Journal article
Using DNA Microarrays To Identify Library-Independent Markers for Bacterial Source Tracking
Applied and environmental microbiology, Vol.72(3), pp.1843-1851
03/2006
Handle:
https://hdl.handle.net/2376/118088
PMCID: PMC1393180
PMID: 16517630
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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Details
- Title
- Using DNA Microarrays To Identify Library-Independent Markers for Bacterial Source Tracking
- Creators
- Marilyn Soule - Department of Microbiology and Pathology, Washington State University, Pullman, WashingtonEdward Kuhn - Department of Microbiology and Pathology, Washington State University, Pullman, WashingtonFrank Loge - Department of Microbiology and Pathology, Washington State University, Pullman, WashingtonJohn Gay - Department of Microbiology and Pathology, Washington State University, Pullman, WashingtonDouglas R Call - Department of Microbiology and Pathology, Washington State University, Pullman, Washington
- Publication Details
- Applied and environmental microbiology, Vol.72(3), pp.1843-1851
- Academic Unit
- Veterinary Clinical Sciences, Department of; Paul G. Allen School for Global Animal Health
- Publisher
- American Society for Microbiology
- Identifiers
- 99900547838601842
- Language
- English
- Resource Type
- Journal article