title: Methods to increase fidelity of repetitive extragenic palindromic PCR fingerprint-based bacterial source tracking efforts.
abstract: The goal of the study was to determine which similarity coefficient and statistical method to use to produce the highest rate of correct assignment (RCA) in repetitive extragenic palindromic PCR-based bacterial source tracking. In addition, the use of standards for deciding whether to accept or reject source assignments was investigated. The use of curve-based coefficients Cosine Coefficient and Pearson's Product Moment Correlation yielded higher RCAs than the use of band-based coefficients Jaccard, Dice, Jeffrey's x, and Ochiai. When enterococcal and Escherichia coli isolates from known sources were used in a blind test, the use of maximum similarity produced consistently higher RCAs than the use of average similarity. We also found that the use of a similarity value threshold and/or a quality factor threshold (the ratio of the average fingerprint similarity within a source to the average similarity of this source's isolates to an unknown) to decide whether to accept source assignments of unknowns increases the reliability of source assignments. Applying a similarity value threshold improved the overall RCA (ORCA) by 15 to 27% when enterococcal fingerprints were used and 8 to 29% when E. coli fingerprints were used. Applying the quality factor threshold resulted in a 22 to 32% improvement in the ORCA, depending on the fingerprinting technique used. This increase in reliability was, however, achieved at the expense of decreased numbers of isolates that were assigned a source.
authors.affiliation: Department of Biological Sciences--USM, 118 College Dr., Hattiesburg, MS 39406-0001, USA.
authors.forename: Wail M
authors.initials: WM
authors.lastname: Hassan
authors.forename: Shiao Y
authors.initials: SY
authors.lastname: Wang
authors.forename: Rudolph D
authors.initials: RD
authors.lastname: Ellender
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D002417:Cattle; D016172:DNA Fingerprinting / Q000379:methods; D004269:DNA, Bacterial / Q000032:analysis; D016002:Discriminant Analysis; D004285:Dogs; D016983:Enterococcus / Q000235:genetics / Q000302:isolation & purification*; D004784:Environmental Monitoring / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics / Q000302:isolation & purification*; D005243:Feces / Q000382:microbiology; D006801:Humans; D015999:Multivariate Analysis; D016133:Polymerase Chain Reaction / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D014876:Water Pollution
chemical_list: D004269:DNA, Bacterial