Photo of Catherine  Carrillo

Catherine Carrillo

Adjunct Research Professor

Degrees:B.Sc. (University of Guelph), Ph.D. (University of Ottawa)
Phone:(343) 998-5128 
Office:Canadian Food Inspection Agency
960 Carling Avenue, Building #22
Ottawa, Ontario, Canada
K1A 0C6

Current Research:

Catherine Carrillo has been employed as a Research Scientist at the Canadian Food Inspection Agency (CFIA) since 2013. Her research program is focused on supporting food microbiology inspection programs at the CFIA. Her current interests include the application of whole-genome sequencing (WGS) technologies for the detection, identification and characterization of foodborne bacterial pathogens. Recent improvements in next-generation sequencing technologies have led to rapid advances in the field of food microbiology, wherein pathogenic bacteria (e.g. Listeria monocytogenes, Salmonella enterica, Verotoxigenic Escherichia coli (VTEC)) can be characterized based on their genetic profile rather than on traditional approaches relying on phenotypic properties. Sequence data derived from foodborne pathogens can be used to determine if strains are related (e.g. to a cluster of illnesses, persistent contamination), or to infer strain phenotypes (e.g. virulence, antimicrobial resistance, serotype) based on identification of genetic markers. Development of tools and processes for making optimal use of this information has led to the implementation of a “real-time” diagnostic sequencing program at the CFIA.  She is also interested in the application of genomic information to the development of improved approaches for recovering pathogens from foods.

Graduate Supervision: if you are interested in working with Dr. Carrillo, research project options for graduate students that are available are as follows. Please send her an email:

Project 1:

Purpose: To evaluate the impacts from exposure to antibiotic and heavy metal residues in the environment on the development of microbiota, resistome and immune system using a mouse model (PhD preferred but, could be an M.Sc. project).

Project 2:

Purpose: To evaluate the influence of prion protein gene polymorphisms on ante-mortem detection of chronic wasting disease in deer (M. Sc.)

Selected Publications:

McMahon T, Bin Kingombe C, Mathews A, Seyer K, Wong A, Blais BW, Carrillo CD.  2022. Microbial antagonism in food-enrichment culture: Inhibition of Shiga toxin-producing E. coli (STEC) and Shigella species. Frontiers in Microbiology; 13: 88004. DOI:10.3389/fmicb.2022.880043

Gill A, Dussault F, McMahon T, Petronella N, Wang X, Cebelinski E, Scheutz F, Weedmark K, Blais BW, Carrillo CD. 2022. Characterisation of atypical Shiga toxin gene sequences and description of Stx2j, a new subtype. Journal of Clinical Microbiology; DOI:10.1128/jcm.02229-21

Carrillo CD, Blais BW. 2021. Whole-genome sequence datasets: A powerful resource for the food microbiology laboratory toolbox. Frontiers in Sustainable Food Systems; 5: 754988. DOI:10.3389/fsufs.2021.754988

Hodges LM, Taboada EN, Koziol A, Mutschall S, Blais BW, Inglis GD, Leclair D, Carrillo CD. 2021. Systematic evaluation of whole-genome sequencing based prediction of antimicrobial resistance in Campylobacter jejuni and C. coli. Frontiers in Microbiology; 12: 776967. DOI:10.3389/fmicb.2021.776967

Cooper AL, Low AJ, Koziol AG, Thomas MC, Leclair D, Tamber S, Wong A, Blais BW and Carrillo CD. 2020. Whole genome sequence-based predictions of serotype and antimicrobial resistance for Salmonella isolates from Canadian poultry. Frontiers in Microbiology; 11: 549. DOI:10.3389/fmicb.2020.00549

Cooper AL, Carrillo CD, Deschênes, M and Blais BW. 2020. Genomic markers for quaternary ammonium compound resistance as a persistence indicator for Listeria monocytogenes contamination in food manufacturing environments. Journal of Food Protection; 84:389-398. DOI:10.4315/jfp-20-328

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. DOI:10.7717/peerj.6995

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.

Full list available at: