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

Location: Produce Safety and Microbiology Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Colicin immunity proteins of pathogenic bacteria detected by antibiotic-induced SOS response, plasmid sequencing, MALDI-TOF-TOF mass spectrometry and top-down proteomic analysis - (Peer Reviewed Journal)

Campylobacter sputorum subsp. bovis subsp. nov., isolated from cattle, and an emended description of Campylobacter sputorum - (Peer Reviewed Journal)
Miller, W.G., Williams, T.G., Wood, D.F., Chapman, M.H. 2024. Campylobacter sputorum subsp. bovis subsp. nov., isolated from cattle, and an emended description of Campylobacter sputorum. International Journal of Systematic and Evolutionary Microbiology. 74(11). Article 006571. https://doi.org/10.1099/ijsem.0.006571.

The inactivation of Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes using isochoric freezing in raw milk and carrot juice - (Peer Reviewed Journal)
Lacombe, A.C., Harvey, B.L., Van Blair, J.B., Chapman, N., Bilbao-Sainz, C., McHugh, T.H., Rubinsky, B., Wu, V.C. 2024. The inactivation of Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes using isochoric freezing in raw milk and carrot juice. Food Control. 618. Article 110957. https://doi.org/10.1016/j.foodcont.2024.110957.

DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle - (Peer Reviewed Journal)
Zhang, Y., Mao, M., Zhang, R., Liao, Y., Wu, V.C. 2024. DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle. PLoS Computational Biology. 20(10). Article e1012525. https://doi.org/10.1371/journal.pcbi.1012525.

Chlorine dioxide is a broad-spectrum disinfectant against Shiga toxin-producing Escherichia coli and Listeria monocytogenes in agricultural water - (Peer Reviewed Journal)
Van Blair, J.B., Lacombe, A.C., Harvey, B.L., Wu, V.C. 2024. Chlorine dioxide is a broad-spectrum disinfectant against Shiga toxin-producing Escherichia coli and Listeria monocytogenes in agricultural water. Frontiers in Microbiology. 15. Article 1469615. https://doi.org/10.3389/fmicb.2024.1469615.

Campylobacter californiensis sp. nov. isolated from cattle and feral swine - (Peer Reviewed Journal)
Miller, W.G., Chapman, M.H., Williams, T.G., Wood, D.F., Bono, J.L., Kelly, D.J. 2024. Campylobacter californiensis sp. nov. isolated from cattle and feral swine. International Journal of Systematic and Evolutionary Microbiology. 74. Article 006524. https://doi.org/10.6084/m9.figshare.26739553.v1.

Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data - (Peer Reviewed Journal)
Pascoe, B., Futcher, G., Pensar, J., Bayliss, S.C., Mourkas, E., Calland, J.K., Hitchings, M.D., Simmons, M., Joseph, L.A., Lane, C.G., Greenlee, T., Arning, N., Wilson, D.J., Corander, J., Parker, C.T., Cooper, K.K., Rose, E., Williams, M.S., Golden, N.J., Hiett, K., Bruce, B.B., Evans, P.S., Sheppard, S.K. 2024. Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data. Journal of Infection. 89(5). Article 106265. https://doi.org/10.1016/j.jinf.2024.106265.

The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0-24 months of age in resource-limited settings - (Peer Reviewed Journal)
Schiaffino, F., Colston, J.M., Paredes-Olortegui, M., Peñataro-Yori, P., Mourkas, E., Pascoe, B., Lima, A.A., Mason, C.J., Ahmed, T., Kang, G., Mduma, E., Samie, A., Zaidi, A., Liu, J., Cooper, K.K., Houpt, E.R., Parker, C.T., Lee, G.O., Kosek, M.N. 2024. The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0-24 months of age in resource-limited settings. eClinicalMedicine. 76. Article 102841. https://doi.org/10.1016/j.eclinm.2024.102841.

Proximity to urbanization is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes - (Peer Reviewed Journal)
Mourkas, E., Valdebenito, J.O., Marsh, H., Hitchings, M.D., Cooper, K.K., Parker, C.T., Székely, T., Johansson, H., Ellström, P., Pascoe, B., Waldenström, J., Sheppard, S.K. 2024. Proximity to urbanization is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes. Nature Ecology and Evolution. 34:1-11. https://doi.org/10.1016/j.cub.2024.07.059.

