Affinity molecular assay for detecting Candida albicans using chitin affinity and RPA-CRISPR/Cas12a.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
28 Oct 2024
28 Oct 2024
Historique:
received:
21
02
2024
accepted:
18
10
2024
medline:
29
10
2024
pubmed:
29
10
2024
entrez:
29
10
2024
Statut:
epublish
Résumé
Invasive fungal infections (IFIs) pose a significant threat to immunocompromised individuals, leading to considerable morbidity and mortality. Prompt and accurate diagnosis is essential for effective treatment. Here we develop a rapid molecular diagnostic method that involves three steps: fungal enrichment using affinity-magnetic separation (AMS), genomic DNA extraction with silicon hydroxyl magnetic beads, and detection through a one-pot system. This method, optimized to detect 30 CFU/mL of C. albicans in blood and bronchoalveolar lavage (BAL) samples within 2.5 h, is approximately 100 times more sensitive than microscopy-based staining. Initial validation using clinical samples showed 93.93% sensitivity, 100% specificity, and high predictive values, while simulated tests demonstrated 95% sensitivity and 100% specificity. This cost-effective, highly sensitive technique offers potential for use in resource-limited clinical settings and can be easily adapted to differentiate between fungal species and detect drug resistance.
Identifiants
pubmed: 39468064
doi: 10.1038/s41467-024-53693-5
pii: 10.1038/s41467-024-53693-5
doi:
Substances chimiques
Chitin
1398-61-4
DNA, Fungal
0
Cas12a protein
EC 3.1.-
Endodeoxyribonucleases
EC 3.1.-
Bacterial Proteins
0
CRISPR-Associated Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
9304Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 82072349
Informations de copyright
© 2024. The Author(s).
Références
Kainz, K., Bauer, M. A., Madeo, F. & Carmona-Gutierrez, D. Fungal infections in humans: the silent crisis. Micro Cell 7, 143–145 (2020).
doi: 10.15698/mic2020.06.718
Fang, W. et al. Diagnosis of invasive fungal infections: challenges and recent developments. J. Biomed. Sci. 30, 42 (2023).
pubmed: 37337179
pmcid: 10278348
doi: 10.1186/s12929-023-00926-2
Arvanitis, M., Anagnostou, T., Fuchs, B. B., Caliendo, A. M. & Mylonakis, E. Molecular and nonmolecular diagnostic methods for invasive fungal infections. Clin. Microbiol. Rev. 27, 490–526 (2014).
pubmed: 24982319
pmcid: 4135902
doi: 10.1128/CMR.00091-13
Alves, J., Alonso-Tarrés, C. & Rello, J. How to identify invasive candidemia in ICU—a narrative review. Antibiotics 11, 1804 (2022).
Lass-Flörl, C., Samardzic, E. & Knoll, M. Serology anno 2021-fungal infections: from invasive to chronic. Clin. Microbiol. Infect. 27, 1230–1241 (2021).
pubmed: 33601011
doi: 10.1016/j.cmi.2021.02.005
Wen, X., Chen, Q., Yin, H., Wu, S. & Wang, X. Rapid identification of clinical common invasive fungi via a multi-channel real-time fluorescent polymerase chain reaction melting curve analysis. Medicine 99, e19194 (2020).
pubmed: 32049856
pmcid: 7035122
doi: 10.1097/MD.0000000000019194
Scorzoni, L. et al. Antifungal therapy: new advances in the understanding and treatment of mycosis. Front. Microbiol. 8, 36 (2017).
pubmed: 28167935
pmcid: 5253656
doi: 10.3389/fmicb.2017.00036
Janbon, G., Quintin, J., Lanternier, F. & d’Enfert, C. Studying fungal pathogens of humans and fungal infections: fungal diversity and diversity of approaches. Genes Immun. 20, 403–414 (2019).
pubmed: 31019254
doi: 10.1038/s41435-019-0071-2
Wiederhold, N. P. Emerging fungal infections: new species, new names, and antifungal resistance. Clin. Chem. 68, 83–90 (2021).
pubmed: 34969112
pmcid: 9383166
doi: 10.1093/clinchem/hvab217
Lockhart, S. R. & Guarner, J. Emerging and reemerging fungal infections. Semin Diagn. Pathol. 36, 177–181 (2019).
