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Is it possible to use whole gene sequence analysis to distinguish between a common source infection and a person-person disease transmission?
Whole-genome sequencing (WGS) is a comprehensive method for analyzing entire genomes. Genomic information has been instrumental in identifying inherited disorders, characterizing the mutations that drive cancer progression, and tracking disease outbreaks. Rapidly dropping sequencing costs and the ability to produce large volumes of data with today’s sequencers make whole-genome sequencing a powerful tool for genomics research.
While this method is commonly associated with sequencing human genomes, the scalable, flexible nature of next-generation sequencing (NGS) technology makes it equally useful for sequencing any species, such as agriculturally important livestock, plants, or disease-related microbes.
Advantages of Whole-Genome Sequencing
- Provides a high-resolution, base-by-base view of the genome
- Captures both large and small variants that might be missed with targeted approaches
- Identifies potential causative variants for further follow-up studies of gene expression and regulation mechanisms
- Delivers large volumes of data in a short amount of time to support assembly of novel genomes
An Uncompromised View of the Genome
Unlike focused approaches such as exome sequencing or targeted resequencing, which analyze a limited portion of the genome, whole-genome sequencing delivers a comprehensive view of the entire genome. It is ideal for discovery applications, such as identifying causative variants and novel genome assembly.
Whole-genome sequencing can detect single nucleotide variants, insertions/deletions, copy number changes, and large structural variants. Due to recent technological innovations, the latest genome sequencers can perform whole-genome sequencing more efficiently than ever.
Compare Whole-Genome & Exome Sequencing
Explore the benefits of each approach to determine which method is best for your research.
Key Whole-Genome Sequencing Methods
Large Whole-Genome Sequencing
Sequencing large genomes (> 5 Mb), such as human, plant, or animal genomes, can provide valuable information for disease research and population genetics.
Small Whole-Genome Sequencing
Small genome sequencing (≤ 5 Mb) involves sequencing the entire genome of a bacterium, virus, or other microbe. Without requiring bacterial culture, researchers can sequence thousands of small organisms in parallel using NGS.
De Novo Sequencing
De novo sequencing refers to sequencing a novel genome where there is no reference sequence available. NGS enables fast, accurate characterization of any species.
Phased sequencing, or genome phasing, distinguishes between alleles on homologous chromosomes, resulting in whole-genome haplotypes. This information is often important for genetic disease studies.
Human Whole-Genome Sequencing
Previously a challenging application, human whole-genome sequencing has never been simpler. It offers the most detailed view into our genetic code.
COVID-19 Host Risk and Response
Understanding host genetic differences and individual responses to the SARS-CoV-2 virus increases understanding of disease susceptibiliity and severity. Read more about the methods for host risk & immune response studies.
Illumina DNA Prep
A fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species.
NovaSeq Reagent Kit
Reagent kits for the NovaSeq 6000 System provide ready-to-use cartridge-based reagents for cluster generation and SBS.
MiSeq Reagent Kit
Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier MiSeq reagent kit versions.
BaseSpace Sequence Hub and iCredits
Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing operations.
Whole-Genome Sequencing Data Analysis
The DRAGEN Bio-IT Platform provides accurate, ultra-rapid analysis of whole-genome sequencing data across a broad range of applications.
How Scientists Use WGS
Investigating the Genetics of COVID-19 Susceptibility
Illumina is providing whole-genome sequencing for a UK-wide study led by Genomics England, designed to compare the genomes of severely and mildly ill COVID-19 patients.
The Time is Now for Microbiome Studies
Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development.
NGS is Revealing the Mysterious World of Microbes
Researchers are using shotgun metagenomics to improve our understanding of human health, disease, and microbial evolution.
Shortening the Journey to Diagnosis
Whole genome sequencing may be the key to helping parents avoid months or years of inconclusive tests. Listen to experts from the Undiagnosed Diseases Network to learn more.
Illumina DNA PCR-Free Prep
A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing.
Cancer Whole-Genome Sequencing
Whole-genome sequencing of tumor samples provides a comprehensive view of the unique mutations in cancer tissue, informing analysis of oncogenes, tumor suppressors, and other risk factors.
Microbial Whole-Genome Sequencing
This method can be utilized to generate accurate microbial reference genomes, identify novel bacteria and viruses, perform comparative genomic studies, and more.
This method allows researchers to identify the organisms present in a given complex sample, analyze bacterial diversity, and detect microbial abundance in various environments.
Noninvasive Prenatal Testing
NGS-based WGS involves analysis of cell-free DNA fragments across the entire genome, which has proven advantages over other prenatal testing methodologies.
Rare Disease Whole-Genome Sequencing
This method can detect multiple variant types in a single assay, and help clinical researchers identify causative genetic variants linked to rare disorders.
Complex Disease Genomics
Researchers can utilize WGS and other methods to identify genetic variants associated with complex diseases and characterize disease mechanisms.
Additional Tips and Training Opportunities
Find Content and Products for Your Field
The user-friendly "Recommended Links" feature allows you to quickly find in-depth content and products relevant to your specific field of interest. You can access this option from the top of any illumina.com page.
What is the PhiX Control v3 Library?
This library is derived from the small, well-characterized bacteriophage genome, PhiX. It is an ideal sequencing control for run quality monitoring.
Interested in receiving newsletters, case studies, and information on genomic analysis techniques?
Flexible Genome Sequencer
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project with the NovaSeq 6000 System.
Compare sequencing platforms by application and specification. Find tools and guides to help you choose the right instrument.
Library Prep and Array Kit Selector
Determine the best kit for your needs based on your project type, starting material, and method of interest.
Find high-quality whole-genome and other sequencing services that deliver analyzed data to researchers.
Sequencing Method Explorer
Use this interactive tool to explore experimental NGS library preparation methods compiled from the scientific literature.
View Sequencing Coverage Tips
Learn how to estimate and achieve the necessary sequencing coverage for your experiment.
At Illumina, our goal is to apply innovative technologies to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. It is mission critical for us to deliver innovative, flexible, and scalable solutions to meet the needs of our customers. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and providing the highest level of quality, we strive to meet this challenge. Illumina innovative sequencing and array technologies are fueling groundbreaking advancements in life science research, translational and consumer genomics, and molecular diagnostics.
