Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections

Abstract

We used whole-genome sequence typing (WGST) to investigate an outbreak of Sarocladium kiliense bloodstream infections (BSI) associated with receipt of contaminated antinausea medication among oncology patients in Colombia and Chile during 2013-2014. Twenty-five outbreak isolates (18 from patients and 7 from medication vials) and 11 control isolates unrelated to this outbreak were subjected to WGST to elucidate a source of infection. All outbreak isolates were nearly indistinguishable (<5 single-nucleotide polymorphisms), and >21,000 single-nucleotide polymorphisms were identified from unrelated control isolates, suggesting a point source for this outbreak. S. kiliense has been previously implicated in healthcare-related infections; however, the lack of available typing methods has precluded the ability to substantiate point sources. WGST for outbreak investigation caused by eukaryotic pathogens without reference genomes or existing genotyping methods enables accurate source identification to guide implementation of appropriate control and prevention measures.

Keywords: Chile; Colombia; Latin America; bloodstream infections; epidemiology; fungal outbreaks; fungi; whole-genome sequencing.

Figure

Whole-genome single-nucleotide polymorphism (SNP) typing of Sarocladium kiliense strains, Chile and Colombia, 2013–2014. All patient (clinical) and drug (vial) isolates from these 2 countries differed by <5 SNPs, and >21,000 SNPs were identified for the control isolates (≈117,000 total SNPs, ≈73,000 parsimoniously informative SNPs). Scale bar indicates nucleotide substitutions per site.