Table 1.
Vibrio cholerae and other Vibrio spp. isolates analysed in this study.
Table 2.
Primers used in this study.
Figure 1.
Phylogenetic relationships of Vibrio cholerae isolates based on neighbour-joining tree. ST is indicated in bracket after strain name for V. cholerae.
Non-O1/non-O139 V. cholerae strains from clinical sources are marked with a dot. Vibrio vulnificus strain CMCP6 was used as an outgroup. Bootstrap values, if greater than 50%, are presented at nodes of the neighbour joining trees.
Figure 2.
Neighbour-net network of Vibrio cholerae isolates analysed in this study.
Four subpopulations (I to IV) as determined by STRUCTURE analysis are indicated with curly brackets. Isolates associated with 6th, pre-7th and 7th pandemics are indicated with an arrow.
Table 3.
Estimates of mutation (θ) and recombination (ρ) rates.
Figure 3.
STRUCTURE analysis of Vibrio cholerae isolates including genome strains.
The four subpopulations are colour-coded with red, green, blue and yellow for subpopulation I, II, III and IV respectively. Each isolate has been allocated to a subpopulation. Isolates were identified by strain name with ST in brackets on the left. Mosaic colours for an isolate indicate mixed population origin from respective populations of matching colour. Y-axis represents percentage of population assignment. Non-O1/non-O139 V. cholerae strains from clinical sources are marked with a dot.
Figure 4.
Relationships of M1086 and pandemic related strains based on minimum spanning tree (MST).
MST was constructed using allelic difference of 26 housekeeping (hk) genes which are either resulted from recombination (r) or mutation (m). Events were marked on the branches with gene symbol (r or m) or for multiple genes as number of hk genes affected. M1086 and V52 were analysed in this study. See Salim et al. [43] for details of others. Changes of Vibrio pathogenicity island (VPI) and cholera toxin (CTX) are also indicated. Sequence data were M1086 from this study, V52 from Chun et al. [62] and others from Salim et al. [43]. Strain names, year of isolation and place of isolation were shown except for the pandemic strains and Australian and US Gulf toxigenic isolates.