Lab Matters Fall 2024 | Page 104

APHL 2024 POSTER ABSTRACTS

Genomic Epidemiology of Candida auris in a Burn Intensive Care Unit

H . Barbian 1 , L . Lie 2 , A . Kittner 3 , A . Harrington 2 , M . Frias 4 , J . Parada 2 , D . Young Kim 3 , S . Black 3 , M . Pacilli 3 , M . Hayden 1 , Rush University Medical Center 1 , Loyola University Medical Center 2 , Chicago Department of Public Health 3 , Cook County Department of Public

Health 4

Background : Candida auris is an emerging fungal pathogen associated with outbreaks in healthcare settings , frequently in intensive care units ( ICUs ). Whole genome sequencing has been used to support C . auris outbreak investigation and response . We used whole genome sequencing and genomic epidemiology to investigate a multi-year outbreak of C . auris in a burn ICU ( BICU ) in Illinois .

Methods : A cluster of four C . auris clinical cases in the BICU in 2021 initiated an outbreak investigation and response , including multimodal mitigation measures like admission and point-prevalence screening , enhanced environmental cleaning , hand hygiene and other infection prevention best practices . Despite this , C . auris continued to be detected in the BICU over the course of two years . To investigate i ) the genetic relationship of C . auris among cases and ii ) whether on-going C . auris detections resulted from its persistence in the BICU or new introductions , available C . auris isolates were subjected to whole genome sequencing ( Illumina NovaSeq6000 ). Sequence data were analyzed using the CDC MycoSNP pipeline and single nucleotide polymorphisms ( SNPs ) and phylogenetic relationships between cases were assessed .

Results : 28 C . auris cases were identified in the BICU over a 2-year period . Weekly point prevalence screens identified 23 ( 82.1 %) cases . Whole genome sequencing was performed on available BICU C . auris isolates ( n = 19 ) and contemporaneous non-BICU C . auris isolates from other units within the hospital and another hospital in the health system ( n = 50 ). All isolates fell within C . auris Clade IV and clustered in a single clade with other publicly available Illinois C . auris sequences . Phylogenetic analysis revealed four distinct clusters of closely related ( differing by 0-6 SNPs ) BICU genomes . These clusters each contained 3-6 cases . Two cases did not cluster closely with any other BICU specimen ( differing by 21-66 SNPs to other BICU cases ). BICU C . auris clusters generally contained specimens collected within a few months from patients with putative epidemiological links , such as shared equipment , staff , or temporal overlap . This suggests that multiple introductions and within-unit spread over a limited timeframe were responsible for the BICU cases , rather than transmission from a long-term source ( e . g . persistent environmental contamination or staff carriage ).

Conclusions : Whole genome sequencing and genomic epidemiology can support C . auris outbreak investigation and response by informing mechanisms of transmission such as multiple new introductions or sustained transmission after a single introduction . This , in turn , can direct targeted interventions such as admission screening for new C . auris introductions and environmental disinfection and hand hygiene for sustained transmission .

Presenter : Hannah Barbian , hannah _ j _ barbian @ rush . edu

Genomic Surveillance of Candida auris Clades and FKS1 Mutations in the Antimicrobial Resistance Laboratory Network ’ s Mountain Region : A Comprehensive Analysis

T . Iverson , K . Oakeson , J . Hergert , Utah Public Health Laboratory

Candida auris , known for its virulent nature , has transcended its role as a causative agent of candidiasis . It has emerged as a formidable global fungal pathogen , characterized by its ability to cause severe illness , spread easily among healthcare facility patients and frequent resistance to antifungal treatments . In the Mountain Region of the Antimicrobial Resistance Laboratory Network , we present an overview of our genomic surveillance efforts . These efforts encompass the analysis of 2,213 C . auris isolates , all of which underwent whole-genome sequencing between December 2021 and December 2023 .

Our primary objectives were to gain a comprehensive understanding of the clade distribution of C . auris within the Mountain Region and investigate the prevalence of specific FKS1 mutations . To achieve this , we leveraged the mycosnp-nf workflow , a Nextflow workflow for performing whole genome sequencing analysis of fungal organisms .

Our findings reveal a detailed distribution of C . auris clades I , III and IV within the Mountain Region . Notably , Clade III predominates in State A , with 961 isolates , while Clade I exhibits a significant presence in both State A ( 696 isolates ) and State B ( 259 isolates ). Additionally , we observed varying frequencies of specific FKS1 mutations across different clades and states . For instance , Clade I is characterized by a predominance of p . Ser639Phe mutations ( 10 isolates ), whereas Clade III predominantly features p . Leu638Trp mutations ( 3 isolates ). Interestingly , Clade I displays a higher occurrence of FKS1 mutations ( 27 ) than Clade III ( 8 ), with approximately 2.77 % of Clade I isolates and 0.72 % of Clade III isolates exhibiting these mutations .

Our data not only aids in tracking the regional epidemiology of this emerging pathogen but also sheds light on the association between clades and specific FKS1 mutations , contributing to our understanding of C . auris evolution and antifungal resistance patterns .

Presenter : Thomas Iverson , Utiverson @ utah . gov

High-accuracy , Long-read Sequencing of Microbial Isolates And Standards Enables AR Profiling , Methylation Detection and Taxonomic Annotation

L . Ly , R . Featherston , S . Midha , P . James , P . West , J . Beaulaurier , G . Dodd , M . Heatly , S . McKenzie , Oxford Nanopore Technologies

Genomic and metagenomic sequencing is revolutionizing the field of microbiology . Previously , tradeoffs between read length and accuracy in short read sequencing and early long read sequencing have limited the completeness and accuracy of genomic and metagenomic analyses ; however , recent advancements in Oxford Nanopore Technologies ’ sequencing have significantly improved long read accuracy for microbial genomic applications .

Here , we use Nanopore sequencing with the latest chemistry and basecalling models to characterize the genomes of 32 bacterial isolates sourced from the FDA CFSAN proficiency panel in triplicate , with 16 samples per MinION flow cell . Nanopore-only assemblies achieved high completeness and accuracy ( mean / median > Q50 ) when compared to publicly available reference genomes . We found