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Ambrosio FJ, Scribner MR, Wright SM, Otieno JR, Doughty EL, Gorzalski A, Siao DD, Killian S, Hua C, Schneider E, Tran M, Varghese V, Libuit KG, Pandori M, Sevinsky JR, Hess D. TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization. Front Public Health 2023; 11:1198213. [PMID: 37593727 PMCID: PMC10428623 DOI: 10.3389/fpubh.2023.1198213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens. Methods TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of C. auris in southern Nevada was investigated. We performed whole-genome sequence analysis of 752 new C. auris isolates from this outbreak. Furthermore, TheiaEuk was utilized to observe the accumulation of mutations in the FKS1 gene over the course of the outbreak, highlighting the utility of TheiaEuk as a monitor of emerging public health threats when combined with whole-genome sequencing surveillance of fungal pathogens. Results A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Candida auris (C. auris). In addition, for several fungal species, it performs dynamic reference genome selection and variant calling, reporting mutations found in genes currently associated with antifungal resistance (FKS1, ERG11, FUR1). Using genome assemblies from the ATCC Mycology collection, the taxonomic identification module used by TheiaEuk correctly assigned genomes to the species level in 126/135 (93.3%) instances and to the genus level in 131/135 (97%) of instances, and provided zero false calls. Application of TheiaEuk to actual specimens obtained in the course of work at a local public health laboratory resulted in 13/15 (86.7%) correct calls at the species level, with 2/15 called at the genus level. It made zero incorrect calls. TheiaEuk accurately assessed clade type of Candida auris in 297/302 (98.3%) of instances. Discussion TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of C. auris and in the identification of mutations known to associate with drug resistance in that organism.
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Affiliation(s)
| | | | | | | | | | | | | | - Steve Killian
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | - Chi Hua
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Emily Schneider
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Michael Tran
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Vici Varghese
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV, United States
| | | | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
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Gorzalski A, Ambrosio FJ, Massic L, Scribner MR, Siao DD, Hua C, Dykema P, Schneider E, Njoku C, Libuit K, Sevinsky JR, Van Hooser S, Pandori M, Hess D. The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada. Front Public Health 2023; 11:1198189. [PMID: 37522005 PMCID: PMC10374848 DOI: 10.3389/fpubh.2023.1198189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/06/2023] [Indexed: 08/01/2023] Open
Abstract
A Candida auris outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 C. auris isolates from patients at several facilities. Genetically distinct subgroups of C. auris were detected from Clade I (3 distinct lineages) and III (1 lineage). Open-source bioinformatic tools were developed and implemented to aid in the epidemiological investigation. The work herein compares three methods for C. auris whole genome analysis: Nullarbor, MycoSNP and a new pipeline TheiaEuk. We also describe a novel analysis method focused on elucidating phylogenetic linkages between isolates within an ongoing outbreak. Moreover, this study places the ongoing outbreaks in a global context utilizing existing sequences provided worldwide. Lastly, we describe how the generated results were communicated to the epidemiologists and infection control to generate public health interventions.
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Affiliation(s)
| | | | - Lauryn Massic
- Nevada State Public Health Laboratory, Reno, NV, United States
| | | | | | - Chi Hua
- Division of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United States
| | - Phillip Dykema
- Division of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United States
| | - Emily Schneider
- Division of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United States
| | - Chidinma Njoku
- Nevada Department of Health and Human Services, Las Vegas, NV, United States
| | - Kevin Libuit
- Theiagen Consulting LLC, Highlands Ranch, CO, United States
| | | | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United States
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV, United States
| | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United States
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