated after the addition of Salmonella selective chemicals to the non-selective initial enrichment broth. The addition of a variety of selective agents was also tested and this new method was compared to the standard method using naturally contaminated samples collected in a commercial broiler slaughter plant. The new method worked as well as the standard method and allowed recovery of the same subtypes of Salmonella. One-stage Salmonella enrichment shows great promise to detect and collect Salmonella from broiler flocks in a shorter amount of time.

5. Rapid and accurate serotyping methods for Salmonella from Burkina Faso. Salmonella enterica is a leading cause of foodborne diseases worldwide with outbreaks tracked by Salmonella serotype. However, serotyping is complex and difficult to implement in countries with limited financial resources. To determine if current serotyping methods can be adapted for use in low- and middle-income countries, ARS researchers in Athens, Georgia, trained a visiting Fulbright Scholar from Burkina Faso in methods to determine Salmonella serotypes. Of the two methods used, whole genome sequencing and SeqSero 2.0 analysis rapidly and accurately determined Salmonella serotypes of isolates from Burkina Faso that were not identified by multiplex PCR. This serotyping method improved the speed and accuracy of serotyping. This study highlighted the necessity for collaboration between researchers from developing countries with those of high-income countries to enable the rapid application of food safety and public health measures to reduce cases of salmonellosis and stop Salmonella outbreaks.

6. Salmonella genomic island detected in Klebsiella. Resistance to frontline and clinically important antimicrobials can originate in human bacterial strains and subsequently move to bacteria from different sources such as food animals. For this reason, it is important to analyze resistance in bacterial pathogens from multiple sources to monitor dissemination of resistance. ARS researchers in Athens, Georgia, and Hiroshima University, Japan and Mansoura University, Egypt, collaborated to detect and characterize a clinical isolate of Klebsiella pneumoniae from Egypt containing a mobile genomic island of resistance genes originally identified in Salmonella. The Klebsiella strain harbored mobile genetic elements and was multidrug resistant. The presence of the Salmonella genomic island in Klebsiella provided evidence of another mechanism of spreading and transfer of antimicrobial resistance and virulence genes. Implementation of screening strategies for the various Salmonella genomic islands among Gram-negative bacteria (not only Salmonella spp.) is essential to prevent the spread of this mobile element to other bacterial pathogens. This data will provide a basis for comparison of resistance genes and mobile elements from human and food animal origin for evaluation of antimicrobial use for the One Health initiative.

7. Core gene multilocus sequence analysis reveals diversity among Listeria monocytogenes. Sequence variant determination of all the core genes (genes found in almost all the members of a given species, usually hundreds to thousands of genes) using raw sequence data of a bacterial species is a difficult process. Core gene multilocus sequence analysis has become a preferred method for genomic analyses of pathogenic bacteria providing a streamlined method for the complex process. ARS researchers in Athens, Georgia, developed a program, Haplo-ST, that analyzed the raw sequence data and returned the gene sequences, determined their type assignments, and identified when different genes were very similar due to gene duplication. The program was applied to the sequence typing for 2554 genes in a panel of 180 Listeria monocytogenes, a major cause of foodborne illness. The analyses showed a non-random association of many genes with the isolate source (hosts or environmental). Twenty-seven genes showed evidence of frequent exchange between strains. This analysis identified genes that may be related to colonization and thus point to critical points for control of Listeria.

8. Multiple carbapenem resistance genes detected in Escherichia coli. Antibiotics in the carbapenem class of antibiotics are often the last line of defense in treatment of human infections. Although carbapenems are not prescribed for use in food animal production, resistance mechanisms for carbapenems exist from both human and animal sources and is cause for concern. ARS researchers in Athens, Georgia, and Hiroshima University, Japan and Mansoura University, Egypt, collaborated to analyze carbapenem resistant clinical Escherichia coli from Egypt. In a single isolate, one carbapenem resistance gene was located on the chromosome while the second gene was located on a conjugative plasmid. Multiple acquired antimicrobial resistance genes were also detected conferring resistance to other antibiotics used to treat human infections. Presence of the carbapenem resistance genes on mobile genetic elements may increase the spread of this E. coli genetic type. Data in this study is useful for surveillance programs for monitoring development and dissemination of resistance.

9. A new chromogenic agar for identification of enterococci from surface water. Enterococci are used as indicator organisms for the presence of fecal contamination and are also monitored to detect trends in antimicrobial resistance. As the aquatic environment contains a diverse group of enterococcal species, a new chromogenic medium, not yet available for commercial purchase, was evaluated by ARS reseachers in Athens, Georgia, for the isolation of enterococci from environmental water and compared to commercially available media. Three consecutive tests were conducted with a newer batch of the medium with improved media composition per batch. Newer batches of media performed better than the previous versions and were comparable to the other two commercial media tested. The new medium resulted in detection of diverse enterococcal species with varying antimicrobial resistance phenotypes in a shorter amount of incubation time. This media offers a good alternative to other media for the isolation of enterococci and will be useful for diagnostic and microbiology laboratories. This new medium will also improve monitoring activities to protect humans from contaminated water.