For Research Use Only. Not for use in diagnostic procedures (except as specifically noted).
Why use Sanger sequencing in your SARS-CoV-2 research?
- Since being developed in 1977, Sanger sequencing has been the most widely used DNA sequencing method for the past 40 years and remains in wide-spread use around the world
- Sanger method remains in wide use for smaller-scale projects and for confirmation of NGS results
- Smaller inquiries with more specific goals can benefit from more focused, less expensive laboratory procedures
Sanger sequencing is the gold standard for sequencing single genes, confirming gene variants, detecting repeat sequences, copy number variation, and single nucleotide changes. Sanger sequencing is perfect for:
- Sequencing single genes and single nucleotide variants
- Targeted sequencing of 100 amplicons or less
- Sequencing up to 96 samples at a time, without barcoding
- NGS confirmation
- High GC-rich sequences
- Microbial identification
- Microsatellite or STR analysis
- Plasmid sequencing
While NGS technologies are common in research labs due to higher throughput capabilities, Sanger sequencing offers a cost-effective solution for your research needs. It does not require expensive equipment and can generate high quality data even for low viral titer samples that do not yield high genome coverage for some NGS technologies.
What are the Challenges of Metagenomic Next Generation Sequencing?
Despite the potential of mNGS, there are many barriers to clear before the technology can become part of the mainstream laboratory, as well as gaps in our understanding about its diagnostic utility. Major reservations include the interpretation of findings (distinguishing contamination and colonization from true pathogens), selection and validation of databases used for analyses, and prediction (or lack thereof) of antimicrobial susceptibilities. A common perception is that mNGS is so incredibly sensitive that it will reveal a diagnosis when all other testing is negative. While mNGS may be analytically more sensitive than standard culturing methods in some cases, the necessary removal of vast amounts of human nucleic acid during sequencing preparation and (by computational methods) during the post-analytic process, can decrease the sensitivity in comparison to targeted PCR approaches for many organisms.
The specificity of mNGS remains the proverbial elephant in the room. Contamination of samples during specimen collection is a large concern given the increased analytical sensitivity of mNGS in comparison to standard culture methods, and there needs to be a validated quality-control process in place for steps from assessing reagent purity to measuring adequate genome coverage controls. Furthermore, with some Illumina platforms, the wrong barcode indices can be designated, leading to false positives on sequencing data. Bioinformatic quality controls are needed to ensure that high quality and validated genomes are available with minimal database errors and there would ideally be bioinformatic personnel available to interpret sequencing results for each test, which is not available at most clinical microbiological laboratories. The Federal Drug Administration (FDA) has collaborated with other federal agencies to curate a database entitled FDA-ARGOS (FDA-database for regulatory-grade microbial sequences), which has been useful to ensure that current mNGS results are reliable and accurate, but these resources need to be updated and maintained.
The greater question remains surrounding the clinical specificity of mNGS: Are the detected sequences from pathogens that are contributing to the patient&rsquos current disease? The analytical specificity of the mNGS testing can be addressed with rigorous controls throughout specimen collection, sequencing library preparation, assay run, and bioinformatic classification, but clinical specificity is not directly addressed by these approaches. Questions that can help determine clinical utility and applicability include: How can we distinguish organisms related to transient bacteremia from oral/gastrointestinal flora or skin colonizers in blood/plasma mNGS testing? How should sequencing depth be reported and how reliable is the relationship of sequence depth to true infection? Does this relationship differ by pathogen/host? How long is the expected detectable half-life of a pathogen by mNGS once the patient is receiving appropriate curative therapy? Studies on clinical utility and cost-effectiveness are greatly needed despite the indisputable power of this technology from a research and discovery perspective.
It&rsquos also worth pointing out that there are no currently FDA-cleared or approved mNGS tests that can be sent for microbial testing, although there are laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA &rsquo88) which offer testing on clinical samples. To date, only a few diagnostic NGS systems have been cleared by the FDA for oncological testing or detection of cystic fibrosis, for example. A recent review describes in detail many of the regulatory hurdles and considerations that will need to be addressed before mNGS could enter mainstream clinical diagnostic laboratories as an FDA-validated test.
In summary, while mNGS testing may likely play a major role in the microbiological diagnostic workflow in the future, particularly as sequencing and bioinformatic processing power evolves, this remains a high-complexity technology for which the clinical utility in our current medical practice environment remains uncertain. Although mNGS testing may offer novel and exciting diagnostic clinical opportunities in the near future, none of it will likely replace an astute clinician anytime soon.
Tweaking COVID-19 Diagnostics and Developing Therapeutics With WGS Data
SARS-CoV-2 sequence data allow scientists to develop new targets for molecular assays and track the trends of mutations that may lead to reduced sensitivity of existing assays. For example, GISAID routinely performs common diagnostic primer checks against high-quality genomes in the collection to monitor trends of mutations that may affect clinical diagnostics testing.
Additionally, the availability of SARS-CoV-2 sequence data allows researchers to identify potential therapeutic targets and provides a basis for epitope mapping and modeling along with the prediction of immune response to the virus, all of which could help guide therapeutics and vaccine development. From the beginning of the pandemic, scientists have been using WGS data to perform epitope mapping and structural modeling. A very recent report in Proceedings of the National Academy of Sciences (PNAS) analyzed 18,514 SARS-CoV-2 sequences sampled since December 2019. The authors noted that the rare mutations across the genomes were likely due to neutral evolution and not adaptive selection. The authors hypothesized that due to the limited genomic diversity seen in SARS-CoV-2, one vaccine may be able to provide universal protection against most, if not all, SARS-CoV-2 strains.
Partially Fake News:
“In some recent scientific publications, the 16S technology has been shown to produce lots of false results. A peer-reviewed study by Edgar determined that 16S sequencing of known bacterial communities resulted in a 56% to 88% false positive rate of predicted genus names.”
