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Antimicrobial Resistance Interagency Task Force
2007 Annual Report (Released June 2008)

Action Items 68—72

Action Item #68: Conduct Further Government-Wide Assessments with External Input on the Scope and Composition of AR Research To Identify Research Opportunities.

Project Title: Novel Antimicrobials in Respiratory Infections

• Agency: NIH
• Description: On February 27-28, 2008, a meeting on novel antimicrobials for respiratory infections was sponsored by NIAID. The sessions addressed the scope of the problem of resistance, mechanisms of resistance, diagnostic assays, novel approaches, and recommendations for future research. Participants included investigators from academia and industry from the US, Europe and Japan.
• Results: An Executive Summary of the meeting will be posted on the NIAID website in 2008 (www.niaid.nih.gov).

Action Item #69: Work with the Appropriate Peer Review Structures To Ensure That the Requisite Expertise Is Applied to the Review Process To Facilitate Funding of Quality AR Research.

• Agency: NIH
• Description: The Panel on Scientific Boundaries for Review has conducted a comprehensive examination of the organization and function of the review process that is carried out by the Center for Scientific Review (CSR) at NIH. The purpose of this evaluation is to position the CSR peer review system so that it fosters expanded research opportunities, as well as permits the review system to keep pace with the accelerating rate of change in the way that health-related research is performed. This examination is being carried out in two phases, with extensive involvement of the extramural research community.
• Results: The Infectious Diseases and Microbiology IRG review by the Expert Working Group was conducted from May – August 2001 and developed a proposed set of guidelines and shared interests for new study sections. NIH's CSR has established a new Study Section, Drug Discovery and Mechanisms of Antimicrobial Resistance (DDR), within the new Infectious Diseases and Microbiology Integrated Review Group (IRG). It will review applications that are concerned with the identification of novel antimicrobial agents, including agents that could be used in bioterrorism, for the prevention and treatment of infectious diseases and the study of the evolution, mechanisms, and transmission of resistance.
  
  NIH's CSR established a Study Section, Drug Discovery and Mechanisms of Antimicrobial Resistance (DDR), within the new Infectious Diseases and Microbiology Integrated Review Group (IRG). It reviews application that are concerned with the identification of novel antimicrobial agents, including agents that could be used in bioterrorism, for the prevention and treatment of infectious diseases and the study of the evolution, mechanisms, and transmission of resistance. DDR held its first meeting in June of 2004, and has met regularly thereafter. In FY2007, over 200 applications were reviewed of which 43 were awarded.

Action Item #70: Provide To the Research Community Genomics and Other Powerful Technologies To Identify Targets in Critical Areas for the Development of New Rapid Diagnostics Methodologies, Novel Therapeutics, and Interventions To Prevent the Emergence and Spread of Resistant Pathogens. Examples Include Tools Such as Microbial Genome Sequences, Information on Comparative Genomics, DNA Chip Technology, Informatics, and Assistance in the Application and Use of These Tools.

Project Title: Microbe project interagency working group

• Agency: NIH, USDA, FDA, EPA, FDA
• Description: NIAID staff is participating in the Microbe Project Interagency Working Group, which coordinates microbial genomics activities across Federal government agencies.
• Results: This working group continues to coordinate genomic activities across federal agencies, including those related to biodefense, and has also focused on issues related to genomic data release and usage, as well as on bioinformatics and microbial sequencing efforts.

Project Title: Research in support of the use of genomics, proteomics and other powerful technologies to identify targets in critical areas for the development of new rapid diagnostic methodologies, novel therapeutics, and interventions to prevent the emergence and spread of resistant pathogens.

• Agency: FDA
• Description: Research in support of the use of genomics, proteomics and other powerful technologies to identify targets in critical areas for the development of new rapid diagnostic methodologies, novel therapeutics, and interventions to prevent the emergence and spread of resistant pathogens.
• Results: Established microarray group and CBER core program (for producing and reading oligonucleotide microarray chips). Initiated several research projects related to vaccine development, AR, pathogen identification and detection. Developed a rapid typing method for Neisseria gonorrhoeae applicable to non-cultured specimens and the identification of ciprofloxacin resistant strains. Also developing rapid DNA assays to detect all four species of human malaria parasites. And developing microarray technology for detecting drug resistance among mycobacteria.

