Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus

Aho, 1973, On finding lowest common ancestors in trees, 253 Al-Wathiqi, 2013, Molecular identification and antifungal susceptibility profile of Aspergillus flavus isolates recovered from clinical specimens in Kuwait, BMC Infectious Diseases, 13, 126, 10.1186/1471-2334-13-126 Altschul, 1990, Basic local alignment search tool, Journal of Molecular Biology, 215, 403, 10.1016/S0022-2836(05)80360-2 Amend, 2010, Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics, Proceedings of the National Academy of Sciences of the United States of America, 107, 13748, 10.1073/pnas.1000454107 Balajee, 2009, Aspergillus alabamensis, a new clinically relevant species in the section Terrei, Eukaryotic Cell, 8, 713, 10.1128/EC.00272-08 Balajee, 2005, Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus, Eukaryotic Cell, 4, 625, 10.1128/EC.4.3.625-632.2005 Balajee, 2009, Molecular identification of Aspergillus species collected for the transplant-associated infection surveillance network, Journal of Clinical Microbiology, 47, 3138, 10.1128/JCM.01070-09 Bittinger, 2014, Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing, Genome Biology, 15, 487, 10.1186/s13059-014-0487-y Black, 2013, Determining fungi rRNA copy number by PCR, Journal of Biomolecular Techniques, 24, 32 Blankenberg, 2010, Galaxy: a web-based genome analysis tool for experimentalists, Current Protocols in Molecular Biology, 11 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Buée, 2009, 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity, New Phytologist, 184, 449, 10.1111/j.1469-8137.2009.03003.x Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, 7, 335, 10.1038/nmeth.f.303 Dannemiller, 2014, Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS), Journal of Basic Microbiology, 54, 315, 10.1002/jobm.201200507 Findley, 2013, Topographic diversity of fungal and bacterial communities in human skin, Nature, 498, 367, 10.1038/nature12171 Fröhlich-Nowoisky, 2009, High diversity of fungi in air particulate matter, Proceedings of the National Academy of Sciences of the United States of America, 106, 12814, 10.1073/pnas.0811003106 Gallo, 2012, Molecular characterization of an Aspergillus flavus population isolated from maize during the first outbreak of aflatoxin contamination in Italy, Phytopathologia Mediterranea, 51, 198 Gardes, 1993, ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts, Molecular Ecology, 2, 113, 10.1111/j.1365-294X.1993.tb00005.x Geiser, 2004 Geiser, 2007, The current status of species recognition and identification in Aspergillus, Studies in Mycology, 59, 1, 10.3114/sim.2007.59.01 Giardine, 2005, Galaxy: a platform for interactive large-scale genome analysis, Genome Research, 15, 1451, 10.1101/gr.4086505 Glass, 1995, Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes, Applied and Environmental Microbiology, 61, 1323, 10.1128/aem.61.4.1323-1330.1995 Goecks, 2010, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biology, 11, R86, 10.1186/gb-2010-11-8-r86 Gugnani, 2003, Ecology and taxonomy of pathogenic aspergilli, Frontiers in Bioscience, 8, s346, 10.2741/1002 Guinea, 2015, Aspergillus citrinoterreus, a new species of section Terrei isolated from samples of patients with nonhematological predisposing conditions, Journal of Clinical Microbiology, 53, 611, 10.1128/JCM.03088-14 Hedayati, 2007, Aspergillus flavus: human pathogen, allergen and mycotoxin producer, Microbiology, 153, 1677, 10.1099/mic.0.2007/007641-0 Herrera, 2009, Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus, Journal of Clinical Microbiology, 47, 1325, 10.1128/JCM.02073-08 Hong, 2005, Polyphasic taxonomy of Aspergillus fumigatus and related species, Mycologia, 97, 1316, 10.1080/15572536.2006.11832738 Hoog, 2000 Hospodsky, 