This is partially correct, but it’s not applicable to uBiome data. The study mentioned above (Edgar) was investigating a very specific bioinformatics analysis pipeline (QIIME) and a very specific 16S rRNA gene reference database (Greengenes). One of the problems identified in this study was that, in the Greengenes database, certain genera were placed under multiple families, thus creating unreliable taxonomic lineages.
As we wrote above, at uBiome we use a proprietary bioinformatics pipeline and a different, manually curated sequence database that does not have these taxonomic overlaps.We have made sure that there are no genera that fall under different taxonomic lineages. So the problem described above does not apply to our bioinformatics analysis. If we label a 16S sequence with a name, you can rest assured that we got the taxonomy right.
Challenges and outstanding questions
There is a lot of potential for the consortium to make huge advances in our understanding of the virus, but it won&rsquot be easy. Whilst WGS is a powerful tool for understanding virus transmission, DNA sequences alone are often not enough to track viral spread without other information such as contact tracing, which follows up a person&rsquos movements and in particular people they may have been in contact with while infectious.
For example, in February the genome of the virus causing COVID-19 found in a German patient who was infected in Italy appeared similar to that detected in a patient in Munich a month earlier. This implied that the virus at the source of the Italian outbreak may have originated in Munich, though it was also considered equally likely both viruses had been imported from China, arriving separately in each country. In this case information suggesting that the Italian outbreak originated in Germany spread before being refuted, causing confusion. This situation highlights that more information is necessary to confirm how the virus is spreading.
The consortium will face several technical challenges in terms of analysing viral DNA &ndash for example, some sample types such as nasal swabs don&rsquot always provide good quality viral RNA (viral DNA is often obtained by using viral RNA as a template) and quantities of genetic material can vary greatly between samples. It is also currently uncertain how many viral genomes it will be possible to sequence with the funding available.
Samples – DNA extraction – Sequencing
The JYD-34 pool of MF was provided by TRS Labs Inc. (Athens, Georgia, USA). JYD-34 D. immitis was originally isolated in 2010 in a heartworm-positive dog from Illinois. The original dog had no known history of treatment with ML products. D. immitis MF were purified from whole canine blood using a protocol previously described . DNA was isolated using the DNeasy extraction kit (Qiagen) following the manufacturer’s instructions. DNA integrity was verified by electrophoresis on a 0.8% agarose gel, and its purity was assessed by measuring the OD ratios at 260/280 nm and 260/230 nm. Frozen DNA was shipped to the Beijing Genomics Institute (www.bgi.com) for whole genome sequencing. DNA was then fragmented randomly. After electrophoresis, DNA fragments of desired length were gel purified. Adapter ligation and DNA cluster preparation were performed and subjected to Solexa sequencing [8,9,10] for next- generation sequencing using the Illumina HiSeq™ 2000. To minimize the likelihood of systematic bias in sampling, two paired-end libraries of the same DNA pool sample with insert size of 500 bp were prepared and were then subjected to whole-genome sequencing to generate 90-bp-paired-end reads. The four FASTQ files generated were sent to McGill University for analysis.
BAM file for JYD-34
Reads were trimmed from the 3-prime-end to generate a Phred quality score [11, 12] of at least 30. Illumina sequencing adapters were removed from the reads, and all trimmed reads were required to have a length of at least 50 bp. Trimming and clipping were performed using Trimmomatic software (http://www.usadellab.org/cms/?page=trimmomatic) . Any DNA read from Canis familiaris were removed from the data. The filtered reads were aligned to the nDi.2.2.D. immitis genome (http://www.nematodes.org/genomes/dirofilaria_immitis/). Each readset was aligned using BWA (http://bio-bwa.sourceforge.net/) , which created a Binary Alignment Map file (BAM).
Comparison of genomes between different D. immitis isolates
PoPoolation 2, adapted for analysis of pooled samples [15, 16], was used. A mpileup file was generated with a minimum quality score of Q20 using BAM files from the JYD-34 genome, and from susceptible and LOE isolates from Bourguinat et al. (2015) that included data pooled from four susceptible isolates (Missouri laboratory isolate, maintained at TRS Labs since 2000 Gran Canaria field isolate Grenada field isolate Italy field isolate) and from four LOE field isolates (Mechanicsville [Virginia], New Orleans [Louisiana], Haywood County [Tennessee] and Monroe [Louisiana]) and separately from the susceptible Missouri laboratory isolate (from TRS Labs). A subsequent synchronized file was generated following PoPoolation 2 directives. FST or fixative index was calculated on each single nucleotide polymorphism (SNP) in the genome, based on the synchronized file. The criteria for FST calculation were set with a minimum nucleotide count of six, a minimum and maximum read coverage of 30 and 10,000, respectively. The distance between two populations (Susceptible versus JYD-34, Susceptible versus LOE, Missouri versus JYD-34, Missouri versus LOE and JYD-34 versus LOE) was calculated as the mean FST value for all SNPs. Clustering was assessed based on filtered SNPs using various minimal FST thresholds ranging from 0 to 0.9 where FST = 0 means no divergence between two population and FST = 1 complete divergence. Dendrograms were built to visualize distance between populations using R (https://www.r-project.org/) and FST means as distances.
Comparison of D. immitis populations using SNP previously reported
Forty-one SNP previously reported  were investigated. The program BVA Tools (https://bitbucket.org/mugqic/bvatools/src) was used to extract, from the JYD-34 BAM file, the nucleotide counts at each of the 41 SNP of interest. The default quality score used was Q10. The nucleotide counts were assimilated to the allele counts, and allele frequencies were calculated. Allele frequencies for the susceptible (SUS), LOE and resistant (RES) populations were retrieved from the genotype frequencies published .
Whole Genome Sequencing Researchers
Below you will find biographies for the CFSAN researchers who are part of FDA’s foods whole genome sequencing program.
Marc Allard, Ph.D.
