Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks.
Establishing an association between possible food sources and clinical isolates requires discriminating the suspected pathogen from an environmental background, and distinguishing it from other closely-related foodborne pathogens. We used whole genome sequencing (WGS) to Salmonella subspecies enterica serotype Tennessee (S. Tennessee) to describe genomic diversity across the serovar as well as among and within outbreak clades of strains associated with contaminated peanut butter. We analyzed 71 isolates of S. Tennessee from disparate food, environmental, and clinical sources and 2 other closely-related Salmonella serovars as outgroups (S. Kentucky and S. Cubana), which were also shot-gun sequenced. A whole genome single nucleotide polymorphism (SNP) analysis was performed using a maximum likelihood approach to infer phylogenetic relationships. Several monophyletic lineages of S. Tennessee with limited SNP variability were identified that recapitulated several food contamination events. S. Tennessee clades were separated from outgroup salmonellae by more than sixteen thousand SNPs. Intra-serovar diversity of S. Tennessee was small compared to the chosen outgroups (1,153 SNPs), suggesting recent divergence of some S. Tennessee clades. Analysis of all 1,153 SNPs structuring an S. Tennessee peanut butter outbreak cluster revealed that isolates from several food, plant, and clinical isolates were very closely related, as they had only a few SNP differences between them. SNP-based cluster analyses linked specific food sources to several clinical S. Tennessee strains isolated in separate contamination events. Environmental and clinical isolates had very similar whole genome sequences; no markers were found that could be used to discriminate between these sources. Finally, we identified SNPs within variable S. Tennessee genes that may be useful markers for the development of rapid surveillance and typing methods, potentially aiding in traceback efforts during future outbreaks. Using WGS can delimit contamination sources for foodborne illnesses across multiple outbreaks and reveal otherwise undetected DNA sequence differences essential to the tracing of bacterial pathogens as they emerge.
Center for Food Science and Applied Nutrition (CFSAN), Food and Drug Administration (FDA), College Park, Maryland, United States of America.
Mark R
MR
Wilson
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Eric
E
Brown
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Chris
C
Keys
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Errol
E
Strain
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Yan
Y
Luo
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Tim
T
Muruvanda
Battelle Memorial Institute, Crystal City, Virginia, United States of America.|Division of Virulence Assessment (DVA), Virulence Mechanisms Branch (VMB), CFSAN/FDA, Office of Applied Research and Safety Assessment (OARSA), Laurel, Maryland, United States of America.
Christopher
C
Grim
Division of Virulence Assessment (DVA), Virulence Mechanisms Branch (VMB), CFSAN/FDA, Office of Applied Research and Safety Assessment (OARSA), Laurel, Maryland, United States of America.
Junia
J
Jean-Gilles Beaubrun
Division of Virulence Assessment (DVA), Virulence Mechanisms Branch (VMB), CFSAN/FDA, Office of Applied Research and Safety Assessment (OARSA), Laurel, Maryland, United States of America.
Karen
K
Jarvis
Division of Virulence Assessment (DVA), Virulence Mechanisms Branch (VMB), CFSAN/FDA, Office of Applied Research and Safety Assessment (OARSA), Laurel, Maryland, United States of America.
Laura
L
Ewing
Division of Virulence Assessment (DVA), Virulence Mechanisms Branch (VMB), CFSAN/FDA, Office of Applied Research and Safety Assessment (OARSA), Laurel, Maryland, United States of America.
Gopal
G
Gopinath
Division of Virulence Assessment (DVA), Virulence Mechanisms Branch (VMB), CFSAN/FDA, Office of Applied Research and Safety Assessment (OARSA), Laurel, Maryland, United States of America.
Darcy
D
Hanes
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Marc W
MW
Allard
Battelle Memorial Institute, Crystal City, Virginia, United States of America.
Steven
S
Musser
D004196:Disease Outbreaks; D005517:Foodborne Diseases / Q000453:epidemiology / Q000382:microbiology*; D016680:Genome, Bacterial; D017720:Molecular Epidemiology; D020641:Polymorphism, Single Nucleotide; D019779:Salmonella enterica / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D065288:Serogroup