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ARS Home » Northeast Area » Wyndmoor, Pennsylvania » Eastern Regional Research Center » Molecular Characterization of Foodborne Pathogens Research » Research » Research Project #430258

Research Project: Molecular Characterization of Foodborne Pathogen Responses to Stress

Location: Molecular Characterization of Foodborne Pathogens Research

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

Complete genome sequence of Escherichia coli strain FEX669, a ColV plasmid-containing isolate from retail chicken meat Reprint Icon - (Peer Reviewed Journal)
Elders, J., Liu, Y., Kanrar, S., Gehring, A.G., Sommers, C.H., Johnston, B.D., Johnson, J.R. 2021. Complete genome sequence of Escherichia coli strain FEX669, a ColV plasmid-containing isolate from retail chicken meat. Microbiology Resource Announcements. Available: Microbiology Resource Announcements.10(8):e01340. https://doi.org/10.1128/MRA.01340-20.

Evaluation of a loop-mediated isothermal amplification (LAMP) method for the detection of Salmonella spp. in terms of sensitivity and applicability Reprint Icon - (Peer Reviewed Journal)
Wang, D., Wang, Y., Zhang, M., Liu, Y. 2020. Evaluation of a loop-mediated isothermal amplification (LAMP) method for the detection of Salmonella spp. in terms of sensitivity and applicability. Journal of Nutrition and Metabolism. 3(2):5-5. https://doi.org/10.31487/j.JFNM.2020.02.03.

The inhibitory effect of plant extracts on growth of the foodborne pathogen, Listeria monocytogenes Reprint Icon - (Peer Reviewed Journal)
Ceruso, M., Clement, J., Zhang, F., Huang, Z., Pepe, T., Anastasio, A., Liu, Y. 2020. The inhibitory effect of plant extracts on growth of the foodborne pathogen, Listeria monocytogenes. Antibiotics. 9(6)available online:doi.org/10.3390. https://doi.org/10.3390/antibiotics9060319.

Draft genomic sequence of three Escherichia coli Sequence Type 131 isolates (H45, H43ii, and H43iii) from patients in Lagos, Nigeria Reprint Icon - (Peer Reviewed Journal)
Yang, Y., Sommers, C.H., Adenipkun, E., Ceruso, M., Jackson, C.R., Woodley, T.A., Barrett, J.B., Hiott, L.M., Liu, Y., Frye, J.G. 2020. Draft genomic sequence of three Escherichia coli Sequence Type 131 isolates (H45, H43ii, and H43iii) from patients in Lagos, Nigeria. Microbiology Resource Announcements. 9:17. https://doi.org/10.1128//mra.asm

Development of a real-time LAMP assay for monofloral honey authentication using rape honey Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Zhang, M., Wang, D., Zhang, Y., Jiao, X., Liu, Y. 2020. Development of a real-time LAMP assay for monofloral honey authentication using rape honey. CyTA - Journal of Food. Available online:doi.org/10.1080/19476337. https://doi.org/10.1080/19476337.2020.1749135.

Co-existence of mphA, oqxAB and blaCTX-M-65 on the IncHI2 plasmid in highly drug-resistant Salmonella enterica serovar Indiana ST17 isolated from retail foods and humans in China Reprint Icon - (Peer Reviewed Journal)
Zhang, Z., Yang, J., Xu, X., Zhou, X., Shi, C., Zhao, X., Liu, Y., Shi, X. 2020. Co-existence of mphA, oqxAB and blaCTX-M-65 on the IncHI2 plasmid in highly drug-resistant Salmonella enterica serovar Indiana ST17 isolated from retail foods and humans in China. Food Control. doi.org/10.1016/j.foodcontrol. https://doi.org/10.1016/j.foodcont.2020.107269.

Natural flagella-templated Au nanowires as a novel adjuvant against Listeria monocytogenes Reprint Icon - (Peer Reviewed Journal)
Du, R., Qu, Y., Qi, P.X., Sun, X., Liu, Y., Zhao, M. 2020. Natural flagella-templated Au nanowires as a novel adjuvant against Listeria monocytogenes. The Royal Society of Chemistry. Nanoscale. 12:5627-5635.

