A5015491153- Antibiotic Resistance in Bacteria
- Pharmaceutical and Antibiotic Environmental Impacts
- Bacteriophages and microbial interactions
- Genetics, Bioinformatics, and Biomedical Research
- Escherichia coli research studies
- Salmonella and Campylobacter epidemiology
- Molecular Biology Techniques and Applications
- Enterobacteriaceae and Cronobacter Research
- Vibrio bacteria research studies
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Poxvirus research and outbreaks
- Biomedical Text Mining and Ontologies
- Mycobacterium research and diagnosis
- Bacterial Identification and Susceptibility Testing
- Viral gastroenteritis research and epidemiology
- Scientific Computing and Data Management
- Bacillus and Francisella bacterial research
- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Listeria monocytogenes in Food Safety
- Identification and Quantification in Food
Centers for Disease Control and Prevention
2021-2023
Waterborne Environmental (United States)
2022
James Madison University
2021
Colorado Department of Public Health and Environment
2019
The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of early infections, these methods are resource intensive require samples high viral DNA concentrations. Given atypical clinical presentation cases associated uncertainty regarding load across both course infection...
We have adopted an open bioinformatics ecosystem to address the challenges of implementation in public health laboratories (PHLs). Bioinformatics for requires practitioners undertake standardized bioinformatic analyses and generate reproducible, validated auditable results. It is essential that data storage analysis are scalable, portable secure, fits within operational constraints laboratory. these requirements using Terra, a web-based platform with graphical user interface connecting users...
The sharing of genome sequences in online data repositories allows for large scale analyses specific genes or gene families. This can result the detection novel subtypes as well development improved methods. Here, we used publicly available WGS to detect a Stx subtype, Stx2n two clinical E. coli strains isolated USA. During this process, additional Stx2 were detected; six Stx2j, one Stx2m strain, and Stx2o, all analyzed variability from originally described subtypes. Complete assembled...
The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many laboratories did not have infrastructure place to handle vast amount of severe acute respiratory syndrome 2 (SARS-CoV-2) sequence data generated. California Department Public Health, partnership with Theiagen Genomics, was an early adopter cloud-based resources bioinformatics and genomic epidemiology, resulting creation a SARS-CoV-2 surveillance system that...
Abstract The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of early mpox infections, these methods are resource intensive require samples high viral DNA concentrations. Given atypical clinical presentation cases associated uncertainty regarding load across both course infection...
The sharing of genome sequences in online data repositories, allows for large scale analyses specific genes or gene families. This can result the detection novel subtypes as well development improved methods. Here we used publicly available WGS to detect a Stx subtype, Stx2n two clinical E. coli strains isolated USA. During this process, additional Stx2 were detected; six Stx2j one Stx2m strain and Stx2o, all analyzed variability from originally described [1,2]. Complete assembled short long...
We have developed and implemented an undergraduate microbiology course in which students isolate, characterize, perform whole genome assembly analysis of Salmonella enterica from stream sediments poultry litter. In the development over three semesters, successive teams collected field samples performed enrichment isolation techniques specific for detection S. enterica. Eighty-eight strains were confirmed using standard microbiological methods PCR invA gene. The isolates' genomes...
In the United States, reports of Salmonella enterica carrying mcr-1 remain rare in humans, but when observed, infection is often associated with travel. Here, we report 14 mcr-1-positive isolates from patients States that reported travel to Dominican Republic within 12 months before illness.
Abstract Antimicrobial resistance (AMR) poses significant risks to human and animal health while the environment can contribute its spread. National AMR surveillance programs are pivotal for assessing prevalence, trends, intervention outcomes, however, integrating advanced tools be difficult. This pilot study, conducted by FAO ECTAD Indonesia DGLAHS, Indonesian Ministry of Agriculture, evaluated costs benefits Nanopore MinION, Illumina MiSeq, Sensititre system into a culture-based...
Salmonella enterica subsp. serovar Corvallis is commonly reported in avian populations and by-products. We report the draft genome sequence of a multidrug-resistant S. strain (NPHL 15376). To our knowledge, this first case isolated from human blood United States.
Laboratories that run Whole Genome Sequencing (WGS) produce a tremendous amount of data, up to 10 gigabytes for some common instruments. There is need standardize the quality assurance and control process (QA/QC). Therefore we have created SneakerNet automate QA/QC WGS.
4. CONCLUSIONS • Transmissible plasmids affect environmental ecosystems via exchange and recombination of antibiotic resistance genes. Exchange occurs between native bacterial populations introduced fecal pathogens selected for in farm animals. Public Health Relevance: Native bacteria aquatic soil habitats may act as incubators sites genes that are subsequently transferred to human pathogens. Plasmid 1-1 1-20