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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » People & Locations » Michelle Carter
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

(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)

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.)
Comparative genomic and phenotypic analyses of virulence potential in Shiga toxin-producing Escherichia coli O121:H7 and O121:H10 Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Laniohan, N.S., Pham, A., Quinones, B. 2022. Comparative genomic and phenotypic analyses of virulence potential in Shiga toxin-producing Escherichia coli O121:H7 and O121:H10. Frontiers in Cellular and Infection Microbiology. 12:1043726. https://doi.org/10.3389/fcimb.2022.1043726.
Comparative genomics applied to systematically assess pathogenicity potential in Shiga toxin-producing Escherichia coli O145:H28 Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Laniohan, N.S., Lo, C., Chain, P.G. 2022. Comparative genomics applied to systematically assess pathogenicity potential in Shiga toxin-producing Escherichia coli O145:H28. Microorganisms. 10(5). Article 866. https://doi.org/10.3390/microorganisms10050866.
Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: transcriptomic data Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Hu, B., Chain, P.S. 2021. Epigenetic regulation of gene expression in Shiga toxin-producing Escherichia coli: transcriptomic data. Data in Brief. 36:107065. https://doi.org/10.1016/j.dib.2021.107065.
Genomic insights into divergent evolution of virulence and fitness traits in Shiga toxin-producing Escherichia coli O121 - (Abstract Only)
DNA Adenine Methylase, not the Pstl restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Pham, A., Huynh, S., Parker, C., Miller, A., He, X., Hu, B., Chain, P. 2020. DNA Adenine Methylase, not the Pstl restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food Microbiology. 96. Article 103722. https://doi.org/10.1016/j.fm.2020.103722.
Differential induction of Shiga toxin in environmental Escherichia coli O145:H28 strains carrying the same genotype as the outbreak strains Reprint Icon - (Peer Reviewed Journal)
Carter, M.Q., Pham, A.C., Du, W.N., He, X. 2020. Differential induction of Shiga toxin in environmental Escherichia coli O145:H28 strains carrying the same genotype as the outbreak strains. International Journal of Food Microbiology. 339. Article 109029. https://doi.org/10.1016/j.ijfoodmicro.2020.109029.
Genomic insight into natural inactivation of Shiga toxin 2 production in an environmental Escherichia coli strain producing Shiga toxin 1 Reprint Icon - (Peer Reviewed Journal)
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.
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.
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 Reprint Icon - (Peer Reviewed Journal)
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.
Top-down proteomic identification of Shiga toxin 1 and 2 from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry Reprint Icon - (Peer Reviewed Journal)
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.
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.
Typing/subtyping Shiga toxin from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis - (Proceedings)
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).
Enhanced formation of shiga toxin-producing Escherichia coli persister variants in environments relevant to leafy greens production Reprint Icon - (Peer Reviewed Journal)
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.
Curli fimbriae confer shiga toxin-producing Escherichia coli a competitive trait in mixed biofilms Reprint Icon - (Peer Reviewed Journal)
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.
Typing/subtyping Shiga toxin from pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry and top-down proteomic analysis - (Abstract Only)
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.
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.
imGLAD: accurate detection and quantification of target organisms in metagenomes Reprint Icon - (Peer Reviewed Journal)
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.
Complete genome sequences of two atypical enteropathogenic Escherichia coli O145 environmental strains Reprint Icon - (Peer Reviewed Journal)
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.
Complete genome sequence of a natural Escherichia coli O145:H11 isolate that belongs to Phylo-group A Reprint Icon - (Peer Reviewed Journal)
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.
Survival of foodborne pathogens on commercially packed table grapes under simulated refrigerated transit conditions Reprint Icon - (Peer Reviewed Journal)
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.
Conditional function of autoaggregative protein cah and common cah mutations in Shiga toxin-producing Escherichia coli Reprint Icon - (Peer Reviewed Journal)
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.
Complete Genome Sequence of a Shiga toxin-producing Enterobacter cloacae Clinical Isolate Reprint Icon - (Peer Reviewed Journal)
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.
Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa - (Peer Reviewed Journal)
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.
Decoding the ecological function of accessory genome - (Review Article)
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.
Curli temper adherence of Escherichia coli O157:H7 to squamous epithelial cells from the bovine recto-anal junction in a strain-dependent manner - (Peer Reviewed Journal)
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.
Curli fimbriae are conditionally required in Escherichia coli O157:H7 for initial attachment and biofilm formation - (Peer Reviewed Journal)
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.
The polymorphic aggregative phenotype of Shiga toxin-producing Escherichia coli O111 depends on rpoS and curli - (Peer Reviewed Journal)
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.
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.
Curli modulates adherence of Escherichia coli O157 to bovine recto-anal junction squamous epithelial cells - (Abstract Only)
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.
Comparative genomic analysis and adherence characteristics of supershedder strains of Escherichia coli O157:H7 - (Abstract Only)
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.
Effect of sulfur dioxide fumigation on survival of foodborne pathogens on table grapes under standard storage temperature - (Peer Reviewed Journal)
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.
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 - (Peer Reviewed Journal)
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.
Characterization of foodborne Staphylococcus aureus isolates: association of toxin gene profile with genotype and food commodities in Shanghai, China - (Peer Reviewed Journal)
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.
Natural rpoS mutations contribute to the phenotypic heterogeneity of clonal populations in Escherichia coli O157:H7 - (Peer Reviewed Journal)
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.
Complete genome sequences of two Escherichia coli O145:H28 outbreak strains of food origin - (Peer Reviewed Journal)
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..
Comparative genomic and phenotypic characterization of super-shedder Escherichia coli O157:H7 - (Abstract Only)
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.
Molecular insights into the unique phenotypes exhibited by super shed shiga toxin producing Escherichia coli O157 - (Abstract Only)
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.
Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7 - (Peer Reviewed Journal)
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.
Genomic and molecular analysis of the hyperadherent phenotype of an Escherichia coli O157:H7 super shedder isolate - (Abstract Only)
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.
The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities - (Peer Reviewed Journal)
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.
Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm - (Peer Reviewed Journal)
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.
RcsB contributes to the distinct stress fitness between Escherichia coli O157:H7 curli variants of 1993 hamburger-associated outbreak strains - (Peer Reviewed Journal)
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.
Functional metagenomics of Escherichia coli O157:H7 interactions with spinach indigenous microorganisms during biofilm formation - (Peer Reviewed Journal)
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.
Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak - (Peer Reviewed Journal)
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.
Evolutionary silence of the acid chaperone protein HdeB in enterohemorrhagic Escherichia coli O157:H7 - (Peer Reviewed Journal)
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.
Salmonella biofilm formation on Aspergillus niger involves cellulose - chitin interactions - (Peer Reviewed Journal)
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.
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.
Molecular Insights into the Phenotypic Divergence in Natural Curli Variants of Escherichia coli O157:H7 - (Abstract Only)
The Pseudomonas aeruginosa Pathogenicity Island PAPI-1 is transferred via a novel Type IV pilus - (Peer Reviewed Journal)
Phenotypic Divergence in Curli Variants of Enterohemorrhagic Escherichia coli O157:H7 - (Abstract Only)
Transcriptome and phenotypic difference of Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak reveals variants in the bag - (Abstract Only)