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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Research Project #440168

Research Project: Elucidating the Factors that Determine the Ecology of Human Pathogens in Foods

Location: Produce Safety and Microbiology Research

2023 Annual Report

1. Improved categorization of pathogenic Escherichia coli (E. coli). Pathogenic Escherichia coli are causative agents of a broad range of enteric human diseases such as colitis, dysentery, hemolytic uremic syndrome as well as other extraintestinal diseases, including sepsis and urinary tract infections. With the combinatorial use of statistics, genomics and bioinformatics, ARS researchers in Albany, California, differentiated a collection of hundreds of pathogenic E. coli isolates recovered from food, animal, environmental and clinical samples based on genetic groups and disease outcome categorization. In particular, some genetic groups were significantly linked to isolation sources, and pathogenicity markers were statistically associated with each detected genetic group in the examined E. coli isolates. These findings provide fundamental information to regulatory agencies as well as public health, academic and food processing laboratories by identifying genetic markers specific to various pathogenic E. coli recovered from distinct isolation sources, including food, animal and human. and Consequently, this research will assist in developing better typing tools for identifying potential transmission routes of contamination.

2. A bacteriophage cocktail lytic against E. coli O157:H7 has been approved for patent application. Antimicrobial intervention, such as chlorination, is commonly used in the food industry because of its easy access, installation, and low cost. However, the major drawbacks are that frequent application results in the development of bacterial resistance, thus compromising the efficacies of these chemical antimicrobials. ARS researchers in Albany, California, have developed a lytic bacteriophage (phage) cocktail containing different well-characterized lytic phages that can effectively control and mitigate Shiga toxin-producing E. coli (STEC) O157:H7. The phage cocktail demonstrated a much stronger antimicrobial activity than a commercial phage product in reducing a four-strain E. coli O157:H7 cocktail by more than 3 logs. This phage cocktail (Invention Disclosure USDA Docket No. 0020.23) is in a patent application process. It will improve the antimicrobial activity of traditional intervention strategies against STEC O157 contamination in pre-harvest or post-harvest environments with better effectiveness, cost-efficiency, and reliability. It is expected that the phage cocktail can be utilized by farmers, food processing plants, and other regulatory agencies to mitigate the contamination of these pathogens in the area where the traditional interventions are not applicable or bacterial resistance to sanitizers have developed.

3. Bacteriophages involved in a new mechanism of ARG transfer within agricultural environments. The continuous emergence of antibiotic-resistance bacteria has caused a serious food safety issue in the United States. ARS researchers in Albany, California, have determined the antibiotic resistance genes (ARG) profile within various agricultural samples and discovered a new mechanism of ARG dissemination in agricultural-associated environments. The results indicate that bacteriophages carry various ARG types and can disperse these genes among the bacterial population, contributing to the development of antibiotic-resistant strains. This pivotal information unveils the controversial phage-associated ARG transmission and provides valuable information in preventing the spread of foodborne pathogens harboring ARG in produce-associated environments. The information could be used by researchers, farmers, and other regulatory agencies for tracking phage-mediated ARG transfer and preventing the emergence of ARG strains.