Research Area Coordinator for Genomics
Marc W. Allard received his Ph.D. in biology in 1990 from Harvard University, Cambridge, MA. Dr. Allard was the Louis Weintraub Associate Professor of Biology (and Genetics) at George Washington University (Washington, DC) for 14 years from 1994 to 2008. He has had appointments to the Visiting Scientists Program both at the Federal Bureau of Investigation’s Counterterrorism and Forensic Science Research Unit (CTFSRU) and in the Chem Bio Sciences Unit (CBSU) for 8 years, where he assisted in the anthrax investigations and human genetics data-basing. Dr. Allard joined FDA's Office of Regulatory Science and the Division of Microbiology in November 2008 and he is using DNA sequence information from the genomes of food borne pathogens to identify unique single nucleotide polymorphisms (SNPs), SAAPs and whole proteins to rapidly identify the various strains of bacteria, particularly Salmonella, E. coli, Shigella and Listeria. Dr. Allard specializes in both phylogenetic analysis and bioinformatics methods, as well as the wet laboratory methods which generate this genetic information.
Uma Babu, Ph.D.
Dr. Uma Babu received her Ph.D. in nutritional sciences from University of Maryland, College Park. She joined CFSAN in 1991 as a Senior Staff Fellow in the Division of Nutrition and became a research biologist in the Division of Science and Applied Technology, Office of Special Nutritionals in 1993. In 1998, she joined the Immunobiology Branch of the Division of Virulence Assessment in the Office of Applied Research and Safety Assessment (OARSA). She is part of a team tasked with developing culture methods for the identification of Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops. These bacterial isolates are sequenced by WGS for source attribution and inclusion in the GenomeTrakr database.
Kannan Balan, Ph.D.
Dr. Kannan Balan received his Ph.D. in biology from Howard University. After postdoctoral training at Brown University, he held research appointments at the University of Miami and Case Western Reserve University. Dr. Balan joined FDA in 2009 as a Commissioner’s Fellow, conducting research in the Office of Applied Research and Safety Assessment’s (OARSA) Immunobiology Branch. He is currently developing culture methods for the detection of Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops, and performs whole genome sequencing on Campylobacter and Arcobacter isolates from surveillance samples to determine source attribution and for inclusion in the GenomeTrakr database.
Rebecca Bell, Ph.D.
Dr. Rebecca Bell is a research microbiologist in the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at the Food and Drug Administration’s Center for Food Safety and Applied Nutrition. Dr. Bell received her Ph.D. in microbiology from The Ohio State University in 2005. Afterwards, she joined CFSAN in 2006 as a postdoctoral fellow in the Division of Analytical Chemistry where she worked on bacterial protein profiling using liquid chromatography/mass spectrometry. In 2008, Dr. Bell moved to MMSB. She continues to collaborate with the DAC on LC/MS work as well as working on molecular subtyping of Salmonella enterica, the development of rapid screening methods for Salmonella contamination of foods and ecological surveillance of the tomato growing environment for Salmonella.
Rachel Binet, Ph.D.
Dr. Rachel Binet has been with FDA’s Center for Food Safety and Applied Nutrition (CFSAN) since 2009 and currently serves as a research microbiologist in the Microbiological Methods Development Branch, within the Division of Microbiology. Dr. Binet was trained as a microbiologist at the Pasteur Institute in France and received her M.Sc. in microbiology in 1994 and her Ph.D. in microbiology in 1998. She began her career using genetics strategies to explore the physiology of various Gram-negative bacteria, including Escherichia coli, Serratia marcescens, Shigella, and Chlamydia. At FDA her research continues to concentrate on microbial genetics and physiology, with the addition of genomics and metagenomics as tools to differentiate and improve the recovery yield of pathogenic E. coli, Shigella, and Salmonella from contaminated food products. Dr. Binet serves as expert in committees related to laboratory biosafety and security of work involving recombinant DNA molecules, pathogens and toxins at FDA and on microbial methods and pathogens for CFSAN and for the International Organization for Standardization (ISO).
Eric Brown, Ph.D.
Director, Division of Microbiology
Dr. Eric W. Brown currently serves as Director of the Division of Microbiology in the Office of Regulatory Science. He oversees a group of 50 researchers and support scientists engaged in a multi-parameter research program to develop and apply microbiological and molecular genetic strategies for detecting, identifying, and differentiating bacterial foodborne pathogens such as Salmonella and shiga-toxin producing E. coli. His early work on horizontal gene transfer among foodborne pathogens has aided in elucidating the etiologies of several emerging pathogens including many of the group I salmonellae as well as enterohemorrhagic and enteropathogenic E. coli. More recently, his laboratory has been instrumental in adapting next-generation sequencing technologies to augment foodborne outbreak investigations at the FDA. Dr. Brown received his Ph.D. in Microbial genetics from The Genetics Program in the Department of Biological Sciences at The George Washington University. He has conducted research in microbial evolution and microbial ecology as a research fellow in the National Cancer Institute, the U.S. Department of Agriculture, and as a tenure-track Professor of Microbiology at Loyola University of Chicago. Dr. Brown came to the Food and Drug Administration in 1999 and has since carried out numerous experiments relating to the detection, identification, and discrimination of foodborne pathogens. He has been a member of the American Society for Microbiology since 1994 and has co-authored more than 70 publications and book chapters on the molecular differentiation and molecular evolution of bacterial pathogens. His primary research interests are currently to investigate the role of next-generation genome sequencing in the resolution of foodborne outbreaks and to continue to employ a variety of methods that allow for rapid and sensitive identification of enteric pathogens from the food supply.
Laurel Burall, Ph.D.
Dr. Laurel Burall is a research microbiologist in CFSAN’s Office of Applied Research and Safety Assessment. She received her Ph.D. in microbiology and immunology from the Department of Microbiology and Immunology at the University of Maryland in 2004 and joined FDA in 2007, initially as an ORISE Fellow. Her research focuses on aspects of Listeria monocytogenes survival in various environments and food matrices, as well as method development. Dr. Burall uses WGS to evaluate strain persistence of L. monocytogenes in different natural environments, particularly as it pertains to the farm and fresh produce. She uses WGS analysis to examine phylogenetic groups that may be implicated in increased persistence or linked to strains that are more transient. She is also working on a method to rapidly subtype L. monocytogenes into distinct, broad phylogenetic groups, prior to sequencing of an isolate, thus aiding the rapid classification of the organism.
