Table 2.

Most relevant features of the subtyping methods for Salmonella Typhimurium.

	PT	AMR	PFGE	MLVA	MLST	CRISPR	RT	WGS
Bacterial culture required	Yes	Yes	Yes	No	No	No	Yes	No
Typeability	Moderate	Low	High	High	High	High	Moderate	High
Repeatability	Moderate	Moderate	High	High	High	High	Moderate	High
Reproducibility	Low	Moderate*	High	Moderate	Moderate	Moderate to high*	Moderate	High
DPa	Moderate to high	Low to moderate*	Moderate*	High*	Low to moderate*	High	Low to moderate	High
Stability	Moderate to high	Moderate	High	Low	High	Moderate	High	High
Level of interpretation	Difficult	Easy	Easy	Easy to moderate	Moderate	Difficult	Difficult	Difficult
Ease of use	Moderate	Easy	Moderate	Moderate	Difficult	Moderate	Moderate	Difficult
High throughput	No	No	No	Yes	Yes	Yes	No	Yes
Costb	Low	Low	Low to moderate	Low to moderate	High	High	Low to moderate	High
Time requiredc	2+	3+	3+	< 2	3+	< 1	2+	< 2*
Notes	Needs experience in interpretation	Depends on number of antimicrobials tested; Not utilized alone for epidemiological correlation	Depends on type and number of enzymes; Depends on the strain (Table 1)	Specific to ST	Depends on the number of and the gene choice; Insufficiently DI for use in outbreak investigations	Depends on databases used; Used mainly in France	–	Depends on the sequencer technology and number of strains
References	Threlfall and Frost, 1990; Rabsch, 2007	Giraud et al., 2003; van Belkum et al., 2007	Foxman et al., 2005; Li et al., 2009; Wattiau et al., 2011	Torpdahl et al., 2007; Lindstedt et al., 2013	Foxman et al., 2005; Li et al., 2009; Sabat et al., 2013	Fabre et al., 2012; Shariat et al., 2013	Foxman et al., 2005; Li et al., 2009	Niedringhaus et al., 2011; Weymann et al., 2017

^aDP, discriminatory power.

^bPer sample for materials, low < EUR 10 < moderate < EUR 100 < high.

^cDays.

PT, Phage typing; AMR, Antimicrobial Resistance Profile; PFGE, Pulsed-field gel electrophoresis; MLVA, Multilocus variable-number tandem repeat analysis; MLST, Multilocus Sequence Typing; CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats; RT, Ribotyping; WGS, Whole genome sequence.

^*See notes.