pubmed: 31010605
doi: 10.1053/j.semdp.2019.04.010
Lockhart, S. R., Chowdhary, A. & Gold, J. A. W. The rapid emergence of antifungal-resistant human-pathogenic fungi. Nat. Rev. Microbiol. 21, 818–832 (2023).
pubmed: 37648790
doi: 10.1038/s41579-023-00960-9
Lenardon, M. D., Munro, C. A. & Gow, N. A. R. Chitin synthesis and fungal pathogenesis. Curr. Opin. Microbiol. 13, 416–423 (2010).
pubmed: 20561815
pmcid: 2923753
doi: 10.1016/j.mib.2010.05.002
Gow, N. A. R., Latge, J.-P. & Munro, C. A. The fungal cell wall: structure, biosynthesis, and function. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.FUNK-0035-2016 (2017).
Bonhomme, J. & d’Enfert, C. Candida albicans biofilms: building a heterogeneous, drug-tolerant environment. Curr. Opin. Microbiol. 16, 398–403 (2013).
pubmed: 23566895
doi: 10.1016/j.mib.2013.03.007
Steinfeld, L., Vafaei, A., Rösner, J. & Merzendorfer, H. Chitin prevalence and function in bacteria, fungi and protists. Adv. Exp. Med. Biol. 1142, 19–59 (2019).
pubmed: 31102241
doi: 10.1007/978-981-13-7318-3_3
Atkinson, E. M. & Long, S. R. Homology of Rhizobium meliloti NodC to polysaccharide polymerizing enzymes. Mol. Plant Microbe Interact. 5, 439–442 (1992).
pubmed: 1472720
doi: 10.1094/MPMI-5-439
Ren, Z. et al. Structural basis for inhibition and regulation of a chitin synthase from Candida albicans. Nat. Struct. Mol. Biol. 29, 653–664 (2022).
pubmed: 35788183
pmcid: 9359617
doi: 10.1038/s41594-022-00791-x
Bowman, S. M. & Free, S. J. The structure and synthesis of the fungal cell wall. Bioessays 28, 799–808 (2006).
pubmed: 16927300
doi: 10.1002/bies.20441
Haydour, Q. et al. Diagnosis of fungal infections. A systematic review and meta-analysis supporting American Thoracic Society practice guideline. Ann. Am. Thorac. Soc. 16, 1179–1188 (2019).
pubmed: 31219341
doi: 10.1513/AnnalsATS.201811-766OC
Mendonca, A., Santos, H., Franco-Duarte, R. & Sampaio, P. Fungal infections diagnosis—past, present and future. Res. Microbiol. 173, 103915 (2022).
pubmed: 34863883
doi: 10.1016/j.resmic.2021.103915
Kontoyiannis, D. P. Antifungal resistance: an emerging reality and a global challenge. J. Infect. Dis. 216, S431–S435 (2017).
pubmed: 28911044
doi: 10.1093/infdis/jix179
Ganguli, A. et al. A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proc. Natl. Acad. Sci. USA 119, e2209607119 (2022).
pubmed: 36161889
pmcid: 9546527
doi: 10.1073/pnas.2209607119
Katevatis, C., Fan, A. & Klapperich, C. M. Low concentration DNA extraction and recovery using a silica solid phase. PLoS One 12, e0176848 (2017).
pubmed: 28475611
pmcid: 5419563
doi: 10.1371/journal.pone.0176848
Kasahara, K., Ishikawa, H., Sato, S., Shimakawa, Y. & Watanabe, K. Development of multiplex loop-mediated isothermal amplification assays to detect medically important yeasts in dairy products. FEMS Microbiol. Lett. 357, 208–216 (2014).
pubmed: 24965944
Kourkoumpetis, T. K., Fuchs, B. B., Coleman, J. J., Desalermos, A. & Mylonakis, E. Polymerase chain reaction-based assays for the diagnosis of invasive fungal infections. Clin. Infect. Dis. 54, 1322–1331 (2012).
pubmed: 22362884
pmcid: 3491854
doi: 10.1093/cid/cis132
Zhao, Y., Chen, F., Li, Q., Wang, L. & Fan, C. Isothermal amplification of nucleic acids. Chem. Rev. 115, 12491–12545 (2015).
