Table 2.

Strengths and weaknesses of different methods for bacterial identification.

Identification Method	Strengths	Weaknesses
Morphology (colony and Gram-stain)	very low cost and time investment	identification only possible for some species examiner-dependent
Biochemical spot tests	very low cost and time investment	low reliability for anaerobes
Antibiotic susceptibility testing	important information for clinical decision making	takes 24 to 48 h low reliability for anaerobes
Automated systems such as VITEK® 2 (see also Box 1)	automated identification plus antimicrobial testing	high costs
MALDI-TOF MS (see also Box 1)	early and reliable identification	initially high cost of instrument sample preparation influences spectrum quality
Partial 16S rRNA gene sequencing analysis (see also Box 1)	reliable identification	time and costs
Metagenomics/next-generation sequencing (see also Box 1)	no bacterial growth necessary discovery of new, uncultured taxa association of microbial signatures with diseases	time and costs limited discrimination between live bacteria and transient DNA results depend on used methodologies