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Article: Rapid genomic diagnosis of fungal infections in the age of next-generation sequencing
Title | Rapid genomic diagnosis of fungal infections in the age of next-generation sequencing |
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Authors | |
Keywords | genomic diagnosis next-generation sequencing NGS fungal infection mycosis |
Issue Date | 2021 |
Publisher | MDPI AG. The Journal's web site is located at https://www.mdpi.com/journal/jof |
Citation | Journal of Fungi, 2021, v. 7 n. 8, p. article no. 636 How to Cite? |
Abstract | 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. |
Persistent Identifier | http://hdl.handle.net/10722/301650 |
ISSN | 2023 Impact Factor: 4.2 2023 SCImago Journal Rankings: 0.929 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Tsang, CC | - |
dc.contributor.author | Teng, LL | - |
dc.contributor.author | Lau, SKP | - |
dc.contributor.author | Woo, PCY | - |
dc.date.accessioned | 2021-08-09T03:42:10Z | - |
dc.date.available | 2021-08-09T03:42:10Z | - |
dc.date.issued | 2021 | - |
dc.identifier.citation | Journal of Fungi, 2021, v. 7 n. 8, p. article no. 636 | - |
dc.identifier.issn | 2309-608X | - |
dc.identifier.uri | http://hdl.handle.net/10722/301650 | - |
dc.description.abstract | 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. | - |
dc.language | eng | - |
dc.publisher | MDPI AG. The Journal's web site is located at https://www.mdpi.com/journal/jof | - |
dc.relation.ispartof | Journal of Fungi | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | genomic diagnosis | - |
dc.subject | next-generation sequencing | - |
dc.subject | NGS | - |
dc.subject | fungal infection | - |
dc.subject | mycosis | - |
dc.title | Rapid genomic diagnosis of fungal infections in the age of next-generation sequencing | - |
dc.type | Article | - |
dc.identifier.email | Tsang, CC: microbioct@connect.hku.hk | - |
dc.identifier.email | Teng, LL: llteng@hku.hk | - |
dc.identifier.authority | Tsang, CC=rp02492 | - |
dc.identifier.authority | Teng, LL=rp00277 | - |
dc.identifier.authority | Lau, SKP=rp00486 | - |
dc.identifier.authority | Woo, PCY=rp00430 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.3390/jof7080636 | - |
dc.identifier.scopus | eid_2-s2.0-85112396325 | - |
dc.identifier.hkuros | 324155 | - |
dc.identifier.volume | 7 | - |
dc.identifier.issue | 8 | - |
dc.identifier.spage | article no. 636 | - |
dc.identifier.epage | article no. 636 | - |
dc.identifier.isi | WOS:000689456000001 | - |
dc.publisher.place | Switzerland | - |