Yi Chen, Ph.D.
Dr. Yi Chen is a research microbiologist and Listeria monocytogenes subject matter expert in CFSAN’s Division of Microbiology. He has developed, compared, and evaluated rapid methods for screening L. monocytogenes in food and environmental matrices, and both led and collaborated on efforts to validate qualitative and quantitative testing methods for the organism. Dr. Chen has studied the behavior of L. monocytogenes in various food matrices to elucidate the relative risk of L. monocytogenes contamination in these foods. He is also an expert on whole genome sequencing analysis of L. monocytogenes, having analyzed strains isolated during regular FDA surveillance and outbreak response. His work has improved understanding of the epidemiology and ecological persistence of this pathogen. He has provided scientific advice on various FDA assignments, outbreak investigations, and laboratory analyses. In addition, Dr. Chen has worked on the method validation and genetic characterization of Cronobacter spp. Dr. Chen received his Ph.D. in Food Science from the Department of Food Science at the Pennsylvania State University in 2007. He currently serves as a member of Microbial Method Validation Subcommittee of FDA, General Referee for AOAC International, Technical Committee member on MicroVal and Editorial Board member for Applied and Environmental Microbiology.
Hediye Nese Cinar, M.D.
Dr. Hediye Nese Cinar is a research biologist on the Parasitology Team, within the Division of Virulence Assessment, at FDA’s Center for Food Safety and Applied Nutrition. Her areas of research specialization include: the study of bacterial virulence mechanisms and immune responses using the model organism Caenorhabditis elegans heavy metal detection and genome-wide responses to heavy metals in C. elegans and developmental genetics and neurobiology of nerve regeneration. Since January 2014, Dr. Cinar has led a project investigating the use of whole genome sequencing for epidemiologic investigations of illness outbreaks involving the foodborne parasite Cyclospora cayetanensis.
Christina Ferreira is molecular microbiologist in the Division of Microbiology's Molecular Methods and Subtyping Branch. She graduated in 2008 from Clarion University of Pennsylvania, with a Bachelor of Science degree in molecular biology and biotechnology. At FDA-CFSAN, her work is primarily focused on development of a mass spectrometry-based assay for rapid identification of Salmonella species in food. She is also working on the validation of assembled genomes through comparisons with whole genome (optical) maps, analysis of the evolution of S. enterica Typhimurium over the last 70 years, and an investigation of SNP variations in clinical STEC strains.
Solomon Gebru, Ph.D.
Dr. Solomon Gebru is a staff fellow in the Division of Molecular Biology’s Molecular Genetics Branch within, at CFSAN’s Office of Applied Research and Safety Assessment. Dr. Gebru received his Ph.D. in molecular biology from Howard University in 2006. He joined FDA in 2007 as a contractor molecular biologist, developing rapid Salmonella and E. coli subtyping methods including multi-locus variable tandem repeats (MLVA) approaches and clustered regularly interspaced short palindromic repeats (CRISPR). He collaborates with FDA’s Center of Veterinary Medicine to explore the suitability of pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP), MLVA, and CRISPR typing approaches for resolving closely related foodborne E. coli and Salmonella outbreak strains. Currently he is working on whole genome sequencing analysis of E. coli strains from Penn State University and USDA’s Food Safety and Inspection Service collections, and from fungi found in foods.
Narjol Gonzalez-Escalona, Ph.D.
Dr. Gonzalez-Escalona is a research microbiologist in the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at FDA’s Center for Food Safety and Applied Nutrition. His research interests include the ecology and evolution of marine bacteria, especially those of the genus Vibrio. Other research interests include tracking, subtyping, evolution, comparative genomics, and the identification of novel pathogenicity targets from foodborne pathogens such as E. coli, Clostridium botulinum, and Salmonella using whole genome sequencing approaches. He has developed new methods to detect Salmonella in produce, S. Enteritidis and S. Heidelberg in egg products, and alternative methods for Salmonella subtyping. He is a member of IAFP and ASM and is the curator of the MLST website for V. parahaemolyticus. Dr. Gonzalez-Escalona received his Ph.D. from the University of Chile in 2004 and completed further postdoctoral training at the Gulf Coast Seafood Laboratory (GCSL), FDA, Dauphin Island, AL.
Christopher J. Grim, Ph.D.
Dr. Grim received his B.S. in marine biology from the University of Miami and his Ph.D. in environmental molecular biology from the University of Maryland, College Park. Dr. Grim joined the FDA in 2016. His research is focused on advanced molecular detection strategies, such as whole genome sequencing, pathogen subtyping and comparative genomics, and metagenomic approaches to complex food safety challenges.
Julie Haendiges is a biologist with the Molecular Methods and Subtyping Branch, in the Division of Microbiology at FDA’s Center for Food Safety and Applied Nutrition (CFSAN). She received her master’s degree from UMBC in biotechnology. She previously was the leader of the core sequencing lab at the Maryland Department of Health where she focused on sequencing foodborne bacterial pathogens and viruses. At CFSAN, her research focuses on functional genomics, preventive controls of Salmonella enterica, and utilizing long-read sequencing technology for transcriptomics.
Kelli L. Hiett, Ph.D.
Director, Division of Virulence Assessment
Dr. Kelli L. Hiett serves as Director of the Division of Virulence Assessment in the Office Applied Research and Safety Assessment (OARSA), CFSAN. Dr. Hiett received her M.S. in molecular genetics, studying operon structure in the fungal model organism, Neurospora crassa, and pathogen, Aspergillus nidulans. She received her Ph.D. in infectious disease from the School of Veterinary Medicine at the University of Georgia, where she investigated molecular mechanisms involved in the colonization of Campylobacter spp. in poultry. Dr. Hiett continued to conduct research on the zoonotic pathogen, Campylobacter spp. as a lead scientist at the U.S. Department of Agriculture’s, Agricultural Research Service. Dr. Hiett came to the FDA in 2017 and has since formed a team to develop culture and molecular methods to recover and detect Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops. Campylobacter and Arcobacter isolates from surveillance samples are identified by whole genome sequencing for source attribution and inclusion in the GenomeTrakr database.
