Metagenomic next-generation sequencing identified Histoplasma capsulatum in the lung and epiglottis of a Chinese patient: A case report

Li, Ying‐Qin; Li, Zizi; Chen, Gongqi; Liu, Xi; Ding, Li

doi:10.1016/j.ijid.2020.09.038

Cited by 11 publications

(10 citation statements)

References 47 publications

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“…Lastly, publications were searched using specific fungal names and after manual examination five extra articles were added. Therefore, in total 52 articles were included in this review [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ].…”

Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

“…It was a case of allergic bronchopulmonary mycosis where A. fumigatus and Schizophyllum commune sequences were detected in the homogenised sputum and mucoid plugs of the patient [ 26 ]. Since then, up to the time of writing, a total of 319 cases of fungal infections diagnosed by NGS were described in the literature, with some in case reports and others in case series or cohorts [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. In 40 out of the 319 cases (12.5%), more than 1 fungus was detected by NGS [ 26 , ...…”

Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

“… Distribution of fungal species detected by next-generation sequencing from clinical samples of patients with suspected infections reported in the literature [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. There was a total of 319 cases with 365 fungi detected.…”

Section: Figurementioning

confidence: 99%

See 2 more Smart Citations

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Tsang

Teng

Lau

et al. 2021

JoF

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Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.

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Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

Section: Laboratory Diagnosis Of Fungal Infections By Ngsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

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Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Tsang

Teng

Lau

et al. 2021

JoF

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“…A reference database has been created to identify H. capsulatum via matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) but little data on performance is available [ 75 , 76 ]. Similarly, while metagenomic next generation sequencing (mNGS) has been used on BAL fluid to diagnose H. capsulatum causing chronic progressive pulmonary lesions and epiglottis lesions, broader performance data are not available [ 77 , 78 ]. Finally, there may be a role for panfungal PCR to diagnose histoplasmosis, but so far use has been exploratory [ 79 ].…”

Section: Histoplasmosismentioning

confidence: 99%

Diagnosis of Pulmonary Infections Due to Endemic Fungi

et al. 2021

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Endemic mycoses including Histoplasma, Blastomyces, Coccidioides, Paracoccidioides, and Talaromyces are dimorphic fungi that can cause a variety of clinical manifestations, including respiratory infections. Their pulmonary presentations are variable, and diagnosis is often delayed as they can mimic other infectious and non-infectious causes of pulmonary disease. Delay in diagnosis can lead to unnecessary antibiotic use, repeat hospitalizations, and increased morbidity and mortality. The diagnosis of endemic fungal pulmonary infections often relies on multiple diagnostic tests including culture, tissue histopathology, antigen assays, and antibody assays. Due to the increased use of immunosuppressive agents and the widening geographic ranges where these infections are being found, the prevalence of endemic fungal infections is increasing. Physicians need to be aware of the clinical manifestations of pulmonary infections due to endemic fungal in order to ensure that the proper diagnostic work up is obtained promptly. A high index of suspicion is particularly important in patients with suspected pulmonary infections who have failed to improve despite antibiotics in the appropriate setting. We present a review diagnostic testing for pulmonary infections due to endemic mycoses.

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“…Direct analysis of sputum samples by shotgun sequencing confirmed the co-infection with Aspergillus fumigatus and Schizophyllum commune . NGS has been successfully employed in the diagnosis of fungal pathogens and many of those have reported the presence of more than one fungal strain involved [ 177 – 183 ]…”

Section: Introductionmentioning

confidence: 99%

Diagnosis of invasive fungal infections: challenges and recent developments

Fang¹,

Junqi

Cheng

et al. 2023

J Biomed Sci

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Background The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow. Main text A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections. Conclusion The review will undoubtedly assist in updating the scientific community’s understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.

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Metagenomic next-generation sequencing identified Histoplasma capsulatum in the lung and epiglottis of a Chinese patient: A case report

Cited by 11 publications

References 47 publications

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

Diagnosis of Pulmonary Infections Due to Endemic Fungi

Diagnosis of invasive fungal infections: challenges and recent developments

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