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Volume 28, Number 7—July 2022
Research

One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016

Amrita BharatComments to Author , 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)

Main Article

Figure 3

Phylogenetic dendrogram of extended-spectrum β-lactamase‒producing Salmonella enterica serovars Infantis from Canada and the United States. Isolates from the United States are from Tate et al. (26). 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 was Salmonella Infantis strain 15-SA01028 (GenBank accession no. CP026660.1). The tree is based on a core genome that represents 97% of the reference genome. Numbers along branches indicate branch support values. Salmonella Infantis containing extended-spectrum β-lactamases were isolated from human sources in Canada (dark orange), human sources from the United States (light orange), a cat from Canada (dark green), poultry or dairy at slaughter from the United States (light green) or retail meat from the United States. Isolate N17-03255 from a cat contained SHV-2, isolate 15-8465 from a human contained CTX-M-3, and all other isolates contained CTX-M-65. The dataset comprises 491 SNVs, and SH-like branch support values are displayed.

Figure 3. Phylogenetic dendrogram of extended-spectrum β-lactamase‒producing Salmonella enterica serovars Infantis from Canada and the United States. Isolates from the United States are from Tate et al. (26). 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 was Salmonella Infantis strain 15-SA01028 (GenBank accession no. CP026660.1). The tree is based on a core genome that represents 97% of the reference genome. Numbers along branches indicate branch support values. Salmonella Infantis containing extended-spectrum β-lactamases were isolated from human sources in Canada (dark orange), human sources from the United States (light orange), a cat from Canada (dark green), poultry or dairy at slaughter from the United States (light green) or retail meat from the United States. Isolate N17-03255 from a cat contained SHV-2, isolate 15-8465 from a human contained CTX-M-3, and all other isolates contained CTX-M-65. The dataset comprises 491 SNVs, and SH-like branch support values are displayed.

Main Article

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