Bacterial Infections - A Medical Dictionary, Bibliography, and Annotated Research Guide to Internet References

BACTERIAL INFECTIONS A M EDICAL D ICTIONARY , B IBLIOGRAPHY , AND A NNOTATED R ESEARCH G UIDE TO I NTERNET R EFERENCES ...

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BACTERIAL INFECTIONS A M EDICAL D ICTIONARY , B IBLIOGRAPHY , AND A NNOTATED R ESEARCH G UIDE TO I NTERNET R EFERENCES

J AMES N. P ARKER , M.D. AND P HILIP M. P ARKER , P H .D., E DITORS

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ICON Health Publications ICON Group International, Inc. 4370 La Jolla Village Drive, 4th Floor San Diego, CA 92122 USA Copyright ©2004 by ICON Group International, Inc. Copyright ©2004 by ICON Group International, Inc. All rights reserved. This book is protected by copyright. No part of it may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without written permission from the publisher. Printed in the United States of America. Last digit indicates print number: 10 9 8 7 6 4 5 3 2 1

Publisher, Health Care: Philip Parker, Ph.D. Editor(s): James Parker, M.D., Philip Parker, Ph.D. Publisher's note: The ideas, procedures, and suggestions contained in this book are not intended for the diagnosis or treatment of a health problem. As new medical or scientific information becomes available from academic and clinical research, recommended treatments and drug therapies may undergo changes. The authors, editors, and publisher have attempted to make the information in this book up to date and accurate in accord with accepted standards at the time of publication. The authors, editors, and publisher are not responsible for errors or omissions or for consequences from application of the book, and make no warranty, expressed or implied, in regard to the contents of this book. Any practice described in this book should be applied by the reader in accordance with professional standards of care used in regard to the unique circumstances that may apply in each situation. The reader is advised to always check product information (package inserts) for changes and new information regarding dosage and contraindications before prescribing any drug or pharmacological product. Caution is especially urged when using new or infrequently ordered drugs, herbal remedies, vitamins and supplements, alternative therapies, complementary therapies and medicines, and integrative medical treatments. Cataloging-in-Publication Data Parker, James N., 1961Parker, Philip M., 1960Bacterial Infections: A Medical Dictionary, Bibliography, and Annotated Research Guide to Internet References / James N. Parker and Philip M. Parker, editors p. cm. Includes bibliographical references, glossary, and index. ISBN: 0-597-84344-9 1. Bacterial Infections-Popular works. I. Title.

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Disclaimer This publication is not intended to be used for the diagnosis or treatment of a health problem. It is sold with the understanding that the publisher, editors, and authors are not engaging in the rendering of medical, psychological, financial, legal, or other professional services. References to any entity, product, service, or source of information that may be contained in this publication should not be considered an endorsement, either direct or implied, by the publisher, editors, or authors. ICON Group International, Inc., the editors, and the authors are not responsible for the content of any Web pages or publications referenced in this publication.

Copyright Notice If a physician wishes to copy limited passages from this book for patient use, this right is automatically granted without written permission from ICON Group International, Inc. (ICON Group). However, all of ICON Group publications have copyrights. With exception to the above, copying our publications in whole or in part, for whatever reason, is a violation of copyright laws and can lead to penalties and fines. Should you want to copy tables, graphs, or other materials, please contact us to request permission (E-mail: [email protected]). ICON Group often grants permission for very limited reproduction of our publications for internal use, press releases, and academic research. Such reproduction requires confirmed permission from ICON Group International, Inc. The disclaimer above must accompany all reproductions, in whole or in part, of this book.

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Acknowledgements The collective knowledge generated from academic and applied research summarized in various references has been critical in the creation of this book which is best viewed as a comprehensive compilation and collection of information prepared by various official agencies which produce publications on bacterial infections. Books in this series draw from various agencies and institutions associated with the United States Department of Health and Human Services, and in particular, the Office of the Secretary of Health and Human Services (OS), the Administration for Children and Families (ACF), the Administration on Aging (AOA), the Agency for Healthcare Research and Quality (AHRQ), the Agency for Toxic Substances and Disease Registry (ATSDR), the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the Healthcare Financing Administration (HCFA), the Health Resources and Services Administration (HRSA), the Indian Health Service (IHS), the institutions of the National Institutes of Health (NIH), the Program Support Center (PSC), and the Substance Abuse and Mental Health Services Administration (SAMHSA). In addition to these sources, information gathered from the National Library of Medicine, the United States Patent Office, the European Union, and their related organizations has been invaluable in the creation of this book. Some of the work represented was financially supported by the Research and Development Committee at INSEAD. This support is gratefully acknowledged. Finally, special thanks are owed to Tiffany Freeman for her excellent editorial support.

