Genotypic, library based |
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|
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Ribotyping |
Quantitative; highly sensitive and reproducible; classifies isolates from multiple sources |
Large isolate database required, geographically specific; labor-intensive and time-consuming; high percentage of inconclusive results |
71, 124
|
Pulsed-field gel electrophoresis |
Sensitive, discriminative, and reproducible; quantitative |
Labor-intensive and time-consuming; may be too sensitive for discriminating multiple sources |
82, 122
|
Phenotypic, library based |
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|
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Antibiotic resistance analysis |
Rapid; classifies isolates from multiple animal sources |
Large isolate database required, geographically specific; isolates have to show antibiotic resistance to be typed; antibiotic resistance traits are not stable; no consensus on combination and dose of antibiotics used |
67, 123
|
Library and culture independent (bacterial host-specific markers) |
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|
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Terminal restriction fragment length polymorphism, length heterogeneity PCR |
Rapid and easy to perform; no database or cultivation required; high accuracy in differentiating human and nonhuman sources |
Survival and distribution of molecular markers in aquatic environments are not well studied; expensive equipment; currently applicable to only a limited number of host groups |
6, 10
|
Direct measurement of host-specific viruses |
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|
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PCR for viral pathogens |
Library independent and directly relates to health risk; rapid and straightforward; detects conserved regions of a viral genome, may not have geographical limits |
Nonquantitative in conventional PCR; requires more sensitive detection methods; limited knowledge of prevalence of animal-specific viruses in aquatic environments; serotyping is expensive and time-consuming |
40, 100, 120
|
PCR and phage typing (e.g., F+ RNA coliphage) |
Subgroups are well-correlated to sources; straightforward |
Serotyping is expensive and time-consuming; low survival in marine and tropical waters; may proliferate in sewage; exceptions in association of coliphage subgroup and host group have been noted |
76, 134
|