The Use of Whole Genome and Next-Generation Sequencing in the Diagnosis of Invasive Fungal Disease

El-Kamand, Sam; Papanicolaou, Alexie; Morton, Oliver

doi:10.1007/s12281-019-00363-5

Cited by 4 publications

(3 citation statements)

References 66 publications

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“…Whole genome sequencing includes two different techniques: de novo genome assembly, when the species to be studied has not been previously sequenced and assembled; or re-sequencing, which identifies genome-wide variants (copy number variants, structural variants, and SNPs and indels) comparing an existing reference assembly with a sequenced isolate through the alignment of sequence reads against the reference [ 49 ]. These variants are significant in studies such as fungal microevolution, fungicide resistance, virulence factors monitoring, and outbreak analysis [ 66 ]. Short-read platforms (e.g., Illumina) allow the detection of single base pair variants (SNVs).…”

Section: Dna-based Molecular Markersmentioning

confidence: 99%

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Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years

Oliveira

Azevedo

2022

JoF

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Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.

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Section: Dna-based Molecular Markersmentioning

confidence: 99%

“…Short-read platforms (e.g., Illumina) allow the detection of single base pair variants (SNVs). In contrast, long-read platforms (e.g., Pacific Biosciences or Oxford Nanopore) allow the detection of large structural variants, copy number variants, or pathogenicity islands [ 66 ].…”

Section: Dna-based Molecular Markersmentioning

confidence: 99%

Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years

Oliveira

Azevedo

2022

JoF

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“…The metagenomic next-generation sequencing (mNGS) technology is a high-throughput DNA or RNA sequencing method that can simultaneously detect a variety of microorganisms, including bacteria, viruses, and fungi, and is widely used for the rapid detection and diagnosis of pathogens ( Gu et al., 2021 ). Although mNGS has disadvantages such as its high cost, susceptibility to exogenous microbial contamination, and reduced efficiency in detecting thick-walled fungi, research has showcased its superior sensitivity and specificity in diagnosing invasive fungal diseases compared to traditional culture and histopathological methods ( El-Kamand et al., 2019 ; Song et al., 2021 ; Wang et al., 2022 ). In certain circumstances, mNGS has a superior positive detection efficiency and can determine fungal pathogens that are difficult to diagnose via conventional diagnostic approaches ( Zheng et al., 2021 ; Wu et al., 2023 ).…”

Section: Introductionmentioning

confidence: 99%

COVID-19 in pulmonary critically ill patients: metagenomic identification of fungi and characterization of pathogenic microorganisms

Huang,

Chang,

et al. 2024

Front. Cell. Infect. Microbiol.

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BackgroundFungal co-infection is prevalent in critically ill patients with COVID-19. The conventional approach applied to fungal identification has relatively low sensitivity and is time-consuming. The metagenomic next-generation sequencing (mNGS) technology can simultaneously detect a variety of microorganisms, and is increasingly being used for the rapid detection and diagnosis of pathogens.MethodsIn this single-center retrospective study, we described the clinical presentation and outcomes of COVID-19 and mNGS positive for fungi in pulmonary critically ill patients during the outbreak of Omicron infection from December 2022 to January 2023.ResultsAmong 43 COVID-19 patients with acute respiratory distress syndrome (ARDS) on a single intensive care unit (ICU), 10 were reported to be fungal positive using the mNGS test. The number of pathogenic microorganisms detected by mNGS was significantly higher than that via traditional methods, especially in the detection of fungi and viruses. Aspergillus infection was dominant, and most of these patients also had concurrent bacterial or viral infections. Probable or possible COVID-19-associated pulmonary aspergillosis (CAPA) was diagnosed in all 10 patients, and the prognosis was poor.ConclusionPatients with COVID-19 may be at increased risk of developing fungal infections as well as concurrent bacterial or viral infections, and mNGS can be a powerful tool in identifying these infections. Clinicians should be aware of the increased risk of fungal infections in COVID-19 patients, particularly those who have underlying immunocompromising conditions, and should monitor for early signs of infection.

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Diagnostics for Fungal Infections in Solid Organ Transplants (SOT)

Stack

Morton

2021

Curr Fungal Infect Rep

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The Use of Whole Genome and Next-Generation Sequencing in the Diagnosis of Invasive Fungal Disease

Cited by 4 publications

References 66 publications

Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years

Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years

COVID-19 in pulmonary critically ill patients: metagenomic identification of fungi and characterization of pathogenic microorganisms

Diagnostics for Fungal Infections in Solid Organ Transplants (SOT)

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