Michelle Qiu Carter
Produce Safety and Microbiology Research
Research Microbiologist
Phone: (510) 559-6180
Fax: (510) 559-6162
Room WAB306-B
USDA, ARS, PWA, WRRC-PSM
800 BUCHANAN STREET
ALBANY, CA 94710
Publications
(Clicking on the reprint icon
will take you to the publication reprint.)
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Genomic insight into natural inactivation of Shiga toxin 2 production in an environmental Escherichia coli strain producing Shiga toxin 1
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(Peer Reviewed Journal)
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Carter, M.Q., Pham, A.C., He, X., Hnasko, R.M. 2020. Genomic insight into natural inactivation of Shiga toxin 2 production in an environmental Escherichia coli strain producing Shiga toxin 1. Foodborne Pathogens and Disease. 17(9):555-567. https://doi.org/10.1089/fpd.2019.2767.
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Metagenomics as a public health risk assessment tool in a
study of natural creek sediments influenced by agricultural
and livestock runoff: potential and limitations
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(Peer Reviewed Journal)
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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.
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Formation of E. coli O157:H7 persister cells in the lettuce phyllosphere and application of differential equation models to predict their prevalence on lettuce plants in the field
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(Peer Reviewed Journal)
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Munther, D.S., Carter, M.Q., Aldric, C.V., Ivanek, R., Brandl, M. 2020. Formation of E. coli O157:H7 persister cells in the lettuce phyllosphere and application of differential equation models to predict their prevalence on lettuce plants in the field. Applied and Environmental Microbiology. 86(2):e01602-19. https://doi.org/10.1128/AEM.01602-19.
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Top-down proteomic identification of Shiga toxin 1 and 2 from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry
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(Peer Reviewed Journal)
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Fagerquist, C.K., Zaragoza, W.J., Carter, M.Q. 2019. Top-down proteomic identification of Shiga toxin 1 and 2 from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry. Microorganisms. 7(488):1-14. https://doi.org/10.3390/microorganisms7110488.
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Complete genome sequences of two Shiga toxin-producing Escherichia coli strains isolated from crows
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(Peer Reviewed Journal)
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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.
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Typing/subtyping Shiga toxin from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis
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(Proceedings)
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Fagerquist, C.K., Zaragoza, W.J., Carter, M.Q. 2019. Typing/subtyping Shiga toxin from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis. Proceedings of the ASMS Conference on Mass Spectrometry and Allied Topics, June 2 - 6, 2019, Atlanta, GA. ID 297530 (ThP 536).
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Enhanced formation of shiga toxin-producing Escherichia coli persister variants in environments relevant to leafy greens production
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(Peer Reviewed Journal)
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Thao, S., Brandl, M., Carter, M.Q. 2019. Enhanced formation of persister variants in shiga toxin-producing Escherichia coli under conditions relevant to fresh produce production. Food Microbiology. 84:103241. https://doi.org/10.1016/j.fm.2019.103241.
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Curli fimbriae confer shiga toxin-producing Escherichia coli a competitive trait in mixed biofilms
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(Peer Reviewed Journal)
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Carter, M.Q., Feng, D., Li, H. 2019. Curli fimbriae confer shiga toxin-producing Escherichia coli a competitive trait in mixed biofilms. Food Microbiology. 82:482-488. https://doi.org/10.1016/j.fm.2019.03.024.
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Typing/subtyping Shiga toxin from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis
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(Abstract Only)
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Fagerquist, C.K., Zaragoza, W.J., Carter, M.Q. 2019. Typing/subtyping Shiga toxin from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis [abstract]. 67th ASMS Conference on Mass Spectrometry and Allied Topics, June 2-6, 2019, Atlanta, GA.
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A clonal shiga toxin-producing Escherichia coli O121:H19 population exhibits diverse carbon utilization patterns
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(Peer Reviewed Journal)
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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.
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imGLAD: accurate detection and quantification of target organisms in metagenomes
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(Peer Reviewed Journal)
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Castro, J.C., Rodriguez, L.M., Harvey, W.T., Weigland, M.R., Hatt, J.K., Carter, M.Q., Konstantinidis, K. 2018. imGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ. 6:e5882. https://doi.org/10.7717/peerj.5882.
