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

被引：5

作者：

Gorzalski, Andrew ^{[1
]}

Ambrosio III, Frank J. J. ^{[2
]}

Massic, Lauryn ^{[1
]}

Scribner, Michelle R. R. ^{[2
]}

Siao, Danielle Denise ^{[1
]}

Hua, Chi ^{[3
]}

Dykema, Phillip ^{[3
]}

Schneider, Emily ^{[3
]}

Njoku, Chidinma ^{[4
]}

Libuit, Kevin ^{[2
]}

Sevinsky, Joel R. R. ^{[2
]}

Van Hooser, Stephanie ^{[1
]}

Pandori, Mark ^{[1
,5
,6
]}

Hess, David ^{[1
,5
]}

机构：

[1] Nevada State Publ Hlth Lab, Reno, NV 89503 USA

[2] Theiagen Consulting LLC, Highlands Ranch, CO USA

[3] Washington State Dept Hlth, Div Dis Control & Hlth Stat, Publ Hlth Labs, Shoreline, WA USA

[4] Nevada Dept Hlth & Human Serv, Las Vegas, NV USA

[5] Univ Nevada, Reno Sch Med, Dept Pathol & Lab Med, Reno, NV 89557 USA

[6] Univ Nevada, Reno Sch Med, Dept Microbiol & Immunol, Reno, NV 89557 USA

来源：

FRONTIERS IN PUBLIC HEALTH | 2023年 / 11卷

关键词：

Candida auris; epidemiology; whole-genome sequencing; bioinformatics; emerging pathogens;

D O I：

10.3389/fpubh.2023.1198189

中图分类号：

R1 [预防医学、卫生学];

学科分类号：

1004 ; 120402 ;

摘要：

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.

引用

页数：12

共 29 条

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