Comparison of methods for microbial source tracking in aquatic environments

Genotypic, library based
    RibotypingQuantitative; highly sensitive and reproducible; classifies isolates from multiple sourcesLarge isolate database required, geographically specific; labor-intensive and time-consuming; high percentage of inconclusive results71, 124
    Pulsed-field gel electrophoresisSensitive, discriminative, and reproducible; quantitativeLabor-intensive and time-consuming; may be too sensitive for discriminating multiple sources82, 122
Phenotypic, library based
    Antibiotic resistance analysisRapid; classifies isolates from multiple animal sourcesLarge 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 used67, 123
Library and culture independent (bacterial host-specific markers)
    Terminal restriction fragment length polymorphism, length heterogeneity PCRRapid and easy to perform; no database or cultivation required; high accuracy in differentiating human and nonhuman sourcesSurvival and distribution of molecular markers in aquatic environments are not well studied; expensive equipment; currently applicable to only a limited number of host groups6, 10
Direct measurement of host-specific viruses
    PCR for viral pathogensLibrary independent and directly relates to health risk; rapid and straightforward; detects conserved regions of a viral genome, may not have geographical limitsNonquantitative in conventional PCR; requires more sensitive detection methods; limited knowledge of prevalence of animal-specific viruses in aquatic environments; serotyping is expensive and time-consuming40, 100, 120
    PCR and phage typing (e.g., F+ RNA coliphage)Subgroups are well-correlated to sources; straightforwardSerotyping 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 noted76, 134