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We present the case of a 51-y-old male with multiple splenic abscesses that failed to resolve despite antimicrobial therapy targeted at Burkholderia pseudomallei. Elective splenectomy was performed to clarify the diagnosis. Pus from the spleen was subjected to universal bacterial 16S rDNA amplification and sequencing. The sequence obtained was 99% identical to 16S rDNA sequences for Burkholderia pseudomallei. Sequencing of the 16S rDNA is a very promising diagnostic tool allowing quick identification of Burkholderia pseudomallei directly from clinical specimen.