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Complete genome sequences of two atypical enteropathogenic Escherichia coli O145 environmental strains
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(Peer Reviewed Journal)
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Carter, M.Q., Pham, A.C. 2018. Complete genome sequences of two atypical enteropathogenic Escherichia coli O145 environmental strains. Genome Announcements. 6:e00418-18. https://doi.org/10.1128/genomeA.00418-18.
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Complete genome sequence of a natural Escherichia coli O145:H11 isolate that belongs to Phylo-group A
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(Peer Reviewed Journal)
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Carter, M.Q., Pham, A.C. 2018. Complete genome sequence of a natural Escherichia coli O145:H11 isolate that belongs to Phylo-group A. Genome Announcements. 6:e000349-18. https://doi.org/10.1128/genomeA.00349-18.
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Survival of foodborne pathogens on commercially packed table grapes under simulated refrigerated transit conditions
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(Peer Reviewed Journal)
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Carter, M.Q., Feng, D., Chapman, M.H., Gabler, F. 2017. Survival of foodborne pathogens on commercially packed table grapes under simulated refrigerated transit conditions. Food Microbiology. 72:199-205. https://doi.org/10.1016/j.fm.2017.12.004.
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Conditional function of autoaggregative protein cah and common cah mutations in Shiga toxin-producing Escherichia coli
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(Peer Reviewed Journal)
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Carter, M.Q., Brandl, M., Kudva, I.T., Katani, R., Moreau, M.R., Kapur, V. 2017. Conditional function of autoaggregative protein cah and common cah mutations in Shiga toxin-producing Escherichia coli. Applied and Environmental Microbiology. 84(1):e01739-17. https://doi.org/10.1128/AEM.01739-17.
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Complete Genome Sequence of a Shiga toxin-producing Enterobacter cloacae Clinical Isolate
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(Peer Reviewed Journal)
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Carter, M.Q., Pham, A.C., Huynh, S., He, X. 2017. Complete Genome Sequence of a Shiga toxin-producing Enterobacter cloacae Clinical Isolate. Genome Announcements. 5(37):e00883-17. https://doi.org/10.1128/genomeA.00883-17.
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Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa
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(Peer Reviewed Journal)
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Phuoc, T., Carter, M.Q., Cosonato, S., Lory, S., Jousson, O. 2017. Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa. BMC Microbiology. (2017) 17:31 DOI 10.1186/s12866-017-0943-4.
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Decoding the ecological function of accessory genome
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Carter, M.Q. 2016. Decoding the ecological function of accessory genome. Trends in Microbiology. 25(1):6-8. doi:org/10.1016/j.tim.2016.11.012.
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Curli temper adherence of Escherichia coli O157:H7 to squamous epithelial cells from the bovine recto-anal junction in a strain-dependent manner
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(Peer Reviewed Journal)
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Kudva, I.T., Carter, M.Q., Sharma, V.K., Stasko, J.A., Giron, J.A. 2016. Curli temper adherence of Escherichia coli O157:H7 to squamous epithelial cells from the bovine recto-anal junction in a strain-dependent manner. Applied and Environmental Microbiology. 83(1):e02594-16. doi: 10.1128/AEM.02594-16.
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Curli fimbriae are conditionally required in Escherichia coli O157:H7 for initial attachment and biofilm formation
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(Peer Reviewed Journal)
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Carter, M.Q., Louie, J.W., Feng, D., Zhong, W.W., Brandl, M. 2016. Curli fimbriae are conditionally required in Escherichia coli O157:H7 for initial attachment and biofilm formation. Food Microbiology. 57: 81-89.
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The polymorphic aggregative phenotype of Shiga toxin-producing Escherichia coli O111 depends on rpoS and curli
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(Peer Reviewed Journal)
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Diodati, M.E., Bates, A.H., Miller, W.G., Carter, M.Q., Zhou, Y., Brandl, M. 2016. The polymorphic aggregative phenotype of Shiga toxin-producing Escherichia coli O111 depends on rpoS and curli. Applied and Environmental Microbiology. 82:1475–1485. doi: 10.1128/AEM.03935-15.