Project Title: The tuberculosis research materials and vaccine testing contract (Colorado State University)

• Agency: NIH
• Description: The contract provides TB research reagents to qualified investigators throughout the world, enabling them to work with consistent, high quality microbiological, immunological and genomic reagents, prepared from contagious and technically demanding mycobacterial pathogens.
• Results: More than 150 new TB vaccine candidates had been evaluated under this contract, several of which have been or are going ot be tested in human clinical trials with several others progressing through various stages of preclinical development. In addition, research reagents, including specialized post-genomic materials, continue to be provided to researchers worldwide and are being used for drug, vaccine and diagnostic development. Contract staff collaborates with the PFGRC for the production and dissemination of mycobacterial specific molecular reagents. and with the NIH Tetramer Facility to provide mycobacterially relevant tetramers. This contract will soon provide optimized cloning vectors for the preparation of mycobacterial mutants with the ultimate goal of finding new drug, diagnostic and vaccine targets in TB.

Project Title: Tuberculosis Animal Research and Gene Evaluation Task Force (TARGET, Johns Hopkins University)

• Agency: NIH
• Description: This contract provides a selection of animal models that collectively reproduce the most critical features of human tuberculosis, and provides services to evaluate M. tuberculosis and M. tuberculosis mutants in mice, guinea pigs, and hollow fibers to assess their virulence, capacity to induce, for example, acute, latent, or progressive tuberculosis, and ultimately to validate novel drugs, vaccine and diagnostic targets. This contract also provides transposon mutants either directly or through the he tuberculosis research materials and vaccine testing contract (Colorado State University)
• This contract continues to serve as a critical component in the process to validate putative therapeutic and preventive targets in TB in animal hosts.

Project Title: NIAID Pathogen Functional Genomics Resource Center (PFGRC)

• Agency: NIH
• Description: The PFGRC was established in FY2001 to provide and distribute to the broader research community a wide range of genomic and related resources and technologies for the functional analysis of microbial pathogens and invertebrate vectors of infectious diseases. The PFGRC was expanded to provide the research community with the needed resources and reagents to conduct both basic and applied research on microorganisms responsible for emerging and re-emerging infectious diseases and those considered agents of bioterrorism and organisms considered agents of bioterrorism.
• Results: The number of organism-specific microarrays produced and distributed to the scientific community has increased to 30 in FY2007 and now includes arrays for viruses, bacteria, fungi, and parasites. In addition, the PFGRC has developed 40 organism-specific protein expression clones since its inception.

Project Title: Sequencing of whole pathogen genomes

• Agency: NIH
• Description: NIAID has made significant investment in large-scale projects to sequence the genomes of medically significant bacterial, fungal, and parasitic pathogens. In addition, NIAID collaborates with other funding agencies to sequence larger genomes of protozoan pathogens such as the organism that causes malaria. A listing of currently active pathogen genome sequencing projects is available at: http://www.niaid.nih.gov/dmid/genomes/mscs/projects.htm
  The availability of microbial and human DNA sequences will open up new opportunities and allow scientists to examine functional analysis of genes and proteins in whole genomes and cells, as well as the host immune response and an individuals' genetic susceptibility to pathogens.
• Results: In FY2007, NIAID supported approximately 40 large scale genome sequencing projects for additional strains of viruses, bacteria, fungi, parasites, and invertebrate vectors and new projects include additional strains of Actinomycetales, Burkholderia, E.coli 0157, Enterococcus, Lactobacillus, drug resistant - including XDR-Mycobacterium tuberculosis (Mtb) strains that were the source of a recent outbreak in HIV co-infected patients in South Africa and drug sensitive Mtb, Neisseria meningitis, Salmonella, Staphylococcus aureus, Plasmodium falciparum, and Rotaviruses.

Project Title: Influenza Genome Sequencing Project

• Agency: NIH
• Description: This project was launched in 2004 and puts influenza sequence data rapidly into the public domain, enabling scientists to further study how influenza flu viruses evolve, spread, and cause disease and may ultimately lead to improved methods of treatment and prevention. This project is a collaborative effort among NIAID, NCBI/NLM, CDC, St. Jude Children's Research Hospital in Memphis and others, bringing together expertise in sequencing and bioinformatics, as well as expertise in human and avian influenza viruses to help NIAID prioritize, select and obtain strains.
• Results: As of February 2007, the entire genetic blueprints of more than 2,000 human and avian influenza viruses taken from samples around the world have been completed and the sequence data made available in a public database. See http://www.niaid.nih.gov/dmid/genomes/mscs/default.htm#influenza for details.

