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DATA ANALYSIS
DATABASES
B.burgdorferi
B.cereus
B.henselae
B.pseudomallei
C.albicans
C.glabrata
C.krusei
C.tropicalis
C.jejuni
C.neoformans var grubii
E.coli
E.faecalis
E.faecium
H.influenzae
H.pylori
Leptospira spp.
M.catarrhalis
N.meningitidis
S.agalactiae
S.aureus
S.dysgalactiae
S.enterica
S.epidermidis
S.pneumoniae
S.pyogenes
S.suis
V.vulnificus
SUBMISSIONS
NEWS
LINKS
 

Introduction

Burkholderia pseudomallei, a saprophytic, gram-negative aerobe, is the causative agent of melioidosis, an infectious disease mainly restricted to South East Asia, Northern Australia and other tropical and non-tropical regions.  Melioidosis manifests itself clinically as abcesses, pneumonia and, at worst, as a fatal septicemia in susceptible hosts. It belongs to a closely related group of organisms, which incude Burkholderia mallei, the causative agent of glanders in horses and other equines, and the avirulent saprophytic species Burkholderia thailandensis, which was thought until recently to be a biotype of B. pseudomallei capable of assimilating arabinose. The MLST scheme developed for B. pseudomallei is also applicable to these two latter species and strains representing these species are available in the database.

REF - Daniel Godoy, Gaynor Randle, Andrew J. Simpson, David M. Aanensen, Tyrone L. Pitt, Reimi Kinoshita, and Brian G. Spratt. Multilocus Sequence Typing and Evolutionary Relationships among the Causative Agents of Melioidosis and Glanders, Burkholderia pseudomallei and Burkholderia mallei. J. Clin. Microbiol. 2003;41 2068-2079

The B. pseudomallei MLST scheme has been developed byDaniel Godoy (Imperial College) and Gaynor Randle (now at the John Radcliffe Hospital, University of Oxford), in the laboratory of Brian Spratt at the Department of Infectious Disease Epidemiology at Imperial College London, in collaboration with Ty Pitt at the Division of Hospital Infection, Central Public Health Laboratory, Colindale, London, and Andrew Simpson at the Royal Free Hospital, University College London, and Reimi Kinoshita of the University of Hong Kong. For further details please contact Erin Price (Erin Price)

Is it really B. pseudomallei?

MLST provides the best method for deciding whether an isolate is B.pseudomallei or another closely related species - see Help box on contatenation page. Click here

Obtaining an allelic profile and comparing your strains with those in our database

The allelic profile of a B. pseudomallei strain is obtained by sequencing internal fragments of seven house-keeping genes. The primers for the amplification and sequencing of these gene fragments can be obtained here. The sequences must be obtained on both strands, and they must be 100% accurate, since even a single error may convert a known allele into a novel allele.

The sequences have to be trimmed so that they correspond exactly to the region that we use to define the alleles. The sequences of the seven loci from a typical pneumococcus can be obtained here and can be used to ensure that your sequences have been trimmed correctly

For a query isolate, the sequences at the seven loci have to be compared with those in our database. Select the B. pseudomallei database, and the  locus query drop-down menu.  Select single locus and paste the correctly trimmed sequence into the box.  Select the appropriate locus in the drop-down menu, followed by submit query.

The software will check that the sequence is the correct length and that it does not contain any unrecognised characters. A check is also made to see if the submitted sequence is at least 70% similar to another allele at that locus (in case you have cut and pasted a sequence into the wrong box).   If the sequence corresponds to a known allele, the allele number will be returned.  If the sequence appears to be a new allele it should be compared with the most similar locus (or loci) to check that any sequence differences are real (this can be done using the Jalview module).  If you are convinced you have a new allele, the forward and reverse traces from the sequencer should be sent to the curator (d.godoy@ic.ac.uk) who will check their quality and if OK will assign a new allele number.

After you have obtained the allele numbers at each locus for your query strain, you select profile query and in the drop-down menu select allelic and enter the seven allele numbers in the appropriate boxes and submit.  If the allelic profile is in the database, the sequence type assigned to this allelic profile will be returned.  Otherwise the most similar allelic profile will be returned. You can then search for isolates that have allelic profiles that are similar to yours. For example, isolates that have at least 4/7, 5/7 or 6/7 matches to the submitted allelic profile and can show the relationships between your query strain and these strains by using the Tree button.

Further details about strains that are identical, or similar, to the submitted strain can be obtained by clicking on the strain names.

Help boxes are available on some pages. 

 
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Profile Query

 
Locus Query

Batch Query