Table 1.

Users, criteria and limitations on use of analytical methods for detection of foodborne pathogens^a.

	Food industry, quality control	Public enforcement, legal/safety control	Clinical outbreak investigation, source trackingb
Molecular targets	A narrow range of pre-defined risk indicators, e.g., particular species specific markers, serotype specific markers, virulence genes	A broader range of risk indicators, pre-defined or not. May also include focus on different sequence variants	At least all case specific markers identified from characterization of patient isolate(s). Often also including a broad range of other risk indicators, pre-defined or not
Purpose of analysis	Ensure that own food product is legally compliant and does not pose an unacceptable risk to consumer (can be perceived as safe)	Ensure that food production/products are legally compliant and safe, and monitoring of prevalence/distribution of contaminants on the market	Identify contaminated product(s) and retract the product(s) from the market as well as clearing non-contaminated products from suspicion
How?	Analytical verification: pre-defined risk indicators are not detectable at a pre-defined limit of detection or in a pre-defined sample size. Sampling based on HACCPc approach	Analytical detection and typing of risk indicators, analysis of traceability documentation and epidemiological analysis. A pre-defined sample size or LODd and quantitative analyses are often applied. Sampling based on specific sampling plans, standards or guidelines	Interviews of patients/family analytical detection targeting case specific markers from patient isolate(s) complemented with epidemiological analysis and sampling partly based on interviews. A pre-defined sample size is often applied, but a pre-defined LOD is usually not
Required time from test to result	Minutes or usually several hours, but may be justifiable with up to days/weeks in case of re-emerging contamination problem	Exceptionally weeks, usually days, but may be shorter in case of products with short shelf life and high turnover	As soon as possible, preferably minutes to hours, but can be days
Resource limitations	Routine on-site detection. Price sensitive market testing costs per unit produced must be very low, but may be justifiable with high costs in case of re-emerging contamination problem	Routine laboratory analyses complemented with in-depth analyses in well-equipped (reference) laboratories. Testing costs per unit can be low to moderate, depending on specific control program. High to very high costs can be justified in particular cases	Emergency conditions: life and health of humans are at stake. Routine and in-depth analyses in advanced laboratories. Testing costs per unit can be moderate to very high
Representative analytical approach	Traditional culturing, PCRe or immuno-assay analyses	Enrichment culturing, biochemical tests and PCR complemented with sequencing of genes	PCR complemented with gene sequencing and WGSf of selected isolates
High throughput sequencing (HTS) applicable? When?	Usually not because of costs and time. May be justifiable to apply HTS based genome typing methods on isolates to investigate/unravel re-emerging contamination problems	Usually not because of costs and time. HTS based amplicon sequencing of one to a few genes in some cases justifiable. Selected isolates from public enforcement/control programs occasionally qualify for WGS	Yes, typically by WGS of selected isolates, possibly limiting bioinformatics to focusing on particular gene panels while facilitating successive in-depth analyses of genome evolution and epidemiology

^aResearch applications are essentially unlimited and therefore not included in this table.

^bPatient treatment and characterization of patient derived isolates is a separate task not included in this table. However, the source tracking rely in part on the data derived from characterization of patient derived isolates.

^cHACCP, hazard analysis (and) critical control point.

^dLOD, limit of detection.

^ePCR, polymerase chain reaction.

^fWGS, whole genome sequencing.