Antimicrobial activity of green synthesized silver and copper oxide nanoparticles against the foodborne pathogen Campylobacter jejuni - (Peer Reviewed Journal)
Rivera-Mendoza, D., Quinones, B., Huerta-Saquero, A., Castro-Longoria, E. 2024. Antimicrobial activity of green synthesized silver and copper oxide nanoparticles against the foodborne pathogen Campylobacter jejuni. Antibiotics. 13(7). Article 650. https://doi.org/10.3390/antibiotics13070650.

Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest - (Peer Reviewed Journal)
Goforth, M., Obergh, V., Park, R., Porchas, M., Brierley, P., Turini, T.A., Patil, B.S., Ravishankar, S., Huynh, S., Parker, C.T., Cooper, K.K. 2024. Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest. PLOS ONE. 19(9). Article e0307477. https://doi.org/10.1371/journal.pone.0307477.

Plasmid-encoded colicin immunity proteins produced by pathogenic Escherichia coli identified by antibiotic induction, MALDI-TOF-TOF-MS/MS and top-down proteomic analysis - (Proceedings)
Fagerquist, C.K., Shi, Y., Park, J. 2024. Plasmid-encoded colicin immunity proteins produced by pathogenic Escherichia coli identified by antibiotic induction, MALDI-TOF-TOF-MS/MS and top-down proteomic analysis. 72nd ASMS Conference on Mass Spectrometry and Allied Topics, June 2-6, 2024, Anaheim, CA. Poster ID 316847, TP476.

Prevalence of environmental microplastics in Taiwan and its impact on the seafood safety: An integrative review - (Review Article)
Lin, M., Wu, V.C., Lin, C. 2024. Prevalence of environmental microplastics in Taiwan and its impact on the seafood safety: An integrative review. Journal of Food Safety. 44(3). Article e13148. http://doi.org/10.1111/jfs.13148.

Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids - (Peer Reviewed Journal)
Miller, W.G., Lopes, B.S., Ramjee, M., Jay-Russell, M., Chapman, M.H., Williams, T.G., Wood, D.F., Gruntar, I., Papic, B., Forbes, K.J. 2024. Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids. International Journal of Systematic and Evolutionary Microbiology. 74(6). Article 006405. https://doi.org/10.1099/ijsem.0.006405.

Characterization of two novel Salmonella phages having biocontrol potential against Salmonella spp. in gastrointestinal conditions - (Peer Reviewed Journal)
Zhang, Y., Chu, M., Liao, Y., Salvador, A., Wu, V.C. 2024. Characterization of two novel Salmonella phages having biocontrol potential against Salmonella spp. in gastrointestinal conditions. Scientific Reports. 14. Article 12294. https://doi.org/10.1038/s41598-024-59502-9.

The stress response of Listeria monocytogenes inoculated on fresh apples exposed to gaseous chlorine dioxide - (Peer Reviewed Journal)
Guan, J., Lacombe, A.C., Rane, B., Van Blair, J.B., Zhang, Y., Tang, J., Sablani, S., Wu, V.C. 2024. The stress response of Listeria monocytogenes inoculated on fresh apples exposed to gaseous chlorine dioxide. Journal of Food Safety. 44(3) Article. e13126. https://doi.org/10.1111/jfs.13126.

Transcriptional analysis of Escherichia coli O157:H7 and a non-pathogenic E. coli in response to the chlorine treatment regulated by the U.S. Environmental Protection Agency - (Abstract Only)

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses - (Peer Reviewed Journal)
Park, J., Fagerquist, C.K. 2024. Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses. PLOS ONE. 19(5). Article e0299287. https://doi.org/10.1371/journal.pone.0299287.

Plasmid-encoded colicin immunity proteins produced by pathogenic Escherichia coli identified by antibiotic induction, MALDI-TOF-TOF-MS/MS and top-down proteomic analysis - (Abstract Only)

A new member of Tequintavirus bacteriophage isolated from sewage water with antimicrobial potential against multidrug-resistant Salmonella Infantis strains - (Abstract Only)

DeepPL: a deep-learning-based tool for the prediction of bacteriophage lifecycle - (Abstract Only)

Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool - (Peer Reviewed Journal)
Schiaffino, F., Parker, C.T., Garcia-Bardales, P.F., Huynh, S., Manzanares Villaneuva, K., Mourkas, E., Pascoe, B., Penataro Yori, P., Paredes-Olortegui, M., Houpt, E.R., Liu, J., Cooper, K.K., Kosek, M.N. 2024. Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool. PLOS Neglected Tropical Diseases. 18(3). Article e0012018. https://doi.org/10.1371/journal.pntd.0012018.

Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States - (Peer Reviewed Journal)
Goforth, M., Obergh, V., Park, R., Porchas, M., Crosby, K.M., Jifon, J.L., Ravishankar, S., Brierley, P., Leskovar, D.L., Turini, T.A., Schultheis, J., Coolong, T., Miller, R., Koiwa, H., Patil, B.S., Cooper, M.A., Huynh, S., Parker, C.T., Guan, W., Cooper, K.K. 2024. Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States. PLOS ONE. 19(4). Article e0293861. https://doi.org/10.1371/journal.pone.0293861.

Genomic analysis points to multiple genetic mechanisms for non-transformable Campylobacter jejuni ST-50 - (Peer Reviewed Journal)
Parker, C.T., Villafuerte, D.A., Miller, W.G., Huynh, S., Chapman, M.H., Hanafy, Z., Jackson III, J.H., Miller, M.A., Kathariou, S. 2024. Genomic analysis points to multiple genetic mechanisms for non-transformable Campylobacter jejuni ST-50. Microorganisms. 12(2). Article 327. https://doi.org/10.3390/microorganisms12020327.

Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru - (Peer Reviewed Journal)
Schiaffino, F., Parker, C.T., Paredes Olortegui, M., Pascoe, B., Manzanares Villaneuva, K., Garcia Bardales, P.F., Mourkas, E., Huynh, S., Penataro Yori, P., Romaina Cachique, L., Gray, H.K., Salvatierra, G., Silva Delgado, H., Sheppard, S.K., Cooper, K.K., Kosek, M.N. 2024. Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru. Journal of Global Antimicrobial Resistance. 36:309-318. https://doi.org/10.1016/j.jgar.2024.01.009.

Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons - (Peer Reviewed Journal)
Goforth, M., Cooper, M.A., Oliver, A.S., Pinzon, J., Skots, M., Obergh, V., Suslow, T.V., Flores, G.E., Huynh, S., Parker, C.T., Mackelprang, R., Cooper, K.K. 2024. Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLOS ONE. 19(4). Article e0297453. https://doi.org/10.1371/journal.pone.0297453.

A new Rogue-like Escherichia phage UDF157lw to control Escherichia coli O157:H7 - (Peer Reviewed Journal)
Liao, Y., Ho, K., Zhang, Y., Salvador, A., Wu, V.C. 2024. A new Rogue-like Escherichia phage UDF157lw to control Escherichia coli O157:H7. Frontiers in Microbiology. 14. Article 1302032. https://doi.org/10.3389/fmicb.2023.1302032.

Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified by top-down proteomic analysis - (Peer Reviewed Journal)
Fagerquist, C.K., Shi, Y., Park, J. 2023. Unusual modifications of protein biomarkers expressed by plasmid, prophage, and bacterial host of pathogenic Escherichia coli identified by top-down proteomic analysis. Rapid Communications in Mass Spectrometry. 38(1). Article e9667. https://doi.org/10.1002/rcm.9667.

Gut phageome—An insight into the role and impact of gut microbiome and their correlation with mammal health and diseases - (Review Article)
Zhang, Y., Sharma, S., Tom, L., Liao, Y., Wu, V.C. 2023. Gut phageome—An insight into the role and impact of gut microbiome and their correlation with mammal health and diseases. Microorganisms. 11(10). Article 2454. https://doi.org/10.3390/microorganisms11102454.

Top-down proteomic identification of plasmid-encoded immunity proteins from pathogenic bacteria using MALDI-TOF-TOF tandem mass spectrometry - (Abstract Only)

Comparative genomic analyses of virulence and antimicrobial resistance in Citrobacter werkmanii, an emerging opportunistic pathogen - (Peer Reviewed Journal)
Aguirre-Sanchez, J.R., Quinones, B., Ortiz-Muñoz, J.A., Prieto-Alvarado, R., Vega-Lopez, I.F., Martinez-Urtaza, J., Lee, B.G., Chaidez, C. 2023. Comparative genomic analyses of virulence and antimicrobial resistance in Citrobacter werkmanii, an emerging opportunistic pathogen. Microorganisms. 11(8). Article 2114. https://doi.org/10.3390/microorganisms11082114.

Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem - (Peer Reviewed Journal)
Zhang, Y., Kitazumi, A., Liao, Y., de los Reyes, B.G., Wu, V.C. 2023. Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem. Microbiology Spectrum. 11(5). Article e00226-23. https://doi.org/10.1128/spectrum.00226-23.

The effects of sanitizing hurdles against foodborne pathogens during blueberry processing - (Peer Reviewed Journal)
Lacombe, A.C., Wu, V.C. 2023. The effects of sanitizing hurdles against foodborne pathogens during blueberry processing. Food Control. 154. Article 109981. https://doi.org/10.1016/j.foodcont.2023.109981.

Understanding gas phase dissociation of singly charged metastable protein ions generated by MALDI using protein structures predicted by Alphafold2 - (Abstract Only)

Efficacy of gaseous chlorine dioxide (ClO2) treatment on quality parameters and against Listeria innocua growth on apple surfaces under controlled atmosphere (CA) storage condition and post-treatment quality analysis - (Peer Reviewed Journal)

Top-down proteomic identification of protein biomarkers of Xylella fastidiosa subsp. fastidiosa using MALDI-TOF-TOF-MS and MS/MS - (Peer Reviewed Journal)
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. https://doi.org/10.1016/j.ijms.2023.117051.

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 - (Peer Reviewed Journal)
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. https://doi.org/10.1002/rcm.9505.

Using protein structures predicted by Alphafold2 to understand the fragmentation of proteins from pathogenic bacteria analyzed by MALDI-TOF-TOF-MS/MS - (Abstract Only)

Biofilm of pathogenic bacteria analyzed by MALDI-TOF imaging mass spectrometry (IMS) and top-down proteomic identification - (Abstract Only)

Microbiome profiles of an organic agricultural environment microcosm: A window to bacteriophage-bacterial population dynamics and the evolution of antibiotic resistance in the agricultural environment microbiome - (Abstract Only)

Comparative metagenomics reveal the effect of diet on the fecal virome and the associations with production traits of beef cattle - (Abstract Only)

Outcomes of stakeholder meeting discussing outreach efforts of waterless, non-thermal food processing technology USDA coordinated agriculture project / speaker's corner - (Abstract Only)

Characterization and encapsulation of a Salmonella phage cocktail for the biocontrol potential of Salmonella spp. in gastrointestinal environments - (Abstract Only)

Antimicrobial potential of a new Rogue-like Escherichia coli phage UDF157lw against E. coli O157:H7 biofilm - (Abstract Only)

Reduction of Aspergillus flavus and aflatoxin AFB1 on almond kernels using gaseous chlorine dioxide fumigation - (Abstract Only)

The role of temperate phages in bacterial pathogenicity - (Review Article)
Gummalla, V., Zhang, Y., Liao, Y., Wu, V.C. 2023. The role of temperate phages in bacterial pathogenicity. Microorganisms. 11(3). Article 541. https://doi.org/10.3390/microorganisms11030541.

A new Kayfunavirus-like Escherichia phage vB_EcoP-Ro45lw with antimicrobial potential of Shiga toxin-producing Escherichia coli O45 strain - (Peer Reviewed Journal)
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. https://doi.org/10.3390/microorganisms11010077.

Shiga toxin-producing Escherichia coli outbreaks in California’s leafy greens production continuum - (Review Article)
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. https://doi.org/10.3389/frfst.2022.1068690.

The bile salt deoxycholate induces Campylobacter jejuni genetic point mutations that promote increased antibiotic resistance and fitness - (Peer Reviewed Journal)
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. https://doi.org/10.3389/fmicb.2022.1062464.

Advances, applications, and limitations of portable and rapid detection technologies for routinely encountered foodborne pathogens - (Review Article)
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. https://doi.org/10.3389/fmicb.2022.1054782.

Characterization of polyvalent Escherichia phage Sa157lw for the biocontrol potential of Salmonella Typhimurium and Escherichia coli O157:H7 on contaminated mung bean seeds - (Peer Reviewed Journal)
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. https://doi.org/10.3389/fmicb.2022.1053583.

Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico - (Peer Reviewed Journal)
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. https://doi.org/10.1016/j.meegid.2022.105380.

“Candidatus Campylobacter infans” detection is not associated with diarrhea in children under the age of 2 in Peru - (Peer Reviewed Journal)
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. https://doi.org/10.1371/journal.pntd.0010869.

Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species - (Peer Reviewed Journal)
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. https://doi.org/10.1371/journal.pntd.0010815.

