Success Stories
Some examples of how scientists are using NCBI Pathogen Detection resources to promote public health and further their research goals.
Outbreak analysis
- FDA GenomeTrakr network has used Pathogen Detection Isolates Browser for 1,056 actions intended to protect consumers from foodborne illness.
2023
- A much longer paper including perspectives from all international partners about the Listeria monocytogenes enoki mushroom outbreak from 2020 is described using Pathogen Detection. See the earlier 2020 paper
- Scientists at CDC and FDA describe Foodborne Sample-Initiated Retrospective Outbreak Investigations using Pathogen Detection.
- Scientists at Harvard Medical School and multiple U.S. public health agencies used Pathogen Detection clustering information to identify cryptic MRSA outbreaks in NICU patients and use AMRFinderPlus to characterize these isolates' AMR and virulence genes.
- Scientists at the University of Washington and Seattle & King County Public Health use Pathogen Detection Isolates Browser to identify multi-drug resistant Shigella outbreak isolates and use AMRFinderPlus to identify these isolates' AMR genes.
2022
- USDA scientists use NCBI Pathogen Detection to evaluate 13,612 Salmonella enterica serovar I 4,[5],12:i:- strain sequences for global distribution, and multi-drug resistance.
- Genomics for Food Safety Interagency Collaboration (CDC, FDA, USDA-FSIS, and NCBI-NLM-NIH) is described including Pathogen Detection.
- Scientists from an international collaboration used NCBI Pathogen Detection to link Salmonella in Trinidad and Tobago to an emergent, widespread multidrug resistance clone of Salmonella Infantis.
- Scientists at Cornell University used NBCI Pathogen Detection to cluster isolates from wildlife with known food-borne isolates and provide detailed descriptions of Listeria monocytogenes.
- Scientists use the Pathogen Detection System to link isolates from Southeast Asia to clinical cases in England and the US , some of which had a history of travel.
2021
- Pro Publica used NCBI Pathogen Detection to track an ongoing multi-drug resistant Salmonella outbreak.
- FDA economists examine the impact of the switch to whole genome sequencing for three foodborne bacterial pathogens in the US and the use of the Pathogen Detection browser with significant impacts economically and for public health.
- Scientists in Oregon public health institutions use NCBI Pathogen Detection Browser to identify pathogenic Escherichia coli O157:H7 from venison from harvested deer and clinical cases from hunters in the same area.
- Scientists at New York State Department of Health use NCBI Pathogen Detection Browser for a retrospective analysis of Clostridium prefringens outbreaks.
- Scientists at multiple institutions use NCBI Pathogen Detection Browser for evaluation of Shigella isolates. Analysis includes evaluation of macrolide resistance, plasmid structure, and identified multiple outbreaks in the United States and evidence of intercontinental transmission.
2020
- Scientists at multiple public health agencies use NCBI Pathogen Detection Browser for international Listeria outbreak.
- Scientists at BWH use NCBI Pathogen Detection Browser to examine Clostridioides difficile transmission.
2019
- Oregon Health Authority uses NCBI Pathogen Detection Browser to uncover outbreak.
Antimicrobial resistance, point mutations, virulence, and stress response genes and genotypes
2023
- The Microbiological Diagnostic Unit Public Health Laboratory (Melbourne, Victoria, Australia) incorporated AMRFinderPlus into an ISO-certified pipeline for the detection of AMR determinants from whole genome sequencing data, with outputs adapted for clinical antibiotic susceptibility prediction and public health microbiology reporting.
- Scientists at the Canadian Food Inspection Agency use genomic AMR data from the Isolates Browser FTP site to develop strain-specific isolation methods for shiga toxin-producing Escherichia coli during foodborne illness outbreak investigations.
- Scientists used AMRFinderPlus to identify novel putative beta-lactamase sequences found in metagenomic samples from Chinese wildlife for functional characterization and to understand the role of wildlife as reservoirs for antibiotic resistance.
2022
- An international group of β-lactamase experts met to develop a consensus for the way naturally-occurring β-lactamase genes should be named and agreed NCBI should be the clearinghouse for allele assignment
- Scientists used output from the Pathogen Detection Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) to identify conserved functional regions in erythromycin resistance methyltransferases.
- Scientists from the University of Liege, Belgium used class D beta-lactamase sequences from the Reference Gene Catalog to identify possible class D beta-lactamase sequences in non-clinical bacterial strains.
- Scientists used AMR and virulence factor data from NCBI Pathogen Detection to characterize Klebsiella pneumoniae from Low-and Middle-Income Countries (LMICs).
- A diverse set of Shigella in Africa and Southeast Asia are examined using AMRFinderPlus to examine AMR genotypes in multi-drug resistant Shigella spp. and to guide policy on treatments and vaccination.
- Cornell uses Pathogen Detection Isolates Browser as a framework leveraging WGS data to identify Salmonella subtypes over- and underrepresented among human clinical cases and then examine genotypes for potential contribution. A particular known virulence gene in Salmonella Saintpaul was confirmed using this method.
- Scientists at the University of Milan used NCBI Pathogen Detection to observe a global increase in AMR genes in Streptococcus agalactiae (Group B streptococci)
- Scientists at the University of Helsinki used AMRFinderPlus to identify AMR genes in neonatal gut Enterococcus faecalis isolates
- Scientists use AMRFinderPlus to screen for heavy metal and biocide resistance genes in clinical Salmonella enterica
2021