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    Genetic diversity of clinical and environmental mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients

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    Author
    Nguyen, M.H.
    Kaul, D.
    Muto, C.
    Cheng, S.J.
    Richter, R.A.
    Bruno, V.M.
    Liu, G.
    Beyhan, S.
    Sundermann, A.J.
    Mounaud, S.
    Pasculle, A.W.
    Nierman, W.C.
    Driscoll, E.
    Cumbie, R.
    Clancy, C.J.
    Dupont, C.L.
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    Date
    2020-11-27
    Journal
    Microbial Genomics
    Publisher
    Microbiology Society
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://doi.org/10.1099/mgen.0.000473
    Abstract
    Mucormycoses are invasive infections by Rhizopus species and other Mucorales. Over 10 months, four solid organ transplant (SOT) recipients at our centre developed mucormycosis due to Rhizopus microsporus (n=2), R. arrhizus (n=1) or Lichtheimia corymbifera (n=1), at a median 31.5 days (range: 13–34) post-admission. We performed whole genome sequencing (WGS) on 72 Mucorales isolates (45 R. arrhizus, 19 R. delemar, six R. microsporus, two Lichtheimia species) from these patients, from five patients with community-acquired mucormycosis, and from hospital and regional environments. Isolates were compared by core protein phylogeny and global genomic features, including genome size, guanine–cytosine percentages, shared protein families and paralogue expansions. Patient isolates fell into six core phylogenetic line-ages (clades). Phylogenetic and genomic similarities of R. microsporus isolates recovered 7 months apart from two SOT recipients in adjoin-ing hospitals suggested a potential common source exposure. However, isolates from other patients and environmental sites had unique genomes. Many isolates that were indistinguishable by core phylogeny were distinct by one or more global genomic comparisons. Certain clades were recovered throughout the study period, whereas others were found at particular time points. In conclusion, mucormycosis cases could not be genetically linked to a definitive environmental source. Comprehensive genomic analyses eliminated false associations between Mucorales isolates that would have been assigned using core phylogenetic or less extensive genomic comparisons. The genomic diversity of Mucorales mandates that multiple isolates from individual patients and environmental sites undergo WGS during epidemiological investiga-tions. However, exhaustive surveillance of fungal populations in a hospital and surrounding community is probably infeasible. Copyright 2020 The Authors.
    Keyword
    Mucorales
    Mucormycosis
    Phylogenetics
    Whole genome sequence
    Identifier to cite or link to this item
    http://hdl.handle.net/10713/14622
    ae974a485f413a2113503eed53cd6c53
    10.1099/mgen.0.000473
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