A5005706405- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Environmental DNA in Biodiversity Studies
- Plant Pathogenic Bacteria Studies
- Microbial Community Ecology and Physiology
- Salmonella and Campylobacter epidemiology
- Bacteriophages and microbial interactions
- Antibiotic Resistance in Bacteria
- Mycotoxins in Agriculture and Food
- Listeria monocytogenes in Food Safety
- Identification and Quantification in Food
- Plant Pathogens and Fungal Diseases
- Pharmaceutical and Antibiotic Environmental Impacts
- Paraoxonase enzyme and polymorphisms
- Marine Bivalve and Aquaculture Studies
- Molecular Biology Techniques and Applications
- Plant Pathogens and Resistance
- Berberine and alkaloids research
- Probiotics and Fermented Foods
- Neonatal Health and Biochemistry
- Protist diversity and phylogeny
- Aquaculture disease management and microbiota
- Water Treatment and Disinfection
- Enterobacteriaceae and Cronobacter Research
- Bacillus and Francisella bacterial research
United States Food and Drug Administration
2018-2025
Center for Food Safety and Applied Nutrition
2018-2024
Food and Drug Administration
2023
University of Maryland, College Park
2019-2021
Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed correct these errors, but it is uncertain if they obtain accuracy needed for high-resolution source tracking foodborne illness outbreaks.
Abstract Prepared and stored feeds, fodder, silage, hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous have played significant roles livestock deaths from forage consumption recent years Western United States including Salvia reflexa . Metagenomic data, genome skims metabarcodes, been used for identification characterization complex matrices diet composition animals, mixed forages, herbal products. Here, chemistry, skims, metabarcoding were to...
Abstract Motivation Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although commonly used, they have not been critically evaluated their effectiveness as basis metagenomic analyses. Results As case study, we investigate one such catalog, Integrated Gene Catalog (IGC), however, our observations apply broadly to most constructed date. We focus on both...
Introduction Identification of chemical toxins from complex or highly processed foods can present ‘needle in the haystack’ challenges for chemists. Metagenomic data be used to guide toxicity evaluations by providing DNA-based description wholistic composition (eukaryotic, bacterial, protozoal, viral, and antimicrobial resistance) suspected harbor toxins, allergens, pathogens. This type information focus chemistry-based diagnostics, improve hazard characterization risk assessment, address...
The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne in over a decade. epidemiological investigation suggested two farms as likely source contamination. However, single nucleotide polymorphism (SNP) analysis whole genome sequencing data showed that none isolates collected from farm regions were linked to clinical isolates-preventing use phylogenetics identification. Here, we explored an alternative method for analyzing driven by hypothesis if strain...
A total of 55 food and clinical S . Schwarzengrund isolates were assayed for plasmid content, among which an IncFIB-IncFIC(FII) fusion plasmid, conferring streptomycin resistance, was detected in 17 isolates. Among the isolates, 9 primarily collected from poultry meat, 8 stool, urine, gallbladder. SNP—based phylogenetic analyses showed that carrying formed a subclade indicating acquired is now maintained by lineage. Phylogenetic analysis suggested it derived avian pathogenic plasmids might...
The National Antimicrobial Resistance Monitoring System (NARMS) has monitored antimicrobial resistance (AMR) associated with pathogens of humans and animals since 1996. In alignment One Health strategic planning, NARMS is currently exploring the inclusion surface waters as an environmental modality for monitoring AMR. From a perspective, function key integrators between humans, animals, agriculture, environment. Surface however, due to their dilute nature present unique challenge critically...
Abstract Background Whole genome sequencing of cultured pathogens is the state art public health response for bioinformatic source tracking illness outbreaks. Quasimetagenomics can substantially reduce amount culturing needed before a high quality be recovered. Highly accurate short read data analyzed single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads much more...
Seventeen Salmonella enterica serovar Schwarzengrund isolates from chicken (n = 9) and clinical samples including stool 6), urine 1), gallbladder 1) were sequenced found to carry an IncFIB-IncFIC (FII) fusion plasmid of approximately 145 Kb. This information provides reference genomic data for comparative studies S. pathogenicity genetics.
Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools make accurate about microbial communities and their functions. More discussion is needed the current state analysis required overcome hurdles preventing development implementation predictive analyses. We summarize ideas generated by participants Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from presentations that...
