Table 3.
Summary of molecular techniques used to genotype M. hyopneumoniae field strains (adapted from Stakenborg, 2005)
| Target of technique | Methodology | Technique(s) used | Reference | Amplicon | Reproducibility | Discriminatory power | Ease of performance | Time required (days) | Ease of interpretation | Cost-efficient |
|---|---|---|---|---|---|---|---|---|---|---|
| Entire genome | Restriction and electrophoresis | FIGE | Frey et al. (1992) | Eco RI | ++ | + | − | 2–3 | + | + |
| PFGE | Blank and Stemke (2000) | ApaI, Sal I, ApaL, Asp718 | ++ | ++ | − | 2–3 | + | + | ||
| Stakenborg et al. (2005) | ||||||||||
| Restriction and hybridisation | REA and DNA specific probe | Ferrell et al. (1989) | IS-like | ± | ± | ++ | 1 | −− | − | |
| Harasawa et al. (1995) | Unknown repetitive sequence | |||||||||
| Restriction and PCR | AFLP | Kokotovic et al. (1999) | Restriction enzymes | + | ++ | ± | 2 | − | + | |
| Stakenborg et al. (2006a) | ||||||||||
| PCR | RAPD (AP-PCR) | Artiushin and Minion (1996) | OPA-3 primer | − | ++ | ++ | <1 | ± | − | |
| Vicca et al. (2003) | ||||||||||
| Stakenborg et al. (2006a) | ||||||||||
| Specific DNA fragment | PCR | PCR | Hsu et al., 1997, Lin, 2001 | P97 | ++ | − | ++ | <1 | + | − |
| PCR of repetitive elements | VNTR | Stakenborg et al. (2006a) | P97 | ++ | ± | ++ | <1 | + | − | |
| de Castro et al. (2006) | VNTR genes | |||||||||
| PCR and restriction | PCR-RFLP | Stakenborg et al. (2006a) | P146 | ++ | ± | ++ | <1 | + | ± | |
| PCR and electrophoresis | PCR-DGGE | McAuliffe et al. (2005) | 16 SrRNA | |||||||
| PCR and sequencing | PCR-seq | Wilton et al. (1998) | P97 | + | ++ | + | 1 | + | + | |
| Mayor et al. (2007a) | p146 | |||||||||
| Mrazek (2006) | mnSSR | NA | ++ | + | 1 | + | + | |||
| MLST | Mayor et al. (2007b) | adk, rpoB, tpiA | ++ | ++ | ± | 2 | + | + | ||
| PCR and hybridisation | Microarray | Madsen et al. (2007) | 125–350 bp PCR products | ++ | ++ | − | 1 | − | − |
PCR, polymerase chain reaction; RAPD, randomly amplified polymorphic DNA; VNTR, variable number tandem repeats; AFLP, amplified fragment length polymorphism; RLFP, restriction fragment length polymorphism; PFGE, pulsed-field gel electrophoresis; DGGE, denaturing gradient gel electrophoresis; Seq, sequencing; REA, restriction endonuclease analysis; AP-PCR, arbitrarily primed PCR; FIGE, field-inversed gel electrophoresis; mnSSR, mononucleotide simple sequence repeats; MLST, multi locus sequence typing; NA, not available; ++, very high; +, high; ±, moderate; −, low; −−, very low.