pubmed: 26551336
doi: 10.1021/acs.chemrev.5b00428
Li, J. & Macdonald, J. Advances in isothermal amplification: novel strategies inspired by biological processes. Biosens. Bioelectron. 64, 196–211 (2015).
pubmed: 25218104
doi: 10.1016/j.bios.2014.08.069
Lobato, I. M. & O’Sullivan, C. K. Recombinase polymerase amplification: basics, applications and recent advances. Trends Anal. Chem. 98, 19–35 (2018).
doi: 10.1016/j.trac.2017.10.015
Najjar, D. et al. A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma. Nat. Biomed. Eng. 6, 968–978 (2022).
pubmed: 35941191
pmcid: 9361916
doi: 10.1038/s41551-022-00919-w
Qin, C. et al. One-pot visual detection of African swine fever virus using CRISPR-Cas12a. Front Vet. Sci. 9, 962438 (2022).
pubmed: 35923823
pmcid: 9339671
doi: 10.3389/fvets.2022.962438
Kaminski, M. M., Abudayyeh, O. O., Gootenberg, J. S., Zhang, F. & Collins, J. J. CRISPR-based diagnostics. Nat. Biomed. Eng. 5, 643–656 (2021).
pubmed: 34272525
doi: 10.1038/s41551-021-00760-7
Chen, J. S. et al. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360, 436–439 (2018).
pubmed: 29449511
pmcid: 6628903
doi: 10.1126/science.aar6245
Lu, S. et al. Fast and sensitive detection of SARS-CoV-2 RNA using suboptimal protospacer adjacent motifs for Cas12a. Nat. Biomed. Eng. 6, 286–297 (2022).
pubmed: 35314803
doi: 10.1038/s41551-022-00861-x
Arizti-Sanz, J. et al. Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nat. Commun. 11, 5921 (2020).
pubmed: 33219225
pmcid: 7680145
doi: 10.1038/s41467-020-19097-x
Malcı, K., Walls, L. E. & Rios-Solis, L. Rational design of CRISPR/Cas12a-RPA based one-pot COVID-19 detection with design of experiments. ACS Synth. Biol. 11, 1555–1567 (2022).
pubmed: 35363475
pmcid: 9016756
doi: 10.1021/acssynbio.1c00617
Zeng, Q. et al. Rapid and sensitive Cas12a-based one-step nucleic acid detection with ssDNA-modified crRNA. Anal. Chim. Acta 1276, 341622 (2023).
pubmed: 37573099
doi: 10.1016/j.aca.2023.341622
Mehmood, M. A., Xiao, X., Hafeez, F. Y., Gai, Y. & Wang, F. Molecular characterization of the modular chitin binding protein Cbp50 from Bacillus thuringiensis serovar konkukian. Antonie Van. Leeuwenhoek 100, 445–453 (2011).
pubmed: 21647612
doi: 10.1007/s10482-011-9601-2
Barboza-Corona, J. E. et al. Cloning, sequencing, and expression of the chitinase gene chiA74 from Bacillus thuringiensis. Appl Environ. Microbiol 69, 1023–1029 (2003).
pubmed: 12571025
pmcid: 143672
doi: 10.1128/AEM.69.2.1023-1029.2003
Bormann, C. et al. Characterization of a novel, antifungal, chitin-binding protein from Streptomyces tendae Tü901 that interferes with growth polarity. J. Bacteriol. 181, 7421–7429 (1999).
pubmed: 10601197
pmcid: 94197
doi: 10.1128/JB.181.24.7421-7429.1999
Vaaje-Kolstad, G., Houston, D. R., Riemen, A. H. K., Eijsink, V. G. H. & van Aalten, D. M. F. Crystal structure and binding properties of the Serratia marcescens chitin-binding protein CBP21. J. Biol. Chem. 280, 11313–11319 (2005).
pubmed: 15590674
doi: 10.1074/jbc.M407175200
Muller, D. A., Corrie, S. R., Coffey, J., Young, P. R. & Kendall, M. A. Surface modified microprojection arrays for the selective extraction of the dengue virus NS1 protein as a marker for disease. Anal. Chem. 84, 3262–3268 (2012).
pubmed: 22424552
doi: 10.1021/ac2034387
Yang, Q. et al. A rapid, visible, and highly sensitive method for recognizing and distinguishing invasive fungal infections via CCP-FRET technology. ACS Infect. Dis. 7, 2816–2825 (2021).