Aquaculture plays an increasingly important role in the growing demand for seafood. Hatchery production of oyster larvae is integral component farming, providing single seed off-bottom farming or setting on larger substrates on-bottom farming. Larvae from certain tanks established aquaculture enterprise were dying unknown etiologic agent. A metagenomic approach was used to examine and water larval with high low survival rates evaluate epidemiological efficacy this approach.
Water from the Hickey Run Tributary of Anacostia River is being collected quarterly (beginning August 2018) and analyzed to create high-resolution baseline taxonomic profiles microbiota associated with this important aquatic ecosystem, which has a long history exposure residential commercial effluents Washington, DC. These United States National Arboretum Microbial Observatory data are available under NCBI BioProject number PRJNA498951.
Abstract Identification of chemical toxins from complex or highly processed foods can present ‘needle in the haystack’ challenges for chemists. Metagenomic data guide toxicity evaluations with DNA-based description wholistic composition (bacterial, eukaryotic, protozoal, viral, and antimicrobial resistance) any food suspected to harbor toxins, allergens, pathogens. This approach focus chemistry-based diagnostics, improve risk assessment, address gaps. There is increasing recognition that...
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and profile microbial communities. However, criticized for being too conserved differentiate between distinct species. We argue that inability is not a unique feature of gene. Rather, we observe gradual loss species-level resolution other nearly-universal marker genes as number sequences increases in reference databases. This trend was strongly correlated with how represented taxonomic group database...
Abstract Surface waters present a unique challenge for the monitoring of critically important antimicrobial resistance. Metagenomic approaches provide unbiased descriptions taxonomy and resistance genes in many environments, but surface water, culture independent data is insufficient to describe To address this expand resistome reporting capacity waters, we apply metagenomic quasimetagenomic (enriched microbiome) examine contrast water from two sites, creek near hospital, reservoir used...
Abstract Background: Rapid pathogen detection is essential for an effective public health response. The Illumina MiSeq short read sequencer has been the workhorse of many whole genome sequencing source tracking programs. However, reads cannot span bacterial genomic repeats, resulting in highly fragmented assemblies. Long can repeats complete assembly genomes. With advancing throughput and accuracy inexpensive long data, it important to evaluate this resource potential inclusion rapid...
Abstract BackgroundMicrobial eukaryotes are nearly ubiquitous in microbiomes on Earth and contribute to many integral ecological functions. Metagenomics is a proven tool for studying the microbial diversity, functions, ecology of microbiomes, but has been underutilized microeukaryotes due computational challenges they present. For taxonomic classification, use eukaryotic marker gene database can improve efficiency, precision sensitivity. However, tools which databases often implement...
ABSTRACT Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast vivo versus vitro bioequivalence response antiparasitic drug administration. The provided unique opportunity evaluate metagenomic profiles canine feces before and after anti-parasitic exposure.
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and profile microbial communities. The criticized for being too conserved differentiate between distinct species. We argue that inability is not a unique feature of gene. Rather, we observe gradual loss species-level resolution other marker genes as number sequences increases in reference databases. demonstrate this effect through analysis three commonly databases nearly-universal genes: SILVA...
Abstract BackgroundMicrobial eukaryotes are nearly ubiquitous in microbiomes on Earth and contribute to many integral ecological functions. Metagenomics is a proven tool for studying the microbial diversity, functions, ecology of microbiomes, but has been underutilized microeukaryotes due computational challenges they present. For taxonomic classification, use eukaryotic marker gene database can improve efficiency, precision sensitivity. However, tools which databases often implement...
Abstract Background The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne in over a decade. epidemiological investigation suggested two farms as likely source contamination. However, single nucleotide polymorphism (SNP) analysis whole genome sequencing data did not find any isolates from farm regions that were closely related to clinical isolates—preventing use phylogenetics identification. Here, we explored an alternative method for analyzing driven by...
Sprouts have been implicated in numerous foodborne illness outbreaks. To better understand baseline microbial profiles of irrigation water and subsequent spent alfalfa sprouts, DNA from was extracted, sequenced, annotated with CosmosID a custom pipeline to provide bacterial, fungal, protist, antimicrobial resistance gene profiles.
Abstract Paraoxonase (PON) comprises a trio of mammalian enzymes that have been reported to number roles including the inhibition bacterial virulence and biofilm formation by microorganisms quorum sense with acylated homoserine lactones (AHLs). PON previously inhibit P. aeruginosa in airways skin. An innate immune role for urinary tract infection has not reported. We performed western blots PON1 urine from patients (UTI), also tested UTI presence AHLs using cellular reporter system. Urine...