title: Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia.
abstract: Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area.
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Ginther
authors.affiliation: Menzies School of Health Research, Casuarina, Northern Territory, Australia.
authors.forename: Mark
authors.initials: M
authors.lastname: Mayo
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America.
authors.forename: Stephanie D
authors.initials: SD
authors.lastname: Warrington
authors.affiliation: Menzies School of Health Research, Casuarina, Northern Territory, Australia.
authors.forename: Mirjam
authors.initials: M
authors.lastname: Kaestli
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America.
authors.forename: Travis
authors.initials: T
authors.lastname: Mullins
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America.
authors.forename: David M
authors.initials: DM
authors.lastname: Wagner
authors.affiliation: Menzies School of Health Research, Casuarina, Northern Territory, Australia.
authors.forename: Bart J
authors.initials: BJ
authors.lastname: Currie
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America; Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Apichai
authors.initials: A
authors.lastname: Tuanyok
authors.affiliation: Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America; Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D016957:Burkholderia pseudomallei / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005843:Geography; D006801:Humans; D008554:Melioidosis / Q000453:epidemiology / Q000382:microbiology*; D008969:Molecular Sequence Data; D015876:Northern Territory / Q000453:epidemiology; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S