Now Reading
Population genomics confirms the acquisition of drug-resistant Aspergillus fuigatus infection by humans.
[vc_row thb_full_width=”true” thb_row_padding=”true” thb_column_padding=”true” css=”.vc_custom_1608290870297{background-color: #ffffff !important;}”][vc_column][vc_row_inner][vc_column_inner][vc_empty_space height=”20px”][thb_postcarousel style=”style3″ navigation=”true” infinite=”” source=”size:6|post_type:post”][vc_empty_space height=”20px”][/vc_column_inner][/vc_row_inner][/vc_column][/vc_row]

Population genomics confirms the acquisition of drug-resistant Aspergillus fuigatus infection by humans.

  • Brown, G. D. et al. Hidden killers: Human fungal infections Sci. Transl. Med. 4, 165rv13 (2012).

    Article
    CAS
    PubMed

    Google Scholar

  • Schauwvlieghe, A. F. A. D. et al. A retrospective cohort study of invasive aspergillosis among severe influenza patients admitted to the ICU. Lancet Respir. Med. 6, 782792 (2018).

    Article
    PubMed

    Google Scholar

  • Armstrong-James, D. et al. How to confront and mitigate the risk of COVID-19-associated pulmonary aspergillosis. Eur. Respir. J. 56, 2002554 (2020).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Baxter, C. G. et al. A novel immunologic classification for aspergillosis in adult cystic Fibrosis. J. Allergy Clin. Immunol. 132, 560566.e10 (2013).

    Article
    PubMed

    Google Scholar

  • Kleinkauf et al. Risk Assessment of the Impact of Environmental Use of Triazoles on Resistance Development and Spread to Medical Triazoles Aspergillus Species (ECDC, 2013).

  • Fisher, M. C., Hawkins, N. J., Sanglard, D. & Gurr, S. J. The worldwide emergence of resistance against antifungal drugs poses a threat to human health and food security. Science 360, 739742 (2018).

    CAS
    Article
    PubMed

    Google Scholar

  • Wiederhold, N. P. et al. First detection of TR34/L98H & TR46/Y121F/T289A Cyp51 Mutations in Aspergillus fumigatusIsolates in the United States J. Clin. Microbiol. 54, 168171 (2016).

    CAS
    Article
    PubMed

    Google Scholar

  • Leonardelli, F. et al. First itraconazole resistant Aspergillus fumigatusClinical isolate showing a G54E mutation in Cyp51Ap South America. Rev. Iberoam. Micol. 34, 4648 (2017).

    Article
    PubMed

    Google Scholar

  • Ullmann, A. J. et al. Management and diagnosis of AspergillusDiseases: Executive Summary of the 2017 ESCMID ECMM-ERS guideline. Clin. Microbiol. Infect. 24, e1e38 (2018).

    Article
    PubMed

    Google Scholar

  • Lestrade, P. P. Voriconazole resistance & mortality in invasive Aspergillosis: A Multicenter Retrospective Cohort Study. Clin. Infect. Dis. 68, 14631471 (2019).

    CAS
    Article
    PubMed

    Google Scholar

  • Howard, S. J. et al. Frequency of azole resistance evolution Aspergillus fumigatusFailure to treat. Emerg. Infect. Dis. 15, 10681076 (2009).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Arendrup, M. C. et al. Development of azole resistant in Aspergillus fumigatusDuring azole treatment associated with a change of virulence PLoS ONE 5, e10080 (2010).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Snelders, E. et al. Possible environmental origin of resistance Aspergillus fumigatusMedical triazoles Appl. Environ. Microbiol. 75, 40534057 (2009).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Verweij, P. E. et al. Azole resistance is the single health problem Aspergillus fumigatus: Current insights and future research agenda. Fungal Biol. Rev. 34, 202214 (2020).

    Article

    Google Scholar

  • Verweij, P. E., Mellado, E. & Melchers, W. J. G. Multiple-triazole-resistant aspergillosis. N. Engl. J. Med. 356, 14811483 (2007).

