Dr. Catherine D. Carrillo

Image Catherine Carrillo
Research Scientist

Method development for food microbiology laboratories

Canadian Food Inspection Agency

Current research and/or projects

Dr. Carrillo's current research program is focused on the application of whole-genome sequencing (WGS) technologies for the detection, identification and characterization of foodborne bacterial pathogens. In the past four years, Dr. Carrillo's laboratory has sequenced several thousand bacterial genomes, and this work has led to the implementation of methods for real-time WGS of bacterial pathogens isolated in CFIA's food testing programs. Her current research interests include the development of tools for bacterial phenotype prediction based on WGS data, and the application of novel technologies (e.g. metagenomics) to improve methods for detection of bacterial pathogens in foods. Dr. Carrillo currently leads the sequencing component of the interdepartmental Genomics Research and Development Initiative project on antimicrobial resistance (GRDI-AMR).

Professional activities / interests



Education and awards

B.Sc. (Hons.) Microbiology, University of Guelph, 1994

Ph. D. Biology, University of Ottawa (2000)

Key publications

Low AJ, Koziol AG, Manninger PA, Blais BW, Carrillo CD. 2019. ConFindr: Rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data. PeerJ 7:e6995 http://doi.org/10.7717/peerj.6995

Carrillo CD, Koziol A, Vary N, Blais BW. Applications of Genomics in Regulatory Food Safety Testing in Canada. 2019. In New Insight into Salmonella, Listeria and E. coli infections (editor Maria Teresa Mascellino), ISBN 978-1-78984-721-5. IntechOpen. DOI: 10.5772/intechopen.86063

Gill A, Carrillo C, Hadley M, Kenwell R, Chui L. Bacteriological analysis of wheat flour associated with an outbreak of Shiga toxin-producing Escherichia coli O121. Food Microbiol 2019;82:474–81. doi:10.1016/j.fm.2019.03.023.

Blais BW, Tapp K, Dixon M, Carrillo CD. 2019. Genomically informed strain-specific recovery of Shiga toxin-producing Escherichia coli during foodborne illness outbreak investigations. J Food Prot;82:39–44. doi:10.4315/0362-028X.JFP-18-340.

McMahon TC, Blais BW, Wong A, Carrillo CD. 2017. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures. Frontiers in Microbiology. 8:332. doi:10.3389/fmicb.2017.00332.

Carrillo, C.D, A. G. Koziol, A. Mathews, N. Goji, D. Lambert, G. Huszczynski, M. Gauthier, K. K. Amoako, B. Blais. 2016. Comparative evaluation of genomic and laboratory approaches for determination of shiga toxin subtypes in Escherichia coli. Journal of Food Protection 79(12):2078-2085. DOI: 10.4315/0362-028X.JFP-16-228

Knowles, M., S. Stinson, D. Lambert, C. D, Carrillo, A. Koziol, M. Gauthier and B. Blais. 2016. Genomic tools for Customized Recovery and Detection of Food-Borne Shiga-Toxigenic Escherichia coli. Journal of Food Protection: 79 (12): 2066-2077. DOI: 10.4315/0362-028X.JFP-16-220.

H. Huang, B.W. Brooks, R. Lowman, C.D. Carrillo. 2015. Campylobacter species in animal, food, and environmental sources, and relevant testing programs in Canada. Canadian journal of microbiology 61 (10), 701-721

D. Lambert*, C. D. Carrillo*, A. G. Koziol, P. Manninger and B. W. Blais. 2015. GeneSippr: a rapid whole-genome approach for the identification and characterization of foodborne pathogens such as priority Shiga toxigenic Escherichia coli. PLOS One. 10 (4), e0122928.

C.D. Carrillo, D. Plante, I. Iugovaz, G. Belanger, F. Boucher, N. Poulin, Y-L. Trottier. Method-dependent variability in determination of the prevalence of Campylobacters pp. in Canadian retail poultry. 2014. Journal of Food Protection.77(10): 1682-1688. doi:10.4315/0362-028X.JFP-14-133

Sproston, EL, Carrillo, CD, J Boulter-Bitzer, J. 2014. The quantitative and qualitative recovery of Campylobacter from raw poultry using USDA and Health Canada methods. Food Microbiology 44: 258–263. DOI: 10.1016/j.fm.2014.06.003

E.N. Taboada, C.G. Clark, E.L. Sproston and C.D. Carrillo. 2013. Current methods for typing Campylobacter species. Journal of Microbiological Methods. 95:24-31. doi:10.1016/j.mimet.2013.07.007

C. D. Carrillo, P. Kruczkiewicz, S. Mutschall, A. Tudor, C. Clark, E. N. Taboada. 2012. Full genome sequence analysis of Campylobacter jejuni and C. coli to assess concordance of molecular typing methods with true strain phylogeny. Front. Cell. Inf. Microbio. 2:57. doi: 10.3389/fcimb.2012.00057

L.C. Carranza, P.A. Alvarez, A. Ghetler, I. Iugovaz, J. Sedman, C.D. Carrillo and A.A. Ismail. 2012. Evaluation of FPA-FTIR as a tool in the differentiation of Campylobacter jejuni from Campylobacter coli isolated from retail chicken samples. Journal of Food Safety. doi:10.1111/j.1745-4565.2012.00379.x

A. Aubry, G. Hussack, W. Chen, R. KuoLee, S. M. Twine, K. M. Fulton, S. Foote, C. D. Carrillo, J. Tanha and S. M. Logan. 2012. Modulation of toxin production by the flagellar regulon in Clostridium difficile. Infection and Immunity. 80(10):3521-32 doi: 10.1128/​IAI.00224-12

Medeiros, D. T., S. S. Sattar, J. M. Farber and C.D. Carrillo2008. The prevalence of Campylobacter spp. in raw and ready-to-eat foods and in a Canadian foodservice operation: results of a two-year study.  Journal of Food Protection. 71(10):2087-93.

Sampathkumar B, S. Napper, C.D. Carrillo, P. Willson, E. Taboada, J.H. Nash, A.A. Potter, L.A. Babiuk and B.J.Allan.  2006.  Transcriptional and translational expression patterns associated with immobilized growth of Campylobacter jejuni. Microbiology. Feb; 152(Pt 2):567-77.

Carrillo, C.D., E. Taboada, J. H. E. Nash, P. Lanthier, J. Kelly, P. Lau, R. Verhulp, O. Mykytczuk, J. Sy, W. A. Findlay, K. Amoako, S. Gomis, P. Willson, J. W. Austin, B. Allan and C. M. Szymanski.  2004. Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. Journal of Biological Chemistry. 279(19):20327-38.