Review Publications
Lacombe, A.C., Quintela, I.A., Liao, Y., Wu, V.C. 2022. Shiga toxin-producing Escherichia coli outbreaks in California’s leafy greens production continuum. Frontiers In Food Science And Technology. 2. Article 1068690.
Fagerquist, C.K. 2023. Top-down identification of Shiga toxin (and other virulence factors and biomarkers) from pathogenic E. coli using MALDI-TOF/TOF tandem mass spectrometry. In: Shah, H.N., Gharbia, S.E., Shah, A.J., Tranfield, E.Y., Thompson, K.C., editors. Microbiological Identification Using MALDI-TOF and Tandem Mass Spectrometry: Industrial and environmental applications. 1st edition. West Sussex, UK: John Wiley & Sons Ltd. p. 71-96.
Garcia Bardales, P., Schiaffino, F., Huynh, S., Paredes Olortegui, M., Penataro Yori, P., Pinedo Vasquez, T., Manzanares Villaneuva, K., Curico Huansi, G., Shapiama Lopez, W., Cooper, K.K., Parker, C.T., Kosek, M.N. 2022. “Candidatus Campylobacter infans” detection is not associated with diarrhea in children under the age of 2 in Peru. PLOS Neglected Tropical Diseases. 16(10). Article e0010869.
Ndraha, N., Huang, L., Wu, V.C., Hsiao, H. 2022. Vibrio parahaemolyticus in seafood: Recent progress in understanding influential factors at harvest and food-safety intervention approaches. Current Opinion in Food Science. 48. Article 100927.
Quintela, I.A., Vasse, T., Lin, C., Wu, V.C. 2022. Advances, applications, and limitations of portable and rapid detection technologies for routinely encountered foodborne pathogens. Frontiers in Microbiology. 13. Article 1054782.
Gummalla, V., Zhang, Y., Liao, Y., Wu, V.C. 2023. The role of temperate phages in bacterial pathogenicity. Microorganisms. 11(3). Article 541.
Parker, C.T., Schiaffino, F., Huynh, S., Paredes Olortegui, M., Penataro Yori, P., Garcia Bardales, P.F., Pinedo Vasquez, T., Curico Huansi, G.E., Manzanares Villaneuva, K., Shapiama Lopez, W.V., Cooper, K.K., Kosek, M.N. 2022. Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLOS Neglected Tropical Diseases. 16(10). Article e0010815.
Aguirre-Sanchez, J.R., Valdez-Torres, J.B., Castro del Campo, N., Martinez-Urtaza, J., Castro del Campo, N., Lee, B.G., Quinones, B., Chaidez-Quiroz, C. 2022. Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico. Infection, Genetics and Evolution. 106. Article 105380.
Fagerquist, C.K., Wallis, C.M., Chen, J. 2023. Top-down proteomic identification of protein biomarkers of Xylella fastidiosa subsp. fastidiosa using MALDI-TOF-TOF-MS and MS/MS. International Journal of Mass Spectrometry. 489. Article 117051.
Fagerquist, C.K., Shi, Y., Dodd, C.E. 2023. Toxin and phage production from pathogenic E. coli by antibiotic induction analyzed by chemical reduction, MALDI-TOF-TOF mass spectrometry and top-down proteomic analysis. Rapid Communications in Mass Spectrometry. 37(10). Article e9505.
Talukdar, P., Crockett, T.M., Gloss, L.M., Huynh, S., Roberts, S.A., Turner, K.L., Lewis, S.T., Herup-Wheeler, T.L., Parker, C.T., Konkel, M. 2022. The bile salt deoxycholate induces Campylobacter jejuni genetic point mutations that promote increased antibiotic resistance and fitness. Frontiers in Microbiology. 13. Article 1062464.
Liao, Y., Zhang, Y., Salvador, A., Ho, K., Cooley, M.B., Wu, V.C. 2022. Characterization of polyvalent Escherichia phage Sa157lw for the biocontrol potential of Salmonella Typhimurium and Escherichia coli O157:H7 on contaminated mung bean seeds. Frontiers in Microbiology. 13. Article 1053583.
Sun, X., Liao, Y., Zhang, Y., Salvador, A., Ho, K., Wu, V.C. 2022. A new Kayfunavirus-like Escherichia phage vB_EcoP-Ro45lw with antimicrobial potential of Shiga toxin-producing Escherichia coli O45 strain. Microorganisms. 11(1). Article 77.
Carter, M.Q., Laniohan, N.S., Pham, A., Quinones, B. 2022. Comparative genomic and phenotypic analyses of virulence potential in Shiga toxin-producing Escherichia coli O121:H7 and O121:H10. Frontiers in Cellular and Infection Microbiology. 12. Article 1043726.
Kirchner, M., Miller, W.G., Osborne, J., Badgley, B., Niedermeyer, J.A., Kathariou, S. 2023. Campylobacter colonization and diversity in young turkeys in the context of gastrointestinal distress and antimicrobial treatment. Microorganisms. 11(2). Article 252.
Bolinger, H., Miller, W.G., Osborne, J., Niedermeyer, J., Kathariou, S. 2023. Campylobacter jejuni and Campylobacter coli from houseflies in commercial turkey farms are frequently resistant to multiple antimicrobials and exhibit pronounced genotypic diversity. Pathogens. 12(2). Article 230.
Meinersmann, R.J., Berrang, M.E., Shariat, N.W., Richards, A.K., Miller, W.G. 2023. Despite shared geography, Campylobacter isolated from surface water are genetically distinct from Campylobacter isolated from chickens. Microbiology Spectrum. 11(2). Article e04147-22.