Clinical chemistry最新文献

Background: Candida auris is an emerging multidrug-resistant pathogen. Interpretation of susceptibility testing can be difficult since minimum inhibitory concentration (MIC) breakpoints have not been fully established.

Methods: All C. auris isolates from unique patients identified at a large urban hospital between 2020 and 2024 (n = 66) underwent whole-genome sequencing (WGS). Genomic DNA was extracted from pure culture isolates and underwent PCR-free library preparation. WGS was performed on an Illumina platform (NextSeq2000) with an average coverage of 50×. Genomic analysis was conducted via an adapted GATK-based pipeline using the B11205 strain as the reference genome based on the CDC (MycoSNP) protocol. All isolates underwent FKS1 gene Sanger sequencing for confirmation of WGS results. Genotypic results were correlated with antifungal susceptibility testing.

Results: All clinical isolates were part of Clade I and carried azole resistance mutations in ERG11, TAC1b, and CDR1, consistent with 100% phenotypic fluconazole resistance. Across all isolates, 5 distinct missense variants in FKS1 were identified: one case with p.Ser639Tyr, one case with both a p.Arg1354Ser and a p.Asp642His, 7 cases with p.Met690Ile, and 9 cases with p.Val1818Ile. Isolates with known echinocandin resistance conferring mutations p.Ser639Tyr and p.Arg1354Ser were resistant to micafungin and anidulafungin. Two isolates with Met690Ile were resistant to caspofungin alone.

Conclusions: With potential resistance to all 3 major antifungal classes of drugs, C. auris is an emerging public health threat. Early detection of echinocandin resistance by molecular methods could impact treatment course to include novel antifungal agents. Further study of the FKS1 Met690Ile variant is warranted.

Background: Massively parallel sequencing (MPS) of nucleic acids has been a transformative technology for basic and applied genomic science, increasing efficiencies and decreasing costs to enable studies of unprecedented scope and impact. In clinical settings, these technological and scientific advances have led to the development of tests that are increasingly fast, comprehensive, and more frequently employed. Practitioners of genomic medicine have applied these tools across clinical settings, including diagnosis of inherited disorders and cancers and infectious disease detection and surveillance. In recent years, the commercial marketplace for MPS sequencers and reagents has been dominated by a few companies. The growing demand for sequencing has led to the recent emergence of several new sequencing platforms with techniques that may provide alternatives or improvements to existing workflows or allow the adoption of sequencing workflows in new settings. Clinical genomics laboratories will evaluate these platforms from a unique perspective, focusing on how technological advancements can improve patient care.

Content: This review describes short-read sequencing platforms provided by Illumina, Element Biosciences, MGI, PacBio, Singular Genomics, Thermo Fisher Scientific, and Ultima Genomics. This review discusses their innovative approaches, principles, workflows, and applications.

Summary: This review aims to inform laboratory geneticists, clinicians, and researchers about emerging short-read technologies and their applications in clinical genomics. By highlighting their principles and potential contributions, we aim to assist laboratories in selecting suitable solutions for their sequencing needs considering key factors such as applications, throughput, and integration with existing laboratory workflows.

Background: Newborn hearing screening is a physiologic screen to identify infants who may be deaf or hard of hearing (DHH) and would benefit from early intervention. Typically, an infant who does not pass the newborn hearing screen is referred for clinical audiology testing, which may be followed by genetic testing to identify the etiology of an infant's DHH.

Content: The current newborn hearing screening paradigm can miss mild cases of DHH or later-onset DHH, leaving a child at risk for unrecognized DHH, which could impact long-term language, communication, and social development. Genomic technologies are improving the diagnosis of DHH in newborns who fail their newborn hearing screen, and a case is being made for genomic screening for DHH in all newborns.

Summary: The genomic era brings a wealth of opportunities to screen newborns for genetic causes of hearing loss on a population wide basis, some of which are already being implemented in a clinical setting.

Background: Genetic testing has traditionally been divided into molecular genetics and cytogenetics, originally driven by the use of different assays and their associated limitations. Cytogenetic technologies such as karyotyping, fluorescent in situ hybridization or chromosomal microarrays are used to detect large "megabase level" copy number variants and other structural variants such as inversions or translocations. In contrast, molecular methodologies are heavily biased toward subgenic "small variants" such as single nucleotide variants, insertions/deletions, and targeted detection of intragenic, exon level deletions or duplications. The boundaries between these approaches are now increasingly blurred as next-generation sequencing technologies and their use for genome-wide analysis are used by both disciplines, therefore eliminating the historic and somewhat artificial separation driven by variant type.

Content: This review discusses the history of genomic nomenclature across both fields, summarizes implementation challenges for the clinical genetics community, and identifies key considerations for enabling a seamless connection of the stakeholders that consume variant descriptions.

Summary: Standardization is naturally a lengthy and complex process that requires consensus building between different stakeholders. Developing a standard that not only fits the multitude of needs across the entities that consume genetic variant information but also works equally well for all genetic variant types is an ambitious goal that calls for revisiting this vision.