Project Title: NIAID pathogen genomics website

• Agency: NIH
• Description: The NIAID genomics website serves as a focal point to disseminate to the scientific community current information about NIAID's microbial genomics research program and related activities, including information on funding opportunities, policies, application procedures, priorities for large-scale genome sequencing projects, press releases, and currently funded large-scale genome sequencing projects.
• Results: Currently available to the scientific community:  www.niaid.nih.gov/dmid/genomes/

Project Title: Network on Antimicrobial Resistance in Staphylococcus aureus (NARSA) contract

• Agency: NIH
• Description: The network includes over two hundred domestic and international investigators made up of basic researchers, clinical laboratorians, epidemiologists, and infectious disease clinicians involved in staphylococcal and antimicrobial resistance research. NARSA supports electronic sharing of information and an annual conference of NIH funded researchers. The eighth annual NARSA meeting took place on March 5-6, 2007. The repository has over two hundred strains of S. aureus including the first three identified VRSA isolates noted above. Additional information is available through www.narsa.net and http://www.niaid.nih.gov/dmid/antimicrob/
• Results: In 2007, NIAID reissued a seven year contract, Network on Antimicrobial Resistance in Staphylococcus aureus (NARSA), to Eurofins Medinet, Inc. in Herndon, VA.   

Project Title: Population Genetics Analysis Program: Immunity to Vaccines/Infections

• Agency: NIH
• Description: The goal of this program is to identify associations between specific immune response gene polymorphisms/genetic variations and susceptibility to infection or response to vaccination with a focus on one or more of NIAID Category A-C pathogens.
• Results: NIAID awarded 6 Centers in 2004 and studies include examining host response to immunization against smallpox, anthrax, typhoid fever, and cholera. In FY06, these centers focused on recruitment of the samples needed for genotyping and have begun genotyping assays. For example, more than 1100 smallpox vaccinated individuals and controls have been recruited and blood and PBMC samples obtained for whole genome association studies in FY07. In addition, one of the centers is using genome-wide linkage approaches to map, isolate, and validate human host genes that confer susceptibility to influenza infection. Approximately 100 individuals are being recruited using an Iceland genealogy database and in FY 2007 the Center has recruited more than 800 individuals and has almost finished genotyping the 800 samples received.

Project Title: Program Project grant “Structural Organization and Proteomics of TB”

• Agency: NIH
• Description: The goal of a global consortium, which involves over 70 laboratories in 12 countries, was to determine and analyze the structures of over 400 functionally relevant Mtb proteins. Originally developed under a Center Grant, which ended in early FY 2006, consortium activities, as well as more scientifically targeted, collaborative programs for specific drug targets in Mycobacterium tuberculosis are continues under a program project grant.  
• Results: All data collated and produced by this consortium is publicly available through web-based databases: /www.webtb.org. Targeted studies mycobacterial proteins relevant for drug development are on-going under this grant.

Project Title: Food and Waterborne Diseases Integrated Research Network (FWDIRN)

• Agency: NIH
• Results: NIAID's FWDIRN network includes multidisciplinary research on all food and waterborne pathogens (bacteria, viruses, and protozoa), as well as toxins, to facilitate the development and evaluation of products to rapidly identify, prevent, and treat food and waterborne diseases that threaten public health. The network includes Immunology (IRU), Microbiology (MRU), Zoonoses (ZRU) and Clinical (CRU) Research Units. The Network is supported by a Coordinating and Biostatistics Center. One of the MRUs will emphasize research aimed at developing and evaluating therapies for botulism.
• Description: The network currently funds:
• Research and development of improved diagnostics for enteric pathogens
• Vaccine research on tularemia vaccine strain LVS, Shigella, and S. typhi
• Therapeutics research for botulinum neurotoxin intoxication and for infections with Shiga-toxin producing E. coli (STEC)
• Research on diagnostics for botulism
• Clinical study to improve response to S. typhi vaccination
• Research on the molecular evolution and transmission of antibiotic-resistance genes in enteric pathogens
• Animal model development for botulinum neurotoxins, STEC-mediated HUS, Campylobacter-mediated enteritis, and Crohn's disease
• Strain repository for STEC  

Project Title: Structural Genomics of Pathogenic Protozoa

• Agency: NIH
• Results: NIAID has cofunded the Structural Genomics of Pathogenic Protozoa (http://depts.washington.edu/sgpp/) to provide the three dimensional structure of many proteins deduced from the genome information of the trypanosomatid and Plasmodium species. This will be valuable information for future drug and vaccine discovery design, as well as information for the discovery of new protein folds and function.
• Description: The overall goal of the project is to solve protein structures for diverse parasitic protozoa to aid in structure/function studies and drug design, emphasizing protein structures that can be exploited by differences with the human enzyme and sharing common features with those of parasitic protozoa.

