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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » People & Locations » Michael Cooley (Mike)

Michael Cooley (Mike)
Produce Safety and Microbiology Research
Research Geneticist (Plants)

Phone: (510) 559-5986
Fax: (510) 559-6162
Room WAB200-E

USDA, ARS, PWA, WRRC-PSM
800 BUCHANAN STREET
ALBANY, CA 94710
Projects
Human Pathogens within the Produce Production Continuum; their Detection, Mechanisms for Persistence, and Ecology
In-House Appropriated (D)
  Accession Number: 438551

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Panoramic MLVA fingerprinting of Brucella melitensis circulating among livestock and cases of sporadic human illness in Egypt Reprint Icon - (Peer Reviewed Journal)
Sayour, A.E., Elbauomy, E., Abdel-Hamid, N.H., Mahrous, A., Carychao, D.K., Cooley, M.B., Elhadidy, M. 2020. Panoramic MLVA fingerprinting of Brucella melitensis circulating among livestock and cases of sporadic human illness in Egypt. Transboundary and Emerging Diseases. 1:1-11. https://doi.org/10.1111/tbed.13581.
Metagenomics as a public health risk assessment tool in a study of natural creek sediments influenced by agricultural and livestock runoff: potential and limitations Reprint Icon - (Peer Reviewed Journal)
Suttner, B.J., Johnston, E.R., Orellana, L.H., Rodriguez, L.M., Hatt, J.K., Carychao, D.K., Carter, M.Q., Cooley, M.B., Konstantinidis, K.T. 2020. Metagenomics as a public health risk assessment tool in a study of natural creek sediments influenced by agricultural and livestock runoff: potential and limitations. Applied and Environmental Microbiology. 86(6):e02525-19. https://doi.org/10.1128/AEM.02525-19.
Complete genome sequences of two Shiga toxin-producing Escherichia coli strains isolated from crows Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Pham, A.C., Carychao, D.K., Cooley, M.B. 2019. Complete genome sequences of two Shiga toxin-producing Escherichia coli strains isolated from crows. Microbiology Resource Announcements. 8(45):e01082-19. https://doi.org/10.1128/MRA.01082-19.
New strategies for the enumeration of enteric pathogens in water Reprint Icon ()
Gorski, L.A., Rivadeneira, P., Cooley, M.B. 2019. New strategies for the enumeration of enteric pathogens in water. Environmental Microbiology Reports. 11(6):765-776. https://doi.org/10.1111/1758-2229.12786.
A clonal shiga toxin-producing Escherichia coli O121:H19 population exhibits diverse carbon utilization patterns Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Tan, Z., Pham, A.C., Carychao, D.K., Cooley, M.B. 2019. A clonal shiga toxin-producing Escherichia coli O121:H19 population exhibits diverse carbon utilization patterns. Foodborne Pathogens and Disease. 16(6):384-393. https://doi.org/10.1089/fpd.2018.2567.
Complete genome sequences of three Shiga toxin-producing Escherichia coli O111:H8 strains exhibiting an aggregation phenotype Reprint Icon - (Peer Reviewed Journal)
Parker, C., Huynh, S., Bono, J.L., Miller, W.G., Cooley, M.B., Brandl, M. 2019. Complete genome sequences of three Shiga toxin-producing Escherichia coli O111:H8 strains exhibiting an aggregation phenotype. Microbiology Resource Announcements. 8(1):e01335-18. https://doi.org/10.1128/MRA.01335-18.
Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California Reprint Icon - (Peer Reviewed Journal)
Parker, C., Cooper, K.K., Huynh, S., Smith, T.P., Bono, J.L., Cooley, M.B. 2018. Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Genome Announcements. 7(1):1-3. https://doi.org/10.1128/MRA.00807-18.
Optimized co-extraction and quantification of DNA from enteric pathogens in surface water samples near produce fields in California Reprint Icon - (Peer Reviewed Journal)
Cooley, M.B., Carychao, D.K., Gorski, L.A. 2018. Optimized co-extraction and quantification of DNA from enteric pathogens in surface water samples near produce fields in California. Frontiers in Microbiology. 9:448. https://doi.org/10.3389/fmicb.2018.00448.
Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and the correlation with STEC bacterial hosts in produce-growing area in Salinas, California Reprint Icon - (Peer Reviewed Journal)
Liao, Y., Quintela, I., Nguyen, K.M., Salvador, A., Cooley, M.B., Wu, V.C. 2018. Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and the correlation with STEC bacterial hosts in produce-growing area in Salinas, California. PLoS One. 13(1):e0190534. https://doi.org/10.1371/journal.pone.0190534.
Concurrent detection of human norovirus and bacterial pathogens in water samples from an agricultural region in Central California Coast Reprint Icon - (Peer Reviewed Journal)
Tian, P., Yang, D., Lei, S., Wang, D., Li, Q., Gorski, L.A., Lee, B.G., Quinones, B., Cooley, M.B. 2017. Concurrent detection of human norovirus and bacterial pathogens in water samples from an agricultural region in Central California Coast. Frontiers in Microbiology. 8:1560. https://doi.org/10.3389/fmicb.2017.01560.
Investigation of environmental factors on the prevalence of free bacteriophages against Shiga toxin-producing Escherichia coli strains in produce pre-harvest environment in Salinas, California - (Abstract Only)
Investigation of environmental factors on the prevalence of free bacteriophages against Shiga toxin-producing Escherichia coli strains in produce pre-harvest environment in Salinas, California - (Proceedings)
Liao, Y., Quintela, I., Nguyen, K.M., Salvador, A., Cooley, M.B., Wu, V.C. 2017. Investigation of environmental factors on the prevalence of free bacteriophages against Shiga toxin-producing Escherichia coli strains in produce pre-harvest environment in Salinas, California. Meeting Proceedings. 2017 USDA-ARS/FSIS Annual Food Safety Meeting. NCTC, Shepherdstown, WV. Section Z, P13.
An environmental shiga toxin-producing Escherichia coli O145 clonal population exhibits high-level phenotypic variation that includes virulence traits - (Peer Reviewed Journal)
Carter, M.Q., Quinones, B., He, X., Louie, J.W., Zhong, W.W., Lee, B.G., Yambao, J.C., Mandrell, R.E., Cooley, M.B. 2015. An environmental shiga toxin-producing Escherichia coli O145 clonal population exhibits high-level phenotypic variation that includes virulence traits. Applied and Environmental Microbiology. doi: 10.1128/AEM.03172-15.
Male-specific coliphages for source tracking fecal contamination in irrigation waters and prevalence of Shiga toxigenic Escherichia coli in a major produce production region of central coast of California - (Peer Reviewed Journal)
Ravva, S.V., Sarreal, C.Z., Cooley, M.B. 2015. Male-specific coliphages for source tracking fecal contamination in irrigation waters and prevalence of Shiga toxigenic Escherichia coli in a major produce production region of central coast of California. Environmental Science: Processes & Impacts. doi: 10.1039/C4EM00537F.
High genotypic and phenotypic similarity among Shiga toxin-producing Escherichia coli O111 environmental and outbreak strains Reprint Icon - (Peer Reviewed Journal)
Diodati, M.E., Bates, A.H., Cooley, M.B., Walker, S., Mandrell, R., Brandl, M. 2015. High genotype and phenotypic similarity among Shiga toxin-producing Escherichia coli O111 environmental and outbreak strains. Foodborne Pathogens and Disease. 12:235-243.
Fitness of outbreak and environmental strains of Escherichia coli O157:H7 in aerosolizable soil and association of clonal variation in stress gene regulation - (Peer Reviewed Journal)
Ravva, S.V., Cooley, M.B., Sarreal, C.Z., Mandrell, R.E. 2014. Fitness of outbreak and environmental strains of Escherichia coli O157:H7 in aerosolizable soil and association of clonal variation in stress gene regulation. Pathogens. 3:528-548. DOI: 10.3390/pathogens3030528.
