TABLE 5

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

Antimicrobial
resistance
category
Presence of gene(s) and WGS-res profileNo. of isolates with
indicated phenotype
Sensitivity (%)bSpecificity (%)c
ResistantSusceptible
Ampicillin resistanceTotal263273
blaTEM-1B2627
Truncated blaTEM-1B02
No blaTEM-1B1264
WGS-res profile: resistant262799.697.4
WGS-res profile: susceptible1266
Co-trimoxazole resistancedTotal233303
dfrA7 + sul1 + sul2205e,i4f,i
dfrA7 + sul1 only2622g
sul2 only1e,i55h,i
None of three1222
WGS-res profile: resistant2312699.191.4
WGS-res profile: susceptible2277
Chloramphenicol resistanceTotal250286
catA1248j7j
Truncated catA101j
No catA12278
WGS-res profile: resistant248799.297.6
WGS-res profile: susceptible2279
Ceftriaxone resistanceTotal1535
blaCTX-M1510
No blaCTX-M150535
WGS-res profile: resistant10100.0NA
WGS-res profile: susceptible0535
  • a Four antimicrobials were considered (ampicillin, co-trimoxazole, chloramphenicol, and ceftriaxone); resistance to these agents is caused mainly by acquisition of resistance genes.

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

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

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

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

  • f 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.

  • g 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.

  • h 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.

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