2010, Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi, Applied and Environmental Microbiology, 76, 7004, 10.1128/AEM.01240-10 Houbraken, 2011, Phylogeny of Penicillium and the segregation of Trichocomaceae into three families, Studies in Mycology, 70, 1, 10.3114/sim.2011.70.01 Houbraken, 2014, Modern taxonomy of biotechnologically important Aspergillus and Penicillium species, Advances in Applied Microbiology, 86, 199, 10.1016/B978-0-12-800262-9.00004-4 Klich, 2002, Biogeography of Aspergillus species in soil and litter, Mycologia, 94, 21, 10.1080/15572536.2003.11833245 Larena, 1999, Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes, Journal of Biotechnology, 75, 187, 10.1016/S0168-1656(99)00154-6 Lee, 2015, Triazole susceptibilities in thermotolerant fungal isolates from outdoor air in the Seoul Capital Area in South Korea, PLoS ONE, 10, e0138725, 10.1371/journal.pone.0138725 Lin, 2001, Aspergillosis case-fatality rate: systematic review of the literature, Clinical Infectious Diseases, 32, 358, 10.1086/318483 Manter, 2007, Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis, Journal of Microbiological Methods, 71, 7, 10.1016/j.mimet.2007.06.016 Mari, 2003, Sensitization to fungi: epidemiology, comparative skin tests, and IgE reactivity of fungal extracts, Clinical and Experimental Allergy, 33, 1429, 10.1046/j.1365-2222.2003.01783.x Nilsson, 2006, Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective, PLoS ONE, 1, e59, 10.1371/journal.pone.0000059 O'Gorman, 2011, Airborne Aspergillus fumigatus conidia: a risk factor for aspergillosis, Fungal Biology Reviews, 25, 151, 10.1016/j.fbr.2011.07.002 Parenicova, 2001, Combined molecular and biochemical approach identifies Aspergillus japonicus and Aspergillus aculeatus as two species, Applied and Environmental Microbiology, 67, 521, 10.1128/AEM.67.2.521-527.2001 Peterson, 2008, Phylogenetic analysis of Aspergillus species using DNA sequences from four loci, Mycologia, 100, 205, 10.1080/15572536.2008.11832477 Pitt, 1993 Samson, 2014, Phylogeny, identification and nomenclature of the genus Aspergillus, Studies in Mycology, 78, 141, 10.1016/j.simyco.2014.07.004 Schoch, 2014, Finding needles in haystacks: linking scientific names, reference specimens and molecular data for fungi, Database, 1 Schoch, 2012, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, Proceedings of the National Academy of Sciences of the United States of America, 109, 6241, 10.1073/pnas.1117018109 Simon-Nobbe, 2008, The spectrum of fungal allergy, International Archives of Allergy and Immunology, 145, 58, 10.1159/000107578 Tedersoo, 2014, Global diversity and geography of soil fungi, Science, 346, 10.1126/science.1256688 Toju, 2012, High-coverage ITS primers for the DNA-based identification of Ascomycetes and Basidiomycetes in environmental samples, PLoS ONE, 7, e40863, 10.1371/journal.pone.0040863 Varga, 2011, New and revisited species in Aspergillus section Nigri, Studies in Mycology, 69, 1, 10.3114/sim.2011.69.01 Visagie, 2014, Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world, Studies in Mycology, 78, 63, 10.1016/j.simyco.2014.07.002 Visagie, 2014, Ochratoxin production and taxonomy of the yellow aspergilli (Aspergillus section Circumdati), Studies in Mycology, 78, 1, 10.1016/j.simyco.2014.07.001 White, 1990 Yamamoto, 2012, Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air, ISME Journal, 6, 1801, 10.1038/ismej.2012.30 Yamamoto, 2014, Identification accuracy and diversity reproducibility associated with ITS-based fungal taxonomic library preparation, Environmental Microbiology, 16, 2764, 10.1111/1462-2920.12338 Yamamoto, 2015, Indoor emissions as a primary source of airborne allergenic fungal particles in classrooms, Environmental Science & Technology, 49, 5098, 10.1021/es506165z