Top-down proteomic identification of Shiga toxin 2 subtypes from Shiga toxin-producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization-Tandem Time of Flight mass spectrometry - (Peer Reviewed Journal)
Fagerquist, C.K., Zaragoza, W.J., Sultan, O., Woo, N., Quinones, B., Cooley, M.B., Mandrell, R.E. 2014. Top-down proteomic identification of Shiga toxin 2 subtypes from Shiga toxin-producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization-Tandem Time of Flight mass spectrometry. Applied and Environmental Microbiology. 8(9):2928-2940.
Comparison of subtypes of Listeria monocytogenes isolates from naturally contaminated watershed samples using a combination of non-selective and selective enrichment methods - (Peer Reviewed Journal)
Gorski, L.A., Walker, S., Liang, A.S., Nguyen, K.M., Govoni, J.A., Carychao, D.K., Cooley, M.B., Mandrell, R.E. 2014. Comparison of subtypes of Listeria monocytogenes isolates from naturally contaminated watershed samples using a combination of non-selective and selective enrichment methods. PLoS One. 9(3):e92467. DOI: 10.1371/journal.pone.009246.
Prevalence of Shiga toxin producing Escherichia coli, Salmonella enterica and Listeria monocytogenes at public access watershed sites in a California central coast agricultural region - (Peer Reviewed Journal)
Cooley, M.B., Quinones, B., Oryang, D., Mandrell, R.E., Gorski, L.A. 2014. Prevalence of Shiga toxin producing Escherichia coli, Salmonella enterica and Listeria monocytogenes at public access watershed sites in a California central coast agricultural region. Frontiers in Cellular and Infection Microbiology. 4:30.
Top-down proteomic identification of Shiga toxin 2 variants from Shiga toxin-producing Escherichia coli (STEC) using MALDI-TOF-TOF-MS/MS-PSD - (Proceedings)
Fagerquist, C.K., Zaragoza, W.J., Sultan, O., Woo, N., Quinones, B., Swimley, M.S., Cooley, M.B., Mandrell, R.E. 2013. Top-down proteomic identification of Shiga toxin 2 variants from Shiga toxin-producing Escherichia coli (STEC) using MALDI-TOF-TOF-MS/MS-PSD. ASMS20139833.3125VER.1.pdf.
Development of a robust methos for isolation of shiga toxin positive Escherichia coli (STEC) from fecal, plant, soil and water samples from leafy greens production region in California - (Peer Reviewed Journal)
Cooley, M.B., Jay-Russell, M., Atwill, E.R., Carychao, D.K., Nguyen, K.M., Quinones, B., Patel, R., Walker, S., Swimley, M., Pierre-Jerome, E., Gordus, A., Mandrell, R.E. 2013. Development of a robust methos for isolation of shiga toxin positive Escherichia coli (STEC) from fecal, plant, soil and water samples from leafy greens production region in California. PLoS One. 8(6):e65716. doi:10.1371/journal.pone.0065716.
Occurrence of generic E. coli, E. coli O157:H7 and Salmonella spp. in water and sediment from leafy green produce farms and streams on the Central California coast - (Peer Reviewed Journal)
Benjamin, L., Atwill, E.R., Jay-Russell, M., Cooley, M.B., Carychao, D.K., Gorski, L.A., Mandrell, R.E. 2013. Occurrence of generic E. coli, E. coli O157:H7 and Salmonella spp. in water and sediment from leafy green produce farms and streams on the Central California coast. International Journal of Food Microbiology. 10.1016/j.ijfoodmicro.2013.04.003 165(1)65-76.
Quantification and characterization of mucosa-associated and intracellular Escherichia coli in inflamatory bowel disease Reprint Icon - (Peer Reviewed Journal)
Elliott, T.R., Hudspith, B.N., Wu, G., Cooley, M.B., Parkes, G., Quinones, B., Randall, L., Mandrell, R.E., Fagerquist, C.K., Brostoff, J., Rayment, N.B., Boussioutas, A., Petrovska, L., Sanderson, J.D. 2013. Quantification and characterization of mucosa-associated and intracellular Escherichia coli in inflamatory bowel disease. Inflammatory Bowel Diseases. 19(11):2326-2338.