Project Title: NIAID Microbial Sequencing Centers

• Agency: NIH
• Description: The Microbial Genome Sequencing Centers address NIAID's need for sequencing of microorganism and invertebrate vectors of disease. The MGSCs provide rapid and cost efficient resources for production of high quality genome sequences of pathogens considered agents of bioterrorism (NIAID category A-C priority list), or causing emerging and re-emerging infectious diseases, their closely related organisms and clinical isolates and invertebrate vectors of disease.
• Results: These Centers have the capacity and are responding to scientific community and national and federal agencies' priorities for genome sequencing, filling in sequence gaps and therefore, providing genome sequencing data for multiple usages including understanding biology of microbe, forensic strain identification and identifying targets for drugs, vaccines and diagnostics. See http://www.niaid.nih.gov/dmid/genomes/mscs/default.htm.

Project Title: Bioinformatics Resource Centers

• Agency: NIH
• Description: NIAID Bioinformatics Resource Centers are designed to develop, populate, and maintain comprehensive, relational databases to collect, store, display, annotate, query, analyze genomic, functional genomic, structural and related data for microorganisms responsible for emerging and re-emerging infectious diseases and for those considered agents of bioterrorism. The center will also develop and provide software tools.
• Results: Eight Centers were funded in FY04: http://www.niaid.nih.gov/dmid/genomes/brc/default.htm. In FY 2007, NIAID has continued to support these eight centers, each publicly accessible BRC web site has continued to be developed, the user interfaces have been improved and a variety of genomics data types have being integrated, including gene expression and proteomics information, host/pathogen interactions and signaling/metabolic pathways data. Visit http://www.brc-central.org for additional information. In FY2007 the National Microbial Pathogen Data Resource (NMPDR http://www.nmpdr.org/) BRC has made available computational server that will provide the scientific community the annotation of bacterial genomes within 48 hours.

Project Title: Biodefense Proteomics Research Centers

• Agency: NIH
• Description: NIAID Proteomic Centers are intended to develop and enhance innovative proteomic technologies and methodologies and apply them to the understanding of the pathogen and/or host cell proteome for the discovery and identification of novel targets for the next generation of drugs, vaccines, diagnostics and immunotherapeutics against microorganisms considered agents of bioterrorism.
• Results: Seven Centers were funded in 2004: http://www.niaid.nih.gov/dmid/genomes/prc/default.htm. In FY 2007, an additional 5 SARS-CoV 3D protein structures were solved and additional project was initiated to solve the structures of two influenza polymerase proteins. Ninety-six percent of the coding genes for B. anthracis have been cloned and will be used to generate unique protein arrays.

Project Title: Novel, all natural citrus-based antimicrobials for cost effective salmonella reduction during organic poultry processing

• Agency: USDA
• Description: Research to determine the MIC for citrus oil fractions in model poultry skis systems, and the effectiveness and economics at 2 process interventions and evaluate antimicrobial activity
• Results: funded NRI, CSREES. Crandell, Univ. of Arkansas

Project Title: Comparative genomic analysis of Salmonella serotypes.

• Agency: USDA
• Description: A multi serotype Salmonella whole genome microarray has been obtained for this study. To determine the genetic elements responsible for these variations, Salmonella serotypes are analyzed by comparative genomic hybridization (CGH).
• Results: Comparative genomic hybridizations have been completed on 20 bovine associated Salmonella serotype Newport isolates and on 11 poultry associated serotype Kentucky isolates. Data analysis is proceeding.

Project Title: Comparative genomic analysis of Campylobacter subtypes.

• Agency: USDA
• Description: To identify and trace Campylobacter isolates responsible for animal and human infections, a multi strain Campylobacter whole genome microarray has been obtained and is being used for comparative genomic hybridizations (CGH).

Project Title: Comparative genomic analysis of Listeria subtypes.

• Agency: USDA
• Description: To identify and trace antimicrobial resistant Listeria monocytogenes from animals, food, and human sources, a Listeria whole genome microarray has been obtained and is being used for comparative genomic hybridizations (CGH).
• Results: Ongoing. Bacterial Epidemiology and Antimicrobial Resistance Research Unit, ARS, Athens, GA.

Action Item #71: Encourage Sharing of AR Data Between Industry and the Research Community, Including Genomics and Other Technologies.