Maria Hoffmann, Ph.D.
Dr. Hoffmann's thesis research was, performed at the U.S. Food and Drug Administration in College Park, Maryland, under Dr. Eric Brown, focused on the molecular evolution and speciation of the genus Vibrio. She completed her Ph.D. work in July 2012 at the University of Hamburg. Currently she is performing analyses to acquire data for differentiation and characterization of pathogens, particularly outbreak isolates from non-outbreak isolates and closely-related antibiotic-resistant Salmonella species using whole genome sequencing (WGS) and comparative genomic analyses. Further using the Pacific Biosciences (PacBio) RS sequencer and their hierarchical genome assembly process (HGAP) we are sequencing different pathogens to completly close reference genomes which will support the pilot studies of testing the applicability of WGS in public health surveillance activities.
Hyein Jang, Ph.D.
Dr. Jang is an ORISE fellow in the Virulence Mechanisms Branch within the Division of Virulence Assessment at CFSAN. She earned a Ph.D. in food science from Rutgers, the State University of New Jersey in 2017, where she studied the microbial safety of fresh produce, particularly molecular interactions and survival of pathogenic E. coli on plants and leafy vegetables. Since joining FDA that same year, she has performed whole genome sequencing to investigate genotypic and phenotypic features of Cronobacter and Salmonella to better understand their virulence traits, genomic diversity, and phylogenetic relatedness, as a part of GenomeTrakr. Dr. Jang currently performs transcriptomic analysis of Cronobacter persister cells grown under stress and developing an isolation and detection method for Cronobacter foods of plant-origin.
Julie Ann Kase, Ph.D.
Julie Ann Kase is a research microbiologist in the Microbial Methods Development Branch within the Division of Microbiology at FDA’s Center for Food Safety and Applied Nutrition. Dr. Kase joined FDA in 2008 and quickly established herself as an agency subject matter expert for Shiga toxin-producing E. coli (STEC) and Brucella spp. She has spent over 25 years at the lab bench encompassing work as a pharmaceutical chemist, public health scientist, and food microbiologist and has authored dozens of peer-reviewed publications and book chapters. Her research activities have touched upon the transmission and detection of infectious agents in the environment, the microbiocidal efficacy of chemical disinfectants, and methods to culture and identify pathogenic STEC and Brucella spp. from various matrices. Much of her current work utilizes the power of nucleic acid sequencing for either a more specific characterization of STEC or the refinement of classical bacteriological culture methods. Dr. Kase has served on numerous committees including the National Advisory Committee on Microbiological Criteria for Foods (NACMCF), the FDA Bacteriological Analytical Manual (BAM) Council, the ILSI North America Committee on Food Microbiology, and currently serves as Chair of the FDA STEC Advisory Council.
Susan R. Leonard, Ph.D.
Dr. Susan Leonard is a research biologist in the Division of Molecular Biology, at CFSAN’s Office of Applied Research and Safety Assessment. Her research interests include utilizing shotgun metagenomic sequencing for the detection and genomic characterization of Shiga toxin-producing Escherichia coli (STEC) in food samples, the characterization of E. coli populations in environmental samples, and for assessing factors that impact STEC contamination or survival during fresh produce production and storage. In addition, her projects include whole genome sequence comparative analyses of STEC isolates as well as other foodborne pathogens. She received her Ph.D. in molecular microbiology and immunology from the University of Maryland, Baltimore.
Sara Lomonaco, Ph.D.
Dumitru Macarisin, Ph.D.
Dumitru Macarisin is a research microbiologist in the Division of Microbiology at FDA’s Center for Food Safety and Applied. He is subject matter expert for Listeria monocytogenes and leads FDA’s development and implementation of research projects related to microbial safety of fresh fruits and vegetables. Dumitru earned his Ph.D. in plant physiology and biochemistry in 2003 and pursued further postdoctoral research in the Agricultural Research Organization at the Volcani Center in Israel. He followed this with an 8-year research tenure at the United States Department of Agriculture’s Agricultural Research Service, where conducted extensive research in postharvest pathology and biocontrol, plant stress response, produce safety, microbiology, parasitology and public health. Dumitru came to FDA in 2013, where his current research focuses on understanding the routes/mechanisms of fresh produce contamination and environmental reservoirs of foodborne pathogens and developing mitigation strategies to improve good agricultural practices in the prevention of produce recalls and foodborne outbreaks. He has represented FDA nationally and internationally on critical food safety issues, providing recommendations on preventive controls, environmental monitoring, and quality control improvements to government agencies and the food industry.
Andrea Ottesen, Ph.D.
Research Area Coordinator for Metagenomics
Dr. Andrea Ottesen is the Research Area Coordinator (RAC) for Metagenomics at FDA's Center for Food Safety and Applied Nutrition (CFSAN) in the Molecular Methods and Subtyping Branch (MMSB) of the Division of Microbiology. She received her Ph.D. in 2000 from the University of Maryland. Ottesen works to provide target and non target metagenomic data to describe ecologies associated with high risk crops. Her ecological data are used to complement and improve Salmonella detection methods and provide data to improve recommendations for Good Agricultural Practices (GAPs).
Isha Patel is a research biologist in CFSAN’s Office of Applied Research and Safety Assessment. Her research focuses on the use of next-generation sequencing methods for detection and characterization of commensal bacteria as well as foodborne pathogens. She has a M.Sc. degree in microbiology from India and pursued further graduate studies at University of Maryland where she earned an M.S. degree in microbiology.
Lisa Harrison Plemons, Ph.D.
Dr. Lisa Plemons received her Ph.D. in medical sciences from the Medical Microbiology and Immunology Department at Texas A&M University in 2004. Following postdoctoral training at the University of Maryland, Baltimore (2004-2009), she joined the Immunobiology Branch of the Division of Virulence Assessment in the Office of Applied Research and Safety Assessment as a Staff Fellow. Currently, Dr. Plemons is a research microbiologist in the Immunobiology Branch and works with a team to develop culture methods to detect Campylobacter and Arcobacter species from the farm environment and ready-to-eat produce crops. Campylobacter and Arcobacter isolates from surveillance samples are identified by whole genome sequencing for source attribution and inclusion in the GenomeTrakr database.
