Table 1 Definitions used to calculate AMR variables. Genetic determinants reported by Pathogenwatch are used to calculate binary resistance prediction variables in TyphiNET

Ampicillin/amoxicillin

bla gene

Azithromycin

acrB-R717Q or acrB-R717L mutation

Ceftriaxone

 ≥ 1 ESBL gene^a

Chloramphenicol

catA1 or cml1 gene

Ciprofloxacin non-susceptible (CipNS)

(MIC, > 0.06 mg/L) [49,50,51]

 ≥ 1 QRDR^b mutation,

and/or ≥ 1 qnr gene

Ciprofloxacin resistant (CipR)

(MIC, > 0.5 mg/L) [49,50,51]

 ≥ 3 QRDR^b mutations,

or ≥ 1 QRDR^b plus ≥ 1 qnr gene^c

Sulphonamides

 ≥ 1 sul gene

Tetracyclines

 ≥ 1 tetA gene

Trimethoprim

 ≥ 1 dfrA gene

Trimethoprim-sulfamethoxazole

 ≥ 1 sul gene

Plus ≥ 1 dfrA gene

Multidrug resistant

(MDR; resistance to chloramphenicol plus ampicillin plus trimethoprim-sulfamethoxazole)

catA1 or cml1 gene

Plus bla gene

Plus ≥ 1 sul gene

Plus ≥ 1 dfrA gene

Extensively drug resistant

(XDR; MDR plus CipR plus ceftriaxone resistant)

As for MDR

Plus CipR

Plus ≥ 1 ESBL gene

Pansusceptible

(No AMR determinants detected)

None