. 2016 May 3;7:644. doi: 10.3389/fmicb.2016.00644

Table 1.

Phenotype- and genotype-based methods for subtyping and molecular serotyping of E. coli.

Phenotype-based methods	O-antigen^a	H-antigen^a	Virulence-related and other genes	SNPs and other markers	Reference
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
NeoSEEK^TM (PCR-mass spectroscopy)	X	X	X	X	Stromberg et al., 2015

^aThe O-somatic and H-flagellar antigens define the E. coli serotype. Agglutination assays using antibodies that react with the specific O- and H-antigens are the basis for traditional serotyping. Molecular serotyping methods are generally based on genetic targets specific to the O- and H-antigens.