Table 2.

Advantages and disadvantages of different molecular diagnostic techniques

Technique	Advantages	Disadvantages
PCR and its modifications	-Suitable for the detection of wide variety of pathogens with various modifications -Suitable for a wide variety of specimen materials -In comparison to antibody or antigen detection far more sensitive and specific	-Specimen contamination will lead to false-positive results -More expensive than, e.g., serological methods -Requires meticulous working techniques and quality control -Requires special facilities and instrumentation
Isothermal amplification	In addition to PCR: -Very efficient method -NASBA is not affected by possible DNA contamination of the sample	In addition to PCR: -Expensive
Fluorescence in situ hybridization	-Allows the detection of nucleic acid directly from the sample without prior nucleic acid amplification -Low cost -Modest technical requirements -The technical part of the analysis is quick -Laboratory contamination of the sample is not an issue -Usually very specific	-Poor sensitivity -Screening of slides slow, unless an expensive automated microscope is available
Genotyping	-Suitable for identifying antimicrobial resistance and high-risk strains -Direct sequencing provides accurate and extensive data -Can be used for phylogenetic analyses	-Direct sequencing requires expensive equipment and technical expertise -Laborious method
Mass spectrometry	-Suitable for typing -Allows detection of both known and new mutations -Very fast compared to DNA sequencing -Suitable for analysis of large number of samples	-Not suitable for the analysis of long oligonucleotides due to decreased sensitivity -Cannot be used for large-scale genomic sequence analysis -MALDI is susceptible to metal contaminants
Microarrays	-Can detect both nucleic acids and antibodies -Very good sensitivity -Ability to detect several pathogens simultaneously -High sample throughput	-Too expensive to be adapted for routine diagnostics -Usually requires nucleic acid amplification prior to analysis

PCR: polymerase chain reaction, NASBA: nucleic acid sequence based amplification, MALDI: matrix-assisted laser desorption/ionization.