AUTHOR=Gorzalski Andrew , Ambrosio Frank J. , Massic Lauryn , Scribner Michelle R. , Siao Danielle Denise , Hua Chi , Dykema Phillip , Schneider Emily , Njoku Chidinma , Libuit Kevin , Sevinsky Joel R. , Van Hooser Stephanie , Pandori Mark , Hess David 

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

JOURNAL=Frontiers in Public Health

VOLUME=11

YEAR=2023

URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2023.1198189

DOI=10.3389/fpubh.2023.1198189

ISSN=2296-2565

ABSTRACT=<p>A <italic>Candida auris</italic> outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 <italic>C. auris</italic> isolates from patients at several facilities. Genetically distinct subgroups of <italic>C. auris</italic> 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 <italic>C. auris</italic> 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.</p>