10. Antimicrobial resistant enterococci identified in a mixed-use watershed. Antimicrobial resistant enterococci released into surface water through human and agricultural wastes are a public health concern. This is not only due to human exposure to these bacteria through water-related activities, but also to potential dissemination of antimicrobial resistance genes to other bacteria present in the environment. ARS researchers in Athens, Georgia, monitored the Upper Oconee Watershed for enterococci and tested multidrug resistant strains to determine the genes responsible for antimicrobial resistance and for plasmids that may carry the resistance genes. Resistance mechanisms could not be determined for many of the resistant isolates indicating that unknown antimicrobial resistance mechanisms exist among environmental enterococci. Environmental enterococci also carried multiple plasmids that could be responsible for transfer of antimicrobial resistance. This work expands knowledge of antimicrobial resistance gene reservoirs and plasmids across a wider range of environments. Surface water may be a suitable environment for the transfer of antimicrobial resistance genes through plasmids harbored by enterococcal isolates in the aquatic environment. Further monitoring and analysis will determine the risk these bacteria pose to human health to target interventions to reduce that risk and protect human health.

11. Retail shrimp harbor diverse antibiotic resistant bacteria. Farm-raised shrimp account for ~80% of the market share in the United States. Farmed shrimp are cultivated as monoculture and are susceptible to infections. The aquaculture industry is dependent on the application of antibiotics for disease prevention, resulting in the selection of antibiotic-resistant bacteria. ARS researchers in Athens, Georgia, collaborated on research that determined prevalence and gut microbiome communities of antibiotic-resistant bacteria in raw and cooked shrimp. Coliforms and opportunistic pathogens obtained were spread across 18 bacterial genera. Isolates from cooked shrimp showed higher resistance to chloramphenicol and tetracycline, while those from raw shrimp exhibited low levels of resistance to nalidixic acid and tetracycline. Compared to wild-caught shrimp, the imported farm-raised shrimp harbored distinct gut microbiota communities and higher prevalence of antibiotic-resistance genes in their gut. A proposal based on these findings was submitted to the Food and Drug Administration for the National Antimicrobial Resistance Monitoring System to develop a surveillance program of antimicrobial resistant bacteria from retail meat and seafood.

12. Cooked shrimp may contain antibiotic resistant bacteria. Enterobacter hormaechei are opportunistic pathogens known to cause urinary and respiratory tract infections in humans. Antibiotic resistant strains of E. hormaechei have been previously isolated from fresh produce and seafood samples. ARS researchers in Athens, Georgia, collected raw shrimp from a supermarket store contained an E. hormaechei strain resistant to nine antibiotics as well as ten putative plasmids. As shrimp samples are cooked using milder heat treatment, consumption of shrimp harboring multidrug resistant strains are possible carriers of resistance genes to human gut microbiota. Changes in processing practices may be necessary to avoid the presence of antibiotic-resistant strains in pre-cooked shrimp in the shrimp industry.

13. Antibiotic resistant staphylococci populations vary in farmed and household chickens. Contamination of poultry with antibiotic resistant staphylococci is a threat to human health. ARS researchers in Athens, Georgia, isolated Staphylococci from the intestines of farmed and household chickens from Pakistan and tested for resistance to antibiotics, presence of resistance genes, and inhibitory activity against other bacteria. Farmed chicken staphylococci were resistant to tigecycline, while household chicken staphylococci were primarily resistant to clindamycin, two drugs used to treat human infections. Isolates from both types of birds were multidrug resistant and produced inhibitory activity against seven clinical bacterial strains. Staphylococcal populations among farmed and household chickens varied by species and the environment or habitat of each bird type may have influenced antimicrobial resistance in the intestinal microflora. This data will help determine control points for development of strategies to prevent transfer of these resistant populations to humans via contamination of poultry meat in different types of poultry production.