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About the Editors James N. Parker, M.D. Dr. James N. Parker received his Bachelor of Science degree in Psychobiology from the University of California, Riverside and his M.D. from the University of California, San Diego. In addition to authoring numerous research publications, he has lectured at various academic institutions. Dr. Parker is the medical editor for health books by ICON Health Publications. Philip M. Parker, Ph.D. Philip M. Parker is the Eli Lilly Chair Professor of Innovation, Business and Society at INSEAD (Fontainebleau, France and Singapore). Dr. Parker has also been Professor at the University of California, San Diego and has taught courses at Harvard University, the Hong Kong University of Science and Technology, the Massachusetts Institute of Technology, Stanford University, and UCLA. Dr. Parker is the associate editor for ICON Health Publications.

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About ICON Health Publications To discover more about ICON Health Publications, simply check with your preferred online booksellers, including Barnes&Noble.com and Amazon.com which currently carry all of our titles. Or, feel free to contact us directly for bulk purchases or institutional discounts: ICON Group International, Inc. 4370 La Jolla Village Drive, Fourth Floor San Diego, CA 92122 USA Fax: 858-546-4341 Web site: www.icongrouponline.com/health

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Table of Contents FORWARD .......................................................................................................................................... 1 CHAPTER 1. STUDIES ON BACTERIAL INFECTIONS ........................................................................... 3 Overview........................................................................................................................................ 3 The Combined Health Information Database................................................................................. 3 Federally Funded Research on Bacterial Infections........................................................................ 4 E-Journals: PubMed Central ....................................................................................................... 43 The National Library of Medicine: PubMed ................................................................................ 44 CHAPTER 2. NUTRITION AND BACTERIAL INFECTIONS ................................................................. 89 Overview...................................................................................................................................... 89 Finding Nutrition Studies on Bacterial Infections ...................................................................... 89 Federal Resources on Nutrition ................................................................................................... 90 Additional Web Resources ........................................................................................................... 91 CHAPTER 3. ALTERNATIVE MEDICINE AND BACTERIAL INFECTIONS ........................................... 93 Overview...................................................................................................................................... 93 National Center for Complementary and Alternative Medicine.................................................. 93 Additional Web Resources ........................................................................................................... 95 General References ....................................................................................................................... 99 CHAPTER 4. DISSERTATIONS ON BACTERIAL INFECTIONS ........................................................... 101 Overview.................................................................................................................................... 101 Dissertations on Bacterial Infections ......................................................................................... 101 Keeping Current ........................................................................................................................ 101 CHAPTER 5. CLINICAL TRIALS AND BACTERIAL INFECTIONS ...................................................... 103 Overview.................................................................................................................................... 103 Recent Trials on Bacterial Infections ......................................................................................... 103 Keeping Current on Clinical Trials ........................................................................................... 108 CHAPTER 6. PATENTS ON BACTERIAL INFECTIONS ...................................................................... 111 Overview.................................................................................................................................... 111 Patents on Bacterial Infections................................................................................................... 111 Patent Applications on Bacterial Infections............................................................................... 136 Keeping Current ........................................................................................................................ 165 CHAPTER 7. BOOKS ON BACTERIAL INFECTIONS.......................................................................... 167 Overview.................................................................................................................................... 167 Book Summaries: Federal Agencies............................................................................................ 167 Book Summaries: Online Booksellers......................................................................................... 174 Chapters on Bacterial Infections ................................................................................................ 177 CHAPTER 8. MULTIMEDIA ON BACTERIAL INFECTIONS ............................................................... 179 Overview.................................................................................................................................... 179 Video Recordings ....................................................................................................................... 179 Audio Recordings....................................................................................................................... 180 CHAPTER 9. PERIODICALS AND NEWS ON BACTERIAL INFECTIONS ............................................ 181 Overview.................................................................................................................................... 181 News Services and Press Releases.............................................................................................. 181 Newsletters on Bacterial Infections............................................................................................ 183 Newsletter Articles .................................................................................................................... 184 Academic Periodicals covering Bacterial Infections................................................................... 186 CHAPTER 10. RESEARCHING MEDICATIONS................................................................................. 189 Overview.................................................................................................................................... 189 U.S. Pharmacopeia..................................................................................................................... 189 Commercial Databases ............................................................................................................... 192 Researching Orphan Drugs ....................................................................................................... 193 APPENDIX A. PHYSICIAN RESOURCES .......................................................................................... 197

