Comparison of methods for microbial source tracking in aquatic environments
| Method | Advantages | Disadvantages | References |
|---|---|---|---|
| Genotypic, library based | |||
| 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 | |||
| 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) | |||
| 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 | |||
| 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 |