TABLE 2.
Non‐DNA and DNA‐based identification methods for Xanthomonas hortorum pathovars. The detection targets, taxonomical level of detection, and primer sequence availability, when applicable, are also reported
| Detection | Targeted pathovar | Specific for the targeted pathovar (antibody, primer, or probe name) b | Reference(s) | Comments c | |||
|---|---|---|---|---|---|---|---|
| method | Type | Target(s) | Taxonomical level a | ||||
| ELISA | Non‐DNA | Polyclonal antibodies | Pathovar | pv. pelargonii | Yes | Balaž et al. (2016) | Commercial ELISA kit |
| ELISA | Non‐DNA | Monoclonal antibodies | Xanthomonas species | pv. pelargonii | Yes (MAb Xpel‐1) | Benedict et al. (1990) | NA |
| ELISA | Non‐DNA | Monoclonal antibodies | Pathovar | pv. pelargonii | Yes (McAb 2H5) | Chittaranjan and De Boer (1997) | NA |
| ELISA | Non‐DNA | Monoclonal antibodies | Xanthomonas species/pathovars | pv. vitians | No | Sahin et al. (2003) | Pattern‐based discrimination |
| SDS‐PAGE | Non‐DNA | Various proteins | Xanthomonas species/pathovars | various: pvs vitians (cluster 7d), hederae (cluster 7e), pelargonii (cluster 12) | No | Vauterin et al. (1991) | Pattern‐based discrimination |
| SDS‐PAGE | Non‐DNA | Various proteins | Xanthomonas species/pathovars | pv. vitians | No | Stefani et al. (1994) | Pattern‐based discrimination |
| SDS‐PAGE | Non‐DNA | Various proteins | Pathovar | pv. gardneri | No | Quezado‐Duval et al. (2004) | Pattern‐based discrimination |
| DDH | DNA | DNA homology groups | Xanthomonas species/pathovars | various: pvs pelargonii, hederae, vitians (group 2) | No | Vauterin et al. (1995) | Clustering‐based discrimination |
| MLSA/MLST | DNA | Various housekeeping genes, including gyrB | Xanthomonas species | various pvs | No | Parkinson et al. (2007); Young et al. (2008); Parkinson et al. (2009) | Clustering‐based discrimination |
| MLSA/MLST | DNA | Various housekeeping genes, including gyrB | Pathovar | pv. vitians | No | Fayette et al. (2016) | Clustering‐based discrimination |
| PCR | DNA | RAPD fragments | Pathovar | pv. carotae | Yes (3S/3SR and 9B/9BR) | Meng et al. (2004) | D.L.: 22 fg (3S) and 2 pg (9B) |
| PCR | DNA | CDS or intergenic regions | Pathovar | pv. carotae | Yes (XhcPP02, PP03, PP04, and PP05) | Kimbrel et al. (2011) | NA |
| PCR | DNA | Based on the target of XhcPP02 (Kimbrel et al., 2011) | Pathovar | pv. carotae | Yes (Xhc‐q2) | Temple et al. (2013) | NA |
| PCR | DNA | AFLP fragments | BSX | pv. gardneri | Yes (Bs‐XgF/Bs‐XgR) | Koenraadt et al. (2009); Pereira et al. (2011) | NA |
| PCR | DNA | 1.2 kb DNA‐fragment | Pathovar | pv. pelargonii | Yes | Manulis et al. (1994); Chittaranjan and De Boer (1997) | NA |
| PCR | DNA | ERIC, REP regions | Pathovar | pv. pelargonii | No | Sulzinski et al. (1995) | Pattern‐based discrimination |
| PCR | DNA | ERIC fragment | Pathovar | pv. pelargonii | Yes (XcpMl/XcpM2) | Sulzinski et al. (1996); Sulzinski et al. (1997); Sulzinski et al. (1998); Sulzinski (2001) | NA |
| PCR | DNA | RAPD fragments | Pathovar | pv. vitians | Yes (B162) | Barak et al. (2001) | NA |
| PCR | DNA | BOXA, ERIC, REP, and 16S‐23S rDNA regions | Xanthomonas species/pathovars | pv. vitians | No | Sahin et al. (2003) | Pattern‐based discrimination |
| PCR | DNA | SNP‐based | Pathovar | pv. vitians | No | Hébert et al. (2021) | C t values |
| Multiplex PCR | DNA | ERIC fragment | X. hortorum pv. pelargonii and Ralstonia solanacearum | pv. pelargonii | Yes (DG1/DG2) | Glick et al. (2002) | NA |
| PCR and multiplex PCR | DNA | AFLP fragments | BSX | pv. gardneri | Yes (Bs‐XgF/Bs‐XgR) | Araújo et al. (2012) | D.L.: DNA: 50 pg/µl; bacterial suspension: 5 × 104 cfu/ml (100 bacterial cells per reaction). |
| Real‐time PCR | DNA | ERIC fragment | Pathovar | pv. pelargonii | Yes (XhqF/XhqR) | Farahani and Taghavi (2016) | D.L.: 200 fg |
| Multiplex real‐time PCR | DNA | lepA | BSX +Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato | pv. gardneri | No | Peňázová et al. (2020) | Cy5 was used for multiplex PCR that targeted BSX together |
| Multiplex real‐time PCR | DNA | hrpB7 primers and probes | BSX | pv. gardneri | Yes, in combination with probe (FP2/RP2) | Strayer, Jeyaprakash, et al. (2016) | D.L.: 5 × 105 cfu/ml |
| LAMP | DNA | Based on PCR product of 9B primer set (Meng et al., 2004) | Pathovar | pv. carotae | Yes (Lace primer set) | Temple and Johnson (2009); Temple et al. (2013) | NA |
| LAMP | DNA | hrpB6 | Pathovar | pv. gardneri | Yes | Stehlíková et al. (2020) | D.L.: 1 pg/µl |
| RPA | DNA | hrpB6 | Pathovar | pv. gardneri | No (XGF/XGR) | Strayer‐Scherer et al. (2019) | D.L.: 5 × 106 cfu/ml; amplified X. hortorum pv. cynarae CFBP 2044 |
a
BSX, the Xanthomonas species causing bacterial spot of tomato and pepper: X. hortorum pv. gardneri, X. vesicatoria, and X. euvesicatoria pvs euvesicatoria and perforans.
b
Primer sequences are available in all the DNA‐based detection methods.
c
D.L., reported detection limits; NA, not available.