TABLE 2.

Overview of common bacterial subtyping methods*.

Method	Application scenarios	Subtype discrimination accuracy	Time to results from a colony	Commercial availability	Relative cost
Phenotypic subtyping
Antibiotic susceptibility test	To select effective antimicrobial drugs.	Worse than DNA-based methods.	1–2 days	Yes (Laboratory medicine)	Low
Phage susceptibility test	To select effective lytic phages.	May perform better than PFGE/MLST for some bacteria but worse for others.	1–2 days	No*	Medium
Immunological test	To applied for the preliminary identification.	Typically worse than DNA-based methods.	<1 day	Yes (Laboratory medicine)	Medium
DNA-based subtyping
Pulsed-field gel electrophoresis (PFGE)	To subtype bacterial species causing infection outbreaks	Gold-standard for many different bacteria	3–4 days	Yes	High
Multiple locus variable number of tandem repeats analysis (MLVA)	Usually been performed for more subtyping details after PFGE.	May perform better than PFGE for some bacteria but worse for others	1–2 days	No	Medium
Multilocus sequence typing (MLST)	To characterize bacterial populations at larger geographic and temporal scales	Typically worse than PFGE	>3 days (send out sequencing)	Yes	High
Whole-genome sequencing (WGS)	To cluster isolates for bacterial outbreak analysis.	Best discrimination among molecular subtyping approaches	2–4 weeks (send out sequencing)	Yes	High

*Mayo Clinic Laboratories (US) and Dr Dangs Lab (India) have announced to commercialize phage susceptibility test in 2020 (Adaptive Phage Therapeutics, 2020a; ANI, 2020).