Real-time application of ITS and D1-D3 nanopore amplicon metagenomic sequencing in fungal infections: Enhancing fungal infection diagnostics

IF 4.5 3区 医学 Q1 MICROBIOLOGY
Seondeuk Kim , Narae Kim , Wan Beom Park , Chang Kyung Kang , Jae Hyeon Park , Soon-Tae Lee , Keun-Hwa Jung , Kyung-Il Park , Sang Kun Lee , Jangsup Moon , Kon Chu
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引用次数: 0

Abstract

While fungal infections cause considerable morbidity and mortality, the performance of the current diagnostic tests for fungal infection is low. Even though fungal metagenomics or targeted next-generation sequencing have been investigated for various clinical samples, the real-time clinical utility of these methods still needs to be elucidated. In this study, we used internal transcribed spacer (ITS) and D1-D3 ribosomal DNA nanopore amplicon metagenomic sequencing to assess its utility in patients with fungal infections. Eighty-four samples from seventy-three patients were included and categorized into ‘Fungal infection,’ ‘Fungal colonization,’ and ‘Fungal contamination’ groups based on the judgement of infectious disease specialists. In the ‘Fungal infection’ group, forty-seven initial samples were obtained from forty-seven patients. Three fungal cases detected not by the sequencing but by conventional fungal assays were excluded from the analysis. In the remaining cases, the conventional fungal assay-negative/sequencing-positive group (n=11) and conventional fungal assay-positive/sequencing-positive group (n=33) were compared. Non-Candida and non-Aspergillus fungi infections were more frequent in the conventional-negative/sequencing-positive group (p-value = 0.031). We demonstrated the presence of rare human pathogens, such as Trichosporon asahii and Phycomyces blakesleeanus. In the ‘Fungal infection’ group and ‘Fungal colonization’ group, sequencing was faster than culturing (mean difference = 4.92 days, p-value < 0.001/ mean difference = 4.67, p-value <0.001). Compared to the conventional diagnostic methods including culture, nanopore amplicon sequencing showed a shorter turnaround time and a higher detection rate for uncommon fungal pathogens.

ITS 和 D1-D3 纳米孔扩增片段元基因组测序在真菌感染中的实时应用:加强真菌感染诊断
虽然真菌感染会导致相当高的发病率和死亡率,但目前针对真菌感染的诊断测试性能却很低。尽管针对各种临床样本的真菌元基因组学或定向下一代测序方法已得到研究,但这些方法的实时临床实用性仍有待阐明。在本研究中,我们使用了内部转录间隔(ITS)和 D1-D3 核糖体 DNA 纳米孔扩增片段元基因组测序技术来评估其在真菌感染患者中的应用。根据传染病专家的判断,73 名患者的 84 份样本被分为 "真菌感染"、"真菌定植 "和 "真菌污染 "三组。在 "真菌感染 "组中,从 47 名患者中获得了 47 份初始样本。分析中排除了三个不是通过测序而是通过传统真菌检测方法检测到的真菌病例。在其余病例中,比较了传统真菌检测阴性/测序阳性组(11 例)和传统真菌检测阳性/测序阳性组(33 例)。在常规真菌检测阴性/测序阳性组中,非念珠菌和非曲霉菌感染更为常见(p 值 = 0.031)。我们发现了罕见的人类病原体,例如旭三孢子菌(Trichosporon asahii)和Phycomyces blakesleeanus。在 "真菌感染 "组和 "真菌定植 "组中,测序比培养更快(平均差异 = 4.92 天,p-value <0.001/平均差异 = 4.67 天,p-value <0.001)。与包括培养在内的传统诊断方法相比,纳米孔扩增片段测序的周转时间更短,对不常见真菌病原体的检出率更高。
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来源期刊
CiteScore
9.70
自引率
0.00%
发文量
18
审稿时长
45 days
期刊介绍: Pathogen genome sequencing projects have provided a wealth of data that need to be set in context to pathogenicity and the outcome of infections. In addition, the interplay between a pathogen and its host cell has become increasingly important to understand and interfere with diseases caused by microbial pathogens. IJMM meets these needs by focussing on genome and proteome analyses, studies dealing with the molecular mechanisms of pathogenicity and the evolution of pathogenic agents, the interactions between pathogens and host cells ("cellular microbiology"), and molecular epidemiology. To help the reader keeping up with the rapidly evolving new findings in the field of medical microbiology, IJMM publishes original articles, case studies and topical, state-of-the-art mini-reviews in a well balanced fashion. All articles are strictly peer-reviewed. Important topics are reinforced by 2 special issues per year dedicated to a particular theme. Finally, at irregular intervals, current opinions on recent or future developments in medical microbiology are presented in an editorial section.
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