Fig 1.
Phylogenetic tree of V. cholerae strains.
Maximum-likelihood (ML) tree was constructed using RAxML-NG v. 1.1 with GTR+G model, using 1,892 core genes. The viuB genotype of each strain is indicated on the right side of the tree. Each strain is color-coded by sample source, with clinical strains in red and environmental strains in blue. Strains from this study are highlighted in bold. The tree is rooted with V. paracholerae strain Cam10 as an outgroup. Bootstrap values from 1,000 replicates are shown at the nodes, with only values greater than 70 indicated. The scale bar represents nucleotide substitutions per site. Subtrees for Clade1 (viuB-25) and Clade2 (viuB-33) were constructed with 3,260 and 3,253 core genes, respectively, with single nucleotide polymorphisms (SNPs) counts noted beside the tree leaf. ST: sequence type using seven housekeeping genes; PG clade: Pandemic-generating clade.
Fig 2.
Heatmap of the virulence gene profile of V. cholerae and V. paracholerae strains isolated from Cameroon waters.
For each gene, presence and similarity are indicated by a color gradient from white (absent) to dark red (identical), according to blast score ratio (BSR). Each row represents a different strain, with V. cholerae El Tor strain N16961 at the top as a reference.
Fig 3.
Network analysis of 260 V. cholerae strains based on core genome MLST (cgMLST) profiles.
Nodes represent individual strains, color-coded based on their country of origin. Strains from the same sublineage (allelic difference equal to or less than 133) are linked together. Strains from Clade1 and Clade2, and strains from different countries that cluster together are labeled.
Fig. 4.
Phylogeny of tcpA (toxin-coregulated pilus subunit A) gene in V. cholerae.
Maximum-likelihood (ML) tree was generated by RAxML-NG v. 1.1 based on the multiple sequence alignment of tcpA genes. Clinical and environmental strains are labeled in red and blue, respectively. Strains from this study are highlighted in bold. The tree is rooted with strains distant from the pandemic clade. Nodes are labeled with bootstrap support from 1,000 replicates. The scale bar represents nucleotide substitutions per site, and the SNP differences between the lineages are indicated beside the tree.