The role of yoaE gene regulated by CpxR in the survival ability of Salmonella Enterica serovar Enteritidis in antibacterial egg white Reprint Icon - (Peer Reviewed Journal)
Huang, X., Hu, M., Zhou, X., Liu, Y., Shi, C., Shi, X. 2020. The role of yoaE gene regulated by CpxR in the survival ability of Salmonella Enterica serovar Enteritidis in antibacterial egg white. mSphere. https://doi.org/10.1128/mSphere.00638-19. https://doi.org/10.1128/mSphere.00638-19.

Development of a real-time loop-mediated isothermal amplification (LAMP) assay and visual LAMP assay for detection of African Swine Fever Virus (ASFV) Reprint Icon - (Peer Reviewed Journal)
Wang, D., Yu, J., Wang, Y., Zhang, M., Li, P., Liu, M., Liu, Y. 2019. Development of a real-time loop-mediated isothermal amplification (LAMP) assay and visual LAMP assay for detection of African Swine Fever Virus (ASFV). Journal of Virological Methods. 27. https://doi.org/10.1016/j.jviromet.2019.113775.

Acidic whey to reduce the prevalence of Campylobacter in poultry products - (Abstract Only)

Characterization of the role of ybgC in lysozyme resistance of Salmonella Enteritidis Reprint Icon - (Peer Reviewed Journal)
Qin, X., Dong, R., He, S., Zhou, X., Zhang, Z., Cui, Y., Shi, C., Liu, Y., Shi, X. 2019. Characterization of the role of ybgC in lysozyme resistance of Salmonella Enteritidis. Food Control. 109:106732. https://doi.org/10.1016/j.foodcont.2019.106732.

Detection of cassava component in sweet potato noodles by real-time loop-mediated isothermal amplification (Real-time LAMP) method Reprint Icon - (Peer Reviewed Journal)
Wang, D., Wang, Y., Zhu, K., Shi, L., Zhang, M., Yu, J., Liu, Y. 2019. Detection of cassava component in sweet potato noodles by real-time loop-mediated isothermal amplification (Real-time LAMP) method. Molecules. 24(11), 2043. https://doi.org/10.3390/molecules24112043.

The evaluation of hydrostatic high pressure and cold storage parameters for the reduction of Campylobacter jejuni in chicken livers Reprint Icon - (Peer Reviewed Journal)
Gunther, N.W., Abdul Wakeel, A.Y., Ramos, R.V., Sheen, S. 2019. The evaluation of hydrostatic high pressure and cold storage parameters for the reduction of Campylobacter jejuni in chicken livers. International Journal of Food Microbiology. 82:249-253. https://doi.org/10.1016/j.fm.2019.02.014.

The evaluation of gamma irradiation and cold storage for the reduction of Campylobacter jejuni in chicken livers Reprint Icon - (Peer Reviewed Journal)
Gunther, N.W., Abdul Wakeel, A.Y., Scullen, O.J., Sommers, C.H. 2019. The evaluation of gamma irradiation and cold storage for the reduction of Campylobacter jejuni in chicken livers. Food Microbiology. 82:249-253. https://doi.org/10.1016/j.fm.2019.02.014.

Transcriptional equencing uncovers survival mechanisms of Salmonella enterica serovar enteritidis in antibacterial egg white Reprint Icon - (Peer Reviewed Journal)
Huang, X., Zhou, X., Jia, B., Li, N., Jia, J., He, M., He, Y., Qin, X., Cui, Y., Shi, C., Liu, Y., Shi, X. 2019. Transcriptional equencing uncovers survival mechanisms of Salmonella enterica serovar enteritidis in antibacterial egg white. mSphere. 4(1). https://msphere.asm.org/content/msph/4/1/e00700-18.full. pdf.

Emerging and re-emerging zoonotic food-borne pathogens Reprint Icon - (Review Article)
Smith, J., Fratamico, P.M. 2018. Emerging and re-emerging zoonotic food-borne pathogens. Foodborne Pathogens and Disease. 15(12). https://doi.org/10.1089/fpd.2018.2493.

Purification and characterization of the thermostable metalloprotease produced by Serratia grimesii isolated from channel catfish Reprint Icon - (Peer Reviewed Journal)
Accumannola, G.M., Richards, V.A., Gunther, N.W., Lee, J. 2018. Purification and characterization of the thermostable metalloprotease produced by Serratia grimesii isolated from channel catfish. Journal of the Science of Food and Agriculture. 99:2428-2437. https://doi.org/10.1002/jsfa.9451.

Campylobacter and hemolytic uremic syndrome Reprint Icon - (Review Article)
Smith, J., Gunther, N.W. 2019. Campylobacter and hemolytic uremic syndrome. Foodborne Pathogens and Disease. 16(2). https://doi.org/10.1089/fpd.2018.2513.

