Michael Feldgarden
A5029324569- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Escherichia coli research studies
- Antimicrobial Resistance in Staphylococcus
- Bacterial Genetics and Biotechnology
- Bacterial biofilms and quorum sensing
- Bacterial Identification and Susceptibility Testing
- Enterobacteriaceae and Cronobacter Research
- Pharmaceutical and Antibiotic Environmental Impacts
- Evolution and Genetic Dynamics
- Antibiotic Use and Resistance
- RNA and protein synthesis mechanisms
- Urinary Tract Infections Management
- Streptococcal Infections and Treatments
- Molecular Biology Techniques and Applications
- Probiotics and Fermented Foods
- Genetics, Bioinformatics, and Biomedical Research
- Marine Ecology and Invasive Species
- Diet and metabolism studies
- Infective Endocarditis Diagnosis and Management
- Identification and Quantification in Food
- Antibiotics Pharmacokinetics and Efficacy
- Clostridium difficile and Clostridium perfringens research
National Center for Biotechnology Information
2016-2025
National Institutes of Health
2016-2025
Broad Institute
2008-2017
Massachusetts Institute of Technology
2010-2017
Harvard University
2010-2013
Digital Research Alliance of Canada
2009
Stony Brook University
2003-2004
Wesleyan University
1999-2003
Yale University
1992-1998
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in microbes occupy habitats such as gut, skin and vagina. Much this diversity remains unexplained, although diet, environment, host genetics early microbial exposure all been implicated. Accordingly, to characterize ecology human-associated communities, Human Microbiome Project has analysed largest cohort set distinct, clinically relevant body so far. We found abundance each habitat's signature vary...
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in health disease. The National Institutes Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting broad range quality-controlled resources data including standardized methods for creating, processing interpreting distinct types high-throughput available scientific community. Here...
Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole-genome sequences, the National Center Biotechnology Information (NCBI) has produced AMRFinder, tool identifies using high-quality curated gene reference database. The Bacterial Resistance Reference Gene Database consists of up-to-date nomenclature, set hidden Markov models (HMMs), and protein family hierarchy. Currently, it contains 4,579...
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...
News from the Inner Tube of Life A major initiative by U.S. National Institutes Health to sequence 900 genomes microorganisms that live on surfaces and orifices human body has established standardized protocols methods for such large-scale reference sequencing. By combining previously accumulated data with new data, Nelson et al. (p. 994 ) present an initial analysis 178 bacterial genomes. The sampling so far barely scratches surface microbial diversity found humans, but work provides...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface New include Comparative Genome Resource (CGR) BLAST ClusteredNR database. Resources receiving significant updates past year PubMed, PMC, Bookshelf,...
The enterococci are Gram-positive lactic acid bacteria that inhabit the gastrointestinal tracts of diverse hosts. However, Enterococcus faecium and E. faecalis have emerged as leading causes multidrug-resistant hospital-acquired infections. mechanism by which a well-adapted commensal evolved into hospital pathogen is poorly understood. In this study, we examined high-quality draft genome data for evidence key events in evolution enterococcal infections, including faecalis, faecium,...
Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences reliable diagnosis of infectious disease agents regulations transport possession organisms economic importance. E. traditionally is thought to live within gastrointestinal tract humans other warm-blooded animals not survive extended periods outside its host; this understanding basis widespread use as fecal contamination indicator. Here, we report genome...
The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on resolution technology used samples studied. Isolates Escherichia coli O104:H4 from centered in Germany May-July 2011, much smaller southwest France June were indistinguishable by standard tests. We report a epidemiological analysis using multiplatform whole-genome sequencing multiple isolates German French outbreaks. showed remarkably little diversity, with...
Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise pathogens in genus. We have sampled, sequenced, assessed diversity genomes validly named tentative species Acinetobacter genus, clade including major nosocomial biotechnologically important species. inferred robust global phylogeny delimited several new putative The genus is very...
Abstract The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface Resources receiving significant updates past year include PubMed, PMC, Bookshelf, SciENcv, NIH Comparative Genomics Resource (CGR), Virus,...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence repository and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 31 distinct repositories knowledgebases. E-utilities serve as programming interface these. Resources receiving significant updates past year include PubMed, PubMed Central, Bookshelf, NIH Comparative Genomics...
Hospital-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a global health burden dominated small number of bacterial clones. The pandemic EMRSA-16 clone (ST36-II) has been widespread in UK hospitals for 20 y, but its evolutionary origin and the molecular basis hospital association unclear. We carried out Bayesian phylogenetic reconstruction on genome sequences 87 S. isolates including 60 27 additional clonal complex 30 (CC30) isolates, collected from...