Genotypic analyses of Shiga toxin-producing Escherichia coli O157 and non-O157 recovered from feces of domestic animals in rural farms in Mexico - (Peer Reviewed Journal)
Amezquita-Lopez, B.A., Quinones, B., Cooley, M.B., Leon-Felix, J., Castro-Del Campo, N., Mandrell, R.E., Jimenez, M., Chaidez, C. 2012. Genotypic analyses of Shiga toxin-producing Escherichia coli O157 and non-O157 recovered from feces of domestic animals in rural farms in Mexico. PLoS One. 7(12):e51565. doi:101371/journal.pone.0051565.
Evidence of norovirus (NV)in a major produce production region watershed and a low density microarray strategy for detecting NV(Abstract) - (Abstract Only)
O-antigen and virulence profiling of Shiga toxin-producing Escherichia coli by a rapid and cost-effective DNA microarray colorimetric method - (Peer Reviewed Journal)
Quinones, B., Swimley, M.S., Narm, K., Patel, R.N., Cooley, M.B., Mandrell, R.E. 2012. O-antigen and virulence profiling of Shiga toxin-producing Escherichia coli by a rapid and cost-effective DNA microarray colorimetric method. Frontiers in Cellular and Infection Microbiology. 10.3389/fcimb.2012.00061/full.
Distinct PFGE and MLVA Genotypes of Shiga Toxin-Producing Escherichia coli (STEC)Recovered from Feces of Farm Animals in the Culiacan Valley, Mexico(Abstract) - (Abstract Only)
Selective recovery by different culture methods of Shiga toxin-producing Escherichia coli genotypes from a major produce production region in California(Abstract) - (Abstract Only)
Curli variants of enterohemorrhagic Escherichia coli O157:H7 display distinct survival fitness - (Peer Reviewed Journal)
Carter, M.Q., Brandl, M., Louie, J.W., Kyle, J.L., Carychao, D.K., Cooley, M.B., Parker, C., Bates, A.H., Mandrell, R.E. 2011. Curli variants of enterohemorrhagic Escherichia coli O157:H7 display distinct survival fitness. Applied and Environmental Microbiology. 77:3685-3695.
Sensitive detection of Shiga toxin 2 and some of its Stx 2 variants in environmental samples by a novel immuno-PCR assay - (Peer Reviewed Journal)
He, X., Qi, W., Quinones, B., Mcmahon, S.A., Cooley, M.B., Mandrell, R.E. 2011. Sensitive detection of Shiga toxin 2 and some of its Stx 2 variants in environmental samples by a novel immuno-PCR assay. Applied and Environmental Microbiology. 77(1):3558-3564. doi:10.1128/AEM.02205-10.
Use of Photopolymerization for Genotyping Shiga Toxin-Producing Escherichia coli Recovered from Produce Production Regions in California - (Abstract Only)
Prevalence, distribution and diversity of salmonella enterica in a major produce region of California - (Peer Reviewed Journal)
Gorski, L.A., Parker, C., Liang, A.S., Cooley, M.B., Jay-Russell, M., Gordus, A., Atwill, R.E., Mandrell, R.E. 2011. Prevalence, distribution and diversity of salmonella enterica in a major produce region of California. Applied and Environmental Microbiology. 77:2734-2748.
Effects of Environmental Stress on Stability of Tandem Repeat in Escherichia coli O157:H7 - (Peer Reviewed Journal)
Cooley, M.B., Carychao, D.K., Nguyen, K.M., Whitehand, L.C., Mandrell, R.E. 2010. Effects of Environmental Stress on Stability of Tandem Repeat in Escherichia coli O157:H7. Applied and Environmental Microbiology. 76(10)3398-3400
Tandem Repeat Stability in Escherichia coli O157:H7 is Dependent on Environmental Stress - (Abstract Only)
Rapid Identification of Protein Biomarkers of E. coli O157:H7 by MALDI-TOF-TOF Mass Spectrometry and Top-Down Proteomics - (Peer Reviewed Journal)
Fagerquist, C.K., Garbus, B.R., Miller, W.G., Williams, K.E., Yee, E., Bates, A.H., Boyle, S., Harden, L.A., Cooley, M.B., Mandrell, R.E. 2010. Rapid Identification of Protein Biomarkers of E. coli O157:H7 by MALDI-TOF-TOF Mass Spectrometry and Top-Down Proteomics. Analytical Chemistry. 82:2717-2725.
