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

From: Increased knowledge of Francisellagenus diversity highlights the benefits of optimised DNA-based assays

Estimated amplification performance Marker id
Amplifies the entire genus 01-16S, 03-16S-Itr-23S, 04-16S-Itr-23S, 08-fabH, 18-groEL, 23-lpnAa, 25-mdh, 30-prfb and 35-tpiA.
Amplifies clade 1 but not clade 2 05-aroA, 07-dnaA, 11-fopA-inaa, 12-fopA-outa, 13-fopAa, 14-FTM19b, 15-FTM19, 19-iglCac, 22-lpnAa, 26-mutS, 27-parCc, 31-putA, 36-tpiA, 37-trpE and 38-uup.
 Amplifies clade 1 but no other Francisella species. 11-fopA-ina, 14-FtM19 and 15-FtM19a
 Amplifies clade 1 as well as F. hispaniensis and W. persica 05-aroA, 07-dnaA, 12-fopA-outa, 27-parCc and 36-tpiA.
 Amplifies clade 1 as well as F. hispaniensis 13-fopAa, 19-iglCc, 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-FTT0376a, 17-FTT0523a, 20-ISFtu2b and 28-pdpDb.
 Amplifies only F. tularensis (only when including the probe). 16-FTT0376a and 17-FTT0523a
 Amplifies F. tularensis subsp. mediasiatica, F. tularensis subsp.holarctica and 6/7 F. tularensis subsp. novicida. 28-pdpDb
 Amplifies isolates from all clade 1 species as well as W. persica. 20-ISFtu2b
Marker with missing sequences as well as mismatches in almost all subspecies represented. 21-ISFtu2a
  1. Successful amplification was defined as having a primer score below two in both the forward and reverse primers.
  2. a Have associated TaqMan probe which is not considered here. bDetection by variable-length amplicon which is not considered here.
  3. cScore of F.noatunensis subsp orientalis <2.