    CAS
    Article
    PubMed

    Google Scholar

  • Seyedmousavi S. Mouton J. W. Melchers W. J. G. Brggemann R. J.M. Verweij P.E. The role of azoles aspergillosis management: From the bench to bedside Drug Resistance Updat. 17, 3750 (2014).

    Article
    PubMed

    Google Scholar

  • van der Linden, J. W. M. et al. Highly resistant to Aspergillosis caused by voriconazole Aspergillus fumigatusThe recovery of genetically related resistant strains from domiciles. Clin. Infect. Dis. 57, 513520 (2013).

    CAS
    Article
    PubMed

    Google Scholar

  • Zhang, J. et al. A novel mutation in environmental azole resistance Aspergillus fumigatusIt could also play a role in sexual reproduction during its emergence. mBio 8, e00791-17 (2017).

    Article
    PubMed
    PubMed Central

    Google Scholar

  • Alvarez-Moreno,C. et. al. Azole-resistant Aspergillus fumigatus harboring TR34/L98H TR46/Y121F/T289A/TR53Colombian mutations in relation to flower fields Sci. Rep. 7, 45631 (2017).

    CAS
    Article

    Google Scholar

  • Macedo, D. et al. Pan-azole resistance is conferred by a novel combination of CYP51A mutations Aspergillus fumigatus. Antimicrob. Agents Chemother. 64, e02501-19 (2020).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Abdolrasouli, A. et al. The whole-genome sequencing has revealed the genomic context of azole resistance mutations in Aspergillus fumigatus. mBio 6, e00536 (2015).

    CAS
    PubMed
    PubMed Central

    Google Scholar

  • K. Dunne, F. Hagen, F. Pomeroy, N. Meis, J. F. and T. R. Rogers Intercountry Transfer of triazole-resistant Aspergillus fumigatusFor more information, see Plant Bulbs. Clin. Infect. Dis. 65, 147149 (2017).

    Article
    PubMed

    Google Scholar

  • Cao, D. et al. Prevalence of azole resistance Aspergillus fumigatusThis is closely associated with azole residues in the field. Environ. Sci. Technol. 55, 30413049 (2021).

    CAS
    Article
    PubMed

    Google Scholar

  • Sewell, T. R. et al. Distribution of azole resistance in the global population is nonrandom Aspergillus fumigatus. mBio 10, e00392-19 (2019).

    Article
    PubMed
    PubMed Central

    Google Scholar

  • Argimn, S. et al. Microreact is a visualizing and sharing of data for genomic epidemiology, phylogeography and other related topics. Microb. Genom. 2, e000093 (2016).

    PubMed
    PubMed Central

    Google Scholar

  • Khoufache, K. et al. Verruculogen is associated with Aspergillus fumigatusThe electrophysiological properties in human nasal epithelial cell cells can be modified by conidia and the hyphae. BMC Microbiol. 7, 5 (2007).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Dasari, P. et al. Aspf2 Aspergillus fumigatusHuman immune regulators are recruited to prevent immune evasion and cell injury. Front. Immunol. 9, 1635 (2018).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Carr, P. D. et al. Low temperatures activate the transposon impala. This is due to the use of a controlled system for transposition to identify genes that are critical for viability. Aspergillus fumigatus. Eukaryot. Cell 9, 438448 (2010).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Tettelin, H. et al. Genome analysis of multiple pathogenic isolates Streptococcus gallactiae: Implications for the microbial pangenome. Proc. Natl Acad. Sci. USA 102, 1395013955 (2005).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • van Paassen, J., Russcher, A., In t Veld-van Wingerden, A. W., Verweij, P. E. & Kuijper, E. J. Emerging aspergillosis is treated with azole-resistant Aspergillus fumigatusThe Netherlands, 2010-2013. Euro Surveill. 21, pii=30300 (2016).

    Article

    Google Scholar

  • Camps, S. M. T. et al. Molecular epidemiology Aspergillus fumigatusIsolates containing the TR34/L98H azole resistance mechanism. J. Clin. Microbiol. 50, 26742680 (2012).

