Table 2.

Quality requirements from both EU and US regulatory authorities for strain characterization.

Required information		Selected tests and assays
Genotyping	Identification at species level	16S rDNA genotyping
	Identification at strain level Antimicrobial resistance genes Virulence genes Presence of mobile genetic elements Plasmid detection Bacteriophage-related DNA insertions Transposons	Whole genome sequencing
Phenotyping	Identification at strain level	MALDI-TOF
	Morphology identification Gram staining Cell shape and size	Microscopy
	Growth characteristics	Growth kinetics, pH tolerance, aerotolerance, bile acid resistance
	Motility and sporulation	Wirtz-Conklin method
	Antibiotic sensitivity profile	Antibiogram along minimum inhibitory concentrations
	Enzymatic activity	API 20A anaerobic test, API rapid ID32A, API ZYM, oxidase, and catalase activity
	Bacterial endotoxins	• Method A: gel-clot technique (12)• Method B: turbidimetric technique (12)• Method C: chromogenic technique (12)