Tracing Origins of the<i>Salmonella</i>Bareilly Strain Causing a Food-borne Outbreak in the United States

Hoffmann, Maria; Luo, Yan; Monday, Steven R.; González-Escalona, Narjol; Ottesen, Andrea; Muruvanda, Tim; Wang, Charles; Kastanis, George; Keys, Christine E.; Janies, Daniel; Senturk, Izzet F.; Çatalyürek, Ümit V.; Wang, Hua; Hammack, Thomas S.; Wolfgang, William J.; Schoonmaker-Bopp, Dianna; Chu, Alvina; Myers, Robert A.; Haendiges, Julie; Evans, Peter; Meng, Jianghong; Strain, Errol; Allard, Marc W.; Brown, Eric W.

doi:10.1093/infdis/jiv297

Cited by 144 publications

(127 citation statements)

References 22 publications

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“…The first case study used whole genome read data from ten Salmonella enterica sequences associated with a 2010 outbreak, and the observed phylogeny inferred from those data [2]. We used a completed Salmonella enterica genome (CFSAN000189, GenBank: CP006053.1) as the anchor sequence, and simulated 200 variable sites under the generalized time reversible (GTR) model at an average coverage of 20 reads per site.…”

Section: Resultsmentioning

confidence: 99%

“…However, these estimates of shared ancestry may rely on only a handful of data points. When the resulting phylogenetic trees are used by public health agencies to make public health decisions, such as to define the scope of foodborne outbreaks [1], to identify the source of these outbreaks [2][3][4] and where appropriate to follow-up with *Correspondence: ejmctavish@ucmerced.edu 1 University of California, Merced, Merced, CA, USA Full list of author information is available at the end of the article regulatory or legal actions, it is particularly important to ensure that the WGS analysis methods used are validated.…”

Section: Introductionmentioning

confidence: 99%

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TreeToReads - a pipeline for simulating raw reads from phylogenies

McTavish

Pettengill

Davis

et al. 2016

Preprint

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Background: Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution. A few of these analysis approaches are well-integrated into the regulatory process of US Federal agencies (e.g. the FDA's SNP pipeline for tracking foodborne pathogens). However, despite extensive validation on benchmark datasets and comparison with other pipelines, we lack methods for fully exploring the effects of multiple parameter values in each pipeline that can potentially have an effect on whether the correct phylogenetic tree is recovered. Results: To resolve this problem, we offer a program, TreeToReads, which can generate raw read data from mutated genomes simulated under a known phylogeny. This simulation pipeline allows direct comparisons of simulated and observed data in a controlled environment. At each step of these simulations, researchers can vary parameters of interest (e.g., input tree topology, amount of sequence divergence, rate of indels, read coverage, distance of reference genome, etc) to assess the effects of various parameter values on correctly calling SNPs and reconstructing an accurate tree. Conclusions: Such critical assessments of the accuracy and robustness of analytical pipelines are essential to progress in both research and applied settings.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

TreeToReads - a pipeline for simulating raw reads from phylogenies

McTavish

Pettengill

Davis

et al. 2016

Preprint

View full text Add to dashboard Cite

show abstract

“…The idea that geographic source attribution could be successful came in 2012 during retrospective WGS. In that study, a Salmonella Bareilly outbreak in the United States was successfully linked by WGS to a scraped tuna product imported from India on the basis of sequence similarity to a 5-year-old historical isolate from the FDA archives that was collected from a processing facility Ͻ8 km away from the source of the 2012 outbreak (182). In addition to this initial observation, later studies have shown that geographic source attribution can be useful as a tool for delineating geographically dispersed outbreaks.…”

Section: Geographic Source Attributionmentioning

confidence: 99%

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

et al. 2016

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SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

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“…The fact that this bacterium survives in soil and water and may be transfered to fish plays an important role in providing information on the nature of the contamination and the possible dissemination route of this bacterium, thus allowing traceability of the microbial source in fish slaughterhouses (SETTI et al, 2009;HOFFMANN et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Salmonella spp. in the fish production chain: a review

et al. 2018

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Salmonella spp is a pathogen responsible for severe foodborne infections, can be introduced into the fish production chain through inadequate handling or hygiene or contact with contaminated water, and is not a biological contaminant originally reported in fish. Fish microbiological safety is a concern for consumers, industries and regulatory agencies worldwide, since fish, an important food category in the international trade and often exported to several countries, can act as a vehicle for Salmonella transmission throughout the production chain. In addition, concerns regarding the misuse of antibiotics in aquaculture are also an issue, as a result of the increased isolation of resistant and multiresistant Salmonella serovars. In this review, we examined aspects associated with the microbiological risks of the presence of Salmonella spp. in fish and their implication in the aquaculture production chain. In addition, incidence and antimicrobial resistance data are presented, as well as strategies for Salmonella prevention and control in fish.

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Tracing Origins of theSalmonellaBareilly Strain Causing a Food-borne Outbreak in the United States

Cited by 144 publications

References 22 publications

TreeToReads - a pipeline for simulating raw reads from phylogenies

TreeToReads - a pipeline for simulating raw reads from phylogenies

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

Salmonella spp. in the fish production chain: a review

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