July 7, 2019  |  

Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes associated with an outbreak linked to cheese, United States, 2013.

Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a non-implicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, minimum spanning tree by the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide the differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering generated by phylogenetically meaningful algorithms on sufficient number of isolates, and SNP/allele threshold alone is not sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b, had an identical inlA sequence, which did not have premature stop codons.IMPORTANCE In this outbreak, multiple analytical approaches were used for maximum discriminatory power. A PFGE-matched, epidemiologically unrelated isolate had high genetic similarity to the outbreak-associated isolates, with as few as only 7 SNP differences. Therefore, the SNP/allele threshold should not be used as the only evidence to define the scope of an outbreak. It is critical that the SNP/allele counts be complemented by WGS clustering generated by phylogenetically meaningful algorithms to distinguish outbreak-associated isolates from epidemiologically unrelated isolates. Careful selection of a variant calling approach and phylogenetic algorithm is critical for core genome-based analyses. The whole genome-based analyses were able to construct the highly resolved phylogeny needed to support the findings of the outbreak investigation. Ultimately, epidemiologic evidence and multiple WGS analyses should be combined to increase the confidence in outbreak investigations. Copyright © 2017 Chen et al.


July 7, 2019  |  

Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States.

Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associated with scraped tuna imported from India.Using next-generation sequencing, we sequenced the complete genome of 100 Salmonella Bareilly isolates obtained from patients who consumed contaminated product, from natural sources, and from unrelated historically and geographically disparate foods. Pathogen genomes were linked to geography by projecting the phylogeny on a virtual globe and produced a transmission network.Phylogenetic analysis of WGS data revealed a common origin for outbreak strains, indicating that patients in Maryland and New York were infected from sources originating at a facility in India.These data represent the first report fully integrating WGS analysis with geographic mapping and a novel use of transmission networks. Results showed that WGS vastly improves our ability to delimit the scope and source of bacterial food-borne contamination events. Furthermore, these findings reinforce the extraordinary utility that WGS brings to global outbreak investigation as a greatly enhanced approach to protecting the human food supply chain as well as public health in general. Published by Oxford University Press for the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.


July 7, 2019  |  

Whole-genome sequencing: opportunities and challenges for public health, food-borne outbreak investigations, and the global food supply.

Food-borne disease is burdensome, af- fecting 1 in 6 persons or an estimated 48 million ill, 128 000 hospitalized, and 3000 deaths in the United States annually. In addition, societal costs from lost lives, lost labor, lost wages, and even lost revenue in the food industry are substan- tial. Globally the burden is even higher, and multinational outbreaks due to the global movement of contaminated foods are being described increasingly. The glo- bal food supply links nations and econo- mies, emphasizing the need to view food safety with an integrated farm-to-fork lens. As predicted, advances in molecular techniques and information management have been transformative for food-borne disease investigation.


July 7, 2019  |  

High-quality draft genome sequences for five non-O157 Shiga toxin-producing Escherichia coli strains generated with PacBio sequencing and optical maps.

Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen. We report here the high-quality draft whole-genome sequences of five STEC strains isolated from clinical cases in the United States. This report is for STEC of serotypes O55:H7, O79:H7, O91:H14, O153:H2, and O156:H25. Copyright © 2016 Lindsey et al.


July 7, 2019  |  

Chromosome and linear plasmid sequences of a 2015 human isolate of the tick-borne relapsing fever spirochete, Borrelia turicatae.

The sequences of the complete linear chromosome and 7 linear plasmids of the relapsing fever spirochete Borrelia turicatae are presented in this report. The 925,547 bp of chromosome and 380,211 bp of plasmid sequence were predicted to contain a total of 1,131 open reading frames, with an average G+C content of 29.7%. Copyright © 2016 Kingry et al.


July 7, 2019  |  

Complete genome sequences of three outbreak-associated Legionella pneumophila isolates.

We report here the complete genome sequences of three Legionella pneumophila isolates that are associated with a Legionnaires’ disease outbreak in New York in 2012. Two clinical isolates (D7630 and D7632) and one environmental isolate (D7631) were recovered from this outbreak. A single isolate-specific virulence gene was found in D7632. These isolates were included in a large study evaluating the genomic resolution of various bioinformatics approaches for L. pneumophila serogroup 1 isolates. Copyright © 2016 Morrison et al.


July 7, 2019  |  

FDA-CDC antimicrobial resistance isolate bank: A publicly-available resource to support research, development and regulatory requirements.

The FDA-CDC Antimicrobial Resistance Isolate Bank was created in July 2015 as a publicly available resource to combat antimicrobial resistance. It is a curated repository of bacterial isolates with an assortment of clinically-important resistance mechanisms that have been phenotypically and genotypically characterized. In the first two years of operation, the Bank offered 14 panels comprising 496 unique isolates and had filled 486 orders from 394 institutions throughout the United States. New panels are being added. Copyright © 2017 American Society for Microbiology.


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