A5028632300- Salmonella and Campylobacter epidemiology
- Genomic variations and chromosomal abnormalities
- Bacteriophages and microbial interactions
- Listeria monocytogenes in Food Safety
- Genetic Associations and Epidemiology
- Viral gastroenteritis research and epidemiology
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Genetic Syndromes and Imprinting
- Traditional and Medicinal Uses of Annonaceae
- Viral Infections and Immunology Research
- Molecular Biology Techniques and Applications
- Vascular Malformations and Hemangiomas
- Probiotics and Fermented Foods
- Vibrio bacteria research studies
- Cancer Genomics and Diagnostics
- Food Safety and Hygiene
- Essential Oils and Antimicrobial Activity
- Chromosomal and Genetic Variations
- Natural product bioactivities and synthesis
- Plant Pathogenic Bacteria Studies
- Vascular Malformations Diagnosis and Treatment
- Aquaculture disease management and microbiota
- Biosensors and Analytical Detection
United States Food and Drug Administration
2018-2024
Center for Food Safety and Applied Nutrition
2016-2020
Johns Hopkins University
2011-2015
Johns Hopkins Medicine
2011-2013
Kennedy Krieger Institute
2013
The Sturge–Weber syndrome is a sporadic congenital neurocutaneous disorder characterized by port-wine stain affecting the skin in distribution of ophthalmic branch trigeminal nerve, abnormal capillary venous vessels leptomeninges brain and choroid, glaucoma, seizures, stroke, intellectual disability. It has been hypothesized that somatic mosaic mutations disrupting vascular development cause both stains, severity extent presentation are determined developmental time point at which occurred....
Whole-genome sequence (WGS) analysis has revolutionized the food safety industry by enabling high-resolution typing of foodborne bacteria. Higher resolving power allows investigators to identify origins contamination during illness outbreaks and regulatory activities quickly accurately. Government agencies stakeholders worldwide are now analyzing WGS data routinely. Although researchers have published many studies that assess efficacy for source attribution, guidance interpreting analyses is...
It is an assumption of large, population-based datasets that samples are annotated accurately whether they correspond to known relationships or unrelated individuals. These annotations key for a broad range genetics applications. While many methods available assess relatedness involve estimates identity-by-descent (IBD) and/or identity-by-state (IBS) allele-sharing proportions, we developed novel approach IBD0, 1, and 2 based on observed IBS within windows. When combined with genome-wide...
Pathogen monitoring is becoming more precise as sequencing technologies become affordable and accessible worldwide. This transition especially apparent in the field of food safety, which has demonstrated how whole-genome (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates WGS performed by public-health agencies other partners providing database with real-time cluster analysis for foodborne pathogen surveillance. Because being support enforcement decisions,...
Tens of thousands lymphoblastoid cell lines (LCLs) have been established by the research community, providing nearly unlimited source material from samples interest. LCLs are used to address questions in population genomics, mechanisms disease, and pharmacogenomics. Thus, it is fundamental importance define extent chromosomal variation LCLs. We measured genotype copy number multiple derived peripheral blood mononuclear cells (PBMCs) single individuals as well two comparison groups: (1) three...
Mosaic somatic alterations are present in all multi-cellular organisms, but the physiological effects of low-level mosaicism largely unknown. Most mosaic remain undetectable with current analytical approaches, although presence such is increasingly implicated as causative for disease.Here, we Parent-of-Origin-based Detection (POD) method chromosomal abnormality detection trio-based SNP microarray data. Our software implementation, triPOD, was benchmarked using a simulated dataset,...
Abstract The US PulseNet and GenomeTrakr laboratory networks work together within the Genomics for Food Safety (Gen-FS) consortium to collect analyze genomic data foodborne pathogen surveillance (species include Salmonella enterica, Listeria monocytogenes, Escherichia coli (STECs), Campylobactor ). In 2017 these two started harmonizing their respective proficiency test exercises, agreeing on distributing a single strain-set following same standard operating procedure (SOP) collection,...
The adoption of whole-genome sequencing within the public health realm for molecular characterization bacterial pathogens has been followed by an increased emphasis on real-time detection emerging outbreaks (e.g., food-borne Salmonellosis). In turn, large databases sequence data are being populated. These currently contain tens thousands samples and expected to grow hundreds a few years. For these be optimal use one must able quickly interrogate them accurately determine genetic distances...
During spring 2018, the U.S. Food and Drug Administration (FDA), Centers for Disease Control Prevention, state local public health agencies responded to a multistate outbreak of gastrointestinal illnesses caused by multiple Salmonella serovars associated with consumption kratom, product harvested from tropical tree native Southeast Asia. The included 199 case-patients reported 41 states, illness onset dates ranging 11 January 2017 8 May leading 54 hospitalizations no deaths. Case-patients...
Correct annotation of the genetic relationships between samples is essential for population genomic studies, which could be biased by errors or omissions. To this end, we used identity-by-state (IBS) and identity-by-descent (IBD) methods to assess relatedness individuals within HapMap phase III data. We analyzed data from 1,397 across 11 ethnic populations. Our results support previous studies (Pemberton et al., 2010; Kyriazopoulou-Panagiotopoulou 2011) assessing unknown present population....
A total of 91 draft genome sequences were used to analyze isolates Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was find mutations disrupting open reading frames (ORFs) and another determine if ORF-disruptive present other sources. 83 between 1995–1998. Isolates separated into two genomic clades 12 subgroups due 742 mutations. Nineteen found, addition, bigA had exceptional heterogeneity requiring additional...
Abstract Salmonella enterica serovar Enteritidis (SE), the most commonly reported of human salmonellosis, has been frequently associated with poultry farms, eggs and egg products. Mice are known vectors SE contamination in these facilities. The objective this study was to use whole-genome sequencing (WGS) analyze from mice obtained at farms Pennsylvania. Documenting pathogen diversity can identify reliable biomarkers for rapid detection speed up outbreak investigations. We sequenced 91...