Whole genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program

AbstractThe All of Us Research Program (AoURP, ‘the program’) is an initiative, sponsored by the National Institutes of Health (NIH), that aims to enroll one million people (or more) across the United States. Through repeated engagement of participants, a research resource is being created to enable a variety of future observational and interventional studies. The program has also committed to genomic data generation and returning important health-related information to participants. To do so, whole genome sequencing (WGS), variant calling processes, data interpretation, and return-of-results procedures had to be created and receive an Investigational Device Exemption (IDE) from the United States Food and Drug Administration (FDA). The performance of the entire workflow was assessed through the largest known cross-center, WGS-based, validation activity that was refined iteratively through interactions with the FDA over many months. The accuracy and precision of the WGS process as a device for the return of certain health-related genomic results was determined to be sufficient, and an IDE was granted. We present here both the process of navigating the IDE application process with the FDA and the results of the validation study as a guide to future projects which may need to follow a similar path. Future supplements to the IDE will be submitted to support additional variant classes, sample types, and any expansion to the reportable regions.

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Whole Genome Sequencing of Mycobacterium bovis Isolated From Livestock in the United States, 1989–2018

Frontiers in Veterinary Science ◽

10.3389/fvets.2018.00253 ◽

2018 ◽

Vol 5 ◽

Cited By ~ 18

Author(s):

Kathy Orloski ◽

Suelee Robbe-Austerman ◽

Tod Stuber ◽

Bill Hench ◽

Mark Schoenbaum

Keyword(s):

United States ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mycobacterium Bovis ◽

The United States ◽

Whole Genome

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Whole Genome Sequencing Resource of the European Larch Canker Pathogen Lachnellula willkommii for Molecular Diagnostic Marker Development

Phytopathology ◽

10.1094/phyto-09-19-0350-a ◽

2020 ◽

Vol 110 (7) ◽

pp. 1255-1259

Author(s):

Emily Giroux ◽

Guillaume J. Bilodeau

Keyword(s):

United States ◽

North America ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Draft Genome ◽

The United States ◽

Molecular Diagnostic ◽

Whole Genome ◽

European Larch ◽

The North

The filamentous ascomycete fungus Lachnellula willkommii is the causal agent of European larch canker (ELC), one of the most destructive diseases of larch in Europe and a regulated plant pathogen of quarantine significance in Canada and the United States. L. willkommii was first detected in Massachusetts, North America in 1927 on a larch plantation cultivated with nursery stock imported from Great Britain. Despite the decades of practices aimed at eliminating the pathogen, it has reappeared in coastal areas of Canada and the United States. There is concern ELC could spread throughout the range of eastern larch, a transcontinental species typical of the Boreal forest that spans the North American landscape. There is geographic range overlap between several nonpathogenic indigenous Lachnellula species and the reported distribution of L. willkommii in North America. Morphological and biological methods to distinguish L. willkommii are often inadequate as the fungus does not always produce the phenotypic structures that distinguish it from these other saprophytic Lachnellula species. Whole genome sequencing technologies were used to obtain the draft genome sequences of L. willkommii and six other Lachnellula species. Molecular markers identified from the genomic data may be used to discriminate L. willkommii from its nonpathogenic relatives.

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Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States

Foodborne Pathogens and Disease ◽

10.1089/fpd.2019.2662 ◽

2019 ◽

Vol 16 (7) ◽

pp. 441-450 ◽

Cited By ~ 17

Author(s):

Eric Brown ◽

Uday Dessai ◽

Sherri McGarry ◽

Peter Gerner-Smidt

Keyword(s):

Public Health ◽

United States ◽

Food Safety ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

The United States ◽

Whole Genome

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SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data

Applied and Environmental Microbiology ◽

10.1128/aem.01746-19 ◽

2019 ◽

Vol 85 (23) ◽

Cited By ~ 25

Author(s):

Shaokang Zhang ◽

Hendrik C. den Bakker ◽

Shaoting Li ◽

Jessica Chen ◽

Blake A. Dinsmore ◽

...

Keyword(s):

Public Health ◽

United States ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Draft Genome ◽

The United States ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Link Type

ABSTRACT SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole-genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here, we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include (i) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes, (ii) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies, and (iii) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common U.S. serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, SeqSero2 is up to 50 times faster than the original SeqSero while maintaining equivalent accuracy for raw reads and substantially improving accuracy for assemblies. SeqSero2 further suggested that 3% of the tested genomes contained reads from multiple serotypes, indicating a use for contamination detection. In addition to short reads, SeqSero2 demonstrated potential for accurate and rapid serotype prediction directly from long nanopore reads despite base call errors. Testing of 40 nanopore-sequenced genomes of 17 serotypes yielded a single H antigen misidentification. IMPORTANCE Serotyping is the basis of public health surveillance of Salmonella. It remains a first-line subtyping method even as surveillance continues to be transformed by whole-genome sequencing. SeqSero allows the integration of Salmonella serotyping into a whole-genome-sequencing-based laboratory workflow while maintaining continuity with the classic serotyping scheme. SeqSero2, informed by extensive testing and application of SeqSero in the United States and other countries, incorporates important improvements and updates that further strengthen its application in routine and large-scale surveillance of Salmonella by whole-genome sequencing.