    Article
    PubMed
    PubMed Central

    Google Scholar

  • Etienne, K. A. et al. Genomic diversity in azole-resistant organisms Aspergillus fumigatusThe United States. mBio 12, e0180321 (2021).

    CAS
    Article
    PubMed Central

    Google Scholar

  • Lofgren, L. A., Ross, B. S., Cramer, R. A. Stajich J. E. Combined pan, population- and phylogenomic analysis Aspergillus fumigatusThis report reveals the population structure as well as lineage-specific diversity. Preprint bioRxiv https://doi.org/10.1101/2021.12.12.472145 (2021).

  • Klaassen, C. H. W., Gibbons, J. G., Fedorova, N. D., Meis, J. F. & Rokas, A. Evidence for genetic differentiation and variable rates of recombination among Dutch populations infected with the opportunistic human disease. Aspergillus fumigatus. Mol. Ecol. 21, 5770 (2012).

    Article
    PubMed

    Google Scholar

  • Raffa N. & Keller N. P. A call of arms: Secondary metabolites are essential for survival and success in combating an opportunistic pathogen. PLoS Pathog. 15, e1007606 (2019).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Gonzlez-Lobato, L., Real, R., Prieto, J. G., lvarez, A. I. Merino, G. Differential inhibitions of murine Bcrp1/Abcg2 & human BCRP/ABCG2 using the mycotoxin fumitremorgin (C. Eur. J. Pharmacol. 644, 4148 (2010).

    Article
    CAS
    PubMed

    Google Scholar

  • Maiya S., Grundmann A., Li S.M. & Turner G. The fumitremorgin cluster of genes Aspergillus fumigatusIdentification of a gene that encodes brevianamide F synthetase Chembiochem 7, 10621069 (2006).

    CAS
    Article
    PubMed

    Google Scholar

  • Barber, A. E. et al. Aspergillus fumigatusPan-genome analysis identifies genes associated with human infections. Nat. Microbiol. 6, 15261536 (2021).

    CAS
    Article
    PubMed

    Google Scholar

  • McCarthy, C. G. P. & Fitzpatrick D.A. Pan-genome analyses for model fungal species. Microb. Genom. 5, e000243 (2019).

    PubMed Central

    Google Scholar

  • Barber, A. E. et al. The effects of agricultural fungicides on Aspergillus fumigatusPopulation structure, antifungal susceptibility, abundance mBio 11, e0221320 (2020).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Zhang, J. et al. Evolution of cross resistance to medical triazoles Aspergillus fumigatusThrough selection pressure of environmental fungalicides Proc. Biol. Sci. 284, 20170635 (2017).

    PubMed
    PubMed Central

    Google Scholar

  • Verweij, P. E., Snelders, E., Kema, G. H. J., Mellado, E. & Melchers, W. J. G. Azole resistance in Aspergillus fumigatusSide-effects of environmental fungicide usage: Lancet Infect. Dis. 9, 789795 (2009).

    CAS
    Article
    PubMed

    Google Scholar

  • Sewell, T. R. et al. An elevated prevalence of azole resistant Aspergillus fumigatusThe United Kingdom has both urban and rural environments. Antimicrob. Agents Chemother. 63, e00548-19 (2019).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Tsitsopoulou, A. et al. The prevalence of triazole resistance within the environment was determined Aspergillus fumigatusThese strains were isolated in South Wales, UK. Front. Microbiol. 9, 43564358 (2018).

    Article

    Google Scholar

  • Samson, R. A. et al. Samson, R. A. et al. Aspergillus. Stud. Mycol. 78, 141173 (2014).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Arendrup, M., Hope, W. & Howard, S. EUCAST Definitive document EDef 9.2 Method to Determine Broth Dilution Minimum inhibitory Concentrations Antifungal Agents For Conidia Forming Moles https://www.eucast.org/ast_of_fungi/ (2014).

