A5033872060- Salmonella and Campylobacter epidemiology
- Genomics and Phylogenetic Studies
- Listeria monocytogenes in Food Safety
- Identification and Quantification in Food
- SARS-CoV-2 detection and testing
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- Food Safety and Hygiene
- Biosensors and Analytical Detection
- COVID-19 diagnosis using AI
- Plant Pathogenic Bacteria Studies
- Data-Driven Disease Surveillance
- Plant and animal studies
- CRISPR and Genetic Engineering
- Plant and Fungal Species Descriptions
- Molecular Biology Techniques and Applications
- Microbial Metabolism and Applications
- Genetic diversity and population structure
- Enzyme Production and Characterization
- Cancer Research and Treatments
- Viral gastroenteritis research and epidemiology
- RNA and protein synthesis mechanisms
- Vibrio bacteria research studies
- Microbial Community Ecology and Physiology
- Antibiotic Resistance in Bacteria
United States Food and Drug Administration
2016-2025
Center for Food Safety and Applied Nutrition
2015-2024
Mondelēz International (India)
2024
Society for Healthcare Epidemiology of America
2024
Food and Drug Administration
2021
University of Minnesota
2011-2015
University of Maryland, College Park
2007-2013
Johns Hopkins Medicine
2005
Johns Hopkins University
2005
University of North Carolina at Greensboro
2003
Abstract Antimicrobial resistance (AMR) is a significant public health threat. With the rise of affordable whole genome sequencing, in silico approaches to assessing AMR gene content can be used detect known mechanisms and potentially identify novel mechanisms. To enable accurate assessment content, as part multi-agency collaboration, NCBI developed comprehensive database, Bacterial Resistance Reference Gene Database detection tool AMRFinder. Here, we describe expansion Database, now called...
The analysis of next-generation sequence (NGS) data is often a fragmented step-wise process. For example, multiple pieces software are typically needed to map NGS reads, extract variant sites, and construct DNA matrix containing only single nucleotide polymorphisms (i.e., SNP matrix) for set individuals. management chaining these their outputs can be cumbersome difficult task. Here, we present CFSAN Pipeline, which combines into package the mapping reads reference genome with Bowtie2,...
Research to understand and control microbiological risks associated with the consumption of fresh fruits vegetables has examined many environments in farm fork continuum. An important data gap however, that remains poorly studied is baseline description microflora may be plant anatomy either endemically or response environmental pressures. Specific anatomical niches plants contribute persistence human pathogens agricultural ways we have yet describe. Tomatoes been implicated outbreaks...
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...
Facile laboratory tools are needed to augment identification in contamination events trace the back source (traceback) of Salmonella enterica subsp. serovar Enteritidis (S. Enteritidis). Understanding evolution and diversity within among outbreak strains is first step towards this goal. To end, we collected 106 new S. Enteriditis isolates Pulsed-Field Gel Electrophoresis (PFGE) pattern JEGX01.0004 close relatives, determined their genome sequences. Sources for these spanned food, clinical...
The enteric pathogen Salmonella enterica is one of the leading causes foodborne illness in world. species extremely diverse, containing more than 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles—some known to be virulent pathogens, while others not. Questions regarding evolution pathogenicity, significance characters, diversity clustered regularly interspaced short palindromic repeat (CRISPR) loci, among others, will remain elusive until...
Salmonella enterica subsp. serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain this was implicated in a large 2011 multistate outbreak resulting from consumption contaminated ground turkey that involved 136 confirmed cases, with death. In study, we assessed evolutionary diversity 44 S. isolates using whole-genome sequencing (WGS) generated by 454 GS FLX (Roche) platform. The isolates, including 30 nearly...
Prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) systems provide adaptive immunity from invasive genetic elements encompass three essential features: (i) cas genes, (ii) a CRISPR array composed of spacers direct (iii) an AT-rich leader sequence upstream the array. We performed in-depth analysis in >600 Salmonella, representing four clinically prevalent serovars. Each feature is extremely conserved CRISPR1 locus more highly than...
As a leading cause of bacterial dysentery, Shigella represents significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also dysentery. Current typing methods have limited ability identify differentiate between these pathogens despite the need for rapid accurate identification clinical treatment outbreak response. We present comprehensive phylogeny EIEC using whole genome sequencing 169 samples, constituting unparalleled...
The accurate identification of SARS-CoV-2 (SC2) variants and estimation their abundance in mixed population samples (
Keeping the global food supply safe necessitates international collaborations between countries. Health and regulatory agencies routinely communicate during foodborne illness outbreaks, allowing partners to share investigational evidence. A 2016-2020 outbreak of Listeria monocytogenes infections linked imported enoki mushrooms required a multinational collaborative investigation among United States, Canada, Australia, France. Ultimately, this included 48 ill people, 36 in States 12 was...