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Overview.................................................................................................................................... 197 NIH Guidelines.......................................................................................................................... 197 NIH Databases........................................................................................................................... 199 Other Commercial Databases..................................................................................................... 201 APPENDIX B. PATIENT RESOURCES ............................................................................................... 203 Overview.................................................................................................................................... 203 Patient Guideline Sources.......................................................................................................... 203 Finding Associations.................................................................................................................. 210 APPENDIX C. FINDING MEDICAL LIBRARIES ................................................................................ 213 Overview.................................................................................................................................... 213 Preparation................................................................................................................................. 213 Finding a Local Medical Library................................................................................................ 213 Medical Libraries in the U.S. and Canada ................................................................................. 213 ONLINE GLOSSARIES................................................................................................................ 219 Online Dictionary Directories ................................................................................................... 219 BACTERIAL INFECTIONS DICTIONARY ............................................................................. 221 INDEX .............................................................................................................................................. 305

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FORWARD In March 2001, the National Institutes of Health issued the following warning: "The number of Web sites offering health-related resources grows every day. Many sites provide valuable information, while others may have information that is unreliable or misleading."1 Furthermore, because of the rapid increase in Internet-based information, many hours can be wasted searching, selecting, and printing. Since only the smallest fraction of information dealing with bacterial infections is indexed in search engines, such as www.google.com or others, a non-systematic approach to Internet research can be not only time consuming, but also incomplete. This book was created for medical professionals, students, and members of the general public who want to know as much as possible about bacterial infections, using the most advanced research tools available and spending the least amount of time doing so. In addition to offering a structured and comprehensive bibliography, the pages that follow will tell you where and how to find reliable information covering virtually all topics related to bacterial infections, from the essentials to the most advanced areas of research. Public, academic, government, and peer-reviewed research studies are emphasized. Various abstracts are reproduced to give you some of the latest official information available to date on bacterial infections. Abundant guidance is given on how to obtain free-of-charge primary research results via the Internet. While this book focuses on the field of medicine, when some sources provide access to non-medical information relating to bacterial infections, these are noted in the text. E-book and electronic versions of this book are fully interactive with each of the Internet sites mentioned (clicking on a hyperlink automatically opens your browser to the site indicated). If you are using the hard copy version of this book, you can access a cited Web site by typing the provided Web address directly into your Internet browser. You may find it useful to refer to synonyms or related terms when accessing these Internet databases. NOTE: At the time of publication, the Web addresses were functional. However, some links may fail due to URL address changes, which is a common occurrence on the Internet. For readers unfamiliar with the Internet, detailed instructions are offered on how to access electronic resources. For readers unfamiliar with medical terminology, a comprehensive glossary is provided. For readers without access to Internet resources, a directory of medical libraries, that have or can locate references cited here, is given. We hope these resources will prove useful to the widest possible audience seeking information on bacterial infections. The Editors

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From the NIH, National Cancer Institute (NCI): http://www.cancer.gov/cancerinfo/ten-things-to-know.

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CHAPTER 1. STUDIES ON BACTERIAL INFECTIONS Overview In this chapter, we will show you how to locate peer-reviewed references and studies on bacterial infections.

The Combined Health Information Database The Combined Health Information Database summarizes studies across numerous federal agencies. To limit your investigation to research studies and bacterial infections, you will need to use the advanced search options. First, go to http://chid.nih.gov/index.html. From there, select the “Detailed Search” option (or go directly to that page with the following hyperlink: http://chid.nih.gov/detail/detail.html). The trick in extracting studies is found in the drop boxes at the bottom of the search page where “You may refine your search by.” Select the dates and language you prefer, and the format option “Journal Article.” At the top of the search form, select the number of records you would like to see (we recommend 100) and check the box to display “whole records.” We recommend that you type “bacterial infections” (or synonyms) into the “For these words:” box. Consider using the option “anywhere in record” to make your search as broad as possible. If you want to limit the search to only a particular field, such as the title of the journal, then select this option in the “Search in these fields” drop box. The following is what you can expect from this type of search: •

Bacterial Infections of the Small Intestine and Colon Source: Current Opinion in Gastroenterology. 15(1): 43-52. January 1999. Contact: Available from Lippincott Williams and Wilkins Publishers. 12107 Insurance Way, Hagerstown, MD 21740. (800) 637-3030. Fax (301) 824-7390. Summary: This article reviews research on bacterial infections of the small and large intestine. The author notes that enterotoxigenic Escherichia coli, Vibrio cholerae O1, Campylobacter jejuni, Salmonella species, and Shigella species are major causes of morbidity and death in diarrheal disease. Children are most severely affected, and the prevalence is higher in subtropical and tropical countries than in temperate ones. Infections are spread almost exclusively via the fecal oral route (e.g., by water, food, and

