Biography
Our laboratory’s research is focussed on two major foodborne bacterial pathogens, Listeria and Cronobacter. The laboratory has research projects that aim to address the phenomena of how foodborne pathogens can enter the farm-2-fork continuum and cause human illness. Our laboratory is interested in the actual mechanism(s) for understanding and tracking foodborne pathogens in the food chain continuum. We do this by developing projects that address questions such as how a pathogen can grow, adapt, and survive in certain foods. A member of the steering committee for PulseNet Canada, I am also a co-director of the Listeriosis Reference Centre for Canada. The LRS participates in PulseNet Canada for real-time molecular surveillance for listeriosis and utilizes whole genomes sequencing for outbreak investigations.
Our research program in the Listeria area focuses on three major areas that include and combine current and novel methodologies, molecular typing and ready-to-eat food safety. All these areas are done in support of our policy, risk assessment and standard setting activities and it is being done in support of a Government of Canada policy on management of potential risks from emerging pathogens.
By the 1980s, Enterobacter sakazakii and was found to severely affect infants and neonates by causing sepsis, necrotic enterocolitis, and meningitis. This organism was reclassified into the new genus Cronobacter, with the type species Cronobacter sakazakii. Other species within this genus now include C. malonaticus, C. turicensis, C. muytjensii, C. dublinensis, C. condiment, and C. universalis. While the natural reservoir for Cronobacter spp. remains unknown, it has been isolated from a variety of foods as well as different environment (hospitals, processing plants, homes, dust, vacuum cleaners, even in the intestines of stable flies). The vast majority of Cronobacter spp. infections happen in hospital neonatal intensive care units. Improper preparation, handling and storage of infant formula are considered the most likely causes of contamination. Cronobacter spp. are also considered emerging pathogens for stroke patients who suffer from dysphagia and aspiration pneumonia.
Selected Publications
Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach. Rumore J, Walker M, Pagotto F, Forbes JD, Peterson CL, Tyler AD, Graham M, Van Domselaar G, Nadon C, Reimer A, Knox N.
BMC Genomics. 2023 Jun 27;24(1):361. doi: 10.1186/s12864-023-09338-w.
Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes. Gopinath GR, Jang H, Beaubrun JJ, Gangiredla J, Mammel MK, Müller A, Tamber S, Patel IR, Ewing L, Weinstein LM, Wang CZ, Finkelstein S, Negrete F, Muruvanda T, Allard M, Sockett DC, Pagotto F, Tall BD, Stephan R. Microorganisms. 2022 Jun 11;10(6):1199. doi: 10.3390/microorganisms10061199.
Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses. Jang H, Chase HR, Gangiredla J, Grim CJ, Patel IR, Kothary MH, Jackson SA, Mammel MK, Carter L, Negrete F, Finkelstein S, Weinstein L, Yan Q, Iversen C, Pagotto F, Stephan R, Lehner A, Eshwar AK, Fanning S, Farber J, Gopinath GR, Tall BD, Pava-Ripoll M. Front Microbiol. 2020 Sep 25;11:561204. doi: 10.3389/fmicb.2020.561204. eCollection 2020.
Distribution, diversity and persistence of Listeria monocytogenes in swine slaughterhouses and their association with food and human listeriosis strains. Cherifi T, Arsenault J, Pagotto F, Quessy S, Côté JC, Neira K, Fournaise S, Bekal S, Fravalo P. PLoS One. 2020 Aug 6;15(8):e0236807. doi: 10.1371/journal.pone.0236807. eCollection 2020.
Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria. Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M. Microb Genom. 2019 Jan;5(1):e000237. doi: 10.1099/mgen.0.000237. Epub 2019 Jan 16.
Occurrence, characterization, and potential predictors of verotoxigenic Escherichia coli, Listeria monocytogenes, and Salmonella in surface water used for produce irrigation in the Lower Mainland of British Columbia, Canada. Falardeau J, Johnson RP, Pagotto F, Wang S. PLoS One. 2017 Sep 27;12(9):e0185437. doi: 10.1371/journal.pone.0185437. eCollection 2017.
Use of a Pan-Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology. Tall BD, Gangiredla J, Grim CJ, Patel IR, Jackson SA, Mammel MK, Kothary MH, Sathyamoorthy V, Carter L, Fanning S, Iversen C, Pagotto F, Stephan R, Lehner A, Farber J, Yan QQ, Gopinath GR. Microarrays (Basel). 2017 Mar 4;6(1):6. doi: 10.3390/microarrays6010006.
Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Ronholm J, Nasheri N, Petronella N, Pagotto F. Clin Microbiol Rev. 2016 Oct;29(4):837-57. doi: 10.1128/CMR.00056-16.