Laboratory Investigation of Salmonella enterica serovar Poona Outbreak in California: Comparison of Pulsed-Field Gel Electrophoresis (PFGE) and Whole Genome Sequencing (WGS) Results

SUMMARYSalmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

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A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type

Applied and Environmental Microbiology ◽

10.1128/aem.06538-11 ◽

2011 ◽

Vol 77 (24) ◽

pp. 8648-8655 ◽

Cited By ~ 72

Author(s):

Henk C. den Bakker ◽

Andrea I. Moreno Switt ◽

Craig A. Cummings ◽

Karin Hoelzer ◽

Lovorka Degoricija ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Gel Electrophoresis ◽

Salmonella Enterica ◽

Pfge Pattern ◽

Pulsed Field Gel Electrophoresis ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type ◽

Pulsed Field

ABSTRACTIn this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak ofSalmonella entericasubsp.entericaserovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIXX01.0011, a common pulsed-field gel electrophoresis (PFGE) pattern associated with isolates from the outbreak. These isolates represented 20 isolates collected from human sources during the period of the outbreak and 27 control isolates collected from human, food, animal, and environmental sources before the outbreak. Based on 253 high-confidence SNPs, we were able to reconstruct a tip-dated molecular clock phylogeny of the isolates and to assign four human isolates to the actual outbreak. We developed an SNP typing assay to rapidly discriminate between outbreak-related cases and non-outbreak-related cases and tested this assay on an extended panel of 112 isolates. These results suggest that only a very small percentage of the human isolates with the outbreak PFGE pattern and obtained during the outbreak period could be attributed to the actual pepper-related outbreak (20%), while the majority (80%) of the putative cases represented background cases. This study demonstrates that next-generation-based SNP typing provides the resolution and accuracy needed for outbreak investigations of food-borne pathogens that cannot be distinguished by currently used subtyping methods.

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Evaluation of Whole Genome Sequencing for outbreak detection of Salmonella enterica serovar Enteritidis

10.26226/morressier.5f4ccc57648d3d8b3f362bad ◽

2020 ◽

Author(s):

Ainhoa Arrieta-Gisasola ◽

Aitor Atxaerandio Landa ◽

Javier Garaizar ◽

Joseba Bikandi ◽

José Karkamo ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Outbreak Detection ◽

Whole Genome ◽

Salmonella Enterica Serovar Enteritidis

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Whole genome sequencing analysis of Salmonella enterica serovar Weltevreden isolated from human stool and contaminated food samples collected from the Southern coastal area of China

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2017.10.032 ◽

2018 ◽

Vol 266 ◽

pp. 317-323 ◽

Cited By ~ 4

Author(s):

Baisheng Li ◽

Xingfen Yang ◽

Hailing Tan ◽

Bixia Ke ◽

Dongmei He ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Coastal Area ◽

Salmonella Enterica ◽

Food Samples ◽

Whole Genome ◽

Sequencing Analysis ◽

Contaminated Food ◽

Human Stool

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Molecular Analyses of Salmonellaenterica Isolates from Fish Feed Factories and Fish Feed Ingredients

Applied and Environmental Microbiology ◽

10.1128/aem.69.2.1075-1081.2003 ◽

2003 ◽

Vol 69 (2) ◽

pp. 1075-1081 ◽

Cited By ~ 36

Author(s):

Live L. Nesse ◽

Kerstin Nordby ◽

Even Heir ◽

Bjarne Bergsjoe ◽

Traute Vardund ◽

...

Keyword(s):

Gel Electrophoresis ◽

Salmonella Enterica ◽

Profile Analysis ◽

Plasmid Profile ◽

Pulsed Field Gel Electrophoresis ◽

Fish Feed ◽

Molecular Analyses ◽

Feed Ingredients ◽

Pulsed Field ◽

Salmonella Serovars

ABSTRACT Isolates of the most commonly observed salmonella serovars in Norwegian fish feed factories from 1998 to 2000 (Salmonella enterica serovar Agona, S. enterica serovar Montevideo, S. enterica serovar Senftenberg, and S. enterica serovar Kentucky) were studied by pulsed-field gel electrophoresis (PFGE) and plasmid profile analysis and compared to isolates of the same serovars from fish feed ingredients, humans, and other sources (a total of 112 isolates). Within each serovar, a variety of distinct PFGE types (with similarity levels less than 90%) were observed in the feed ingredients and other sources, while only two distinct types of each serovar were identified in the factories. The combined results of PFGE and plasmid analyses showed that each factory harbored only a few S. enterica clones. Some of these clones persisted for at least 3 years in the factories, indicating that there was long-lasting contamination probably due to inadequate decontamination procedures.

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