Phenotypic Divergence in Curli Variants of Enterohemorrhagic Escherichia coli O157:H7 - (Abstract Only)
An Engineered R-Type Pyocin Is a Highly Specific and Sensitive Bactericidal Agent for the Food-Borne Pathogen Escherichia coli O157:H7 - (Peer Reviewed Journal)
Scholl, D., Cooley, M.B., Williams, S.R., Gebhart, D., Martin, D., Bates, A.H., Mandrell, R.E. 2009. An Engineered R-Type Pyocin Is a Highly Specific and Sensitive Bactericidal Agent for the Food-Borne Pathogen Escherichia coli O157:H7. Antimicrobial Agents and Chemotherapy. 53(7):3074-3080.
Escherichia coli O157:H7 strains isolated from environmental sources differ significantly in acid resistance compared to human outbreak strains - (Peer Reviewed Journal)
Oh, D., Pan, Y., Berry, E.D., Cooley, M.B., Mandrell, R.E., Breidt, F. 2009. Escherichia coli O157:H7 strains isolated from environmental sources differ significantly in acid resistance compared to human outbreak strains. Journal of Food Protection. 72(3):503-509.
Incidence and tracking of Escherichia coli O157:H7 in a major produce production region in California - (Peer Reviewed Journal)
Cooley, M.B., Carychao, D.K., Crawford-Miksza, L., Jay, M.T., Myers, C., Rose, C., Key, C., Farrar, J., Mandrell, R.E. 2007. Incidence and tracking of Escherichia coli O157:H7 in a major produce production region in California. PLoS One. 0001159, www.plosone.org
Survival of Escherichia coli O157:H7 Isolates in Acetic Acid Solutions is Influenced by the Source of Isolation - (Abstract Only)
Oh DH, Pan Y, Berry ED, Mandrell RE, Cooley MB, Breidt F. 2007. Survival of Escherichia coli O157:H7 Isolates in Acetic Acid Solutions is Influenced by the Source of Isolation. International Association for Food Protection Proceedings.
Escherichia coli O157:H7 in Feral Swine Near Spinach Fields and Cattle, Central California Coast - (Peer Reviewed Journal)
Jay, M.T., Cooley, M.B., Carychao, D.K., Wiscomb, G.W., Sweitzer, R.A., Crawford-Miksza, L., Farrar, J.A., Lau, D.K., O'Connell, J., Millington, A., Asmundson, R.V., Atwill, E.R., Mandrell, R.E. 2007. Escherichia coli O157:H7 in Feral Swine Near Spinach Fields and Cattle, Central California Coast. Emerging Infectious Diseases. 13:12.
ESCHERICHIA COLI O157:H7 SURVIVAL AND GROWTH ON LETTUCE IS ALTERED BY THE PRESENCE OF EPIPHYTIC BACTERIA - (Peer Reviewed Journal)
Cooley, M.B., Chao, D.K., Mandrell, R.E. 2006. Escherichia coli O157:H7 survival and growth on lettuce is altered by the presence of epiphytic bacteria. Journal of Food Protection.69:10:2329-2335
COLONIZATION OF ARABIDOPSIS THALIANA WITH SALMONELLA ENTERICA AND ENTEROHEMORRHAGIC ESCHERICHIA COLI 157:H7 AND COMPETITIAN BY ENTEROBACTOR ASBURIAE - (Peer Reviewed Journal)
COOLEY, M.B., MILLER, W.G., MANDRELL, R.E. COLONIZATION OF ARABIDOPSIS THALIANA WITH SALMONELLA ENTERICA AND ENTEROHEMORRHAGIC ESCHERICHIA COLI 157:H7 AND COMPETITIAN BY ENTEROBACTOR ASBURIAE. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2003. v 68(8) p.4915-4926
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