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United States Department of Agriculture

Agricultural Research Service

Research Project: Molecular Biology of Human Pathogens Associated with Food

Location: Produce Safety and Microbiology Research

Title: Whole-Genome Sequencing Reveals Laboratory Salmonella Typhimurium Strain 14028s as a Likely Source of Outbreak Isolates from 2009-2010

Authors
item Parker, Craig
item Gorski, Lisa
item Huynh, Steven
item Liang, Anita

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: February 20, 2013
Publication Date: N/A

Technical Abstract: Background: Next-generation sequencing (NGS) of bacterial isolates has emerged as valuable tool for tracking of an outbreak source. Between 2009 and 2011, clinical isolates of Salmonella Typhimurium sharing the JPXX01.0014 (XbaI) PFGE type were isolated across the U.S. The initial isolates were associated with an outbreak from an unidentified food source, while 2010 isolates were linked with exposure to microbiology laboratories. To determine if the isolates could be distinguished, we performed NGS and analyzed the whole-genome shotgun (WGS) assemblies of 12 clinical strains from 2009, two clinical strains from 2010, and four environmental strains possessing the same XbaI PFGE type collected in 2002 and 2009. Methods: Both 454 (8-20X coverage) and MiSeq (>200X coverage) were used to sequence the 18 Salmonella Typhimurium isolates. The 454 sequencing reads were assembled using Newbler and the contigs were compared with seven completed S. Typhimurium genomes to identify the closest match. Subsequently, 454 and MiSeq sequence reads were utilized to identify SNPs in the non-repetitive regions of the genome for each isolate. Suspected SNPs were verified by Sanger sequencing in each strain. Results: Genomic comparisons identified S. Typhimurium strain 14028s, commonly used in clinical and teaching laboratories, as the most similar to the outbreak isolates. Eleven of the 2009 clinical strains were distinct from strain 14028s by three SNPs. One 2009 clinical isolate with a reported distinct MLVA had over 10,000 SNPs. One 2010 clinical isolate had no SNPs when compared to strain 14028s, while the other 2010 clinical strain from the same laboratory, possessed the three SNPs found in the 2009 strains. The four environmental isolates had the same three SNPs. A 2002 isolate and a 2009 isolate were identical to the 2009 clinical strains, whereas, the two other 2009 isolates had 3 and 4 additional SNPs, respectively. Conclusion: This study confirms the resolving ability of whole-genome analysis to distinguish clonal isolates. Our data also suggests the presence of S. Typhimurium clonal isolates that may be genomically stable over several years.

Last Modified: 10/25/2014