Understanding the fine-structure molecular architecture of bacterial epidemics has been a long-sought goal infectious disease research. We used short-read-length DNA sequencing coupled with mass spectroscopy analysis SNPs to study pathogenomics three successive invasive infections involving 344 serotype M3 group A Streptococcus in Ontario, Canada. Sequencing genome 95 strains from epidemics, 280 biallelic all strains, revealed an unexpectedly complex population structure composed dynamic...
Carbapenem-resistant Enterobacteriaceae (CRE) are among the most severe threats to antibiotic era. Multiple different species can exhibit resistance due many mechanisms, and mobile elements capable of transferring between lineages. We prospectively sampled CRE from hospitalized patients three Boston-area hospitals, together with a collection single California hospital, define frequency characteristics outbreaks determine whether there is evidence for transfer strains within hospitals which...
ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) strains are leading causes of hospital-acquired infections in the United States, and clonal cluster 5 (CC5) is predominant lineage responsible for these infections. Since 2002, there have been 12 cases vancomycin-resistant S. (VRSA) infection States—all CC5 strains. To understand this genetic background what distinguishes it from other lineages, we generated analyzed high-quality draft genome sequences all available VRSA Sequence...
The initial report of the mcr-1 (mobile colistin resistance) gene has led to many reports variants and other mcr genes from different bacterial species originating human, animal environmental samples in geographical locations. Resistance nomenclature is complex unfortunately problems such as names being used for same gene/protein or name genes/proteins are not uncommon. Registries exist some families, bla (β-lactamase) genes, but there yet no agreed scheme genes. National Center...
Clonal complex 5 methicillin-resistant Staphylococcus aureus (CC5-MRSA) includes multiple prevalent clones that cause hospital-associated infections in the Western Hemisphere. Here, we present a phylogenomic study of these MRSA to reveal their phylogeny, spatial and temporal population structure, evolution selected traits. We studied 598 genome sequences, including 409 newly generated from 11 countries Central, North, South America, references Asia Europe. An early-branching CC5-Basal clade...
ABSTRACT Pseudomonas aeruginosa is a clinically important Gram-negative pathogen responsible for wide variety of serious nosocomial and community-acquired infections. Antibiotic resistance major concern, as this organism has mechanisms, including chromosomal class C ( bla PDC ) D OXA-50 family) β-lactamases, efflux pumps, porin channels, the ability to readily acquire additional β-lactamases. Surveillance studies can reveal diversity distribution β-lactamase alleles but are difficult...
ABSTRACT The enterococci are low-GC Gram-positive bacteria that have emerged as leading causes of hospital-acquired infection. They also commensals the gastrointestinal tract healthy humans and most other animals with flora important for food fermentations. Here we report availability draft genome sequences 28 enterococcal strains diverse origin, including species Enterococcus faecalis , E. faecium casseliflavus gallinarum .
Whole-genome sequencing of a collection 103 Acinetobacter strains belonging to 22 validly named species and another 16 putative allowed detection genes for 50 new class D β-lactamases 65 Acinetobacter-derived cephalosporinases (ADC). All oxacillinases (OXA) contained the three typical motifs β-lactamases, STFK, (F/Y)GN, K(S/T)G. The phylogenetic tree drawn from OXA sequences led an increase in number groups 7 18. topologies RpoB trees were similar, supporting ancient acquisition blaOXA by...
Abstract Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify acquired AMR genes in whole genome sequences, the National Center Biotechnology Information (NCBI) has produced high-quality, curated, gene reference database consisting of up-to-date protein and nomenclature, set hidden Markov models (HMMs), curated family hierarchy. Currently, Bacterial Resistance Reference Gene Database contains 4,579...
Unlike for classes A and B, a standardized amino acid numbering scheme has not been proposed the class C (AmpC) β-lactamases, which complicates communication in field. Here, we propose developed through collaborative approach that considers both sequence structure, preserves traditional of catalytically important residues (Ser64, Lys67, Tyr150, Lys315), is adaptable to new variants or enzymes yet be discovered includes variation genetic epidemiological applications.
Antimicrobial resistance (AMR) is a significant public health threat. Low-cost whole-genome sequencing, which often used in surveillance programmes, provides an opportunity to assess AMR gene content these genomes using silico approaches. A variety of bioinformatic tools have been developed identify genomic elements. Most those rely on reference databases nucleotide or protein sequences and collections models rules for analysis. While the are critical identification genes, themselves also...
Abstract The detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development number different bioinformatic AMR prediction tools. Although many may implement similar principles, these tools differ significantly their supported inputs, search algorithms, parameterisation, underlying reference databases. Each generates report detected genes variants distinct,...