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Whole Genome Sequencing to Investigate the Emergence of Clonal Complex 23 Neisseria meningitidis Serogroup Y Disease in the United States

PLoS ONE ◽

10.1371/journal.pone.0035699 ◽

2012 ◽

Vol 7 (4) ◽

pp. e35699 ◽

Cited By ~ 19

Author(s):

Mary G. Krauland ◽

Julie C. Dunning Hotopp ◽

David R. Riley ◽

Sean C. Daugherty ◽

Jane W. Marsh ◽

...

Keyword(s):

United States ◽

Neisseria Meningitidis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clonal Complex ◽

The United States ◽

Whole Genome

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Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands

Antibiotics ◽

10.3390/antibiotics10030267 ◽

2021 ◽

Vol 10 (3) ◽

pp. 267

Author(s):

Elton Burnett ◽

Maria Ishida ◽

Sofia de Janon ◽

Sohail Naushad ◽

Marc-Olivier Duceppe ◽

...

Keyword(s):

United States ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

The United States ◽

Galapagos Islands ◽

Multi Drug Resistance ◽

Whole Genome ◽

Galápagos Islands ◽

Extended Spectrum ◽

Surveillance Programs

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.

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Use of whole-genome sequencing for Campylobacter surveillance from NARMS retail poultry in the United States in 2015

Food Microbiology ◽

10.1016/j.fm.2018.01.018 ◽

2018 ◽

Vol 73 ◽

pp. 122-128 ◽

Cited By ~ 20

Author(s):

Chris A. Whitehouse ◽

Shenia Young ◽

Cong Li ◽

Chih-Hao Hsu ◽

Gordon Martin ◽

...

Keyword(s):

United States ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

The United States ◽

Whole Genome

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Genomic Analysis of a Pan-Resistant Isolate ofKlebsiella pneumoniae, United States 2016

mBio ◽

10.1128/mbio.00440-18 ◽

2018 ◽

Vol 9 (2) ◽

Cited By ~ 16

Author(s):

Tom J. B. de Man ◽

Joseph D. Lutgring ◽

David R. Lonsway ◽

Karen F. Anderson ◽

Julia A. Kiehlbauch ◽

...

Keyword(s):

Public Health ◽

United States ◽

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

The United States ◽

Whole Genome ◽

Beta Lactams ◽

Content Type

ABSTRACTAntimicrobial resistance is a threat to public health globally and leads to an estimated 23,000 deaths annually in the United States alone. Here, we report the genomic characterization of an unusualKlebsiella pneumoniae, nonsusceptible to all 26 antibiotics tested, that was isolated from a U.S. patient. The isolate harbored four known beta-lactamase genes, including plasmid-mediatedblaNDM-1andblaCMY-6, as well as chromosomalblaCTX-M-15andblaSHV-28, which accounted for resistance to all beta-lactams tested. In addition, sequence analysis identified mechanisms that could explain all other reported nonsusceptibility results, including nonsusceptibility to colistin, tigecycline, and chloramphenicol. Two plasmids, IncA/C2 and IncFIB, were closely related to mobile elements described previously and isolated from Gram-negative bacteria from China, Nepal, India, the United States, and Kenya, suggesting possible origins of the isolate and plasmids. This is one of the firstK. pneumoniaeisolates in the United States to have been reported to the Centers for Disease Control and Prevention (CDC) as nonsusceptible to all drugs tested, including all beta-lactams, colistin, and tigecycline.IMPORTANCEAntimicrobial resistance is a major public health threat worldwide. Bacteria that are nonsusceptible or resistant to all antimicrobials available are of major concern to patients and the public because of lack of treatment options and potential for spread. AKlebsiella pneumoniaestrain that was nonsusceptible to all tested antibiotics was isolated from a U.S. patient. Mechanisms that could explain all observed phenotypic antimicrobial resistance phenotypes, including resistance to colistin and beta-lactams, were identified through whole-genome sequencing. The large variety of resistance determinants identified demonstrates the usefulness of whole-genome sequencing for detecting these genes in an outbreak response. Sequencing of isolates with rare and unusual phenotypes can provide information on how these extremely resistant isolates develop, including whether resistance is acquired on mobile elements or accumulated through chromosomal mutations. Moreover, this provides further insight into not only detecting these highly resistant organisms but also preventing their spread.

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