AUTHOR=Peng Liang , Liu Chen-Fei , Wu Hong , Jin Hai , Deng Xiao-Yan , Zeng Li-Ting , Xiao Yi , Deng Cong , Yang Zhi-Kai 

TITLE=Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.834015

DOI=10.3389/fcimb.2022.834015

ISSN=2235-2988

ABSTRACT=<p>Over the past decade, <italic>Apiotrichum mycotoxinivorans</italic> has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of <italic>A. mycotoxinivorans</italic> infections. Therefore, to investigate the genetic basis for the pathogenicity of <italic>A. mycotoxinivorans</italic>, we performed whole-genome sequencing and comparative genomic analysis of <italic>A. mycotoxinivorans</italic> GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that <italic>A. mycotoxinivorans</italic> exhibited the closest evolutionary affinity to <italic>A. veenhuisii</italic>, and both the <italic>A. mycotoxinivorans</italic> strains and the formerly <italic>Trichosporon cutaneum</italic> ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to <italic>A. mycotoxinivorans</italic>. Comparisons of three <italic>A. mycotoxinivorans</italic> strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the <italic>Trichosporonaceae</italic> family, we identified potential key genetic factors associated with <italic>A. mycotoxinivorans</italic> infection or pathogenicity. In addition, we also deduced that <italic>A. mycotoxinivorans</italic> had great potential to inactivate some antibiotics (<italic>e.g.</italic>, tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the <italic>Trichosporonaceae</italic> family, uncover the underlying genetic basis of <italic>A. mycotoxinivorans</italic> infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.</p>