Project Title: Collaboration on genomics technologies and resources

• Agency: NIH, DoD
• Description: NIAID continued its agreement with the Defense Advanced Research Project Agency (DARPA) in support of genomics efforts targeted at pathogens of potential bioterrorist threat.
• Results: Through this collaboration with DARPA large-scale genome sequencing projects for Brucella suis and Coxiella burneti have previously been completed. In 2006 sequencing of a multi-drug resistant strain of plague from Madagascar was completed (see reference: Ravel et al., 2007, PLoS ONE, Issue 3:e309). In addition, DARPA provides funds for the Poxvirus Bioinformatics Resource Center (http://www.poxvirus.org). This resource for the scientific community provides sequencing and functional comparisons of orthopox genes and the design and maintenance of a relational database to store, display, annotate, and query genome sequences, structural information, phenotypic data and bibliographic information. It also serves as a repository of well-documented viral strains.

Project Title: Reagent development

• Agency: FDA
• Description: Facilitation of research through reagent development for the scientific community: Pertussis, H. influenzae, TB, influenza and S. pneumoniae.
• Results: WHO, Aeras Global Tuberculosis Foundation CBER collaboration - standard reagents for pre-clinical testing of new TB vaccines. Influenza reagents for live and inactivated influenza vaccine including products of reassortant influenza viruses with high growth characteristics. Collaborative research with CDC and WHO supporting the development of vaccines against influenza virus, including the H5NI strain. Ongoing research project to develop new pneumococcal reference serum.

Action Item #72: Bring New Researchers into the Field, by Utilizing Appropriate Strategies such as Training and Research Opportunities.

Project Title: Research Scholar Development Award (RSDA)(K22)

• Agency: NIH
• Description: The RSDA will provide support for postdoctoral fellows who are moving to assistant professor positions in an academic institution. The purpose of the RSDA is to ease the transition to an academic position by enabling the recipient to focus on the establishment of his/her research laboratory prior to submitting applications for grant support. This is intended to establish new young investigators in needed fields, including AR.
• Results: (PAR-07-347) released April 2, 2007; remains active.

Project Title: Other ongoing training and research fellowship awards

• Agency: NIH
• Description: PA-06-512 Mentored Clinical Scientist Development Award (K08)  PA-05-143 Mentored Patient Oriented Research Career Development Award (K23) PA-04-107 Mid-career Investigator Award in Patient Oriented Research (K24).
• Results: Important ongoing programs are fostering the development of young scientists and clinical investigators. Recent awards include: An In Vitro System to Study Antiviral Strategies Against Hepatitis C virus, Effect of Suppressive Therapy on Behavioral Determinants of HSV-2 Transmission, and Preventing the Establishment of Enfuvirtide-resistance in the Latent Reservoir.

Project Title: NIH Exploratory/Developmental Research Grant Award (R21)

• Agency: NIH
• Description: This announcement redefines the National Institutes of Health (NIH) Exploratory/Developmental Research Grant Award (R21) mechanism, and extends its use as an investigator-initiated mechanism to a variety of Institutes and Centers (ICs) listed in the announcement. The R21 is intended to encourage exploratory and developmental research projects by providing support for the early and conceptual stages of these projects. This is an important mechanism for attracting new investigators to a field of study and providing sufficient support to allow development of preliminary data that will enable successful long-term funding.
• Results: Examples of recent R21 awards include: Novel Targets for Treatment of Pseudomonas aeruginosa, The NTHI Sap Transporter: A Mechanism of Antimicrobial Peptide Resistance, and Targets for Short-Course TB Therapy.

Project Title: Investigator-initiated small research grant award program announcement (R03)

• Agency: NIH
• Description: The R03 award supports small research projects that can be carried out in a short period of time, with limited resources. This solicitation extends its use to unsolicited applications in addition to its use in individual Requests for Applications (RFA) and Program Announcements (PA). This is an important mechanism for attracting new investigators to a field of study and providing sufficient support to allow development of preliminary data that will enable successful long-term funding.
• Results: Program Announcement PA-06-180 was released on March 2, 2006; expiration date: May 2, 2009. Examples of awards made in FY2007 include: Antiretroviral Treatment Strategies with Optional Switching Times, Antibiotics Discovery from the Great Lakes, and Susceptibility of Mycobacterium tuberculosis Clinical Isolates to Moxifloxacin.

<— Previous Section: Action Item 67        Next Section: Action Items 73–79—>

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