From: Choosing an appropriate bacterial typing technique for epidemiologic studies
Typing Technique | Relative discriminatory power | Relative repeatability | Relative reproducibility | Dispersed or focal parts of the genome* | Days required post culture | Relative Cost** | Notes |
---|---|---|---|---|---|---|---|
Sequencing of entire genome | High | High | High | Entire genome | Months to years | Very high | Â |
Comparative hybridization against array containing entire gene sequence | High | Medium to high | Medium to high | Dispersed | Weeks to months | High | Microarrays are increasingly available for human pathogens – not all genes will be present in the sequenced strain |
Direct sequencing of one or more genetic regions | Moderate to high (depends on gene choice) | High | High | Focal if only one region | 2–3 | Equipment: Medium to High Labor & Supplies: Medium to High | Initial selection of target genes might be time consuming. |
Multilocus sequence typing (MLST) | Moderate to high (depends on gene choice) | High | High | Dispersed | 3+ | Equipment: Medium to High Labor & Supplies: High | Initial selection of target genes might be time consuming. Species specific. |
Binary typing (presence/absence of selected genes or alleles across the genome) | Moderate to high (depends on gene choice) | High | Potentially High | Dispersed (if chose different genes across the genome) | 2–3 | Equipment: medium Labor & Supplies: Medium | Reliability dependent on DNA yield and purity |
Pulsed-field gel electrophoresis (PFGE) | Moderate to high (depends on number of bands observed) | Medium=> High (depending on species) | Medium =>High | Dispersed | 3 | Equipment: High Labor & Supplies: High | Discrimination depends on type and number of enzymes selected. |
Restriction fragment length polymorphism (RFLP) | Moderate to High (depends on number of bands observed) | Medium=>High | Medium | Dispersed | 1–3 | Medium |  |
Amplification of a single target gene specific to a pathogen | Moderate to high (depends on gene choice) | High | Medium=>High | Focal | <1 | Equipment: Low to Medium Labor & Supplies: Low | Â |
Amplified fragment length polymorphism (AFLP) | Moderate to high | High | Medium=>High | Dispersed | 2 | Equipment: Low to Medium Labor & Supplies: Low | Â |
Automated ribotyping | Moderate | High | High | Focal | 1 | Equipment: High Labor & Supplies: High | Works for most bacterial species |
Ribosomal RNA gel electrophoresis | Moderate | High | High | Focal | 1 | Equipment: Low Labor & Supplies: Medium | Â |
Targeting known repetitive gene sequences (enterobacterial repetitive intergenic consensus sequences (ERIC), repetitive extragenic palindromic sequences (REP), DRE (double repetitive element), BOX, insertional sequence (IS), polymorphic GC-rich repetitive sequences (PGRS)) | Low to moderate | Medium | Low | Generally dispersed | 1 | Equipment: Low to Medium Labor & Supplies: Low | Patterns vary with equipment used |
Random primers (randomly amplified polymorphic DNA (RAPD), arbitrary primed PCR (AP-PCR)) | Low to moderate | Low | Low | Dispersed | 1 | Equipment: Low to Medium Labor & Supplies: Low | Patterns vary with equipment used |
Restriction endonuclease on a single amplified product | Low to moderate (depends on amplicon) | High | High | Focal | 1–2 | Equipment: Low to Medium Labor & Supplies: Low |  |
Plasmid profiles | Low | High | Medium | Focal | 1 | Equipment: Low Labor & Supplies: Low | Â |