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

Abstract

Extended-spectrum β-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012-2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were bla_SHV-2 and bla_CTX-M-1 IncI1 plasmids_, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-bla_SHV-2 plasmid differed by only 1-7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying bla_CTX-M-65, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.

Keywords: Canada; ESBL; One Health; Salmonella enterica; antimicrobial resistance; bacteria; extended-spectrum β-lactamases; food animals; food safety; food-borne infections; genomic analysis; pets; retail meats; zoonoses.

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.

Figure 2

Phylogenetic dendrogram of extended-spectrum β-lactamase‒producing Salmonella enterica serovars Typhimurium and 4,5,12,i:-, 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 Typhimurium strain LT2 (GenBank accession no. NC_003197.2). The tree is based on a core genome that represents 96% of the reference genome. Numbers along branches indicate branch support values. Sample N17-03254 was a clinical isolate from a sick pig (green), and all other samples were from human sources (orange, n = 14). Extended-spectrum β-lactamase genes are indicated to the right of the 3 largest clusters. The dataset comprises 1,599 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.

Figure 4

Alignment of Salmonella bla_SHV-2 plasmids from human and animals/meat sources, Canada. Closed plasmids were produced by hybrid assembly of short and long read sequencing by using Unicycler (https://bio.tools/unicycler). Plasmids were aligned by using the pangenome feature of the GView server (https://server.gview.ca). Animals/meat sample identifications start with the letter N, and human sample identifications start with a 2-digit number. Plasmids were classified as Type A, B, or C based on their resistance gene profiles and overall similarity. All plasmids belong to the IncI1 incompatibility group.

Figure 5

Alignment of Salmonella bla_CTX-M plasmids from human and animals/meat sources, Canada. Alignments of bla_CTX-M-1 IncI1 (A), bla_CTX-M-1 IncN (B), and bla_CTX-M-55 IncN (C) plasmids are shown. Plasmids were aligned by using the BLAST feature of the GView server (https://server.gview.ca) and representative closed plasmids (bottom-most plasmid in each alignment) from this study. Animals/meat sample identifications start with the letter N, and human sample identifications start with a 2-digit number.