The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada
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 line...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-07-01
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| Series: | Frontiers in Public Health |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpubh.2023.1198189/full |
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| author | Andrew Gorzalski Frank J. Ambrosio Lauryn Massic Michelle R. Scribner Danielle Denise Siao Chi Hua Phillip Dykema Emily Schneider Chidinma Njoku Kevin Libuit Joel R. Sevinsky Stephanie Van Hooser Mark Pandori Mark Pandori Mark Pandori David Hess David Hess |
| author_facet | Andrew Gorzalski Frank J. Ambrosio Lauryn Massic Michelle R. Scribner Danielle Denise Siao Chi Hua Phillip Dykema Emily Schneider Chidinma Njoku Kevin Libuit Joel R. Sevinsky Stephanie Van Hooser Mark Pandori Mark Pandori Mark Pandori David Hess David Hess |
| author_sort | Andrew Gorzalski |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T23:45:44Z |
| format | Article |
| id | doaj.art-d476c96b47524fb0864e4d6758d6790d |
| institution | Directory Open Access Journal |
| issn | 2296-2565 |
| language | English |
| last_indexed | 2024-03-12T23:45:44Z |
| publishDate | 2023-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj.art-d476c96b47524fb0864e4d6758d6790d2023-07-14T09:54:11ZengFrontiers Media S.A.Frontiers in Public Health2296-25652023-07-011110.3389/fpubh.2023.11981891198189The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern NevadaAndrew Gorzalski0Frank J. Ambrosio1Lauryn Massic2Michelle R. Scribner3Danielle Denise Siao4Chi Hua5Phillip Dykema6Emily Schneider7Chidinma Njoku8Kevin Libuit9Joel R. Sevinsky10Stephanie Van Hooser11Mark Pandori12Mark Pandori13Mark Pandori14David Hess15David Hess16Nevada State Public Health Laboratory, Reno, NV, United StatesTheiagen Consulting LLC, Highlands Ranch, CO, United StatesNevada State Public Health Laboratory, Reno, NV, United StatesTheiagen Consulting LLC, Highlands Ranch, CO, United StatesNevada State Public Health Laboratory, Reno, NV, United StatesDivision of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United StatesDivision of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United StatesDivision of Disease Control and Health Statistics, Washington State Department of Health, Public Health Laboratories, Shoreline, WA, United StatesNevada Department of Health and Human Services, Las Vegas, NV, United StatesTheiagen Consulting LLC, Highlands Ranch, CO, United StatesTheiagen Consulting LLC, Highlands Ranch, CO, United StatesNevada State Public Health Laboratory, Reno, NV, United StatesNevada State Public Health Laboratory, Reno, NV, United StatesDepartment of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United StatesDepartment of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV, United StatesNevada State Public Health Laboratory, Reno, NV, United StatesDepartment of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United StatesA 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.https://www.frontiersin.org/articles/10.3389/fpubh.2023.1198189/fullCandida aurisepidemiologywhole-genome sequencingbioinformaticsemerging pathogens |
| spellingShingle | Andrew Gorzalski Frank J. Ambrosio Lauryn Massic Michelle R. Scribner Danielle Denise Siao Chi Hua Phillip Dykema Emily Schneider Chidinma Njoku Kevin Libuit Joel R. Sevinsky Stephanie Van Hooser Mark Pandori Mark Pandori Mark Pandori David Hess David Hess The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada Frontiers in Public Health Candida auris epidemiology whole-genome sequencing bioinformatics emerging pathogens |
| title | The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada |
| title_full | The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada |
| title_fullStr | The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada |
| title_full_unstemmed | The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada |
| title_short | The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada |
| title_sort | use of whole genome sequencing and development of bioinformatics to monitor overlapping outbreaks of candida auris in southern nevada |
| topic | Candida auris epidemiology whole-genome sequencing bioinformatics emerging pathogens |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2023.1198189/full |
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