Draft whole genome sequence of seven L. monocytogenes strains with variation in virulence and stress responses Reprint Icon - (Peer Reviewed Journal)
Liu, Y., Xu, A., Fratamico, P.M., Sommers, C.H., Rotundo, L., Boccia, F., Jiang, Y., Ward, T.J. 2018. Draft whole genome sequence of seven L. monocytogenes strains with variation in virulence and stress responses. Microbiology Resource Announcements. 7(13). https://doi.org/10.1128/MRA.01038-18.

Commentary: Campylobacter and hemolytic uremic syndrome Reprint Icon - (Review Article)
Smith, J., Gunther, N.W. 2019. Commentary: Campylobacter and hemolytic uremic syndrome. Foodborne Pathogens and Disease. 16(2):90-93. https://doi.org/10.1089/fpd.2018.2513.

Draft genome sequences of seven strains of Shiga toxin-producing Escherichia coli O111 with variation in their sensitivity to novobiocin Reprint Icon - (Peer Reviewed Journal)
Rotundo, L., Boccia, F., Fratamico, P.M., Xu, A., Sommers, C.H., Liu, Y., Bono, J.L., Pepe, T. 2018. Draft genome sequences of seven strains of Shiga toxin-producing Escherichia coli O111 with variation in their sensitivity to novobiocin. Microbiology Resource Announcements. 7(10). https://doi.org/10.1128/MRA.01030-18.

Antimicrobial activities of olive leaf extract and its potential use in food industry Reprint Icon - (Book / Chapter)
Liu, Y., Mckeever, L., Suo, Y., Jin, Z.T., Malik, N.S. 2018. Antimicrobial activities of olive leaf extract and its potential use in food industry. ACS Symposium Series. In: Fan, X., Ngo, H., and Wu, C.Natural and Bio-Based Antimicrobials for Food. 119-132.. https://org/doi/abs/10.1021/bk-2018-1287.ch006.

Quaternary ammonium compounds with multiple cationic moieties (multiQACs) provide antimicrobial activity against Campylobacter jejuni - (Peer Reviewed Journal)
Gunther, N.W., Abdul Wakeel, A.Y., Reichenberger, E.R., Al-Khalifa, S., Minbiole, K.P. 2018. Quaternary ammonium compounds with multiple cationic moieties (multiQACs) provide antimicrobial activity against Campylobacter jejuni. Food Control. https://doi.org/10.1016/j.foodcont.2018.06.038.

Comparison of the Diatheva STEC FLUO with BAX system kits for detection of O157:H7 and Non-O157 Shiga Toxin-Producing Escherichia coli (STEC) in ground beef and bean sprout samples using different enrichment protocols - (Peer Reviewed Journal)
Rotundo, L., Fratamico, P.M., Amagliani, G., Carloni, E., Omiccioli, E., Magnani, M. 2018. Comparison of the Diatheva STEC FLUO with BAX system kits for detection of O157:H7 and Non-O157 Shiga Toxin-Producing Escherichia coli (STEC) in ground beef and bean sprout samples using different enrichment protocols. Journal of Food Analytical Methods. https://doi.org/10.1007/s12161-018-1269-z.

Interlaboratory evaluation of the FDA-ECID microarray for profiling Shiga toxin-producing Escherichia coli - (Peer Reviewed Journal)
Patel, I.R., Gangiredla, J., Lacher, D.W., Mammel, M.K., Bagi, L.K., Baranzoni, G., Fratamico, P.M., Roberts, E.L., Debroy, C., Lindsey, R.L., Stripling, D., Martin, H., Smith, P., Strockbine, N.A., Elkins, C.A., Scheutz, F., Feng, P.C. 2018. Interlaboratory evaluation of the FDA-ECID microarray for profiling Shiga toxin-producing Escherichia coli. Journal of Food Protection. 81:1275-1282.

Comparative transcriptome RNA-Seq analysis of Listeria monocytogenes with sodium lactate adaptation - (Peer Reviewed Journal)
Suo, Y., Gao, S., Baranzoni, G., Xie, Y., Liu, Y. 2018. Comparative transcriptome RNA-Seq analysis of Listeria monocytogenes with sodium lactate adaptation. Food Control. 91:193-201.

