Immunological O/H typing (serotyping) |
X |
X |
|
|
Ørskov et al., 1977 |
Bacteriophage typing |
|
|
|
X |
Ahmed et al., 1987; Krause et al., 1996
|
Multilocus enzyme electrophoresis (MLEE) |
|
|
|
X |
Ochman and Selander, 1984; Selander et al., 1986; Campos et al., 1994
|
MALDI-TOF |
|
X |
|
X |
Chui et al., 2015 |
Genotype-based methods |
|
|
|
|
|
Restriction length polymorphism (RFLP) |
X |
X |
X |
|
Coimbra et al., 2000; Beutin et al., 2005; Moreno et al., 2006; Abbadi and Strockbine, 2007
|
Luminex-based suspension assay |
X |
|
|
|
Lin et al., 2011; Clotilde et al., 2015
|
Amplified fragment length polymorphisms (AFLP) |
|
|
|
X |
Hahm et al., 2003; Leung et al., 2004
|
Optical mapping |
|
|
X |
X |
Kotewicz et al., 2007, 2008; Miller, 2013
|
Ribotyping |
|
|
|
X |
Martin et al., 1996; Carson et al., 2001
|
Multilocus variable number tandem repeat analysis (MLVA) |
|
|
|
X |
Hyytiä-Trees et al., 2006; Byrne et al., 2014
|
Pulsed-field gel electrophoresis |
|
|
X |
X |
Krause et al., 1996; Ribot et al., 2006
|
Multilocus sequence typing (MLST) |
|
|
|
X |
Eichhorn et al., 2015; Manges et al., 2015
|
High throughput real-time PCR |
X |
X |
X |
|
Bugarel et al., 2010a,b, 2011a,b; Delannoy et al., 2013; Tseng et al., 2014
|
Multiplex PCR |
X |
X |
X |
|
Fratamico and DebRoy, 2010; Botkin et al., 2012; Doumith et al., 2012; Fratamico et al., 2014; Iguchi et al., 2015b
|
Whole genome sequencing and SNP analysis |
X |
X |
X |
X |
Zhang et al., 2006; Eppinger et al., 2011; Norman et al., 2012, 2015; Joensen et al., 2014, 2015; Griffing et al., 2015; DebRoy et al., 2016; Ison et al., 2016
|
Virulence gene profiles |
|
|
|
X |
Nandanwar et al., 2014; Manges et al., 2015
|
CRISPRs |
|
|
|
X |
Shariat and Dudley, 2014; Delannoy et al., 2015
|
Microarray |
X |
X |
X |
X |
Liu and Fratamico, 2006; Hegde et al., 2013; Lacher et al., 2014
|
NeoSEEKTM (PCR-mass spectroscopy) |
X |
X |
X |
X |
Stromberg et al., 2015 |