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Bacterial Infections

vegetables tainted by water containing manure and small children putting contaminated fingers or items in their mouths). Infections of the small intestine are mediated mainly by bacteria attaching to the epithelium and are aggravated by production of toxins. They generally induce a severe loss of fluid and rarely invade the intestinal wall. Bacteria causing infections of the colon often invade the epithelium. Bacterial species traversing the intestinal epithelium, such as Salmonella and Campylobacter species, commonly cause systemic disease and can be localized to either the small or large intestine. More recently recognized pathogens are V. cholerae O139 and enterohemorrhagic E. coli. In addition to this, several presumptive virulence factors have been identified in diarrheagenic E. coli and in other species. The author concludes that, to confirm these as virulence factors, physicians need good diagnostic tools and good epidemiologic studies, which are of vital importance in creating vaccines for diarrheal diseases. 2 tables. 72 references (43 annotated).

Federally Funded Research on Bacterial Infections The U.S. Government supports a variety of research studies relating to bacterial infections. These studies are tracked by the Office of Extramural Research at the National Institutes of Health.2 CRISP (Computerized Retrieval of Information on Scientific Projects) is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other institutions. Search the CRISP Web site at http://crisp.cit.nih.gov/crisp/crisp_query.generate_screen. You will have the option to perform targeted searches by various criteria, including geography, date, and topics related to bacterial infections. For most of the studies, the agencies reporting into CRISP provide summaries or abstracts. As opposed to clinical trial research using patients, many federally funded studies use animals or simulated models to explore bacterial infections. The following is typical of the type of information found when searching the CRISP database for bacterial infections: •

Project Title: ACTIN BASED MOTILITY OF A BACTERIAL PATHOGEN Principal Investigator & Institution: Theriot, Julie A.; Assistant Professor; Biochemistry; Stanford University Stanford, Ca 94305 Timing: Fiscal Year 2002; Project Start 01-DEC-1994; Project End 28-FEB-2005 Summary: Listeria rnonocytogenes is a ubiquitous Gram-positive bacterium that can cause serious food-borne infections in pregnant women, newborns and immunocompromised adults. The bacterium grows directly in the cytoplasm of infected host cells and moves rapidly throughout and between infected cells using a form of actin-based motility. An L. rnonocytogenes protein, ActA, induces polymerization of host cell actin to form a "comet tail" structure that pushes the bacterium through the host cell cytoplasm. The overall goal of this proposal is to understand the mechanism of the actin-based motility of L. monocytogenes. Three complementary approaches will be used to study this problem: biochemical, biophysical, and cell biological. A major goal is the establishment of a simplified biochemical system that can support L. monocytogenes

2 Healthcare projects are funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Healthcare Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH).