Shashi Sharma, Ph.D.
Ben Tall, Ph.D.
Acting Branch Chief, Virulence Mechanisms Branch
Dr. Ben Tall currently serves as Acting Branch Chief of the Virulence Mechanisms Branch, in the Office of Applied Research and Safety Assessment’s Division of Virulence Assessment. He oversees a group of researchers and support scientists engaged in a research program focused on the development of microbiological and molecular genetic approaches for detecting, identifying, and differentiating bacterial foodborne pathogens such as Salmonella, Cronobacter, Bacillus cereus, marine Vibrios, and Listeria spp. His early work on development of vaccines for Vibrio cholerae, Salmonella typhi, Shigella spp., and enteropathogenic E. coli was performed at the Center for Vaccine Development, University of Maryland School of Medicine. More recently, his laboratory has been instrumental in adapting next-generation sequencing technologies to augment FDA foodborne illness outbreak investigations involving Cronobacter and several serovars of Salmonella enteritidis. Dr. Tall received his Ph.D. in microbiology from the Department of Microbiology, University of Maryland Dental School in 1988. Dr. Tall came to FDA in 1990 and has since carried out numerous studies relating to the detection, identification, and characterization of foodborne pathogens. He has been a member of the American Society for Microbiology since 1977 and has co-authored more than 130 publications and book chapters on the molecular detection, identification, and characterization of foodborne bacterial pathogens. His primary research interests currently are investigating the application of next-generation genome sequencing to characterization of foodborne pathogens and employing a variety of methods that allow for rapid and sensitive identification of enteric foodborne pathogens, which is a prerequisite towards development of future countermeasures against these pathogens.
Sandra M. Tallent, Ph.D.
Chief, Molecular Methods and Subtyping Branch
Sandra Tallent serves as Chief of the Molecular Methods and Subtyping Branch, within the Division of Microbiology, at FDA’s Center for Food Safety and Applied Nutrition. Dr. Tallent began her career as a clinical microbiologist, but the continued challenges of antimicrobial resistance prompted her to alter her career focus to public health research. She earned her Ph.D. from the Medical College of Virginia in Richmond prior to selection as a CDC Emerging Infectious Disease Research Fellow with Virginia’s Division of Consolidated Laboratory Services. Dr. Tallent accepted an appointment with FDA in 2008, where her research continues to concentrate on virulence and pathogenicity of Staphylococcus aureus, but also includes numerous experiments on Bacillus cereus. As a research microbiologist, Dr. Tallent has validated new protocols in an effort to update the FDA’s Bacteriological Analytical Manual. She is currently developing new methods that are based on genomic sequence information.
Carmen Tartera, Ph.D.
Dr. Carmen Tartera received her Ph.D. in microbiology from the University of Barcelona, Spain. In 2009, she joined the Division of Molecular Biology at the Center of Food Safety and Applied Nutrition. Currently, she is leading a study to examine foods supplemented with live microbes. The objective of this research program is to identify adulteration in these products sold in the U.S., using WGS analysis through metagenomics.
Ruth Timme, Ph.D.
Ruth Timme is a research microbiologist at the FDA’s Office of Regulatory Science. She received her Ph.D. in 2006 in Plant Biology at The University of Texas at Austin. Her research background is focused mainly on utilizing comparative genomics and phylogenetics methods to answer evolutionary questions. Although her training is in botany, her published research spans a diversity of organisms, including sunflowers (Helianthus), Dinoflagellates, Charophyte green algae, and Salmonella. At the FDA she is implementing phylogenomic methods for tracking foodborne pathogens through the US food supply.
Zhihui Yang, M.D.
Dr. Yang joined CFSAN in 2012 and is currently a research biologist on the Molecular Virology Team, within the Office of Applied Research and Safety Assessment’s Division of Molecular Biology. Her research mainly focuses on the application of genomic-scale molecular biology techniques (next-generation sequencing) for the detection and further identification/genotyping of epidemiologically important foodborne viruses, including but not limited to, norovirus hepatitis A, and newly emergent viral species. Her research interests also include: development of novel sequencing methodologies for virus detection and analysis, and application of these methodologies to issues of virus carriage in foods, clinical and environmental samples, and exploration of the virome through a metagenomics approach.
Jie Zheng, Ph.D.
Dr. Jie Zheng currently serves as a staff microbiologist of the Molecular Methods and Subtyping Branch within the Division of Microbiology. Dr. Zheng finished her Ph.D. in Food Science from University of Maryland at College Park, MD in 2006 and her dissertation is on "Campylobacter jejni/coli – Host Intestinal Epithelial Cell Interaction". Dr. Zheng joined the laboratories at the Center for Food Safety and Applied Nutrition (CFSAN) in July of 2008 after her two-year post-doctoral training at UM. She is interested in development of SNP-based detection, identification and subtyping methods for various phyletic and pathovar divisions of pathogenic Salmonella. She is also engaged in reducing carriage of Salmonella Newport on tomato plants with bio-control intervention method.
Phillip Curry, Ph.D.
Research Microbiologist, PulseNet Team
Research Microbiologist, PulseNet Team
Eric Stevens, Ph.D.
Statistics and Bioinformatics
Jayanthi Gangiredla is a biologist in FDA’s Office of Applied Research and Safety Assessment and has been working its Division of Molecular Biology’s Molecular Genetics Branch since 2008. With an M.S. degree in biochemistry and an M.S. in bioinformatics, she uses bioinformatics to compare the genomics of foodborne pathogens. She is involved with several metagenomics and metatranscriptomics projects that require extensive analysis of microbial populations from both the gut and the environment and conducts functional profiling of microbes in community-wide studies. She provides key bioinformatic analyses for the beneficial microbiome project, analyzing whole genome sequences of Gram positive, commensal, food, and probiotic bacteria associated with dietary supplements.
Gopal R. Gopinath, Ph.D.
