Table 1

Comparison of Common Bacterial Typing Techniques by Relative Discriminatory Power, Reproducibility, Repeatability, and Whether They Give Information on Dispersed or Focal Parts of the Genome, Time Required and Cost
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
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
Amplified fragment length polymorphism (AFLP)	Moderate to high	High	Medium=>High	Dispersed	2	Equipment: Low to Medium Labor & Supplies: Low
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
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

Focal corresponds to interrogating a single loci. Dispersed means multiple loci are interrogated. *Per isolate costs in US dollars in 2005, assuming all equipment are available, and the investigator has access to automatic sequencing, for PCR reactions are ~$5, PFGE~$20, MLST ~$140, comparative hybridization~$1000 to $2000 and total genomic sequencing (assuming a strain has already been sequenced)~$100,000 to $500,000. Note: For a summary and details of these techniques, and assessments of repeatability and reproducibility, see Tenover, 1997 [1], Gurtler and Mayall 2001 [2] and VanBelkum, 2003 [3]. In general, sequence-based methods are most repeatable and reproducible. Gel-based methods are less so, because of the inherent variability of the technique.
Foxman et al. Epidemiologic Perspectives & Innovations 2005 2:10 doi:10.1186/1742-5573-2-10