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An environmental shiga toxin-producing Escherichia coli O145 clonal population exhibits high-level phenotypic variation that includes virulence traits
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(Peer Reviewed Journal)
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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.
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Curli modulates adherence of Escherichia coli O157 to bovine recto-anal junction squamous epithelial cells
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(Abstract Only)
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Kudva, I.T., Giron, J.A., Carter, M.Q., Sharma, V.K., Arthur, T.M. 2015. Curli modulates adherence of Escherichia coli O157 to bovine recto-anal junction squamous epithelial cells [abstract]. American Society for Microbiology. Abstract No. 1557.
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Comparative genomic analysis and adherence characteristics of supershedder strains of Escherichia coli O157:H7
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(Abstract Only)
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Katani, R., Moreau, M.R., Kudva, I.T., Carter, M.Q., Garay, J.A., Cote, R., Li, L., Arthur, T.M., Debroy, C., Mwangi, M., Kapur, V. 2015. Comparative genomic analysis and adherence characteristics of supershedder strains of Escherichia coli O157:H7 [abstract]. American Society for Microbiology. Abstract No. 973.
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Effect of sulfur dioxide fumigation on survival of foodborne pathogens on table grapes under standard storage temperature
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(Peer Reviewed Journal)
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Carter, M.Q., Chapman, M.H., Gabler, F., Brandl, M. 2015. Effect of sulfur dioxide fumigation on survival of foodborne pathogens on table grapes under standard storage temperature. Food Microbiology. 49:189-196. doi: 10.1016/j.fm.2015.02.002.
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Comparative analysis of super-shedder strains of Escherichia coli O157:H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells
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(Peer Reviewed Journal)
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Cote, R., Katani, R., Mathew, M.R., Kudva, I.T., Arthur, T.M., DebRoy, C., Mwangi, M.M., Albert, I., Garay, J.R., Li, L., Brandl, M., Carter, M.Q., Kapur, V. 2015. Comparative analysis of super-shedder strains of Escherichia coli O157:H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells. PLoS One. 10(2):e0116743. DOI: 10.1371/journal.pone.0116743.
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Characterization of foodborne Staphylococcus aureus isolates: association of toxin gene profile with genotype and food commodities in Shanghai, China
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(Peer Reviewed Journal)
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Song, M., Yalong, B., Jie, X., Carter, M.Q., Chunlei, S., Shi, X. 2014. Characterization of foodborne Staphylococcus aureus isolates: association of toxin gene profile with genotype and food commodities in Shanghai, China. International Journal of Food Microbiology. doi: 10.1016/j.ijfoodmicro.2014.11.020.
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Natural rpoS mutations contribute to the phenotypic heterogeneity of clonal populations in Escherichia coli O157:H7
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(Peer Reviewed Journal)
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Carter, M.Q., Louie, J.W., Huynh, S., Parker, C. 2014. Natural rpoS mutations contribute to the phenotypic heterogeneity of clonal populations in Escherichia coli O157:H7. Food Microbiology. 44:108-118.
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Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin
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(Peer Reviewed Journal)
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Cooper, K.K., Mandrell, R.E., Louie, J.W., Korlach, J., Clark, T.A., Parker, C., Huynh, S., Chain, P.S., Ahmed, S., Carter, M.Q. 2014. Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin. Genome Announcements. 2(3):e00482-14. DOI: 10.1128/genomeA.00482-14..
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Comparative genomic and phenotypic characterization of super-shedder Escherichia coli O157:H7
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(Abstract Only)
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Katani, R., Cote, R., Moreau, M.R., Kudva, I.T., Brandl, M., Carter, M.Q., Arthur, T.M., Debroy, C. 2014. Comparative genomic and phenotypic characterization of super-shedder Escherichia coli O157:H7 [abstract]. American Society for Microbiology. Abstract No. 59.
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Molecular insights into the unique phenotypes exhibited by super shed shiga toxin producing Escherichia coli O157
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(Abstract Only)
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Moreau, M.R., Katani, R., Cote, R., Kudva, I.T., Brandl, M., Carter, M.Q., Arthur, T.M., Debroy, C., Goodfield, L., Li, L., Kapur, V. 2014. Molecular insights into the unique phenotypes exhibited by super shed shiga toxin producing Escherichia coli O157 [abstract]. American Society for Microbiology. Abstract No. 179.
