Fig 1.
Geographic and temporal origin of the 242 V. cholerae collected in Canada.
a. Collection year of V. cholerae isolates according to serogroup. Four NOVC isolates did not have a collection year recorded. b. V. cholerae isolates were received by provincial laboratories and sent to the NML in Winnipeg, Manitoba for characterization and whole genome sequencing. The diameter of each circle scales with the number of isolates to have been collected from the indicated province. Geographic data were unavailable for nine isolates. The bar graphs (a) and pie charts (b) are colored by the original source of isolation. It should be noted that the peak in NOVC isolates in 2018 are a result of the small outbreak on Vancouver Island, British Columbia which required increased environmental sampling to trace the outbreak source. Map was created using Tableau Public 2021.4 [37] using base map and data from OpenStreetMap and OpenStreetMap Foundation..
Table 1.
Clustering thresholds of V. cholerae based on cgMLST alleles.
Fig 2.
In silico cgSNP tree of Canadian V. cholerae isolates with virulence gene profiles a. Maximum likelihood tree showing phylogenetic relationships between 242 clinical and environmental isolates with lineage, region within Canada, isolation source, collection year, serogroup, and b. Heatmap showing the presence (colored in box) and absence (white box) of virulence and secretion system encoding genes, Vibrio pathogenicity islands, and Vibrio seventh pandemic islands.
Tip labels describing isolation origin, source, year and serogroup were colored purple to represent isolates of clinical samples, green to represent environmental samples and black if sample type was not known. Aside from the reference (V. cholerae O1 strain N16961; Bangladesh), all samples were isolated in Canada. Tip labels were left blank when data was not provided. Scale bar denotes the number of mutations per variable site. An interactive version of this figure is available on Microreact (https://microreact.org/project/nGCx8mpZEkvX2jZW2QriJj-fig-2).
Fig 3.
Proportion of virulence genes detected among clinical and environmental NOVC in Canada.
a. NOVC by host information. b. NOVC by detailed host information. (*) represents genes with statistically significant differences p < 0.05 between groups. One NOVC isolate did not have a recorded origin.
Fig 4.
Maximum likelihood tree of 242 Canadian V. cholerae isolates based on non-recombined cgSNPs.
a. Tree nodes and colors represent lineages. The absence of a node means the isolate was not assigned to a lineage. b. The ring represents the five major clades as determined by FastBaps. An interactive phylogenetic tree is available on Microreact (https://microreact.org/project/nGCx8mpZEkvX2jZW2QriJj-fig-2).
Fig 5.
Neighbour-joining phylogenetic tree of 223 global V. cholerae isolates.
The tree was reconstructed using the cgMLST scheme established by Liang and others [48] and plotted using Phylocanvas [121] in Vibriowatch. a. Inner ring represents clustering by sequence type based on the 7-gene MLST scheme by Octavia and colleagues [55], whereas the outer ring represents clustering based on the sublineage threshold (i.e., 133 allelic difference) designated by Liang and colleagues [48]. Tree nodes are colored by the host in which the isolate originated (green = environmental, purple = clinical). All groups inside the 7th pandemic lineage have been collapsed and are shown in the popup box (b). b Outbreak clusters (≤ 40 allelic differences) and geographical origin of V. cholerae serogroup O1 collected in Canada. Tree nodes are colored by outbreak clusters. An interactive version of this figure is available on Microreact (https://microreact.org/project/cLqNBRRphmNt1aoBeh9jmJ-fig-5)..
Fig 6.
Predicted antimicrobial resistance among V. cholerae isolated in Canada.
a. NOVC by host information. b. NOVC by detailed host information. Scale bar represents proportion of resistance present (1) or absent (0) among antibiotic classes based on resistance gene presence or absence; TMP, trimethoprim; nitrofurans (FZD, furazolidone; NIT, nitrofurantoin); TET, tetracycline; MEM, meropenem; RIF, rifampicin; AZM, azithromycin; sulfonamides (SMZ, sulfamethoxazole; SFS, sulfisoxazole); CHL, chloramphenicol; STR, streptomycin; CIP, ciprofloxacin; NAL, nalidixic acid; beta-lactams (FEP, cefepime; CRO, ceftriaxone; CEF, broad spectrum cephalosporins; CAR, carbapenems; AMP, ampicillin; CAZ, ceftazidime). One NOVC isolate did not have a recorded origin.