Genomic Analysis of B. pseudomallei Isolates

Illumina short reads of the environmental B. pseudomallei isolates from this study were submitted to the Sequence Read Archive under the NCBI accession ERR9146399 (IND_S3) an ERR9138530 (IND_S14). Whole genome sequencing data of B. pseudomallei strains were analyzed in SeqSphere (Ridom GmbH, Germany) using our previously published B. pseudomallei core genome MLST (cgMLST) scheme (Lichtenegger et al., 2021 (link)). A UPGMA tree and a minimum spanning tree were constructed based on the allelic profiles of the isolates. Columns with missing values for at least one sample were removed before analysis, resulting in 3635 targets/distance columns. Figures were created and annotated with Ridom SeqSphere.

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Shaw T., Assig K., Tellapragada C., Wagner G.E., Choudhary M., Göhler A., Eshwara V.K., Steinmetz I, & Mukhopadhyay C. (2022). Environmental Factors Associated With Soil Prevalence of the Melioidosis Pathogen Burkholderia pseudomallei: A Longitudinal Seasonal Study From South West India. Frontiers in Microbiology, 13, 902996.

Publication 2022

SeqSphere

Allelic Genome Strains Tree

Corresponding Organization : Medical University of Graz

Other organizations : M S Ramaiah University of Applied Sciences, Karolinska Institutet, Central Soil Salinity Research Institute, Federal Institute for Risk Assessment

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Variable analysis

independent variables

Whole genome sequencing data of B. pseudomallei strains

dependent variables

Allelic profiles of the isolates
UPGMA tree
Minimum spanning tree

control variables

B. pseudomallei core genome MLST (cgMLST) scheme

Annotations

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