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Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7
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(Peer Reviewed Journal)
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Cooper, K.K., Mandrell, R.E., Louie, J.W., Korlach, J., Clark, T.A., Parker, C., Huynh, S., Chain, P.S., Ahmed, S., Carter, M.Q. 2014. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. Biomed Central (BMC) Genomics. doi: 10.1186/1471-2164-15-17.
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Genomic and molecular analysis of the hyperadherent phenotype of an Escherichia coli O157:H7 super shedder isolate
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Moreau, M.R., Cote, R., Katani, R., Kudva, I.T., Carter, M.Q., Brandl, M., Kapur, V. 2013. Genomic and molecular analysis of the hyperadherent phenotype of an Escherichia coli O157:H7 super shedder isolate [abstract]. In: Proceedings of Molecular Biology, Sensing and Signaling Across the Mucosa: From Homeostasis to Pathogenesis, June 4-6, 2013, University Park, Pennsylvania. p. 92.
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The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities
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(Peer Reviewed Journal)
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Lee, Y., Van Nostrand, J.D., Tu, Q., Lu, Z., Cheng, L., Yuan, T., Deng, Y., Carter, M.Q., He, Z., Wu, L., Zhou, J. 2013. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. doi: 10.1038/ismej.2013.88.
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Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm
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(Peer Reviewed Journal)
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Fagerquist, C.K., Sultan, O., Carter, M.Q. 2012. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm. Journal of American Society for Mass Spectrometry. 23(12):2102-2114.
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RcsB contributes to the distinct stress fitness between Escherichia coli O157:H7 curli variants of 1993 hamburger-associated outbreak strains
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(Peer Reviewed Journal)
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Carter, M.Q., Parker, C., Louie, J.W., Huynh, S., Fagerquist, C.K., Mandrell, R.E. 2012. RcsB contributes to the distinct stress fitness between Escherichia coli O157:H7 curli variants of 1993 hamburger-associated outbreak strains. Applied and Environmental Microbiology. doi:10.0028/AEM.02157-12.
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Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation
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(Peer Reviewed Journal)
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Carter, M.Q., Xue, K., Brandl, M., Liu, F., Wu, L., Louie, J.W., Mandrell, R.E., Zhou, J. 2012. Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation. PLoS One. 9:e44186.
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Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak
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(Peer Reviewed Journal)
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Parker, C., Kyle, J.L., Huynh, S., Carter, M.Q., Brandl, M., Mandrell, R.E. 2012. Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak. Applied and Environmental Microbiology. 78:455-463.
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Evolutionary silence of the acid chaperone protein HdeB in enterohemorrhagic Escherichia coli O157:H7
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(Peer Reviewed Journal)
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Carter, M.Q., Louie, J.W., Fagerquist, C.K., Sultan, O., Miller, W.G., Mandrell, R.E. 2012. Evolutionary silence of the acid chaperone protein HdeB in enterohemorrhagic Escherichia coli O157:H7. Applied and Environmental Microbiology. 78:1004-1014.
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Salmonella biofilm formation on Aspergillus niger involves cellulose - chitin interactions
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(Peer Reviewed Journal)
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Brandl, M., Carter, M.Q., Parker, C., Chapman, M.R., Huynh, S., Zhou, Y. 2011. Salmonella biofilm formation on Aspergillus niger involves cellulose - chitin interactions. PloS ONE 6(10):e25553.
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Curli variants of enterohemorrhagic Escherichia coli O157:H7 display distinct survival fitness
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(Peer Reviewed Journal)
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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.
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Molecular Insights into the Phenotypic Divergence in Natural Curli Variants of Escherichia coli O157:H7
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(Abstract Only)
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The Pseudomonas aeruginosa Pathogenicity Island PAPI-1 is transferred via a novel Type IV pilus
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(Peer Reviewed Journal)
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Phenotypic Divergence in Curli Variants of Enterohemorrhagic Escherichia coli O157:H7
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(Abstract Only)
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Transcriptome and phenotypic difference of Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak reveals variants in the bag
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(Abstract Only)
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