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Analysis of clinical Bordetella pertussis isolates using whole genome sequences reveals novel genomic regions associated with recent outbreaks in the United States of America

Glen Otero, Benjamin M. Althouse, Samuel V. Scarpino
doi: https://doi.org/10.1101/047886
Glen Otero
1Independent researcher
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  • For correspondence: gotero@linuxprophet.com
Benjamin M. Althouse
2Institute for Disease Modeling, Bellevue, WA
3Santa Fe Institute, Santa Fe, NM
4Department of Biology, New Mexico State University, Las Cruces, NM
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  • For correspondence: althouse@santafe.edu
Samuel V. Scarpino
3Santa Fe Institute, Santa Fe, NM
5Department of Mathematics and Statistics, University of Vermont, Burlington, VT
6Complex Systems Center, University of Vermont, Burlington, VT
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  • For correspondence: scarpino@santafe.edu
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Abstract

Background: Despite high-levels of vaccination, whooping cough, primarily caused by Bordetella pertussis (BP), has persisted and resurged. It remains a major cause of infant death worldwide and is the most prevalent vaccine-preventable disease in developed countries. To date, most genomic studies have focused on a small subset of the BP genome, biasing our clinical understanding and public health awareness.

Methods: We performed a Genome-Wide Association Study (GWAS) on 76 U.S. BP whole genomes, including strains from recent outbreaks.

Results: A GWAS of the 76 BP isolates revealed a sharp increase in genetic variation associated with the Minnesota 2012 outbreak and identified 52 variants unique to the Minnesota outbreak and 19 unique to the California and Washington outbreaks. None of the identified variants were shared between the outbreaks and the vast majority were previously uncharacterized. We further identified variation associated with pertactin negative strains and acellular vaccination.

Conclusions: We identified novel genomic regions associated with recent BP outbreaks. Our results underscore the need for increased whole genome sequencing of BP isolates, which can reduce costly misdiagnosis and improve surveillance. The genes containing these variants warrant further investigation into their possible roles in BP pathogenicity and the ongoing resurgence in the U.S.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 09, 2016.
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Analysis of clinical Bordetella pertussis isolates using whole genome sequences reveals novel genomic regions associated with recent outbreaks in the United States of America
Glen Otero, Benjamin M. Althouse, Samuel V. Scarpino
bioRxiv 047886; doi: https://doi.org/10.1101/047886
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Analysis of clinical Bordetella pertussis isolates using whole genome sequences reveals novel genomic regions associated with recent outbreaks in the United States of America
Glen Otero, Benjamin M. Althouse, Samuel V. Scarpino
bioRxiv 047886; doi: https://doi.org/10.1101/047886

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