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T10-05 Differentiation of Closely Related Salmonella enterica Serotype Heidelberg Isolates by Comparative Genomic Analysis

Wednesday, July 31, 2013: 9:30 AM
213D (Charlotte Convention Center)
Maria Hoffmann, University of Maryland-College Park, College Park, MD
Shaohua Zhao, U.S. Food and Drug Administration, Laurel, MD
James Pettengill, U.S. Food and Drug Administration, College Park, MD
Yan Luo, U.S. Food and Drug Administration, College Park, MD
Tim Muruvanda, U.S. Food and Drug Administration, College Park, MD
Jason Abbott, U.S. Food and Drug Administration, Laurel, MD
Sherry Ayers, U.S. Food and Drug Administration, Laurel, MD
Jason Folster, Centers for Disease Control and Prevention-NCEZID-DFWED-EDLB-NARMS, Atlanta, GA
Marc Allard, U.S. Food and Drug Administration, College Park, MD
Jianghong Meng, University of Maryland-College Park, College Park, MD
Eric Brown, U.S. Food and Drug Administration, College Park, MD
Patrick McDermott, U.S. Food and Drug Administration, Laurel, MD
Recorded Presentation
Introduction: Salmonella enterica serovar Heidelberg is one of the top serovars responsible for numerous human outbreaks, including a 2011 multistate outbreak involving 136 confirmed cases and one death, resulting from consumption of contaminated ground turkey.

Purpose: Our objectives were to explore how whole genome sequencing (WGS) can differentiate outbreak isolates of Salmonella Heidelberg from non-outbreak isolates that share the same pulsed-field gel electrophoresis (PFGE) pattern, and provide a better understanding of the evolution and ecology of Salmonella Heidelberg.

Methods: DNA from 44 Salmonella Heidelberg isolates with 20 having a nearly indistinguishable PFGE Xbal and BlnI pattern collected from various sources over 30 years, including the 2011 outbreak, was sequenced using the 454 GS FLX (Roche) platform. Phylogenetic analyses were conducted on a matrix of variable single nucleotide polymorphisms (SNPs) identified with the program kSNP. DNA from a clinical 2011 outbreak isolate was sequenced and assembled using the Pacific Biosciences (PacBio) RS sequencer and their hierarchical genome assembly process.

Results: SNP analysis found a total of 860/4,053 SNPs informative and distinguished isolates sharing the same PFGE patterns. The outbreak isolates clustered together having only 2 diagnostic SNP differences among them. Furthermore, the outbreak isolates contained a VirB/D4 virulence plasmid that carries the Type IV secretion system, and an incompatibility group (Inc) I antimicrobial resistance plasmid encoding resistance to gentamicin (aacC2), beta-lactams (bl2b_tem-1), streptomycin (aadAI) and tetracycline (tetA, tetR). Additionally, the complete, closed genome/plasmids sequence from a clinical isolate was rapidly determined using the PacBio system providing more nucleotide sequences for analyses.

Significance: This study shows that WGS, in combination with other methods, is a powerful tool for separating strains considered clonal by indistinguishable PFGE profiles. The timely application of WGS technology will advance investigations to identify bacterial sources of infections and to understand the outbreak transmission dynamics of Salmonella.

Back to: Technical Session 10 - Pathogens
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