title: Comparison of genome diversity of Brucella spp. field isolates using Universal Bio-signature Detection Array and whole genome sequencing reveals limitations of current diagnostic methods.
abstract: The detection and identification of bio-threat agents and the study of host-pathogen interactions require a high-resolution detection platform capable of discerning closely related species. Diverse analysis methods are used to identify pathogens, specifically Brucella species or biovars. In this study, we compared four diagnostic approaches including serology-based biochemical test, PCR assay, microarray analysis using a Universal Bio-signature Detection Array (UBDA) and whole genome "deep" sequencing for Brucella organisms including a number of field isolates. We found that although there was frequent agreement among the different tests, some tests gave compound/contradictory results that were a consequence of species diversity due to mixed infections or minor contaminants as measured by UBDA and validated from whole genome sequence. By comparing these analysis techniques, we demonstrate that standard diagnostics used in the field are limited in their ability to identify genomic DNA contaminants in field isolates while UBDA and sequencing analysis are highly sensitive in tracing genomic differences among the isolates.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA.
authors.forename: Shamira J
authors.initials: SJ
authors.lastname: Shallom
authors.forename: Hongseok
authors.initials: H
authors.lastname: Tae
authors.forename: Luciana
authors.initials: L
authors.lastname: Sarmento
authors.forename: Dale
authors.initials: D
authors.lastname: Preston
authors.forename: Lauren
authors.initials: L
authors.lastname: McIver
authors.forename: Christopher
authors.initials: C
authors.lastname: Franck
authors.forename: Allan
authors.initials: A
authors.lastname: Dickerman
authors.forename: L Garry
authors.initials: LG
authors.lastname: Adams
authors.forename: Harold R
authors.initials: HR
authors.lastname: Garner
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques; D001431:Bacteriological Techniques; D002002:Brucella / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D002006:Brucellosis / Q000175:diagnosis / Q000382:microbiology / Q000662:veterinary; D002007:Brucellosis, Bovine / Q000175:diagnosis / Q000382:microbiology; D002417:Cattle; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D034421:Sus scrofa
chemical_list: D004269:DNA, Bacterial