Figure 2. Maximum-likelihood phylogeny of 208 Salmonella enterica serovar Typhi isolates in study of emergence of genotype 2.3.1 MDR Salmonella Typhi strain, West Africa, 2021–2025. Included are 207 genotype 2.3.1 isolates (167 from France’s National Reference Center for Escherichia coli, Shigella, and Salmonella and 40 published genomes) and the reference genome CT18. CT18 (genotype 3.2.1) was used as the outgroup of the tree (its associated characteristics in terms of geographic origin, antimicrobial-resistance genes, and plasmid types are not indicated). Red color on dendrogram indicates nodes with bootstrap support >98%. Light orange rectangle indicates emerging MDR strain. Year of isolation is indicated, together with the travel information (when available) for the isolate, to the right of the tree, because those parameters serve as a proxy for the probable origin of the isolates. Resistance to certain antimicrobial drugs and the presence (black) or absence (white) of antimicrobial-resistance genes (names given along bottom of tree) also are indicated to the right of the tree. The MDR profiles are indicated in red (for profile A; bla_TEM-1, strA, strB, aadA1, sul1, sul2, dfrA1, and tet(B)) or blue (for profile B; bla_TEM-1–like, strA, strB, sul2, dfrA14, and tet(A)). The presence of plasmid markers is indicated in blue (for IncN) or red (for IncHI1). Scale bar indicates number of nucleotide substitutions per variable site. Information displayed in this figure can be found for each individual strain in Appendix 2 (https://wwwnc.cdc.gov/EID/article/32/10/26-0813-App2.xlsx). AG, aminoglycosides; MDR, multidrug-resistant; PEN, penicillins; QUI, quinolones; SUL, sulfonamides; TET, tetracyclines; TMP, trimethoprim.