Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation
David M. Engelthaler, Tom Chiller, James A. Schupp, Joshua Colvin, Stephen M. Beckstrom-Sternberg, Elizabeth M. Driebe, Tracy Moses, Waibhav Tembe, Shripad Sinari, James S. Beckstrom-Sternberg, Alexis Christoforides, John V. Pearson, John Carpten, Paul Keim, Ashley Peterson, Dawn Terashita, and S. Arunmozhi Balajee
Author affiliations: Author affiliations: Translational Genomics Research Institute, Phoenix, Arizona, USA (D.M. Engelthaler, J.A. Schupp, J. Colvin, S.M. Beckstrom-Sternberg, E.M. Driebe, T. Moses, W. Tembe, S. Sinari, A. Christoforides, J.V. Pearson, J. Carpten, P. Keim); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (T. Chiller, S.A. Balajee); Northern Arizona University, Flagstaff, Arizona, USA (S.M. Beckstrom-Sternberg, J.S. Beckstrom-Sternberg, P. Keim); Los Angeles County Department of Public Health, Los Angeles, California, USA (A. Peterson, D. Terashita)
Figure 2. Alignment of Coccidioides immitis whole-genome sequence reads flanking a confirmed single-nucleotide polymorphism (RSv3 supercontig 1, position 6729646, highlighted in blue in panel B) among the 3 cluster isolates. Isolates from patients X, Y, and Z, who had coccidioidomycosis, are shown in panels A, B, and C, respectively. The alignment was created by using SolScape, a short-read sequence-alignment viewer developed in house (J. Pearson et al., unpub. data; tool available upon request). Reference sequence position is given at the top of each panel; actual reference sequence is highlighted in white at the center of each panel. Bases differing from the reference sequence are highlighted in pink, green, or yellow.
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