  • Rex, J. H., Alexander, B. D., Andes, D. & Arthington-Skaggs, B. Broth Dilution Antifungal Susceptibility Testing of Yaeasts: Approved Standards(Clinical and Laboratory Standards Institute 2008).

  • Nierman, W. C. et al. Genomic sequence for the allergenic and pathogenic filamentous fungus Nierman, W. C. et al. Aspergillus fumigatus. Nature 438, 11511156 (2005).

    CAS
    Article
    PubMed

    Google Scholar

  • Li, H. Aligning sequence sequences, clone sequencings, and assembly contigs using BWAMEM. Preprint arXiv https://arxiv.org/pdf/1303.3997.pdf (2013).

  • Li, H. et al. The Sequence Alignment/Map Format and SAMtools. Bioinformatics 25, 20782079 (2009).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • McKenna, A. et al. The Genome Analysis Toolkit is a MapReduce framework that allows you to analyze next-generation DNA sequence data. Genome Res. 20, 12971303 (2010).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Van der Auwera, G. A. et al. From FastQ data and highconfidence variant calls: The Genome Analysis Toolkit best practice pipeline. Curr. Protoc. Bioinformatics 43, 11.10.111.10.33 (2013).


    Google Scholar

  • Smit, A., Hubley, R. & Green, P. RepeatMasker Open4.0 20132015 http://www.repeatmasker.org/ (2015).

  • Nash, A. et al. MARDy is Mycology Antifungal Resistance Databank. Bioinformatics 34, 32333234 (2018).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Ramrez, F. et al. deepTools2: A next-generation web server that allows deep-sequencing data analysis. Nucleic Acids Res. 44, W160W165 (2016).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Stamatakis A. RAxMLVI-HPC: Maximum likelihood-based phylogenetic analyses using thousands of taxa and mixed model. Bioinformatics 22, 26882690 (2006).

    CAS
    Article
    PubMed

    Google Scholar

  • T. Jombart and I. Ahmed, adegenet 1.2-1: New tools for the analysis genome-wide SNP data. Bioinformatics 27, 30703071 (2011).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Nelson, C. W. & Hughes A. L. Within-host Nucleotide Diversity of Viral Populations: Insights from Next-Generation Sequencing Infect. Genet. Evol. 30, 17 (2015).

    CAS
    Article
    PubMed

    Google Scholar

  • Walker, T. M. et al. Whole-genome sequencing for delineating Mycobacterium tuberculosisAn observational retrospective study of outbreaks. Lancet Infect. Dis. 13, 137146 (2013).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 21562158 (2011).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Jombart T., Devillard S., & Balloux F. Discriminant Analysis of Principal Components: A new method to analyze genetically-structured populations BMC Genet. 11, 94 (2010).

    Article
    PubMed
    PubMed Central

    Google Scholar

  • Falush, D. Stephens, M. and Pritchard J. K. Inferences about population structure using multilocus genetic data: linked loi and correlated allele frequency. Genetics 164, 15671587 (2003).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Lawson, D. J. Hellenthal and Myers, S., & Falush D. Inferences of population structure using dense haplotype information. PLoS Genet. 8, e1002453 (2012).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • F. Tajima Genetics 123, 585595 (1989).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Kamvar Z. N., Tabima J. F., & Grnwald N. J. Poppr – An R package for genetic analysis in populations with clonal/partially clonal and/orsexual reproduction. PeerJ 2, e281 (2014).

    Article
    PubMed
    PubMed Central

    Google Scholar

  • Collins, C. & Didelot, X. A phylogenetic method for performing genome-wide association studies in microbes. It accounts for population structure as well as recombination. PLoS Comput. Biol. 14, e1005958 (2018).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Basenko, E. Y. et al. FungiDB: An integrated bioinformatic resource to oomycetes as well as fungi. J. Fungi (Basel) 4, 39 (2018).

