Single-nucleotide polymorphism typing analysis for molecular subtyping of Tennessee isolates associated with the 2007 nationwide peanut butter outbreak in the United States.

BACKGROUND

In 2007, a nationwide Tennessee outbreak occurred via contaminated peanut butter. Here, we developed a single-nucleotide polymorphism (SNP)-typing method for . Tennessee to determine the clonal subtypes of . Tennessee that were associated with the peanut butter outbreak.

METHODS AND RESULTS

One seventy-six . Tennessee isolates from various sources, including humans, animals, food, and the environment, were analyzed by using the SNP technique. Eighty-four representative SNP markers were selected by comparing the sequences of three representative . Tennessee strains with different multi-locus sequence typing and variable number tandem repeats from our collection. The set of eighty-four SNP markers showed 100% typeability for the 176 strains, with the nucleotide diversity ranging from 0.011 to 0.107 (mean = 0.049 ± 0.018, median = 0.044) for each marker. Among the four clades and nine subtypes generated by the SNP typing, subtype 1, which comprised 142 . Tennessee strains, was the most predominant. The dominance of single-strain clones in subtype 1 revealed that . Tennessee is highly clonal regardless of outbreak-association, source, or period of isolation, suggesting the presence of an . Tennessee strain prototype. Notably, a minimum 18 SNP set was able to determine clonal . Tennessee strains with similar discrimination power, potentially allowing more rapid and economic strain genotyping for both outbreaks and sporadic cases.

CONCLUSIONS

The SNP-typing method described here might aid the investigation of the epidemiology and microevolution of pathogenic bacteria by discriminating between outbreak-related and sporadic clinical cases. In addition, this approach enables us to understand the population structure of the bacterial subtypes involved in the outbreak.