TABLE 1.

Overview of Salmonella characterization and subtyping methods.

Method	Ability to identify or predict serovars	Ability to provide sensitive subtype discrimination	Time to results from a single colony	Commercial availability (time to results that can be expected from commercial labs)	Summary of value for food industry	Estimated reagent cost per isolate (instrument and labor cost not included)1	Service cost per isolate (provided by commercial labs)1
Classical White–Kauffman serotyping	While Salmonella serovars are based on White–Kauffmann serotyping, serotyping does provide frequent misclassification (Petersen et al., 2002).	Very poor subtype discrimination; only valuable as subtyping method for rare and unusual serovars.	2–17 days (usually >5 days) (ECDC, 2015; Bopp et al., 2016)	2–4 weeks	Classical serotyping is likely to be replaced rapidly by WGS-based serovar prediction. Main value for industry is as a rapid confirmation and subtype screen if access exists to lab that can provide rapid turnaround time.	$5–65 (ECDC, 2015; Bopp et al., 2016)	∼$175
Pulsed-field gel electrophoresis (PFGE)	Intermediate ability to predict serovars	Good subtyping discrimination for most serovars. Some PFGE patterns are very common within some serovars (e.g., Pattern 4 for Salmonella Enteritidis)	4–6 days (ECDC, 2015; Bopp et al., 2016)	2–3 weeks	Has been the gold standard subtyping method for Salmonella, is likely to be replaced rapidly by WGS, starting with public health authorities and food regulators.	$7–50 (ECDC, 2015; Bopp et al., 2016)	$130–200
Multiple locus variable number of tandem repeats (VNTR) analysis (MLVA)	Intermediate ability to predict serovars	Good subtyping discrimination for most serovars. May perform better than PFGE for some serovars but worse for others.	1–2 days	NA2	Has been used as a secondary subtyping method to compensate the low discriminatory power of serotyping and PFGE for some Salmonella serovars; it is likely to be replaced rapidly by WGS, starting with public health authorities and food regulators.	$9–36 (Amirkhanian et al., 2006; Top et al., 2008; Schouls et al., 2009; ECDC, 2015)	NA2
Legacy multilocus sequence typing (legacy MLST)	Intermediate ability to predict serovars	Better than conventional serotyping and riboprinting, worse than PFGE and WGS.	1–2 days	2–3 days	Main value for industry is as a rapid confirmation and subtype screen, can be used to select the reference genome for WGS data analysis.	$30–82 (Ranieri et al., 2013; Shi et al., 2015)	∼$280
Whole-genome sequencing (WGS)	Currently available serovar-prediction software using WGS data work well for less common serovars. May not work for extremely rare serovars.	Best discrimination among molecular subtyping approaches	3–17 days (ECDC, 2015) (depends on sequencing capabilities. Usually 1 day after sequencing is finished).	2–8 weeks	For companies with high demand of isolates to be subtyped, WGS is probably the most affordable and fastest method that provides the best discrimination. In addition, in silico serotyping and in silico MLST can be done from the data to allow for comparison with historical isolates that have not been whole-genome-sequenced. Other information, such as presence of antibiotic resistance genes and virulence genes can be easily retrieved from the data. For companies with low demand, the costs of real-time sequencing may be prohibitive, requiring that old isolates must wait until more isolates are collected to be submitted together.	$60–230 (ECDC, 2015)	$100 (using Illumina HiSeq X series)–up to more than $500 (using Illumina MiSeq)

¹These cost estimates per isolate are based on (i) previous cost estimation reports and studies, (ii) official prices available on Internet, and/or (iii) personal communication with service providers and product vendors, as of June 2018, true costs may vary considerably based on number of isolates tested per run, labor costs, and region/country, etc. ²NA, not available.