title: Improved detection of Rhodococcus coprophilus with a new quantitative PCR assay.
abstract: Agricultural practices, such as spreading liquid manure or the utilisation of land as animal pastures, can result in faecal contamination of water resources. Rhodococcus coprophilus is used in microbial source tracking to indicate animal faecal contamination in water. Methods previously described for detecting of R. coprophilus in water were neither sensitive nor specific. Therefore, the aim of this study was to design and validate a new quantitative polymerase chain reaction (qPCR) to improve the detection of R. coprophilus in water. The new PCR assay was based on the R. coprophilus 16S rRNA gene. The validation showed that the new approach was specific and sensitive for deoxyribunucleic acid from target host species. Compared with other PCR assays tested in this study, the detection limit of the new qPCR was between 1 and 3 log lower. The method, including a filtration step, was further validated and successfully used in a field investigation in Switzerland. Our work demonstrated that the new detection method is sensitive and robust to detect R. coprophilus in surface and spring water. Compared with PCR assays that are available in the literature or to the culture-dependent method, the new molecular approach improves the detection of R. coprophilus.
authors.affiliation: Federal Office of Public Health, 3003, Bern, Switzerland. Melanie.Wicki@gmx.ch
authors.forename: Melanie
authors.initials: M
authors.lastname: Wicki
authors.forename: Adrian
authors.initials: A
authors.lastname: Auckenthaler
authors.forename: Richard
authors.initials: R
authors.lastname: Felleisen
authors.forename: Marianne
authors.initials: M
authors.lastname: Liniger
authors.forename: Caroline
authors.initials: C
authors.lastname: Loutre
authors.forename: Isabel
authors.initials: I
authors.lastname: Niederhauser
authors.forename: Marcel
authors.initials: M
authors.lastname: Tanner
authors.forename: Andreas
authors.initials: A
authors.lastname: Baumgartner
mesh_terms: D000818:Animals; D001431:Bacteriological Techniques / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012240:Rhodococcus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D012680:Sensitivity and Specificity; D013557:Switzerland; D014871:Water Microbiology; D014876:Water Pollution
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S