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motility, and development of quantitative assays so that the precise role of each component in actin-based motility can be assessed. The amount of force generated by moving bacteria will be measured directly using a laser force trap (optical tweezers) and compliant microneedles. The mechanism of coupling between actin filament polymerization and production of a motile force will be examined. Finally, videomicroscopy techniques will be used to observe the process of bacterial spread from one host cell to another, and a combination of genetic and pharmacological perturbations will be used to define the contributions of the bacterium, the host cell, and the actin-rich comet tail associated with the moving bacterium, to the process of intercellular spread. Successful completion of our research goals would give significant insight into the mechanisms by which pathogenic bacteria such as L. monocytogenes communicate specifically with the cells of their human hosts. This understanding might pave the way for the development of new ways to prevent and cure bacterial infections. In addition, the results of our research would contribute to our understanding of a wide variety of basic biological process involving actin-based cell movement, including wound healing, immune system responses, and embryonic development. Furthermore, since most malignant tumors do not become lethal until the cancer cells move away from the tumor site and invade other tissues, a detailed understanding of the basic mechanisms that regulate actin-based motility may also be important in the development of therapeutic strategies for combating metastatic cancers. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: ASM CONFERENCE ON POLYMICROBIAL DISEASES Principal Investigator & Institution: Brogden, Kim A.; American Society for Microbiology 1752 N St Nw Washington, Dc 20036 Timing: Fiscal Year 2003; Project Start 01-AUG-2003; Project End 31-JUL-2004 Summary: (provided by applicant): Animals and humans can become infected with more than one pathogen and the resulting clinical diseases and lesions are far greater than that capable from each pathogen alone. These are called polymicrobial diseases and originate from multiple viral infections, multiple bacterial infections, viral and bacterial infections, multiple mycotic infections, and opportunistic infections secondary to microbe-induced immunosuppression. Polymicrobial Diseases is the topic of an American Society for Microbiology sponsored conference October 2003, at the Hotel and Conference Center in Lake Tahoe, Nevada, USA. The purpose of the conference is a) to bring together a diverse group of investigators like physicians, dentists, veterinarians, molecular biologists, and researchers with backgrounds in virology, bacteriology, parasitology, and mycology, b) to discuss the complex etiology and pathogenesis of polymicrobial diseases, and c) to foster interdisciplinary research, possibly leading to productive collaborations. The format is typical of ASM sponsored conferences. Throughout the sessions and discussion periods, we have the following aims for the conference. Aim 1. To increase our understanding of the etiologic agents of polymicrobial disease. In this conference, we will identify and discuss the complex interactions among etiologic agents and the methods to study polymicrobial interactions in vitro and in vivo, which may lead to more effective diagnostic strategies. Aim 2. To increase our understanding of the determinants of polymicrobial pathogenicity and the underlying mechanisms of polymicrobial disease pathogenesis. In this conference we will identify and discuss the determinants that increase the virulence of two or more microorganisms or strains of microorganisms and delineate the common underlying mechanisms of polymicrobial disease pathogenesis. This includes identifying both host and microbial factors that increase the susceptibility of the host to multiple infections.

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Aim 3. To increase our understanding of immune or probiotic intervention of polymicrobial infections. In this conference, we will identify and discuss methods to prevent polymicrobial infections, which may lead to more effective prevention and treatment strategies. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: AUTOIMMUNE DETERMINANTS OF HUMAN CARDIAC MYOSIN Principal Investigator & Institution: Cunningham, Madeline W.; George Lynn Cross Research Professor; Microbiology and Immunology; University of Oklahoma Hlth Sciences Ctr Health Sciences Center Oklahoma City, Ok 73126 Timing: Fiscal Year 2002; Project Start 01-AUG-1997; Project End 30-JUN-2007 Summary: (provided by applicant): Myocarditis and rheumatic carditis are sequelae of viral and bacterial infections, respectively, and occur in humans and animal models following coxsackievirus infection, group A streptococcal infection, or immunization with cardiac myosin. The pathogenesis of these diseases may be due to molecular mimicry between the infectious pathogen and the host autoantigen cardiac myosin. Although cardiac myosin can induce myocarditis in animals, the molecular pathogenesis of the disease in humans is unclear. In addition, there are few studies in humans, which define the immunological parameters of disease. The goal of the proposed work is to define the parameters of the autoimmune response to human cardiac myosin in humans and in a cardiac myosin-induced rat model of myocarditis and valvulitis. We will test the hypothesis that molecular mimicry and the influence of the cytokine environment leads to development of disease. We plan: 1)To produce and investigate human T cell clones from myocarditis patients which are crossreactive with human cardiac myosin, streptococcal M protein and coxsackievirus and their peptides; to determine cytokine responses of human T cell clones as well as HLA class I and II restriction of responses and cell surface antigens by FACS analysis 2)To evaluate expression of genes by crossreactive CD4+/- and CD8+ T cell clones and by normal and myocarditis patient peripheral blood CD4+ and CD8+ lymphocytes in response to stimulation with myosin, M protein and coxsackievirus or their peptides by DNA array analysis, cytokine production, and to study the cell surface markers on T lymphocytes by FACS analysis 3) To investigate a Lewis rat cardiac S2 peptide-induced model of severe myocarditis for parameters of inflammatory heart disease including the role of molecular mimicry and cytokines in susceptible, resistant, and tolerized rat strains (Lewis and BB/DR), to determine the epitope specificity of the heart specific infiltrating T cells from hearts in the Lewis rat model and to determine cytokine expression in hearts using the RNase protection assay for TH1/TH2 cytokines and expression of a large group of genes using DNA arrays. We will establish a tolerance model to investigate the downregulation of myosin specific I cells, antibodies and cytokines in disease. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

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Project Title: BACTERIAL INFECTION INDUCES CYTOKINE PRODUCTION Principal Investigator & Institution: Marriott, Ian; Biology; University of North Carolina Charlotte Office of Research Services Charlotte, Nc 282230001 Timing: Fiscal Year 2002; Project Start 12-APR-2001; Project End 31-JAN-2004 Summary: Staphylococcus aureus and Salmonella are common causes of bone and joint infections in humans. Unfortunately, the pathogenesis of bacterial bone and joint infections are poorly understood. Bacteria, including S. aureus, can infect osteoblasts

