ArticleApplied and environmental microbiology2006
Using DNA microarrays to identify library-independent markers for bacterial source tracking.
Article in Applied and environmental microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 35 citations in OpenAlex.
- Genes Indicative of Zoonotic and Swine Pathogens Are Persistent in Stream Water and Sediment following a Swine Manure Spill.Applied and environmental microbiology · 2015Article
- Molecular Approach to Microbiological Examination of Water Quality in the Grand Bay National Estuarine Research Reserve (NERR) in Mississippi, USA.Environmental health insights · 2013Article
- Enterococci in the environment.Microbiology and molecular biology reviews : MMBR · 2012Review
- A Java-based tool for the design of classification microarrays.BMC bioinformatics · 2008Article
- Validation of mixed-genome microarrays as a method for genetic discrimination.Applied and environmental microbiology · 2007Article
- Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways.Applied and environmental microbiology · 2006Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial source tracking is used to apportion fecal pollution among putative sources. Within this context, library-independent markers are genetic or phenotypic traits that can be used to identify the host origin without a need for library-dependent classification functions. The objective of this project was to use mixed-genome Enterococcus microarrays to identify library-independent markers. Separate shotgun libraries were prepared for five host groups (cow, dog, elk/deer, human, and waterfowl), using genomic DNAs (gDNAs) from ca. 50 Enterococcus isolates for each library. Microarrays were constructed (864 probes per library), and 385 comparative genomic hybridizations were used to identify putative markers. PCR assays were used to screen 95 markers against gDNAs from isolates from known sources collected throughout the United States. This validation process narrowed the selection to 15 markers, with 7 having no recognized homologues and the remaining markers being related to genes involved in metabolic pathways and DNA replication. In most cases, each marker was exclusive to one of four Enterococcus species (Enterococcus casseliflavus, E. faecalis, E. hirae, or E. mundtii). Eight markers were highly specific to either cattle, humans, or elk/deer, while the remaining seven markers were positive for various combinations of hosts other than humans. Based on microarray hybridization data, the prevalence of host-specific markers ranged from 2% to 45% of isolates collected from their respective hosts. A 20-fold difference in prevalence could present challenges for the interpretation of library-independent markers.
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