title: Whole-genome comparison of Aspergillus fumigatus strains serially isolated from patients with aspergillosis.
abstract: The emergence of azole-resistant strains of Aspergillus fumigatus during treatment for aspergillosis occurs by a mutation selection process. Understanding how antifungal resistance mechanisms evolve in the host environment during infection is of great clinical importance and biological interest. Here, we used next-generation sequencing (NGS) to identify mutations that arose during infection by A. fumigatus strains sequentially isolated from two patients, one with invasive pulmonary aspergillosis (IPA) (five isolations) and the other with aspergilloma (three isolations). The serial isolates had identical microsatellite types, but their growth rates and conidia production levels were dissimilar. A whole-genome comparison showed that three of the five isolates from the IPA patient carried a mutation, while 22 mutations, including six nonsynonymous ones, were found among three isolates from the aspergilloma patient. One aspergilloma isolate carried the cyp51A mutation P216L, which is reported to confer azole resistance, and it displayed an MIC indicating resistance to itraconazole. This isolate harbored five other nonsynonymous mutations, some of which were found in the afyap1 and aldA genes. We further identified a large deletion in the aspergilloma isolate in a region containing 11 genes. This finding suggested the possibility that genomic deletions can occur during chronic infection with A. fumigatus. Overall, our results revealed dynamic alterations that occur in the A. fumigatus genome within its host during infection and treatment.
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan dhagi@chiba-u.jp.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Hagiwara
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan Division of Control and Treatment of Infectious Diseases, Chiba University Hospital, Chiba, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Watanabe
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan.
authors.forename: Azusa
authors.initials: A
authors.lastname: Takahashi-Nakaguchi
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan.
authors.forename: Susumu
authors.initials: S
authors.lastname: Kawamoto
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan Division of Control and Treatment of Infectious Diseases, Chiba University Hospital, Chiba, Japan.
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Kamei
authors.affiliation: Medical Mycology Research Center (MMRC), Chiba University, Chiba, Japan.
authors.forename: Tohru
authors.initials: T
authors.lastname: Gonoi
mesh_terms: D000935:Antifungal Agents / Q000494:pharmacology; D001228:Aspergillosis / Q000382:microbiology*; D001232:Aspergillus fumigatus / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification*; D001393:Azoles / Q000494:pharmacology; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics*; D025141:Drug Resistance, Fungal; D016681:Genome, Fungal; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007564:Japan; D008137:Longitudinal Studies; D008826:Microbial Sensitivity Tests; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D009154:Mutation; D017422:Sequence Analysis, DNA
chemical_list: D000935:Antifungal Agents; D001393:Azoles; D004271:DNA, Fungal