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.

TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization

“…Since its development, TheiaEuk has been used to analyze 961 C. auris isolates from an ongoing outbreak in southern Nevada. Genomic and phylogenetic analysis of the first 209 samples were reported in Gorzalski et al ( 29 ) and the remaining 752 samples are reported for the first time in this study. These 752 specimens were isolated from samples obtained from either patients presenting with symptoms or through screening of long-term care patients between April 2022 to February 2023.…”

“…The relevance of this analysis in the southern Nevada outbreak was examined by two methods. Firstly, the accumulation of FKS1 mutations over time was examined during the outbreak using data from this work and Gorzalski et al ( Figure 3 ) ( 29 ). These mutations occur in strains that share the complete genetic background of non- FKS1 mutant isolates in the Nevada outbreak.…”

“…The workflow utilizes many existing bioinformatics tools as cited in the sections below and produces outputs with industry standard file formats to facilitate downstream analyses. Comparison of TheiaEuk to other pipelines that have been deployed for fungal genome analysis, MycoSNP ( 27 ) and Nullarbor ( 28 ), was presented in Gorzalski et al ( 29 ). The structure of the pipeline is described below and illustrated in Figure 1 .…”

“…C. auris specimens from an ongoing outbreak in southern Nevada were isolated from clinical samples collected from April 2022 to February 2023. Genomic data from 752 specimens is reported for the first time in this study, but several analyses utilize all sequenced isolates from the southern Nevada outbreak including an additional 209 specimens reported in Gorzalski et al ( 29 ).…”

“…Samples were analyzed using the TheiaEuk workflow v1.0.0 with default parameters on Terra. Analysis of clade assignments and FKS1 mutations among these samples and an additional 209 specimens reported in Gorzalski et al ( 29 ) was visualized using R and RStudio with the tidyverse package ( 58–60 ). Twelve samples with either assembly lengths greater than 14 Mbp or BUSCO completeness scores less than 90% were excluded from this analysis as noted in Supplementary Table S4 .…”