    Article
    CAS

    Google Scholar

  • Zhao, C. et al. High-throughput gene replacement Aspergillus fumigatus. Curr. Protoc. Microbiol. 54, e88 (2019).

    CAS
    Article
    PubMed

    Google Scholar

  • Furukawa, T. et al. The key regulator of drug resistance is the negative cofactor 2-complex. Aspergillus fumigatus. Nat. Commun. 11, 427 (2020).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Bertuzzi, M. et al. On the lineage Aspergillus fumigatusIsolates in common laboratory usage Med. Mycol. 59, 713 (2021).

    CAS
    Article
    PubMed

    Google Scholar

  • Arendrup, M. C. et al. EUCAST technical notice on Aspergillusamphotericin A, itraconazole, posaconazole, and amphotericin C. Clin. Microbiol. Infect. 18, E248E250 (2012).

    CAS
    Article
    PubMed

    Google Scholar

  • Bolger, A. M. Lohse and Usadel, B. Trimmomatic is a flexible trimmer for Illumina sequence information. Bioinformatics 30, 21142120 (2014).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Li, D. Liu, C.M., Luo R., Sadakane K. & Lam T.-W. MEGAHIT is an ultra-fast single node solution for large and complicated metagenomics assembly via succinct Bruijn graph. Bioinformatics 31, 16741676 (2015).

    CAS
    Article
    PubMed

    Google Scholar

  • Hubley, R. et al. The Dfam database of repetitive genetic DNA families. Nucleic Acids Res. 44, D81D89 (2016).

    CAS
    Article
    PubMed

    Google Scholar

  • Bushnell, B. BBMap: A Fast, Accurate and Splice-Aware Aligner. https://www.osti.gov/servlets/purl/1241166 (2014).

  • Brna, T., Lomsadze, A. Borodovsky M. GeneMark EP+: Eukaryotic gene prediction using self-training in space of genes or proteins NAR Genom. Bioinformatics 2, lqaa026 (2020).

    Article
    CAS

    Google Scholar

  • Kriventseva, E. V. et al. OrthoDB version 10: Sampling the diversity in animal, plant, fungal and protist genomes to provide evolutionary and functional annotations of orthologs. Nucleic Acids Res. 47, D807D811 (2019).

    CAS
    Article
    PubMed

    Google Scholar

  • National Center for Biotechnology Information. User Manual for BLAST Command Line Applications. https://www.ncbi.nlm.nih.gov/books/NBK279690/ (2008).

  • Fouts, D. E., Brinkac, L., Beck, E., Inman, J. PanOCT: automatic clustering of orthologs by using conserved gene neighborhoods for pan-genomic analysis bacterial strains and closely related organisms. Nucleic Acids Res. 40, e172 (2012).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Durinck, S.; Spellman P. T.; Birney E. & Huber W. Mapping identifiers to integrate genomic datasets with R/Bioconductor package BiomaRt. Nat. Protoc. 4, 11841191 (2009).

    CAS
    Article
    PubMed
    PubMed Central

    Google Scholar

  • Buchfink, B. Xie. C. & Huson. D. H. Fast and sensitive alignment of proteins using DIAMOND. Nat. Methods 12, 5960 (2015).

    CAS
    Article
    PubMed

    Google Scholar

  • Kans, J. Entrez Direct: E -utilities on UNIX Command Line(National Center for Biotechnology Information 2021).

  • Snipen L. & Liland K. H. Micropan: An R-package for microbial Pan-Genomics. BMC Bioinformatics 16, 79 (2015).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Brynildsrud O., Bohlin J., Scheffer L., & Eldholm V. Rapid scoring genes in microbial pangenome-wide association studies using Scoary. Genome Biol. 17, 238 (2016).

    Article
    CAS
    PubMed
    PubMed Central

    Google Scholar

  • Larsson, J. Eulerr – Area-proportional euler & Venn diagrams using ellipses. R package version 6.1.0 https://cran.r-project.org/web/packages/eulerr/index.html (2020).

  • View Comments (0)

    Leave a Reply

    Your email address will not be published.