Dr. Gopal Gopinath is a geneticist in CFSAN’s Office of Applied Research and Safety Assessment. His research focuses on genomics and bioinformatics of foodborne parasites like Cyclospora cayetanensis, and bacterial pathogens including Cronobacter spp., Salmonella spp., and Bacillus cereus. Dr. Gopinath was one of the earliest members of GenomeTrakr team at OARSA. As part of the Parasitology Team, Dr. Gopinath is working on consolidating parasite genomics efforts as part of CycloTrakr, a component BioProject of GenomeTrakr, dedicated for foodborne parasites. As part of this project, he has started to implement bioinformatic workflows developed for the Parasitology Team on CFSAN’s GalaxyTrakr platform. Dr. Gopinath graduated with a doctorate in biotechnology from the Center for Biotechnology, Anna University, Chennai, India in 1999. After completing postdoctoral fellowships at Brandeis University and the University of California, Berkeley (2001), he left laboratory research for a career in bioinformatics and biological databases, first at the Medical College of Wisconsin and later at the Cold Spring Harbor Laboratory in New York. His primary research interests are in comparative genomics, bioinformatics, data mining, and the use of next generation sequencing technology to obtain an “-omic” perspective of research questions in food safety.
David W. Lacher, Ph.D.
Dr. Lacher is a research microbiologist in the Division of Molecular Biology, within CFSAN’s Office of Applied Research and Safety Assessment. His research interests include the evolutionary genetics of virulence and the molecular subtyping of bacterial pathogens. He is currently examining the genetic diversity present within Escherichia coli and Shigella spp. through the use of whole genome sequence analyses.
Mark K. Mammel
Mark Mammel is a research microbiologist in CFSAN’s Office of Applied Research and Safety Assessment. With an M.S. degree in microbiology and an M.S. in computer science, he uses bioinformatics for comparative genomics of foodborne pathogens. He develops methods for analyzing whole genome shotgun sequencing of metagenomic samples to identify the microbial composition and detect pathogens in food or environmental samples.
James B. Pettengill, Ph.D.
Dr. Pettengill uses metagenomic approaches (i.e., the sequencing of DNA contained in an environmental sample) to investigate important agricultural and food safety questions. Specifically, he and other scientists at the FDA have employed metagenomics to describe the effects of different bacterial enrichment procedures and how they might impact our ability to detect specific pathogens. They are also evaluating how different pesticides alter microbial diversity and the prevalence of certain pathogens within the ecosystem.
Hugh Rand, Ph.D.
Supervisory Mathematical Statistician
Hugh Rand is a Team Leader in the Biostatistics Branch at the FDA’s Center for Food Safety and Applied Nutrition. He received his Ph.D. in 1995 in applied mathematics at the University of Washington. His research interests focus on the application of mathematical and statistical tools to the analysis of biological problems, primarily in the area of human health. Much of his early work involved the applications of bioinformatics in drug discovery within inflamation and oncology. Currently, a major focus of his efforts at the FDA are in the use of genomic sequencing for aiding in tracking foodborne pathogens through the U.S. food supply.
George Kastanis is part of the genomics team working under the supervision of Dr. Marc Allard. His primary function is to run the MiSeq personal sequencing of various isolates that come through the pipeline.
Anna I. Maounounen-Laasri
Anna I. Maounounen-Laasri received her M.Sc. in biology and chemistry in 1994 from State Pedagogical University, in Saint Petersburg, Russia. Mrs. Maounounen-Laasri served as a teacher and practical adviser for biology, chemistry, and ecology at the Kaskolovka School, in Kingisepp, Russia from 1994 to 2001. In 2010, she joined FDA’s Center for Biologics Evaluation and Research as a volunteer researcher in the Laboratory of Method Development, within the Office of Vaccine Research and Review, where she developed molecular methods for evaluation and identification of viral vaccine strains. In November 2010, she came to FDA’s Center for Food Safety and Applied Nutrition as an ORISE fellow, working in its Division of Microbiology. Mrs. Maounounen-Laasri is currently a biologist in the division, conducting research focused on improvement, validation, and evaluation of culture-based and molecular methods for the detection, typing, and isolation of Salmonella, Escherichia coli O157:H7, non-O157 Shiga toxin-producing E. coli (STEC), and Listeria monocytogenes in food products and environment. She also serves as a microbial strain curator and sample custodian for the division.
Tim Muruvanda collects and analyzes NGS data from the Pacific Biosciences RS II sequencers. He is primarily focused on generating closed microbial reference genomes to support the applicability of WGS in public health.
Justin Payne is an integration and bioinformatics developer and the author of "Bootsie", a statistical tool for RFLP analysis. He graduated in 2011 from the University of Nebraska, Lincoln with a Bachelor of Science degree in biochemistry. At FDA-CFSAN, his work is primarily focused on database development, high-throughput assembly of NGS data, and transparent integration with NCBI data stores.
Day Zero Diagnostics Wins $300K NIH Grant to Refine HAI Outbreak Analysis Service
NEW YORK — Infectious disease startup Day Zero Diagnostics last week received a $300,000 grant from the National Institutes of Health to further develop its nanopore sequencing-based technology for the analysis of healthcare-associated infection (HAI) outbreaks.
Day Zero said that it will use the Phase I Small Business Innovation Research funding to integrate Oxford Nanopore Technologies' (ONT) ultra-long read genomic sequencing into its EpiXact service, in which it sequences and analyzes isolates sent from healthcare facilities to help determine the relationships between infections during a suspected outbreak.
"Precision and speed are essential for identifying and controlling HAI outbreaks," Mohamad Sater, director of computational biology at Day Zero, said in a statement. "This award from the NIH will help accelerate the integration of ONT's ultra-long read genomic sequencing into our service and allow us to provide accurate decision-making information to infection control professionals faster than ever before."
Day Zero said that EpiXact can currently provide a determination of pathogen relatedness within two days. According to the grant's abstract, the addition of ultra-long read genomic sequencing into the service is expected to result in a 24-hour turnaround time.
In mid-2019, the Boston-based company received a $224,000 NIH grant to develop an algorithm used in the service.