One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016
, Laura Mataseje, E. Jane Parmley, Brent P. Avery, Graham Cox, Carolee A. Carson, Rebecca J. Irwin, Anne E. Deckert, Danielle Daignault, David C. Alexander, Vanessa Allen, Sameh El Bailey, Sadjia Bekal, Greg J. German, David Haldane, Linda Hoang, Linda Chui, Jessica Minion, George Zahariadis, Richard J. Reid-Smith, and Michael R. Mulvey
Author affiliations: Public Health Agency of Canada, Winnipeg, Manitoba, Canada (A. Bharat, L. Mataseje, G. Cox, M.R. Mulvey); University of Manitoba, Winnipeg (A. Bharat, G. Cox, M.R. Mulvey); Public Health Agency of Canada, Guelph, Ontario, Canada (E.J. Parmley, B.P. Avery, C.A. Carson, R.J. Irwin, A.E. Deckert, R.J. Reid-Smith); University of Guelph, Guelph (E.J. Parmley); Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada (D. Daignault); Cadham Provincial Laboratory, Winnipeg (D.C. Alexander); Public Health Ontario Laboratories, Toronto, Ontario, Canada (V. Allen); Horizon Health Network, Saint John, New Brunswick, Canada (S. El Bailey); Laboratoire de Santé Publique du Quebec, Sainte-Anne-de-Bellevue, Quebec, Canada (S. Bekal); Queen Elizabeth Hospital, Charlottetown, Prince Edward Island, Canada (G.J. German); Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia, Canada (D. Haldane); British Columbia Center for Disease Control, Vancouver, British Columbia, Canada (L. Hoang); Public Health Laboratory, Edmonton, Alberta, Canada (L. Chiu); University of Alberta, Edmonton (L. Chui); Roy Romanow Provincial Laboratory, Regina, Saskatchewan, Canada (J. Minion); Newfoundland and Labrador Public Health and Microbiology Laboratory, St. John’s, Newfoundland, Canada (G. Zahariadis)
Figure 1. Phylogenetic dendrogram of Salmonella enterica serovar Heidelberg containing extended-spectrum β-lactamase genes, Canada. The maximum-likelihood dendrogram was created by using the single-nucleotide variant (SNV) phylogenomics (SNVPhyl) pipeline (https://snvphyl.readthedocs.io/en/latest) based on SNVs in the core genome. The reference genome is Salmonella Heidelberg strain 12-4374 (GenBank accession no. CP012924.1). The tree is based on a core genome that represents 94% of the reference genome. Numbers along branches indicate branch support values. Salmonella Heidelberg containing extended-spectrum β-lactamases were from animals (green, n = 5), food (blue, n = 1), and humans (orange, n = 16). Extended-spectrum β-lactamase genes are indicated to the right of the 3 largest clusters. The dataset comprises 394 SNVs, and SH-like branch support values are displayed.
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