This week we say farewell to Dr. Sheridan Baker, who joined us in early 2021 as lead molecular biologist for our Ontario Genomics Coalition (ONCoV) and Canadian COVID-19 Genomics Network (CanCOGeN) sequencing and molecular epidemiology of SARS-CoV-2 variants for the Province of Ontario and Government of Canada. Sheridan was essential in tracking COVID-19 variants in our community by sequencing thousands of isolates from across Ontario. Most notably, in the last few years he was worked very closely with Hamilton Health Sciences to ensure timely reporting of variants in our local community.

Since January 2023, Sheridan has been a Mitacs Elevate Postdoctoral Fellow, translating the research of the McArthur Lab to the clinic setting of St. Joseph’s Healthcare Hamilton towards diagnostics and outbreak tracing for the gut pathogen C. difficile.

We wish you much success, Sheridan!

Publications

  • Baker et al. Investigating in-hospital transmission of Clostridioides difficile from asymptomatic patients. Antimicrobial Stewardship & Healthcare Epidemiology, in revision.
  • Baker et al. Whole-genome sequencing confirms Shigella flexneri infection in a child with shock and suspected Multisystem Inflammatory Syndrome in Children. Pediatric Infectious Disease Journal, in revision.
  • Baker et al. 2024. Chronic COVID-19 infection in an immunosuppressed patient shows changes in lineage over time. Virology Journal, 21, 8.
  • Nasir et al. 2024. SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemake workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes. NAR Genomics and Bioinformatics, 6, lqae176.
  • Alcock et al. 2023. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51, D690-D699.
  • Jacob et al. 2023. SARS-CoV-2 R.1 lineage variants are sensitive to neutralizing antibodies but resistant to type I interferons. Cell Host and Microbe, 29, 1386-1396.
  • Tsang et al. 2023. SARS-CoV-2 outbreak investigation using contact tracing and whole genome sequencing in an Ontario Tertiary Care hospital. Microbiology Spectrum, 11, e0190022.

Presentations

  • Baker, S.J.C. et al. 2024. Designing a multiplex typing PCR assay for assessing in-hospital outbreaks of Clostridioides difficile. Presentation at the AMMI Canada – CACMID Annual Conference, Vancouver, Canada.
  • Baker, S.J.C. et al. 2024. Designing a multiplex PCR assay for typing of C. difficile. Presentation at the Canadian Society of Microbiologists, London, Canada.
  • McCarthy, M.C. et al. 2024. Targeted capture and sequencing of Clostridioides (clostridium) difficile genomic DNA for high resolution, culture-free outbreak detection. Presentation at the Canadian Society of Microbiologists, London, Canada.
  • Baker, S.J.C. et al. 2023. Investigating the transmission of Clostridioides difficile from asymptomatic patients. Oral presentation at the 33rd European Congress of Clinical Microbiology & Infectious Diseases, Copenhagen, Denmark.
  • Baker, S.J.C. et al. 2023. Investigating the transmission patterns of Clostridioides difficile in Hamilton-area hospitals. Poster presentation at the AMMI Canada – CACMID Annual Conference, Toronto, Canada.
  • Baker, S.J.C. et al. 2023. Investigating the transmission of Clostridioides difficile from asymptomatic patients. Oral presentation at the Annual Meeting of the Canadian Society of Microbiologists, Halifax, Nova Scotia.
  • Nasir et al. 2023. Designing viral bait capture platforms for pulmonary infections based on symptomology. Poster presentation at the Annual Meeting of the Canadian Society of Microbiologists, Halifax, Nova Scotia.
  • Nirmalarajah et al. 2023. Temporal dynamics, genomics, and clinical characteristics of SARS-CoV-2 in COVID-19 patients from Toronto, Canada. Presentation at the 33rd European Congress of Clinical Microbiology & Infectious Diseases, Copenhagen, Denmark.
  • Nirmalarajah et al. 2023. Temporal dynamics, genomics, and clinical characteristics of SARS-CoV-2 in COVID-19 patients from Toronto, Canada. Presentation at the AMMI Canada – CACMID Annual Conference, Toronto, Canada.
  • Nirmalarajah et al. 2023. SARS-CoV-2 temporal dynamics, genomic surveillance, and disease severity of COVID-19 patients from Toronto, Canada. Poster presentation at the International Nidovirus Symposium, Montreux, Switzerland.
  • Baker et al. 2022. Investigating the transmission patterns of Clostridioides difficile in Hamilton-area hospitals. Poster presentation at the Canadian Society of Microbiologists Annual Meeting, Guelph, Ontario.
  • Kotwa et al. 2022. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients with Delta variant infection in Toronto, Ontario, Canada. Poster presentation at the AMMI Canada – CACMID Annual Conference [online].
  • Nasir et al. 2022. Fishing for a diagnosis: design and application of respiratory virus baits. Virtual poster presentation at the Viral Genomics and Evolution Conference. [online]
  • Nirmalarajah et al. 2022. Associations of SARS-CoV-2 variants, clinical characteristics, and hospitalization in COVID-19 patients from Toronto Canada, 2020- 2021. Presentation at the AMMI Canada – CACMID Annual Conference [online].
  • Nirmalarajah et al. 2022. SARS-CoV-2 variants and clinical characteristics associated with hospitalization in COVID-19 patients from Toronto, Canada, 2020-2021. Presentation at the LMP Research Conference and Product Show, Toronto, Ontario, Canada.
  • Tsang et al. 2022. SARS-CoV-2 outbreak investigation using contact tracing and whole genome sequencing in a Canadian hospital. Poster presentation at the Annual Canadian Society for Virology conference, Edmonton, Alberta, Canada.

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