Table 1.

Strengths and weaknesses of culture techniques and molecular methods. Abbreviations: PCR, polymerase chain reaction; RT, real time; NGS, next generation sequencing; MIC, minimum inhibitory concentration.

	Culture Testing	PCR/RT-PCR	Genomic Technologies
Advantages	Widely available and cheaper than NGS	Rapidly completed in 4–8 h	Pathogen identification and characterisation independent of culturing and microbe isolation
	Only basic equipment necessary	Increased identification of less common organisms such as viruses	Reduced time for slow growing pathogen identification, typing and characterisation
		Test multiple targets in one sample	Faster identification of outbreak clusters
		Higher sensitivity than culture testing	Higher sensitivity and specificity, better resolution
Disadvantages	Failures in the identification of fastidious bacteria and organisms that cannot be cultured	Higher costs than culturing	Higher costs than culturing
	Increased time for slow-growing pathogen identification and typing	High specific design of primers and need for a list of potential pathogens	Requirement of highly specialised laboratory equipment and trained personnel
	Requires special media and specific condition for the different microorganisms	Inability to determine the MIC of a compound	Inability to determine the MIC of a compound