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and survive intracellularly within these bone-forming cells which begins to explain how bone infections might be chronic, and how the host's immune response might have difficulty in eliminating these pathogens. While osteoblasts can internalize and harbor bacteria, it is not at all clear if infected osteoblasts contribute to the immune responses to the invasion. Recently, we have described the surprising ability of osteoblasts to secrete significant amounts of bioactive IL-12. These cells are stimulated to produce this key proinflammatory cytokine when exposed to bacteria previously demonstrated to reside intracellularly. Such a finding is particularly significant given the central role IL-12 plays in the preferential initiation of Th1-type, cell- mediated, immune responses. Such immune responses are essential for the successful elimination of intracellular pathogens. The ability of these non-leukocytic cells to produce this IL-12 may point to a previously unrecognized role for osteoblasts in the generation of protective inflammatory responses and the resolution of infection. In the present application, we propose to investigate the mechanisms responsible for inducing the production of this important cytokine by osteoblasts. We will utilize RT-PCR and immunofluorescent techniques to determine whether IL-12 induction in human and mouse osteoblasts occurs as either a direct or indirect consequence of bacterial invasion. Furthermore, we will determine whether the production of IL-12 seen in vitro is reproducible in vivo using an animal model developed in our laboratory. Finally we will attempt to determine the biological significance of IL-12 production by osteoblasts in infected tissues in vivo by monitoring bacterial burden and T-cell infiltration utilization immunofluorescence techniques. In this manner, we will examine whether IL-12 attenuates or exacerbates bacterial infection of osteoblasts and local inflammation, thereby expanding the recognized role of these cells to include being integral components in the host responses to intracellular pathogens at these sites. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: BACTERIAL ANTIMICROBIALS

RNASE

P

AS

A

TARGET

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Principal Investigator & Institution: Eder, Paul S.; Message Pharmaceuticals, Inc. 30 Spring Mill Dr Malvern, Pa 19355 Timing: Fiscal Year 2002; Project Start 15-MAR-2002; Project End 31-DEC-2002 Summary: (provided by applicant): Antibiotic resistance is a growing health threat worldwide. Small-molecule screens that target specific complexes that are essential for bacterial metabolism will be useful in identifying new classes of microbial inhibitors. Bacterial RNase P represents an excellent target for developing novel anti-infectives: it is essential for viability of bacteria; it is well-characterized enzymatically and structurally; and it differs structurally and functionally from mammalian RNase P. Message Pharmaceuticals is dedicated to developing drugs that target RNA via posttranscriptional regulation. With its high-throughput capacity, Message has screened nearly 150,000 compounds for inhibitors of Neisseria gonorrhoeae RNase P. More than fifty compounds among six classes have exhibited dose-dependent inhibition of N. gonorrhoeae RNase P in vitro. Message proposes to develop these classes of leads further by: 1) determining their minimal inhibitory concentration endpoint against known bacterial isolates; 2) measuring the inhibition of RNase P enzymes from other evolutionarily diverse pathogenic bacteria; 3) comparing the inhibition to that of human RNase P; 4) assessing cytotoxicity in mammalian cells in culture. In addition to identifying novel anti-infectives, the results will advance our understanding of the function of an evolutionarily ancient RNA enzyme, and, more importantly, reveal new classes of small molecules that interact with structured RNAs. PROPOSED

