Aspergillus Outbreak in an Intensive Care Unit: Source Analysis with Whole Genome Sequencing and Short Tandem Repeats

Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but is scarcely used in mycology. Here, we used WGS for genotyping isolates from a potential outbreak in an intensive care unit (ICU) during construction work. After detecting the outbreak, fungal culture...

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Bibliographic Details
Published in:Journal of fungi (Basel) 2024-01, Vol.10 (1), p.51
Main Authors: Hiel, Stephan J P, Hendriks, Amber C A, Eijkenboom, Jos J A, Bosch, Thijs, Coolen, Jordy P M, Melchers, Willem J G, Anröchte, Paul, Camps, Simone M T, Verweij, Paul E, Zhang, Jianhua, Dommelen, Laura van
Format: Article
Language:English
Subjects:
Aspergillus
Aspergillus fumigatus
Bacteriology
Comparative analysis
construction work
Epidemics
Fungi
Genomes
Genotyping
Intensive care
Mortality
Outbreaks
Outdoor air quality
Patients
Phenols
Phylogeny
Sepsis
Short tandem repeats
Single-nucleotide polymorphism
source analysis
Spores
Surveillance
Whole genome sequencing
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Summary:Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but is scarcely used in mycology. Here, we used WGS for genotyping isolates from a potential outbreak in an intensive care unit (ICU) during construction work. After detecting the outbreak, fungal cultures were performed on all surveillance and/or patient respiratory samples. Environmental samples were obtained throughout the ICU. WGS was performed on 30 isolates, of which six patient samples and four environmental samples were related to the outbreak, and twenty samples were unrelated, using the Illumina NextSeq 550. A SNP-based phylogenetic tree was created from outbreak samples and unrelated samples. Comparative analysis (WGS and short tandem repeats (STRs), microsatellite loci analysis) showed that none of the strains were related to each other. The lack of genetic similarity suggests the accumulation of spores in the hospital environment, rather than a single source that supported growth and reproduction of . This supports the hypothesis that the outbreak was likely caused by release of spores during construction work. Indeed, no new cases were observed in the ICU after cessation of construction. This study demonstrates that WGS is a suitable technique for examining inter-strain relatedness of in the setting of an outbreak investigation.
ISSN:2309-608X
2309-608X
DOI:10.3390/jof10010051