Whole genome multiple-locus sequence typing as an epidemiological tool for tracking Tier 1 pathogens
Abstract
Plague and tularemia are severe zoonotic diseases caused by the Tier 1 bacterial pathogens, Yersinia pestis (Yp) and Francisella tularensis (Ft), respectively. Tier 1 agents are those “that present the greatest risk of... [ view full abstract ]
Plague and tularemia are severe zoonotic diseases caused by the Tier 1 bacterial pathogens, Yersinia pestis (Yp) and Francisella tularensis (Ft), respectively. Tier 1 agents are those “that present the greatest risk of deliberate misuse with the most significant potential for mass casualties or devastating effects to the economy, critical infrastructure; or public confidence”. Molecular epidemiological tools for Yp and Ft are essential for surveillance of strains causing natural cases of disease in the US, to identify sources of human exposure, to define outbreaks as well as to identify events due to deliberate misuse. The cost for whole genome sequencing (WGS) of bacterial genomes has decreased exponentially, which makes whole genome sequencing (WGS) a viable option for comprehensive strain typing. Using current and archived isolates, over 100 Yp and Ft strains have been sequenced using both the PacBio RSII and Illumina MiSeq platforms. A whole genome multi-locus sequence typing (wgMLST) approach was developed for Yp and Ft that uses WGS data and rapidly compares every gene in the bacterial genome to all other sequenced strains. Our results indicate this method accurately identifies epidemiologic relationships among strains and with higher resolution than the currently used method, PFGE. Allelic databases, utilizing sequences generated on the Illumina MiSeq, are under development for standardization of whole genome comparisons. Comparison of long-read and short-read sequence data demonstrates the complementary value of using the two types of sequence data for comprehensive strain typing, which include nucleotide sequence data as well as structural rearrangements of the genome.
Authors
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Luke Kingry
(Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO)
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John Young
(Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO)
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Ryan Pappert
(Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO)
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Martin Schriefer
(Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO)
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Jeannine Petersen
(Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Fort Collins, CO)
Topic Areas
Sequencing applications for metagenomics, transcriptomics, diagnostics, and biosurveillanc , Comparative genomics, re-sequencing, SNPs, structural variation , Human, non-human, and infectious disease applications
Session
OS-9 » Pathogen Sequencing & Detection (13:50 - Thursday, 18th May, La Fonda Ballroom)
Presentation Files
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