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Volume 22, Number 12—December 2016

Investigation of and Response to 2 Plague Cases, Yosemite National Park, California, USA, 2015

Mary Danforth, Mark Novak, Jeannine Petersen, Paul S. Mead, Luke Kingry, Matthew Weinburke, Danielle Buttke, Gregory Hacker, James Tucker, Michael Niemela, Bryan Jackson, Kerry Padgett, Kelly Liebman, Duc Vugia, and Vicki L. KramerComments to Author 
Author affiliations: California Department of Public Health, Sacramento, California, USA (M. Danforth, M. Novak, G. Hacker, J. Tucker, M. Niemela, B. Jackson, K. Padgett, K. Liebman, D. Vugia, V. Kramer); Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (J. Petersen, P. Mead, L. Kingry); National Park Service, El Portal, California, and Fort Collins, Colorado, USA (M. Weinburke, D. Buttke)

Main Article

Table 2

MLST alleles in whole-genome sequences of Yersinia pestis isolates recovered from humans, animals, and fleas, Yosemite National Park, California, USA, August 2015*†

MLST allele, ORF Y. pestis strain CO92 genome position Mutation type‡ Group 1 isolates§ Group 2 isolates¶
YPCD1.31 22450 SNP T C
YPMT1.46 48841 SNP T C
YPO0193 211446 6-bp VNTR Loss
YPO0445 467549 1-bp INDEL Deletion
YPO0776 Multiple 9-bp VNTR Loss Gain
YPO0894 980089 15-bp VNTR Gain
YPO0968 1072143 SNP C T
YPO0976 1084232 SNP G T
YPO1332 1498571 SNP T C
YPO1422 1617725 18-bp VNTR Loss
YPO1705 1946021 SNP C T
YPO2153 2423508 SNP C G
YPO2253 2531428 SNP T A
YPO2556 2871852 6-bp VNTR Gain
YPO2840 3170905 SNP T A
YPO2842 3172167 SNP T G
YPO2859 3196474 SNP A T
YPO3032 3385894 SNP A G
YPO3339 3725154 SNP T C
YPO3409 3807578 SNP T C
YPO3419 3821161 SNP C T
YPO3481 3886839 SNP C T
YPO3490 3898668 SNP T C
YPO3828 4296699 8-bp INDEL Insertion
YPO4068 4587603 SNP G T

*INDEL, insertion/deletion; MLST, multilocus sequence typing; ORF, open reading frame; SNP, single-nucleotide polymorphism; VNTR, variable number of tandem repeats; –, none.
†PacBio (Pacific Biosciences, Menlo Park, CA, USA) sequencing of patient isolates yielded an average read length of 15,541 bp with 83,608 average filtered subreads and an average quality and coverage of 84.5% and 202×, respectively. Illumina MiSeq sequencing of flea and animal isolates yielded an average ContigN50 of 40,440 for the 6 assemblies and an average read coverage depth of 84.35×.
‡Gain/loss and insertion/deletion are relative to the CO92 reference genome. All identified SNPs, VNTRs, and INDELs demonstrated at least 10× sequence coverage and 100% of the base calls confirming the mutation.
§Group 1; patient 1, flea pool from Crane Flat, animals from Tuolumne Meadows.
¶Group 2; patient 2.

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Page created: November 16, 2016
Page updated: November 16, 2016
Page reviewed: November 16, 2016
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