Table 3 Summary of estimated amplification performance of primer pairs representing published DNA-based markers targeting Francisella

Amplifies the entire genus

01-16S, 03-16S-Itr-23S, 04-16S-Itr-23S, 08-fabH, 18-groEL, 23-lpnA^a, 25-mdh, 30-prfb and 35-tpiA.

Amplifies clade 1 but not clade 2

05-aroA, 07-dnaA, 11-fopA-ina^a, 12-fopA-out^a, 13-fopA^a, 14-FTM19^b, 15-FTM19, 19-iglC^ac, 22-lpnA^a, 26-mutS, 27-parC^c, 31-putA, 36-tpiA, 37-trpE and 38-uup.

 Amplifies clade 1 but no other Francisella species.

11-fopA-in^a, 14-FtM19 and 15-FtM19^a

 Amplifies clade 1 as well as F. hispaniensis and W. persica

05-aroA, 07-dnaA, 12-fopA-out^a, 27-parC^c and 36-tpiA.

 Amplifies clade 1 as well as F. hispaniensis

13-fopA^a, 19-iglC^c, 22-lpnA, 31-putA, 37-trpE and 38-uup.

 Amplifies clade 1 as well as W. persica

26-mutS

Amplifies clade 2 but not clade 1

10-fopA

Amplifies noatunensis but not the other species

24-lpnB

Amplifies all isolates except some certain species.

02-16S-Itr-23S, 06-atpA, 09-fopA, 29-pgm, 32-rpoA, 33-rpoB and 34-sdhA.

 Amplifies all except F. hispaniensis and W. persica

09-fopA

 Amplifies all except F. hispaniensis

33-rpoB

 Amplifies all except F. tularensis, W. persica and F. hispaniensis

34-sdhA

 Amplifies all except W. persica

02-16S-Itr-23S, 29-pgm

 Amplifies all except F. noatunensis subsp. orientalis

06-atpA

 Amplifies all except F. noatunensis

32-rpoA

Markers with data missing for clade 2 and W. persica

16-FTT0376^a, 17-FTT0523^a, 20-ISFtu2^b and 28-pdpD^b.

 Amplifies only F. tularensis (only when including the probe).

16-FTT0376^a and 17-FTT0523^a

 Amplifies F. tularensis subsp. mediasiatica, F. tularensis subsp.holarctica and 6/7 F. tularensis subsp. novicida.

28-pdpD^b

 Amplifies isolates from all clade 1 species as well as W. persica.

20-ISFtu2^b

Marker with missing sequences as well as mismatches in almost all subspecies represented.

21-ISFtu2^a