Detection of Shiga toxin-producing Escherichia coli (STEC) in food: evaluation of culture enrichment conditions - (Peer Reviewed Journal)
Amagliani, G., Rotundo, L., Carloni, E., Omiccioli, E., Magnani, M., Brandi, G., Fratamico, P.M. 2018. Detection of Shiga toxin-producing Escherichia coli (STEC) in food: evaluation of culture enrichment conditions. Food Research International. 103:398-405.

Genome sequences of 34 Shiga toxin-producing E. coli isolated from swine and other sources - (Peer Reviewed Journal)
Baranzoni, G., Fratamico, P.M., Kim, G., Reichenberger, E.R., Funk, J., Manning, S. 2017. Genome sequences of 34 Shiga toxin-producing E. coli isolated from swine and other sources. Genome Announcements. https://doi.org/10.1128/genomeA.01214-17.

Molecular genotyping of Escherichia coli O-serogroups - (Review Article)
Debroy, C., Fratamico, P.M., Roberts, E. 2018. Molecular genotyping of Escherichia coli O-serogroups. Animal Health Research Reviews. https://doi.org/10.1017/S1466252317000093.

Escherichia coli pathotypes - (Book / Chapter)
Smith, J., Fratamico, P.M. 2018. Escherichia coli pathotypes. Pathogenic E. coli: Evolution, Omics, Detection, and Control – Caister Academic Press, United KingdomBook Chapter. https://doi.org/10.21775/9781910190777.

Sequence-based and other methods for molecular serotyping of E. coli - (Proceedings)
Fratamico, P.M. 2017. Sequence-based and other methods for molecular serotyping of E. coli. In: Proceedings of the United States-Japan Cooperative Program in Natural Resources (UJNR), November 12-18, 2017, Japan. p.1.

Complete genome sequence of Campylobacter jejuni RM1246-ERRC that exhibits resistance to Quaternary Ammonium Compounds Reprint Icon - (Peer Reviewed Journal)
Gunther, N.W., Reichenberger, E.R. 2017. Complete genome sequence of Campylobacter jejuni RM1246-ERRC that exhibits resistance to Quaternary Ammonium Compounds. Genome Announcements. https://doi.org/10.1128/genomeA.00978-17.

LMOf2365_0442 encoding for a fructose specific PTS permease IIA may be required for virulence in L. monocytogenes Strain F2365 - (Peer Reviewed Journal)
Liu, Y., Yoo, B., Hwang, C., Suo, Y., Sheen, S., Khosravi, P., Huang, L. 2017. LMOf2365_0442 encoding for a fructose specific PTS permease IIA may be required for virulence in L. monocytogenes Strain F2365. Frontiers in Microbiology. 8:01611.

A multi-pathogen selective enrichment broth for simultaneous growth of Salmonella enteria, Escherichia coli O157:H7 and Shigella flexneri - (Peer Reviewed Journal)
Suo, Y., Gao, S., Xie, Y., Liu, Y., Qu, Y., Shen, Y., Zhou, C. 2017. A multi-pathogen selective enrichment broth for simultaneous growth of Salmonella enteria, Escherichia coli O157:H7 and Shigella flexneri. Journal of Food Safety. doi:10.1111/jfs.12388.

Prevalence and characteristics of Shiga toxin-producing Escherichia coli in finishing pigs: implications on public health - (Peer Reviewed Journal)
Cha, W., Fratamico, P.M., Ruth, L., Bowman, A., Nolting, J., Manning, S., Funk, J. 2018. Prevalence and characteristics of Shiga toxin-producing Escherichia coli in finishing pigs: implications on public health. International Journal of Food Microbiology. 264:8-15.

Assessment of the antimobial activity of olive leaf extract against foodborne bacterial pathogens - (Peer Reviewed Journal)
Liu, Y., McKeever, L., Malik, N.S. 2017. Assessment of the antimobial activity of olive leaf extract against foodborne bacterial pathogens. Frontiers in Microbiology. doi: 10.3389/fmicb.2017.00113.

Detection and isolation of the "Top 7" Shiga toxin-producing Escherichia coli in ground beef: comparison of the Rapidfinder kits to the USDA microbiology laboratory guidebook method Reprint Icon - (Peer Reviewed Journal)
Fratamico, P.M., Bagi, L.K., Abdul Wakeel, A.Y. 2017. Detection and isolation of the "Top 7" Shiga toxin-producing Escherichia coli in ground beef: comparison of the Rapidfinder kits to the USDA microbiology laboratory guidebook method. Journal of Food Protection. 80:829-836.

