Whole Genome Sequence Typing to Investigate the <em>Apophysomyces</em> Outbreak following a Tornado in Joplin, Missouri, 2011

<div><p>Case reports of <em>Apophysomyces</em> spp. in immunocompetent hosts have been a result of traumatic deep implantation of <em>Apophysomyces</em> spp. spore-contaminated soil or debris. On May 22, 2011 a tornado occurred in Joplin, MO, leaving 13 tornado victims with <em>Apophysomyces trapeziformis</em> infections as a result of lacerations from airborne material. We used whole genome sequence typing (WGST) for high-resolution phylogenetic SNP analysis of 17 outbreak <em>Apophysomyces</em> isolates and five additional temporally and spatially diverse <em>Apophysomyces</em> control isolates (three <em>A. trapeziformis</em> and two <em>A. variabilis</em> isolates). Whole genome SNP phylogenetic analysis revealed three clusters of genotypically related or identical <em>A. trapeziformis</em> isolates and multiple distinct isolates among the Joplin group; this indicated multiple genotypes from a single or multiple sources. Though no linkage between genotype and location of exposure was observed, WGST analysis determined that the Joplin isolates were more closely related to each other than to the control isolates, suggesting local population structure. Additionally, species delineation based on WGST demonstrated the need to reassess currently accepted taxonomic classifications of phylogenetic species within the genus <em>Apophysomyces</em>.</p> </div

WGST phylogeny of outbreak and background Apophysomyces isolates.

<p>A single maximum parsimony tree was reconstructed using ∼28K SNPs from 22 whole genome sequences, resulting in a CI of 0.62. The tree was rooted with Apo-7449 (A. variabilis). The root was derived from an expanded phylogenetic analyses that included a distant outgroup, which enabled the identification of the most basal member of the samples in the dataset described in this figure (data not shown). Genomes are labeled with a Strain ID # (APO-XXXX) and a Cluster ID #-Letter (CX-A). Clusters of identical and nearly identical genome SNP profiles are also labeled. Branch lengths represent genetic distance based on the number of SNP differences; bar represents 1000 SNPs. Tree constructed using MEGA5.</p

List of strains used in study, by isolation site, species and geographic location, along with sequencing coverage results.

<p>NA = Not Applicable; N/A = Not Available; C = Cluster;</p>*<p>indicates multiple isolates from the same patient.</p

<i>De novo</i> assembled reference statistics for Strain Apo-097.

<p><i>De novo</i> assembled reference statistics for Strain Apo-097.</p