pubmed: 34585580
doi: 10.1021/acsinfecdis.1c00393
Louie, A. et al. Pharmacodynamics of fluconazole in a murine model of systemic candidiasis. Antimicrob. Agents Chemother. 42, 1105–1109 (1998).
pubmed: 9593135
pmcid: 105753
doi: 10.1128/AAC.42.5.1105
Clancy, C. J. & Nguyen, M. H. Finding the “missing 50%“ of invasive candidiasis: how nonculture diagnostics will improve understanding of disease spectrum and transform patient care. Clin. Infect. Dis. 56, 1284–1292 (2013).
pubmed: 23315320
doi: 10.1093/cid/cit006
Robbins, N., Caplan, T. & Cowen, L. E. Molecular evolution of antifungal drug resistance. Annu Rev. Microbiol. 71, 753–775 (2017).
pubmed: 28886681
doi: 10.1146/annurev-micro-030117-020345
Lee, Y., Puumala, E., Robbins, N. & Cowen, L. E. Antifungal drug resistance: molecular mechanisms in Candida albicans and beyond. Chem. Rev. 121, 3390–3411 (2021).
pubmed: 32441527
doi: 10.1021/acs.chemrev.0c00199
Uno, N., Li, Z., Avery, L., Sfeir, M. M. & Liu, C. CRISPR gel: a one-pot biosensing platform for rapid and sensitive detection of HIV viral RNA. Anal. Chim. Acta 1262, 341258 (2023).
pubmed: 37179057
pmcid: 10187225
doi: 10.1016/j.aca.2023.341258
Ding, X. et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat. Commun. 11, 4711 (2020).
pubmed: 32948757
pmcid: 7501862
doi: 10.1038/s41467-020-18575-6
Feng, W. et al. Integrating reverse transcription recombinase polymerase amplification with CRISPR technology for the one-tube assay of RNA. Anal. Chem. 93, 12808–12816 (2021).
pubmed: 34506127
doi: 10.1021/acs.analchem.1c03456
Joung, J. et al. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N. Engl. J. Med. 383, 1492–1494 (2020).
pubmed: 32937062
doi: 10.1056/NEJMc2026172
Ma, Y. et al. Efficient magnetic enrichment cascade single-step RPA-CRISPR/Cas12a assay for rapid and ultrasensitive detection of Staphylococcus aureus in food samples. J. Hazard Mater. 465, 133494 (2024).
pubmed: 38228008
doi: 10.1016/j.jhazmat.2024.133494
Lin, M. et al. Glycerol additive boosts 100-fold sensitivity enhancement for one-pot RPA-CRISPR/Cas12a assay. Anal. Chem. 94, 8277–8284 (2022).
pubmed: 35635176
doi: 10.1021/acs.analchem.2c00616
Yin, K. et al. Dynamic aqueous multiphase reaction system for one-pot CRISPR-Cas12a-based ultrasensitive and quantitative molecular diagnosis. Anal. Chem. 92, 8561–8568 (2020).
pubmed: 32390420
pmcid: 7588651
doi: 10.1021/acs.analchem.0c01459
Li, J., Macdonald, J. & von Stetten, F. Review: a comprehensive summary of a decade development of the recombinase polymerase amplification. Analyst 144, 31–67 (2018).
pubmed: 30426974
doi: 10.1039/C8AN01621F
Yan, L. et al. Isothermal amplified detection of DNA and RNA. Mol. Biosyst. 10, 970–1003 (2014).
Daher, R. K., Stewart, G., Boissinot, M. & Bergeron, M. G. Recombinase polymerase amplification for diagnostic applications. Clin. Chem. 62, 947–958 (2016).
pubmed: 27160000
pmcid: 7108464
doi: 10.1373/clinchem.2015.245829
James, A.S. & Alawneh, J.I. COVID-19 infection diagnosis: potential impact of isothermal amplification technology to reduce community transmission of SARS-CoV-2. Diagnostics 10, 399 (2020).
Piepenburg, O., Williams, C. H., Stemple, D. L. & Armes, N. A. DNA detection using recombination proteins. PLoS Biol. 4, e204 (2006).
pubmed: 16756388
pmcid: 1475771
doi: 10.1371/journal.pbio.0040204