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The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada.

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.

SUBMITTER: Gorzalski A

PROVIDER: S-EPMC10374848 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada.

Gorzalski Andrew A Ambrosio Frank J FJ Massic Lauryn L Scribner Michelle R MR Siao Danielle Denise DD Hua Chi C Dykema Phillip P Schneider Emily E Njoku Chidinma C Libuit Kevin K Sevinsky Joel R JR Van Hooser Stephanie S Pandori Mark M Hess David D

Frontiers in public health 20230713

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 ...[more]

PMID: 37522005

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Project description:Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris. IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing.

Dataset Information

The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada.

Publications

The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of <i>Candida auris</i> in southern Nevada.

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Dataset Information

The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada.

Publications

The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of &lt;i&gt;Candida auris&lt;/i&gt; in southern Nevada.

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OmicsDI is part of the ELIXIR infrastructure

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The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of <i>Candida auris</i> in southern Nevada.