Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays

Jon Ahlinder; Caroline Öhrman; Kerstin Svensson; Petter Lindgren; Anders Johansson; Mats Forsman; Pär Larsson; Andreas Sjödin

doi:10.1186/1471-2180-12-220

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-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

Successful amplification was defined as having a primer score below two in both the forward and reverse primers.
^a Have associated TaqMan probe which is not considered here. ^bDetection by variable-length amplicon which is not considered here.
^cScore of F.noatunensis subsp orientalis <2.

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