TABLE 5.
Antimicrobial resistance category |
Presence of gene(s) and WGS-res profile | No. of isolates with indicated phenotype |
Sensitivity (%)b | Specificity (%)c | |
---|---|---|---|---|---|
Resistant | Susceptible | ||||
Ampicillin resistance | Total | 263 | 273 | ||
blaTEM-1B | 262 | 7 | |||
Truncated blaTEM-1B | 0 | 2 | |||
No blaTEM-1B | 1 | 264 | |||
WGS-res profile: resistant | 262 | 7 | 99.6 | 97.4 | |
WGS-res profile: susceptible | 1 | 266 | |||
Co-trimoxazole resistanced | Total | 233 | 303 | ||
dfrA7 + sul1 + sul2 | 205e ,i | 4f ,i | |||
dfrA7 + sul1 only | 26 | 22g | |||
sul2 only | 1e ,i | 55h ,i | |||
None of three | 1 | 222 | |||
WGS-res profile: resistant | 231 | 26 | 99.1 | 91.4 | |
WGS-res profile: susceptible | 2 | 277 | |||
Chloramphenicol resistance | Total | 250 | 286 | ||
catA1 | 248j | 7j | |||
Truncated catA1 | 0 | 1j | |||
No catA1 | 2 | 278 | |||
WGS-res profile: resistant | 248 | 7 | 99.2 | 97.6 | |
WGS-res profile: susceptible | 2 | 279 | |||
Ceftriaxone resistance | Total | 1 | 535 | ||
blaCTX-M15 | 1 | 0 | |||
No blaCTX-M15 | 0 | 535 | |||
WGS-res profile: resistant | 1 | 0 | 100.0 | NA | |
WGS-res profile: susceptible | 0 | 535 |
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.
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).