Vibrio parahaemolyticus in seafood: Recent progress in understanding influential factors at harvest and food-safety intervention approaches - (Peer Reviewed Journal)
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. https://doi.org/10.1016/j.cofs.2022.100927.

Reduction of Aspergillus flavus and aflatoxin AFB1 on almond kernels using gaseous chlorine dioxide fumigation - (Peer Reviewed Journal)

Identification of protein biomarkers of Xylella fastidiosa using MALDI-TOF-TOF-MS/MS and top-down proteomic analysis - (Proceedings)
Fagerquist, C.K., Wallis, C.M., Chen, J. 2022. Identification of protein biomarkers of Xylella fastidiosa using MALDI-TOF-TOF-MS/MS and top-down proteomic analysis. Proceedings of the ASMS Conference on Mass Spectrometry and Allied Topics. ID 310588.

Prevalence and genomic diversity of Salmonella enterica recovered from river water in a major agricultural region in northwestern Mexico - (Peer Reviewed Journal)
Gonzalez-Lopez, I., Medrano-Felix, J.A., Castro-del Campo, N., Lopez-Cuevas, O., Gonzalez-Gomez, J.P., Valdez-Torres, J.B., Aguirre-Sanchez, J.R., Martinez-Urtaza, J., Gomez-Gil, B., Lee, B.G., Quinones, B., Chaidez, C. 2022. Prevalence and genomic diversity of Salmonella enterica recovered from river water in a major agricultural region in northwestern Mexico. Microorganisms. 10(6). Article 1214. https://doi.org/10.3390/microorganisms10061214.

Differences in the propensity of different antimicrobial resistance determinants to be disseminated via transformation in Campylobacter jejuni and Campylobacter coli - (Peer Reviewed Journal)
Hanafy, Z., Osborne, J.A., Miller, W.G., Parker, C.T., Olson, J.W., Jackson III, J.H., Kathariou, S. 2022. Differences in the propensity of different antimicrobial resistance determinants to be disseminated via transformation in Campylobacter jejuni and Campylobacter coli. Microorganisms. 10(6). Article 1194. https://doi.org/10.3390/microorganisms10061194.

Identification of protein biomarkers of Xylella fastidiosa using MALDI-TOF-TOF-MS/MS and top-down proteomic analysis - (Abstract Only)

Whole-genome analysis of Escherichia phage vB_EcoM-S1P5QW, isolated from manures collected from cattle farms in Maine - (Peer Reviewed Journal)
Quintela, I.A., Hwang, A., Vasse, T., Salvador, A., Zhang, Y., Liao, Y., Wu, V.C. 2022. Whole-genome analysis of Escherichia phage vB_EcoM-S1P5QW, isolated from manures collected from cattle farms in Maine. Microbiology Resource Announcements. 11(4). Article e00041-22. https://doi.org/10.1128/mra.00041-22.

Top-down identification of Shiga toxin (and other virulence factors and biomarkers) from pathogenic E. coli using MALDI-TOF-TOF tandem mass spectrometry - (Book / Chapter)
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. https://doi.org/10.1002/9781119814085.ch3.

Overview of methodologies for the culturing, recovery and detection of Campylobacter - (Peer Reviewed Journal)
Soto-Beltran, M., Lee, B.G., Amezquita-Lopez, B.A., Quinones, B. 2022. Overview of methodologies for the culturing, recovery and detection of Campylobacter. International Journal of Environmental Health Research. https://doi.org/10.1080/09603123.2022.2029366.

Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry - (Peer Reviewed Journal)
Fagerquist, C.K., Dodd, C.E. 2021. Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry. PLoS ONE. 16(11). Article e0260650. https://doi.org/10.1371/journal.pone.0260650.

Top-down proteomic identification of Shiga toxin and acid-stress proteins from pathogenic Escherichia coli using antibiotic induction and MALDI-TOF-TOF-MS/MS - (Proceedings)
Fagerquist, C.K., Dodd, C.E. 2021. Top-down proteomic identification of Shiga toxin and acid-stress proteins from pathogenic Escherichia coli using antibiotic induction and MALDI-TOF-TOF-MS/MS [abstract]. Proceedings of the 69th ASMS Conference on Mass Spectrometry and Allied Topics. Citation ID: 305536. Session: Microorganisms and the Microbiome (Remote Posters).

