title: Use of a variable amplicon typing scheme reveals considerable variation in the accessory genomes of isolates of Burkholderia pseudomallei.
abstract: Melioidosis, a disease caused by the bacterium Burkholderia pseudomallei, is endemic in southeast Asia and northern Australia. We used suppression subtractive hybridization (SSH) to identify sequences that varied between two B. pseudomallei isolates from Australia and determined the distribution of 45 SSH-derived sequences among a panel of B. pseudomallei and B. thailandensis isolates. Sequences exhibiting variable prevalence were included in a variable amplicon typing (VAT) scheme designed to score the presence or absence of 14 PCR amplicons. VAT analysis was carried out with 48 isolates from Thailand, which were typed by multilocus sequence typing (MLST), and 44 isolates from Australia of known MLST type. The VAT scheme could be used to divide the 48 isolates from Thailand into 23 VAT types and the 44 isolates from Australia into 36 VAT types. Some of the sequences included in the VAT scheme were more commonly PCR positive among isolates from Australia than among isolates from Thailand, and vice versa. No isolate from Australia was PCR positive for genomic island 11 or a putative transposase sequence, whereas four SSH-derived sequences were far more prevalent among the Australian isolates. Analysis based on the VAT scheme indicated that the isolates clustered into groups, some of which were mainly or exclusively from one geographical origin. One cluster included Australian isolates that were mostly associated with severe disease, including rare neurological melioidosis, suggesting that the content of the accessory genome may play an important role in determining the clinical manifestation of the disease.
authors.affiliation: Division of Medical Microbiology, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, United Kingdom. C.Winstanley@liv.ac.uk
authors.forename: Kwanjit
authors.initials: K
authors.lastname: Duangsonk
authors.forename: Daniel
authors.initials: D
authors.lastname: Gal
authors.forename: Mark
authors.initials: M
authors.lastname: Mayo
authors.forename: C Anthony
authors.initials: CA
authors.lastname: Hart
authors.forename: Bart J
authors.initials: BJ
authors.lastname: Currie
authors.forename: Craig
authors.initials: C
authors.lastname: Winstanley
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D016957:Burkholderia pseudomallei / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D008875:Middle Aged; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial