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

<b>Abstract</b>Mucormycoses are invasive infections by Rhizopus spp. and other Mucorales. Over 10-months, 4 solid organ transplant (SOT) recipients at our center developed mucormycosis due to R. microsporus (n=2), R. arrhizus (n=1) or Lichtheimia corymbifera (n=1), at 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, 6 R. microsporus, 2 Lichtheimia spp.) from these patients, 5 patients with community-acquired mucormycosis, and 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 paralog expansions. Patient isolates fell into 6 core phylogenetic lineages (clades). Phylogenetic and genomic similarities of R. microsporus isolates recovered 7 months apart from 2 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 an environmental source. Comprehensive genomic analyses eliminated false-linkages between Mucorales isolates that would have been assigned using core phylogenetic or less extensive genomic comparisons. Genomic diversity of Mucorales mandates that multiple isolates from individual patients and environmental sites undergo WGS during epidemiologic investigations. However, exhaustive surveillance of fungal populations in a hospital and surrounding community is likely infeasible.<br><b><br></b><b>README</b><br><i>final_June2020_RAxML_all_isolates_sequences.aligned.fasta.gz:</i><br>Concatenated sequences of conserved core marker proteins predicted in all isolate genomes<br><br><i>orfs.zip, proteins.zip:</i>Zipped folder for all nucleotide coding sequences and protein sequences predicted from the isolate genomes.<br><i>final_newNames_June2020_RAxML_all_isolates_phylogeny.nex</i>: Phylogenetic tree depicting relatedness across Mucorales isolates based on concatenated sequences of conserved core marker proteins. <i><br></i><i>old_new_isolate_names_orderedByClade_June17th2019_wRefs.txt</i>: A tab delimited metadata file providing the naming convention for the isolate names included in the study. #OldNames were changed to #NewNames in the exported svg file post tree-building analysis. To view the phylogeny in figtree, simply import the naming key as "Annotations", and select "#NewName" as the Tip label to Display.<br><i>final_June2020_RAxML_ITS_sequences.aligned.fasta.gz, final_June2020_RAxML_D1D2_sequences.aligned.fasta.gz</i>: <br>ITS and D1/D2 aligned sequences for all isolates<br><i>final_June2020_RAxML_ITS_phylogeny.nex, final_June2020_RAxML_D1D2_phylogeny.nex</i>:<br>ITS and D1/D2 phylogenetic trees for all isolates<br>