Identifying Candida auris transmission in a hospital outbreak investigation using whole-genome sequencing and SNP phylogenetic analysis.

Autor:	Mitchell BI; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA., Kling K; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA.; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA., Bolon MK; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.; Department of Healthcare Epidemiology and Infection Prevention, Northwestern Memorial Hospital, Chicago, Illinois, USA., Rathod SN; Department of Healthcare Epidemiology and Infection Prevention, Northwestern Memorial Hospital, Chicago, Illinois, USA., Malczynski M; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA., Ruiz J; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA., Polanco W; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA., Fritz K; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA., Maali S; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA., Stosor V; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA., Zembower TR; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA.; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.; Department of Healthcare Epidemiology and Infection Prevention, Northwestern Memorial Hospital, Chicago, Illinois, USA., Qi C; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.; Clinical Microbiology Laboratory, Northwestern Memorial Hospital, Chicago, Illinois, USA.
Jazyk:	angličtina
Zdroj:	Journal of clinical microbiology [J Clin Microbiol] 2024 Oct 16; Vol. 62 (10), pp. e0068024. Date of Electronic Publication: 2024 Sep 16.
DOI:	10.1128/jcm.00680-24
Abstrakt:	Candida auris poses a global public health challenge, causing multiple outbreaks within healthcare facilities. Despite advancements in strain typing for various infectious diseases, a consensus on the genetic relatedness threshold for identifying C. auris transmission in local hospital outbreaks remains elusive. We investigated genetic variations within our local isolate collection using whole-genome-based single nucleotide polymorphism (SNP) phylogenetic analysis. A total of 74 C . auris isolates were subjected to whole-genome sequencing (WGS) and SNP phylogenetic analysis via the QIAGEN CLC Genomics Workbench. Isolates included known related strains from the same patient, strains from different hospitals, strains from our hospital patients with no epidemiological link, and 19 patient isolates from a recent C. auris outbreak. All but three isolates were identified to be Clade IV. By examining the genetic diversities of C. auris within patients and between patients, we identified a SNP variation range of 0-13 for identifying related isolates. During an outbreak investigation, utilizing this range, maximum likelihood phylogenetic analysis revealed two distinct clusters that aligned with the epidemiological links. Determining a SNP variation range to delineate genetic relatedness among isolates is crucial for the application of WGS and SNP phylogenetic analysis in identifying C. auris transmission during hospital outbreak investigations. The use of WGS SNP phylogenetic analysis via the CLC Genomics Workbench has emerged as a valuable method for typing C. auris in clinical microbiology laboratories. Competing Interests: The authors declare no conflict of interest.
Databáze:	MEDLINE
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