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.

Genomic characterization of recurrent mold infections in thoracic transplant recipients

“…Another study of serial A. fumigatus isolates from patients noted a non‐synonymous mutation in the cyp51A gene of an itraconazole‐resistant isolate as previously noted by targeted sequencing . We did not observe non‐synonymous mutations in cyp51A or cyb51b in the 2 collected isolates in this study that match known resistance mutations, consistent with the lack of measured azole resistance in vitro …”

“…[7][8][9] Another study of serial A. fumigatus isolates from patients noted a non-synonymous mutation in the cyp51A gene of an itraconazole-resistant isolate as previously noted by targeted sequencing. 10,11 We did not observe non-synonymous mutations in cyp51A or cyb51b in the 2 collected isolates in this study that match known resistance mutations, consistent with the lack of measured azole resistance in vitro. 10 In Case 2, we hypothesize that this patient suffered from a chronic, Biofilms are formed when microorganisms attach irreversibly to the surface of an anatomic site or medical device, grow, and produce extracellular polymers to facilitate matrix formation.…”

“…10,11 We did not observe non-synonymous mutations in cyp51A or cyb51b in the 2 collected isolates in this study that match known resistance mutations, consistent with the lack of measured azole resistance in vitro. 10 In Case 2, we hypothesize that this patient suffered from a chronic, Biofilms are formed when microorganisms attach irreversibly to the surface of an anatomic site or medical device, grow, and produce extracellular polymers to facilitate matrix formation. 12 The formation of an extracellular matrix can alter the organism's phenotype by modifying growth rate and gene transcription, leading to decreased antimicrobial susceptibility.…”

A Novel Zn2-Cys6 Transcription Factor AtrR Plays a Key Role in an Azole Resistance Mechanism of Aspergillus fumigatus by Co-regulating cyp51A and cdr1B Expressions

“…The clinical strain IFM 61567 was isolated in 2011 in Japan from a patient with itraconazole treatment. The mutation in cyp51A gene in the strain was identified as a procedure described previously [60]. The fungal strains used in this study are listed in Table 4.…”

On the evolution of azole resistance in Aspergillus fumigatus

“…With greater access to this technology studies are emerging that apply NGS to clinical Aspergillus isolates, reporting both accumulation of mutations and genomic deletions that appeared to have occurred randomly in isolates recovered from an aspergilloma. 71,72 Genomic changes could also provide clues to the mode of reproduction from which the changes originated. The observed genetic changes need to be correlated to phenotypic changes, such as resistance or general fitness, which might prove difficult given the diversity of stress factors the fungus is exposed to.…”