Evaluation of the performance of the IQ-check kits and the USDA microbiology laboratory guidebook methods for detection of Shiga Toxin-Producing E. coli (STEC) and STEC and Salmonella simultaneously in ground beef Reprint Icon - (Peer Reviewed Journal)
Baranzoni, G., Fratamico, P.M., Boccia, F., Bagi, L.K., Kim, G., Anastasio, A., Pepe, T. 2017. Evaluation of the performance of the IQ-check kits and the USDA microbiology laboratory guidebook methods for detection of Shiga Toxin-Producing E. coli (STEC) and STEC and Salmonella simultaneously in ground beef. Journal of Applied Microbiology. 122:809-816.

Methods for detecting pathogens in the beef food chain: detecting particular pathogens - (Book / Chapter)
Fratamico, P.M., Bosilevac, J.M., Schmidt, J.W. 2017. Methods for detecting pathogens in the beef food chain: detecting particular pathogens. In: Acuff, G., Dickson, J. Ensuring safety and quality in the production of beef. Volume 1: Safety. Cambridge, UK: Burleigh Dobbs Science. p.59-72.

Food safety trends in the U.S. and update on pathogenic E. coli - (Proceedings)
Fratamico, P.M., Baranzoni, G. 2016. Food safety trends in the U.S. and update on pathogenic E. coli. In: Proceedings of the United States-Japan Cooperative Program in Natural Resources (UJNR), November 7-10, 2016, Honolulu, Hawaii. p. 27-28.

Editorial: Emerging approaches for typing, detection, characterization, and traceback of Escherichia coli - (Other)
Fratamico, P.M., Debroy, C., Needleman, D.S. 2016. Editorial: Emerging approaches for typing, detection, characterization, and traceback of Escherichia coli. Frontiers in Microbiology. DOI.org/10.3389/fmicb.2016.02089.

A systems biology approach to investigate the antimicrobial activity of oleuropein - (Peer Reviewed Journal)
Li, X., Liu, Y., Jia, Q., Lamacchia, V., O'Donoghue, K., Huang, Z. 2016. A systems biology approach to investigate the antimicrobial activity of oleuropein. Journal of Industrial Microbiology and Biotechnology. 43(12):1705-1717.

Methods for detecting pathogens in the beef food chain: an overview - (Book / Chapter)
Fratamico, P.M., Bosilevac, J.M., Schmidt, J.W. 2017. Methods for detecting pathogens in the beef food chain: an overview. In: Acuff, G., Dickson, J. Ensuring safety and quality in the production of beef. Volume 1: Safety. Cambridge, UK: Burleigh Dobbs Science. p.35-51.

Complete genome sequences of Escherichia coli O157:H7 strains SRCC 1675 and 28RC that vary in acid resistance Reprint Icon - (Peer Reviewed Journal)
Baranzoni, G., Fratamico, P.M., Reichenberger, E.R., Kim, G., Breidt, F., Kay, K., Oh, D. 2016. Complete genome sequences of Escherichia coli O157:H7 strains SRCC 1675 and 28RC that vary in acid resistance. Genome Announcements. 4:4. doi: 10.1128/genomeA.00743-16.

Advances in genoserotyping and subtyping of Escherichia coli - (Review Article)
Fratamico, P.M., Debroy, C., Liu, Y., Needleman, D.S., Baranzoni, G., Feng, P. 2016. Advances in genoserotyping and subtyping of Escherichia coli. Frontiers in Microbiology. 7:644.

Characterization of shiga toxin subtypes and virulence genes in Porcine shiga toxin-producing Escherichia coli Reprint Icon - (Peer Reviewed Journal)
Baranzoni, G., Fratamico, P.M., Gangiredla, J., Patel, I., Bagi, L.K., Delannoy, S., Fach, P., Boccia, F., Anastasio, A., Pepe, T. 2016. Characterization of shiga toxin subtypes and virulence genes in Porcine shiga toxin-producing Escherichia coli. Frontiers in Microbiology. 7:574.

Complete genome sequence of UV-resistant Campylobacter jejuni RM3194, including an 81.08-kilobase plasmid - (Peer Reviewed Journal)
Gunther, N.W., Reichenberger, E.R., Bono, J.L. 2016. Complete genome sequence of UV-resistant Campylobacter jejuni RM3194, including an 81.08-kilobase plasmid. Genome Announcements. 4(2):e00305-16.