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COMMERCIAL APPLICATION: With the worldwide emergence and expansion of antibiotic resistance in both the nosocomial and community settings, new classes of antibiotics are needed to combat the resistance. The results from this grant will contribute to the development of novel classes of antibiotics for a variety of resistant bacterial infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: BIOCHEMICAL ROLE OF AIRWAY MUCINS IN CYSTIC FIBROSIS Principal Investigator & Institution: Sachdev, Goverdhan P.; Pharmaceutical Sciences; University of Oklahoma Hlth Sciences Ctr Health Sciences Center Oklahoma City, Ok 73126 Timing: Fiscal Year 2002; Project Start 01-AUG-2001; Project End 31-JUL-2004 Summary: (provided by applicant): Cystic Fibrosis (CF) is the most lethal genetic disease in Caucasians and is characterized by production of excessive amounts of viscous mucus secretions in the airways of the patient. This causes airway obstruction as well as chronic bacterial infections which eventually lead to respiratory failure. Mucins provide protection to epithelia through interaction of their saccharides with bacterial adhesins. Chronic colonization with Pseudomonas aeruginosa, is considered the principal cause of death in CF patients. Our laboratory and others have shown that P. aeruginosa had considerably stronger binding affinity for CF airway mucin than normal airway mucin. These observations implicate altered glycosylation of CF mucins. Indeed, aberrant glycosylation has been reported for CF mucin. However, to date, the molecular basis of increased interaction between P. aeruginosa and CF airway mucin has not been established. We hypothesize that altered glycosylation of CF mucin is responsible for its stronger binding with P. aeruginosa. We will determine structural features of the CF mucin carbohydrate ligand(s) that provide increased binding to P. aeruginosa by preparing glycopeptides and individual saccharides from CF and control mucins. The glycopeptide(s) which show high inhibition of asialo-GM; binding to P. aeruginosa will be used to isolate 0-linked glycans for further testing of inhibitory activity and structural determination using state-of-the-art highly sensitive mass spectrometry and enzymnatic methods. Affinity gels containing selected mucin glycopeptide or mucin saccharide will be used to purify the P. aeruginosa adhesins which interact with airway mucins and glycolipids, respectively. The primary structure of the major adhesins will be determined using molecular cloning techniques. Structural characterization of major adhesins will open additional approaches to prevent the binding of P. aeruginosa to airway epithelial cells and mucins of CF patients. Information on the adhesin binding sites will permit molecular modeling, design and synthesis of potent 0-glycan inhibitors of the P. aeruginosa infection. The overall long-term goal of this study is to prevent and/or treat lung infections in CF patients. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

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Project Title: BIOFILM ANTIBIOTIC RESISTANCE IN STAPHYLOCOCCUS Principal Investigator & Institution: O'toole, George A.; Assistant Professor; Microbiology and Immunology; Dartmouth College 11 Rope Ferry Rd. #6210 Hanover, Nh 03755 Timing: Fiscal Year 2003; Project Start 01-APR-2003; Project End 31-MAR-2005 Summary: (provided by applicant): Biofilms are complex bacterial communities attached to a surface. The most widely recognized property of biofilm bacteria is their increased resistance to antimicrobial agents. The recalcitrance of biofilm-related

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infections to conventional antibiotic therapy has a profound impact on the medical industry and human health. Although this problem has been studied in numerous different model systems, little is known about the molecular mechanisms that confer antibiotic resistance to biofilm cells. Recent work suggests that a genetic program controls biofilm formation and we have genetic evidence that indicates that the development of antibiotic resistance in biofilms is similarly regulated. Furthermore, socalled "small colony variants" or SCV have been proposed to play a role in biofilmmediated resistance in P. aeruginosa. The role of SCV in S. aureus biofilm resistance has not yet been investigated. The central hypothesis of this application is that antimicrobial resistance of biofilm-grown cells requires specific genetic elements. We propose to identify genetic elements required for the development of biofilm antibiotic resistance by Staphylococcus aureus using techniques developed in our previous studies in Pseudomonas aeruginosa. The identification of genes required for biofilm antibiotic resistance may provide new targets for anti-biofilm therapies and increase our understanding of biofilm antibiotic resistance. The Specific Aims of this application are: Specific Aim 1. Identify genetic elements required for biofilm antibiotic resistance in S. aureus. Specific Aim 2. Characterize mutants defective in biofilm antibiotic resistance. Specific Aim 3. Determine the role of small colony variants (SCV) in biofilm antibiotic resistance. The studies proposed here explore a poorly characterized aspect of microbial resistance that is elaborated when microbes grow in a biofilm. No genetic elements contributing to biofilm resistance have been identified in S. aureus. We propose a genetic screen (already validated in P. aeruginosa) with the goal of identifying genes involved in this process. Future studies will uncover the mechanisms of resistance mediated by the genes identified as a result of this work. We will also perform studies to determine whether SCV, thought to be generated in chronic bacterial infections in vivo: i) play a role in biofilm resistance and ii) utilize the same genetic pathways as biofilmgrown cells to resist the action of antibiotics. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: BIOFILM FORMATION AND DISPERSAL MECHANISMS Principal Investigator & Institution: Romeo, Tony; Professor; Microbiology and Immunology; Emory University 1784 North Decatur Road Atlanta, Ga 30322 Timing: Fiscal Year 2003; Project Start 19-SEP-2003; Project End 31-AUG-2007 Summary: (provided by applicant): In the natural environment, bacteria grow predominantly within sessile, matrix-enclosed communities known as biofilms, rather than as unattached planktonic cells. Biofilms protect resident bacteria from attack by the immune system, compromise antimicrobial therapy, and disperse planktonic cells, which promote the spread of infection to distant body sites. Biofilms complicate about 65 percent of recalcitrant bacterial infections. Nevertheless, the regulatory mechanisms of biofilm development, especially biofilm dispersal, remain poorly defined in any species. Our studies revealed that the RNA-binding global regulatory protein CsrA is a potent repressor of biofilm formation in Escherichia coli K-12 and pathogenic relatives. This effect is mediated primarily through its regulation of intracelluar glycogen synthesis and turnover. Further evidence supports a role for glycogen in the synthesis of a polysaccharide adhesin. Mutations that inhibit biofilm formation were isolated in a 4gene operon, which was cloned and found to needed for the production of a GIcN-rich polysaccharide. Remarkably, csrA-induction within cells of a preformed biofilm caused extensive dispersal, releasing viable planktonic cells. This finding offers a key to unlock the biochemical and genetic bases of biofilm dispersal. The Aims of this proposal are to: 1) Characterize a novel polysaccharide adhesin needed for E. coli biofilm formation. The

