. 2018 Nov 13;9(6):e02112-18. doi: 10.1128/mBio.02112-18

TABLE 5.

Evaluation of the ability of WGS-res profiles to predict S. Typhi resistance phenotypes of our isolates^a

Antimicrobial resistance category	Presence of gene(s) and WGS-res profile	No. of isolates with indicated phenotype		Sensitivity (%)^b	Specificity (%)^c
Antimicrobial resistance category	Presence of gene(s) and WGS-res profile	Resistant	Susceptible	Sensitivity (%)^b	Specificity (%)^c
Ampicillin resistance	Total	263	273
	bla_TEM-1B	262	7
	Truncated bla_TEM-1B	0	2
	No bla_TEM-1B	1	264
	WGS-res profile: resistant	262	7	99.6	97.4
	WGS-res profile: susceptible	1	266	99.6	97.4

Co-trimoxazole resistance^d	Total	233	303
	dfrA7 + sul1 + sul2	205^e ^,ⁱ	4^f ^,ⁱ
	dfrA7 + sul1 only	26	22^g
	sul2 only	1^e ^,ⁱ	55^h ^,ⁱ
	None of three	1	222
	WGS-res profile: resistant	231	26	99.1	91.4
	WGS-res profile: susceptible	2	277	99.1	91.4

Chloramphenicol resistance	Total	250	286
	catA1	248^j	7^j
	Truncated catA1	0	1^j
	No catA1	2	278
	WGS-res profile: resistant	248	7	99.2	97.6
	WGS-res profile: susceptible	2	279	99.2	97.6

Ceftriaxone resistance	Total	1	535
	bla_CTX-M15	1	0
	No bla_CTX-M15	0	535
	WGS-res profile: resistant	1	0	100.0	NA
	WGS-res profile: susceptible	0	535	100.0	NA

Four antimicrobials were considered (ampicillin, co-trimoxazole, chloramphenicol, and ceftriaxone); resistance to these agents is caused mainly by acquisition of resistance genes.

Sensitivity data represent proportions of isolates identified as phenotypically resistant by the WGS-res profile.

Specificity data represent proportions of isolates identified as phenotypically susceptible by the WGS-res profile.

For co-trimoxazole (sxt), we considered the presence of dfrA7, plus sul1 and/or sul2 genes to exert the resistance (R) phenotype.

A total of 206 detected sul2 genes matched three different GenBank IDs: FJ197818 (n = 74), GQ421466 (n = 1), and HQ840942 (n = 131).

Of the four sul2 genes, two matched FJ197818 and two HQ840942. One sul1 gene had unreliable bases (N) in its sequence; that result was considered a sequencing error, and the complete sequence was used in calculations.

One sul1 gene had unreliable bases (N) in its sequence; that result was considered a sequencing error, and the complete sequence was used in calculations.

A total of 54 genes matched GQ421466 and one HQ840942.

ⁱ

Only sul2 genes that matched HQ840942 had complete sequences. Genes that matched FJ197818 and GQ421466 were either truncated or mutated.

All catA1 gene sequence had one silent mutation in amino acid 195 (lysine) (CTG→TTG).