Molecular Characterization of Bacteriophages for Microbial Source Tracking in Korea

Abstract

We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F ؉ -specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F ؉ coliphages in all of the tested fecal samples. We further characterized 311 F ؉ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F ؉ coliphages from various sources. F ؉ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F ؉ RNA coliphages, most F ؉ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F ؉ RNA coliphages isolated from various sources were divided into two main clusters. All F ؉ RNA coliphages isolated from human wastewater were grouped with Q␤-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F ؉ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F ؉ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F ؉ RNA coliphages can effectively distinguish fecal sources.

Relevance of Bacteroidales and F-Specific RNA Bacteriophages for Efficient Fecal Contamination Tracking at the Level of a Catchment in France

“…Presence of FRNAPH I in WWTP effluents in the present study (11%) was similar to that previously reported in South Carolina (11%, n ϭ 133) (34) or Korea (28%, n ϭ 38) (18). This could have been due either to FRNAPH I presence in human effluents or to the presence of feces from wild animals such as seagull, duck, or dog in the WWTP effluents.…”

Coliphages as Model Organisms in the Characterization and Management of Water Resources

“…If we consider the percentage of human and animal individuals excreting phages and the amounts of phages excreted, the inputs of somatic coliphages [89][90][91] in the water environment directly from feces are greater than those of F-specific coliphages [90][91][92][93].…”

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins

“…First of all, the distribution of phage subgroups is not absolute. (i) FRNAPH-III, generally associated with humans, has been isolated in high proportions in swine wastewater (12,19), (ii) FRNAPH-I has been detected in municipal wastewater (20), and (iii) even if FRNAPH-II seems to be highly associated with humans (21), it has also been found in animal feces (22). The second limitation is due to the variable survival rates of FRNAPH in the environment.…”

“…We explored in particular the possibility of minimizing both drawbacks described above. The first objective was to determine whether genome sequencing within each subgroup could allow better differentiation between animal and human fecal contamination as recently suggested (20,30). To achieve this, we isolated by culture FRNAPH strains from samples of known origin (animal feces, urban wastewater, and slaughterhouse wastewater).…”