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Origin of Sarocladium kiliense outbreak determined by whole-genome sequencing

November 14 2016

Whole-genome sequence typing (WGST) determines the genetic relationships amongst isolates by the phylogenetic analysis of single-nucleotide polymorphism differences. Typically, fewer observed differences means that strains are more closely related, and that they are more likely to have a single point source. This technology is therefore a particularly useful tool in outbreak investigations since differentiating between fungal infections originating from a single contaminated source and those independently acquired from the environment is difficult.

Whole-genome single-nucleotide polymorphism (SNP) typing of Sarocladium kiliense strains (click for bigger image)
 

Researchers from the Centers for Disease Control and Prevention (CDC) in Georgia investigated an outbreak of Sarocladium Kiliense (previously known as Acremonium kiliense) in Columbia and Chile during 2013-2014. 25 outbreak isolates and 11 control isolates (unrelated to this outbreak) were subjected to WGST in order to determine the source or sources of infection. Genomic DNA was extracted from cells grown on Sabouraud dextrose agar by using the DNeasy Blood and Tissue kit (QIAGEN, Hilden, Germany) and the 36 samples were prepared for Illumina sequencing (Illumina, San Diego, CA, USA) by using the KAPA Biosystems Library Preparation with Standard PCR kit (KAPA BBiosystems, Wilmington, MA, USA) protocol.

Sarocladium kiliense - often, these hyphae tend to form bundles or cords as they cling together. Long thin, delicate phialides bear conidia at their tips. (Image by Mr. Yuri E. Amatnieks, website here)
 

Isolates were taken both from patients and from  the antinausea medication vials as the epidemiological investigation suggested that contaminated antinausea medication could be the source. Patient isolates from Chile and Colombia were virtually genetically indistinguishable (i.e. ≤5 single nucleotide polymorphisms) from those recovered from medication vials, while control isolates were unrelated (>21000 single nucleotide polymorphisms). These results were indicative of a point source for the outbreak, confirming the evidence from the epidemiological investigation.
WGST enables accurate deduction of genetic relationships among strains in rare fungal outbreaks for which current typing methods are ineffective or non-existent. 

Article (DOI: 10.3201/eid2203.151193)