Open AccessGenetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients
Author(s) -
M. Hong Nguyen,
Drishti Kaul,
Carlene A. Muto,
Shaoji Cheng,
Robin Richter,
Vincent M. Bruno,
Guojun Liu,
Sinem Beyhan,
Alexander Sundermann,
Stephanie Mounaud,
A. William Pasculle,
William C. Nierman,
Eileen Driscoll,
R Cumbie,
Cornelius J. Clancy,
Christopher L. Dupont
Publication year - 2020
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.476
H-Index - 28
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000473
Subject(s) - mucorales , biology , mucormycosis , rhizopus arrhizus , clade , phylogenetic tree , phylogenetics , zygomycosis , genetic diversity , evolutionary biology , genetics , microbiology and biotechnology , gene , medicine , amphotericin b , pathology , population , antifungal , biochemistry , environmental health , lipase , enzyme
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 lineages (clades). Phylogenetic and genomic similarities of R. microsporus isolates recovered 7 months apart from two SOT recipients in adjoining 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 investigations. However, exhaustive surveillance of fungal populations in a hospital and surrounding community is probably infeasible.