Abstract The data provided to the Genetic Analysis Workshop 14 (GAW 14) was result of a collaboration among several different groups, catalyzed by Elizabeth Pugh from Center for Inherited Disease Research (CIDR) and organizers GAW 14, Jean MacCluer Laura Almasy. DNA, phenotypic characterization, microsatellite genomic survey were Collaborative Study on Genetics Alcoholism (COGA), nine-site national funded National Institute Alcohol (NIAAA) Drug Abuse (NIDA) with overarching goal identifying...
Salmonella Newport has ranked in the top three serotypes associated with foodborne outbreaks from 1995 to 2011 United States. In current study, we selected 26 S. strains isolated diverse sources and geographic locations then conducted 454 shotgun pyrosequencing procedures obtain 16-24 × coverage of high quality draft genomes for each strain. Comparative genomic analysis 28 (including 2 reference genomes) 15 outgroup identified more than 140,000 informative SNPs. A resulting phylogenetic tree...
The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact NGS, it is paramount to ensure standardisation 'wet' laboratory and bioinformatic protocols promote comparability methods employed by different laboratories their outputs. Therefore, one ambitious goals Global Microbial Identifier (GMI) initiative (http://www.globalmicrobialidentifier.org/) been establish a mechanism for inter-laboratory NGS proficiency testing (PT). This...
Salmonella enterica is a common cause of foodborne gastroenteritis in the United States and associated with outbreaks fresh produce such as cilantro. culture-based detection methods are complex time consuming, improvments to increase sensitivity will benefit consumers. In this study, we used 16S rRNA sequencing determine microbiome We also investigated changes microbial community prior after 24-hour nonselective pre-enrichment culture step commonly by laboratory analysts resuscitate...
Salmonella enterica subsp. serovar Kentucky is frequently isolated from healthy poultry and dairy cows occasionally people with clinical disease. A genomic analysis of 119 isolates collected in the United States cows, ground beef, products, human cases was conducted. Results demonstrated that majority bovine-associated S. were sequence type (ST) 152. Several (n = 3) food product ST198, a Northern Africa, Europe Southeast Asia. phylogenetic indicated both STs are more closely related to other...
ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 wastewater sites across United States. This initiative required evaluation, optimization, development, and publication new methods analytical tools spanning sample collection through variant analyses. Version-controlled...
DNA barcoding has been proposed as a useful technique within many disciplines (e.g., conservation biology and forensics) for determining the taxonomic identity of sample based on nucleotide similarity to samples known taxonomy. Application plants primarily focused evaluating success candidate barcodes across broad spectrum evolutionary divergence. Less attention paid performance when distinguishing congeners or differential analytical techniques despite fact that practical application...
Mating systems are among the most labile characteristics of flowering plants, with transitions frequently occurring populations or in association speciation. The frequency mating system shifts has made it difficult to reconstruct historical evolutionary dynamics unless have been very recent. Here, we examine molecular and phenotypic variation determine polarity, timescale, causes a transition between outcrossing self-fertilization sister subspecies Clarkia xantiana. Phylogenetic analyses...
Abstract This article documents the addition of 283 microsatellite marker loci to Molecular Ecology Resources Database. Loci were developed for following species: Agalinis acuta ; Ambrosia artemisiifolia Berula erecta Casuarius casuarius Cercospora zeae‐maydis Chorthippus parallelus Conyza canadensis Cotesia sesamiae Epinephelus acanthistius Ficedula hypoleuca Grindelia hirsutula Guadua angustifolia Leucadendron rubrum Maritrema novaezealandensis Meretrix meretrix Nilaparvata lugens...
Contamination of tomatoes by Salmonella can occur in agricultural settings. Little is currently understood about how inputs such as pesticide applications may impact epiphytic crop microflora and potentially play a role contamination events. We examined the two materials commonly used Virginia tomato agriculture: acibenzolar-S-methyl (crop protectant) copper oxychloride (pesticide) to identify effects these exert on baseline incidence three specific genera; Salmonella, Xanthomonas...
The ability to detect a specific organism from complex environment is vitally important many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles foodborne outbreaks due strains Salmonella but few studies ever recovered tomato phyllosphere environment. Precision culturing techniques that target agents associated with depend on factors. One factor better understand which species co-enrich during enrichment procedures and how...
Abstract The origins of hybrid zones between parapatric taxa have been particular interest for understanding the evolution reproductive isolation and geographic context species divergence. One challenge has to distinguish allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative histories. Here, we use complementary phylogeographic population genetic analyses investigate recent two subspecies Clarkia xantiana formation a zone...
ABSTRACT Three multistate outbreaks between 2014 and 2016, involving case patients in outside the United States, were linked to stone fruit, caramel apples, packaged leafy green salad contaminated with Listeria monocytogenes singleton sequence type 382 (ST382), a serotype IVb-v1 clone limited genomic divergence. Isolates from these other ST382 isolates not associated analyzed by whole-genome sequencing (WGS) analysis. The primary differences among strains single nucleotide polymorphisms...