Table 1.
Comparison table of selected molecular techniques.
| Molecular techniques | Advantages | Limitations | Reference |
|---|---|---|---|
| PCR | ∙ High sensitivity ∙ High specificity | ∙ False-positive results ∙ Negative results | Qin et al., 2003; Cattoir et al., 2010 |
| Multiplex PCR | ∙ Provide internal controls ∙ Low reagent costs ∙ Able to preserve precious samples ∙ Able to determine the quality and quantity of template more effectively | ∙ Primer designing ∙ No standard protocol | De Vos et al., 1997; da Silva Filho et al., 2004; Anuj et al., 2009; Thong et al., 2011; Salman et al., 2013; Aghamollaei et al., 2015 |
| qPCR | ∙ Reproducible methods (less than 5 h) ∙ Direct detection from sputum samples ∙ Availability of commercial kits in the market | ∙ Expensive instrument ∙ High cost of maintenance | Deschaght et al., 2009; Cattoir et al., 2010; Clifford et al., 2012; Carlesse et al., 2016 |
| LAMP | ∙ Low detection limit with high sensitivity ∙ Rapid detection (∼20 min) without DNA purification ∙ Only required basic inexpensive equipment with minimal operator training | ∙ Primer designing ∙ Less develop multiplexing approach | Zhao et al., 2011 |
| PSR | ∙ Low detection limit with high sensitivity ∙ Rapid detection (∼60 min) without an initial denaturation ∙ Only required basic inexpensive equipment with minimal operator training | ∙ Still in the progress on method development | Dong et al., 2015 |
| PFGE | ∙ Inexpensive ∙ Excellent typeability ∙ High sensitivity ∙ Easy interpretation | ∙ Lack of standardized protocols ∙ Limited reproducibility ∙ Labor-intensive method ∙ Technical expertise required | Grundmann et al., 1995; Morales et al., 2004; Libisch, 2013 |
| MLVA | ∙ Highly reproducible and easy interpretation ∙ Rapid approach with high resolution ∙ Suitable for large-scale automated platforms | ∙ Assay-specific for different organisms ∙ Lacks standardization of assay | Onteniente et al., 2003; Sobral et al., 2012; Maâtallah et al., 2013 |
| MLST | ∙ Accessibility of online-based MLST reference databases ∙ Standardization of MLST data ∙ Highly reproducible | ∙ High cost ∙ Insufficiently discerning for routine use in local surveillance and outbreaks ∙ Lack the discriminatory power to differentiate certain bacteria | Curran et al., 2004 |
| DL rep-PCR | ∙ Standardization of assay ∙ Improved reproducibility ∙ User-friendly internet-based computer-assisted data analysis | ∙ Validation for each bacterial species is necessary ∙ Lack of a suitable cutoff values from the manufacturer ∙ High cost of reagents and kits ∙ Necessity to use different fingerprint kits for each bacterial species ∙ High instrument installation and maintenance costs | Fluit et al., 2010; Deplano et al., 2011; Brossier et al., 2015 |
| NGS | ∙ Requires less amount of DNA ∙ High quality, robustness and lower noise background sequence data ∙ Reproducible ∙ Analytically sensitive, and accurate assessment of the identity and relative abundance of organisms present in polymicrobial samples | ∙ Technical expertise required to perform the wet lab, analyze, and interpret the data ∙ Computational infrastructures and software need to be upgraded in order to store and analyze large bioinformatics datasets | Quick et al., 2014; Blanc et al., 2016 |
PCR, polymerase chain reaction; qPCR, quantitative real-time PCR, LAMP, loop-mediated isothermal amplification; PSR, polymerase spiral reaction; PFGE, pulsed-field gel electrophoresis; MLVA, multiple locus variable-number tandem repeat analysis; MLST, multilocus sequencing typing; DL rep-PCR, DiversiLab repetitive-sequence-based PCR; NGS, next generation sequencing.