Fig. 3: Maximum-likelihood phylogeny of 1471 seventh pandemic Vibrio cholerae O1 El Tor isolates, including 34 collected in Lebanon in 2022.

A6 was used as the outgroup. Blue arrows represent the three genomic waves and the black arrow indicates the acquisition of the ctxB7 allele. The colour coding in the first column shows the geographic origins of the isolates, and African sublineages (AFR1, AFR3–AFR15) are shown on the left. The red colour in the second column indicates the Lebanese origin of the isolates. A magnification of the clades containing the two strains from Lebanon (red square corresponding to the predominant strain and blue square corresponding to the multidrug-resistant minor strain) is shown on the left with red text indicating the Lebanese isolates. For each genome, its name (or accession number), the country in which contamination occurred and the year of sample collection are indicated at the tip of the branch. Scale bars indicate the number of nucleotide substitutions per variable site. Blue dots correspond to bootstrap values ≥ 90%.