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 1,332 actions intended to protect consumers from foodborne illness.
2024
- Researchers at FDA and CDC used the Isolates Browser to identify Salmonella from imported shrimp products and clinical cases are related during a multistate sample‐initiated retrospective outbreak investigation (SIROI).
- Researchers at the University of New Mexico and New Mexico Dept. of Health use the Isolates Browser to identify isolates belonging to a Shigella outbreak in humans that spread to non-human primates at a wildlife park. The researchers also use AMRFinderPlus to identify resistance genes in order to track the gain and loss of resistance genes in these isolates during the course of the outbreak.
- Researchers at FDA/CFSAN used Pathogen Detection to determine how often environmental isolates were closely linked for four food-borne pathogens and to understand the implications of those patterns when prioritizing surveillance strategies.
- Researchers from the Oregon Health Authority used Pathogen Detection to link backyard poultry and a neonate infection.
- Researchers from the FDA and USDA used Pathogen Detection to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella.
- Scientists in Pennsylvania used Pathogen Detection to link Salmonella obtained from wastewater to a previously known foodborne outbreak.
- Scientists in both the US and Ethiopia used Pathogen Detection in part to show the link of an Listeria isolate in Ethiopia to a clinical case in the US.
- Researchers in the US used Pathogen Detection in part to obtain genome sequences of certain Salmonella serovar associated with a turkey outbreak to evaluate genetic changes that may have contributed to the outbreak.
- Scientists at the FDA Center for Food Safety and Nutrition created an R Shiny interface to download and analyze Pathogen Detection "rapid reports" to investigate the most recently submitted isolates during foodborne outbreak investigations.
2023
- Researchers at Cornell University used Pathogen Detection to identify a ciprofloxacin-resistant outbreak among wildlife patients at a veterinary hospital.
- Scientists in Australia describe using Pathogen Detection for investigation of a Vancomycin Resistance Enterococcus faecium ST78 outbreak at a hospital.
- Scientists at Virginia Department of Health describe using Pathogen Detection for Gram-negative Carbapenem-Resistant Organisms (CRO) - for example, the use of Pathogen Detection increased the number of isolates potentially related to a Proteus mirabilis outbreak from 3 to 10 - spanning a much longer period than originally investigated.
- Pathogen Detection was used to rapid identify a food product contaminated with Salmonella before it was large enough to be identified using the standard multistate outbreak detection methods.
- 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.
- Scientists at multiple institutions use NCBI Pathogen Detection Browser for evaluation of Salmonella isolates from imported papaya products as part of a cross-border investigation
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
2024
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Researchers at Cornell University use the Isolates Browser to identify isolates and obtain their genomes for detailed phylogenetic analysis of Salmonella evolutionary rates, to identify AMR genes, and to link clades of Salmonella with animal or environmental sources.
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Researchers use the AMR genetic element data in MicroBIGG-E to identify mcr-positive Escherichia coli (MCRPEC), characterize their AMR gene content and place these isolates into phylogenetic context.
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Researchers use the Pathogen Detection system to identify isolates with tigecycline resistant elements to study the epidemiology of Klebsiella pneumoniae with plasmid-borne tigecycline resistance.
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Dutch researchers use the antibiotic resistance data in the Isolates Browser to find Pseudomonas aeruginosa NDM-1 positive isolates with an antibiotic resistance gene profile similar to a P. aeruginosa NDM-1 positive isolate responsible for a clinical outbreak in the Netherlands.
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Researchers at the Veterinary Laboratory Investigation and Response Network (Vet-LIRN/CVM/FDA) use the Pathogen Detection pipeline to identify Enterobacterales isolates that have carbapenemases in cat and dog feces.
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Researchers use MicroBIGG-E to identify thousands of mcr-1 containing genomes in order analyze the changes in the mcr-1 genetic background after colistin usage restrictions around the world.
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Researchers at Veterinary Laboratory Investigation and Response Network (Vet-LIRN/CVM/FDA) and others use AMRFinderPlus to identify AMR and stress response genes in aquatic pathogens.
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Researchers of the University of Oxford use MicroBIGG-E to identify isolates and contigs with GES carbapenemases and the Reference Gene Catalog to obtain all known GES carbapenemase alleles to understand the global distribution of GES carbapenemases in integrons.
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Researchers at the University of Utah use AMRFinderPlus as part of ReGAIN, an analytical pipeline which detects the co-occurence of antimicrobial resistance genes in bacterial pathogens.
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Scientists at the Canadian Food Inspection Agency and others use Pathogen Detection data to survey 639,087 ESCAPEE organisms and their AMR, biocide, and metal resistance genes.
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Scientists and Clinicians at the Brigham & Women's Hospital and NCBI use Pathogen Detection Isolates Browser, MicroBIGG-E, and AMRFinderPlus to show how Pathogen Detection can be used to further One Health efforts to improve research, detection, tracking, surveillance, and prevention of C. botulinum, C. difficile, and C. perfringens infection
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.
- NARMS researchers used AMRFinderPlus gene calls in Pathogen Detection to assess the prevalence and mechanisms of azithromycin-resistance in Salmonella from food animal products from 2011–2021 in the United States.
- Investigators at Virginia's Division of Consolidated Laboratory Services use Pathogen Detection to identify carbapenem-resistant organisms for further analysis and investigation.
- Researchers at the National Centre for Infectious Diseases, Singapore, while evaluating the efficacy of phenotypic carbapenemase detection tests, use AMRFinderPlus to verify the presence of carbapenemases in control and test strain genomes.
- Researchers use AMRFinderPlus to identify AMR genes in metagenome-assembled genomes (MAGs) to understand the effects of wastewater discharge on AMR gene dissemination.
- In collaboration with the CDC, CFSAN (FDA), Statens Serum Institut, and the Uniformed Services University of the Health Sciences, Pathogen Detection researchers at NCBI/NLM describe the characterization and discovery of a new form of type 2 Shiga Toxin that was first identified by the Pathogen Detection system's virulence gene detection function in AMRFinderPlus.
- Researchers used AMR data from the Pathogen Detection system to assess the geographic, host, and serovar distribution of fosfomycin resistance genes in Salmonella.
- 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.
- Researchers used Pathogen Detection analyses to characterize Salmonella collected from food products in retail markets in Mexico for AMR, serovar, metal resistance, and virulence factors.
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
2020
- FDA scientists at the Center for Vetrinary Medicine discover after AMRFinderPlus results in Pathogen Detection showed a high frequency occurrence of MCR-9 in Salmonella that it does NOT correlate with phenotypic resistance.