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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

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

 

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

 
  1. *Focal corresponds to interrogating a single loci. Dispersed means multiple loci are interrogated.
  2. **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.
  3. 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.