Dr. Catherine D. Carrillo

Image Catherine Carrillo
Research Scientist

Method development for food microbiology laboratories

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 to improve methods for detection of bacterial pathogens in foods. Dr. Carrillo currently co-leads the interdepartmental Genomics Research and Development Initiative project on antimicrobial resistance (GRDI-AMR2).

Professional activities / interests



Education and awards

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

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

Key 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.

Research facility

960 Carling Road
Ottawa, ON K1A0Z2


Carleton University