Journal article
A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type
Applied and environmental microbiology, Vol.77(24), pp.8648-8655
12/2011
Handle:
https://hdl.handle.net/2376/108825
PMCID: PMC3233099
PMID: 22003026
Abstract
In this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak of
Salmonella enterica
subsp.
enterica
serovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIXX01.0011, a common pulsed-field gel electrophoresis (PFGE) pattern associated with isolates from the outbreak. These isolates represented 20 isolates collected from human sources during the period of the outbreak and 27 control isolates collected from human, food, animal, and environmental sources before the outbreak. Based on 253 high-confidence SNPs, we were able to reconstruct a tip-dated molecular clock phylogeny of the isolates and to assign four human isolates to the actual outbreak. We developed an SNP typing assay to rapidly discriminate between outbreak-related cases and non-outbreak-related cases and tested this assay on an extended panel of 112 isolates. These results suggest that only a very small percentage of the human isolates with the outbreak PFGE pattern and obtained during the outbreak period could be attributed to the actual pepper-related outbreak (20%), while the majority (80%) of the putative cases represented background cases. This study demonstrates that next-generation-based SNP typing provides the resolution and accuracy needed for outbreak investigations of food-borne pathogens that cannot be distinguished by currently used subtyping methods.
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Details
- Title
- A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type
- Creators
- Henk C den Bakker - Department of Food Science, Cornell University, Ithaca, New York 14853Andrea I Moreno Switt - Department of Food Science, Cornell University, Ithaca, New York 14853Craig A Cummings - Life Technologies Corporation, 850 Lincoln Centre Drive, Foster City, California 94404Karin Hoelzer - Department of Food Science, Cornell University, Ithaca, New York 14853Lovorka Degoricija - Life Technologies Corporation, 850 Lincoln Centre Drive, Foster City, California 94404Lorraine D Rodriguez-Rivera - Department of Food Science, Cornell University, Ithaca, New York 14853Emily M Wright - Department of Food Science, Cornell University, Ithaca, New York 14853Rixun Fang - Life Technologies Corporation, 850 Lincoln Centre Drive, Foster City, California 94404Margaret Davis - Veterinary Clinical Sciences Department, Washington State University, P.O. Box 646610, Pullman, Washington 99164Tim Root - New York State Department of Health, Empire State Plaza, P.O. Box 22002, Albany, New York 12201Dianna Schoonmaker-Bopp - New York State Department of Health, Empire State Plaza, P.O. Box 22002, Albany, New York 12201Kimberlee A Musser - New York State Department of Health, Empire State Plaza, P.O. Box 22002, Albany, New York 12201Elizabeth Villamil - New York State Department of Health, Empire State Plaza, P.O. Box 22002, Albany, New York 12201HaeNa Waechter - New York City Department of Health and Mental Hygiene, 455 First Ave., New York, New York 10016Laura Kornstein - New York City Department of Health and Mental Hygiene, 455 First Ave., New York, New York 10016Manohar R Furtado - Life Technologies Corporation, 850 Lincoln Centre Drive, Foster City, California 94404Martin Wiedmann - Department of Food Science, Cornell University, Ithaca, New York 14853
- Publication Details
- Applied and environmental microbiology, Vol.77(24), pp.8648-8655
- Academic Unit
- Paul G. Allen School for Global Animal Health
- Publisher
- American Society for Microbiology; 1752 N St., N.W., Washington, DC
- Number of pages
- 8
- Identifiers
- 99900547797801842
- Language
- English
- Resource Type
- Journal article