TABLE 1.

Candidate canonical SNPs delineating Samoan genotype 3.5.4 sublineages^a

Genotype	n/Nb	Ref. allele	Alt. allele	CT18 position	Gene	Protein
3.5.4.1	96/96	G	Ad	3960783	STY4102	Putative l-lactate dehydrogenase
		G	Ad	4794120	gpmB	Probable phosphoglycerate mutase 2
3.5.4.2	77/77	C	Td	1731534	STY1812	Exodeoxyribonuclease III
		C	Td	1945934	STY2094	Glucose 6-phosphate dehydrogenase
3.5.4.3	106/107c	C	Te	295362	STY0278	Putative drug efflux protein

^aGenotype, suggested sublineage designation; n/N, number of S. Typhi isolates in Samoa over total number of S. Typhi isolates in the sublineage; Ref. allele, CT18 allele; Alt. allele, alternative SNP candidates in the genotype sublineage.

^bAll SNPs were detected in 100% of their designated genotype groupings (N) and absent from 100% of out-grouped isolates (5,240 global S. Typhi genomes were analyzed).

^cOne 3.5.4.3 isolate is of unknown origin.

^dSynonymous intragenic silent mutation.

^eNonsynonymous intragenic missense mutation.