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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Publications at this Location » Publication #297102

Title: Whole Genome Shotgun Analysis: the Resolving Power to Distinguish 2009 and 2010 Clinical Isolates of Salmonella Typhimurium Possessing the Same PFGE Type

item Parker, Craig
item Gorski, Lisa
item Cooper, Kerry
item Huynh, Steven
item Liang, Anita

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 8/5/2013
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Between 2009 and 2011, Salmonella enterica subsp. enterica serovar Typhimurium with the JPXX01.0014 pulse field gel electrophoresis (PFGE) type was isolated across the United States. The 2009 isolates were associated with an outbreak from an unidentified food source, while later isolates were linked with exposure to microbiology laboratories. To determine if higher resolution methods could distinguish these strains, we sequenced and analyzed the whole genome shotgun (WGS) assemblies of 8 clinical isolates from 2009 and two isolates from 2010. Three additional isolates possessing the same PFGE type collected from celery in 2002, raw pecans in 2009, and from California pond water in 2009 were also sequenced. Comparison of these 13 WGS assemblies with seven completed S. Typhimurium genomes clearly revealed that all of the JPXX01.0014 isolates were most related to S. Typhimurium strain 14028s. One 2010 clinical isolate was identical to strain 14028s, which is commonly used in clinical and teaching laboratories. The2009 clinical isolates, the other 2010 clinical isolate and the 2002 isolate from celery were distinct from strain 14028s by the same three SNPs. The strains isolated in 2009 from water and pecans had the same three SNPs and several different additional SNPs, including distinct rpoS alleles. Broadly, these results confirm the resolving ability of whole genome analysis to distinguish isolates that were seemingly identical by other molecular typing methods. More specifically, the results suggest that not all 2010 isolates were necessarily associated with the same source exposure. With decreasing sequencing costs, WGS analysis is poised to become a common tool in outbreak traceback.