A review: Gaseous interventions for Listeria monocytogenes control in fresh apple cold storage - (Review Article)
Guan, J., Lacombe, A.C., Rane, B., Tang, J., Sablani, S., Wu, V.C. 2021. A review: Gaseous interventions for Listeria monocytogenes control in fresh apple cold storage. Frontiers in Microbiology. 12. Article 782934. https://doi.org/10.3389/fmicb.2021.782934.

Sequestration of the ionizing proton in singly charged metastable protein ions generated by MALDI - (Peer Reviewed Journal)
Fagerquist, C.K., Dodd, C.E. 2021. Sequestration of the ionizing proton in singly charged metastable protein ions generated by MALDI. International Journal of Mass Spectrometry. 471. Article 116736. https://doi.org/10.1016/j.ijms.2021.116736.

Gaseous chlorine dioxide inactivation of microbial contamination on whole black peppercorns - (Peer Reviewed Journal)
Rane, B., Lacombe, A.C., Guan, J., Bridges, D.F., Sablani, S., Tang, J., Wu, V.C. 2021. Gaseous chlorine dioxide inactivation of microbial contamination on whole black peppercorns. Journal of Food Safety. Article e12948. https://doi.org/10.1111/jfs.12948.

Detecting glucose fluctuations in the Campylobacter jejuni N-glycan structure - (Peer Reviewed Journal)
Nothaft, H., Bian, X., Shajahan, A., Miller, W.G., Bolick, D.T., Guerrant, R.L., Azadi, P., Ng, K.K., Szymanski, C.M. 2021. Detecting glucose fluctuations in the Campylobacter jejuni N-glycan structure. ACS Chemical Biology. 16(11):2690-2701. https://doi.org/10.1021/acschembio.1c00498.

Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation - (Peer Reviewed Journal)
Shu, X., Singh, M., Karampudi, N., Bridges, D.F., Kitazumi, A., Wu, V.C., De los Reyes, B.G. 2021. Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation. PLoS ONE. 16(10). Article e0256324. https://doi.org/10.1371/journal.pone.0256324.

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent - (Peer Reviewed Journal)
Luna, E., Parkar, S., Kirmiz, N., Hartel, S., Hearn, E., Hossine, M., Kurdian, A., Mendoza, C., Orr, K., Padilla, L., Ramirez, K., Salcedo, P., Serrano, P., Choudhury, B., Paulchakrabarti, M., Parker, C.T., Huynh, S., Cooper, K.K., Flores, G.E. 2021. Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent. Applied and Environmental Microbiology. 88(1). Article e01487-21. https://doi.org/10.1128/AEM.01487-21.

A review of epidemic investigation on cold-chain food-mediated SARS-CoV-2 transmission and food safety consideration during COVID-19 pandemic - (Review Article)
Lu, L., Quintela, I.A., Lin, C., Lin, T., Lin, C., Wu, V.C., Lin, C. 2021. A review of epidemic investigation on cold-chain food-mediated SARS-CoV-2 transmission and food safety consideration during COVID-19 pandemic. Journal of Food Safety. 41(6). Article e12932. https://doi.org/10.1111/jfs.12932.

RNA and sugars, unique properties of bacteriophages infecting multidrug resistant Acinetobacter radioresistens strain LH6 - (Peer Reviewed Journal)
Crippen, C.S., Zhou, B., Andersen, S., Patry, R.T., Muszynski, A., Parker, C.T., Cooper, K.K., Szymanski, C.M. 2021. RNA and sugars, unique properties of bacteriophages infecting multidrug resistant Acinetobacter radioresistens strain LH6. Viruses. 13(8). Article 1652. https://doi.org/10.3390/v13081652.

Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans - (Peer Reviewed Journal)
Peters, S., Pascoe, B., Wu, Z., Bayliss, S.C., Zeng, X., Edwinson, A., Veerabadhran-Gurunathan, S., Jawahir, S., Calland, J.K., Mourkas, E., Patel, R., Wiens, T., Decuir, M., Boxrud, D., Smith, K., Parker, C.T., Farrugia, G., Zhang, Q., Sheppard, S.K., Grover, M. 2021. Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans. Communications Biology. 4. Article 1015. https://doi.org/10.1038/s42003-021-02554-8.

Top-down proteomic identification of Shiga toxin and acid-stress proteins from pathogenic Escherichia coli using antibiotic induction and MALDI-TOF-TOF-MS/MS - (Abstract Only)