Review Publications
Rincon, A., Kumar, S., Ritz, C., Jackson, J.S., Jackson, C.R., Frye, J.G., Cook, K.L., Hinton Jr, A., Singh, M., Cosby, D.E., Cox Jr, N.A., Thippareddi, H. 2020. Antimicrobial interventions to reduce Salmonella and Campylobacter populations and improve shelf life of quail carcasses. Poultry Science. 99(11): 5977-5982. https://doi.org/10.1016/j.psj.2020.07.012.
Mcmillan, E.A., Frye, J.G., Jackson, C.R. 2020. Transferable plasmids of Salmonella enterica associated with antibiotic resistance genes. Frontiers in Microbiology. 11:e562181. https://doi.org/10.3389/fmicb.2020.562181.
Louha, S., Meinersmann, R.J., Abdo, Z., Berrang, M.E., Glenn, T. 2020. An open-source program (Haplo-ST) for whole-genome sequence yping shows extensive diversity among Listeria monocytogenes isolates in outdoor environments and poultry Processing Plants. Applied and Environmental Microbiology. 87:e02248. https://doi.org/10.1128/AEM.02248-20.
Kagambega, A., Hiott, L.M., Boyle, D., Mcmillan, E.A., Sharma, P., Gupta, S., Ramadan, H., Cho, S., Humayoun, S.B., Woodley, T.A., Barro, N., Jackson, C.R., Frye, J.G. 2021. Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing. BMC Microbiology. 21(29):e2021. https://doi.org/10.1186/s12866-021-02085-6.
Mcmillan, E.A., Frye, J.G., Jackson, C.R., Wasilenko, J.L., Tagg, K.A., Chen, J.C., Simmons, M., Gupta, S.K., Tillman, G.E., Folster, J. 2020. Carriage and gene content variability of the pESI-like plasmid associated with Salmonella Infantis recently established in United States poultry production. Genes. 11(12):1516. https://doi.org/10.3390/genes11121516.
Sharma, L., Nagpal, R., Jackson, C.R., Patel, D., Singh, P. 2021. Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from United States versus imported farm-raised retail shrimp. Scientific Reports. 11:e3356. https://doi.org/10.1038/s41598-021-82823-y.
Ramirez, G., Richardson, E., Clark, J., Kishri, J., Dreschler, Y., Berrang, M.E., Meinersmann, R.J., Cox Jr, N.A., Oakley, B. 2020. Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects. PLoS ONE. 15(11). Article e0242108. https://doi.org/10.1371/journal.pone.0242108.
Cho, S., Hiott, L.M., Woodley, T.A., Frye, J.G., Jackson, C.R. 2020. Evaluation of a new chromogenic agar for the detection of environmental Enterococcus. Journal of Microbiological Methods. 178:e106082. https://doi.org/10.1016/j.mimet.2020.106082.
Achtman, M., Zhoua, Z., Alikhan, N., Tyne, W., Parkhill, J., Cormican, M., Chiou, C., Torpdahl, M., Litrup, E., Meinersmann, R.J., Prendergast, D.M., Moore, J.E., Strain, S., Kornschober, C., Uesbeck, A., Weill, F., Coffey, A., Andrews-Polymenis, H., Curtiss, R., Fanning, S. 2021. The UoWUCC 10K Salmonella genomes project. Wellcome Open Research. 5:223. https://doi.org/10.12688/wellcomeopenres.16291.2.
Soliman, A., Ramadan, H., Zarad, H.O., Yo, S., Liansheng, Y., Motoyuki, S., Shimamoto, T., Hiott, L.M., Frye, J.G., Jackson, C.R., Shimamoto, T. 2021. Co-production of Tet(X7) conferring high-level tigecycline resistance, fosfomycin FosA4 and colistin Mcr-1.1 in Escherichia coli strains from chickens in Egypt. Antimicrobial Agents and Chemotherapy. 65(6). Article e33820767. https://doi.org/10.1128/AAC.02084-20.
Rasamsetti, S., Berrang, M.E., Cox Jr, N.A., Shariat, N. 2021. Selective pre-enrichment method to lessen time needed to recover Salmonella from commercial poultry processing samples. Food Microbiology. 99:e103818. https://doi.org/10.1016/j.fm.2021.103818.
Cho, S., Barrett, J.B., Frye, J.G., Jackson, C.R. 2020. Antimicrobial resistance gene detection and plasmid typing among multidrug resistant enterococci isolated from environmental water. Microorganisms. 8(9):1338. https://doi.org/10.3390/microorganisms8091338.
Syed, M., Ullah, H., Tabassum, S., Fatima, B., Woodley, T.A., Ramadan, H., Jackson, C.R. 2020. Staphylococci in poultry intestines: a comparison between farmed and household chickens. Poultry Science. 99(9):4549-4557. https://doi.org/10.1016/j.psj.2020.05.051.
Soliman, A., Ramadan, H., Zarad, H., Nariya, H., Shimamoto, T., Hiott, L.M., Jackson, C.R., Frye, J.G., Shimamoto, T. 2020. Draft genome sequence of a blaNDM-1- and blaOXA-244-carrying multidrug-resistant Escherichia coli D: ST69 clinical isolate from Egypt. Journal of Global Antimicrobial Resistance. 22:832-834. https://doi.org/10.1016/j.jgar.2020.07.015.
Indugu, N., Sharma, L., Jackson, C.R., Singh, P. 2020. Whole genome sequence analysis of multi-drug resistant Enterobacter hormaechei isolated from imported retail shrimp. Microbiology Resource Announcements. 9:e01103-20. https://doi.org/10.1128/MRA.01103-20.
Feldgarden, M., Brover, V., Gonzalez-Escalona, N., Frye, J.G., Haendiges, J., Haft, D.H., Pettengill, J.B., Prasad, A.B., Tillman, G.E., Tyson, G.H., Klimke, W. 2021. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Nature Scientific Reports. 11:12728. https://doi.org/10.1038/s41598-021-91456-0.