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molecular genetics of its synthesis, its chemistry, and its function in biofilm formation will be assessed. 2) Investigate the genetic and metabolic determinants of polysaccharide production. The precursor-product relationship of glycogen to the polysaccharide adhesin will be examined by ELISA analysis of existing mutants and by 13C NMR labeling studies in conjunction with appropriate structural and regulatory mutations. The genetic regulation of its biosynthesis will be examined with reporter fusions and other approaches. 3) Biofilm dispersal will be assessed systematically by examining the effects of csrA induction on the polysaccharide adhesin, membrane and periplasmic proteins, LPS and the transcriptome. Results will pave the way for studies defining the mechanisms of the dispersal process.The long-range goal of these studies is to develop a full understanding of the regulatory factors, metabolic pathways and structural elements that interact in biofilm formation, and thereby obtain useful information for combating biofilm infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: BIOFILM FORMATION AND P. AERUGINOSA INFECTION OF THE EYE Principal Investigator & Institution: Zegans, Michael E.; Surgery; Dartmouth College 11 Rope Ferry Rd. #6210 Hanover, Nh 03755 Timing: Fiscal Year 2002; Project Start 01-AUG-2002; Project End 31-JUL-2007 Summary: (Applicant's Abstract) Bacterial infections of the eye can have visionthreatening complications and often are associated with prosthetic devices such as contact lenses, scleral buckles, and intraocular lenses. Pseudomonas aeruginosa (PA) is one of the most common causes of bacterial keratitis. The central hypothesis of this proposal is that biofilm formation plays an important role in the pathogenesis of ocular infections of PA and that an understanding of the biology and genetics of Pseudomonas aeruginosa biofilm formation will have relevance to the development of novel antimicrobial therapies. Bacteria grow as planktonic (or free-living) cells or as surfaceattached communities known as biofilms. Biofilm formation contributes to the pathogenesis of many clinical infections associated with prosthetic devices by allowing bacteria to persist on abiotic surfaces which come in contact with the body, by facilitating colonization of biotic surfaces and by rendering bacteria more resistant to antimicrobial agents. However, the relevance of biofilm formation to ocular infections has not been extensively studied. Bacterial keratitis caused by PA will be the model system studied in this project. Existing biofilm mutants of PA, as well as additional mutants that will be developed in the course of the project, will be used to elucidate the biology and genetics related to PA biofilm formation on abiotic and biotic surfaces relevant to the eye. The functions mutated in these strains may define novel drug targets. In addition, inhibitor studies may identify new classes of compounds that prevent and/or eliminate eye infections. The ability of growth in a biofilm to render PA resistant to the innate immune system, specifically the human B-defensin (hBD) 1 and 2 will be investigated. hBD 1 and 2 are recently described antimicrobial peptides secreted by the corneal and conjunctival epithelium. hBD 1 and 2 are active against PA under planktonic conditions, but have not been tested against organisms growing in a biofilm. If biofilm-based resistance exists, it would presumably contribute to keratitis and identification of genes that play a role in this process may be novel targets for rendering biofilm bacteria sensitive to antibiotics and defensins. If biofilm and planktonic cells are as equally sensitive to hBD-l and hBD-2, this would suggest that B-defensins can bypass biofilm-specific biocide resistance, and furthermore, these compounds (or derivatives) might make excellent therapeutics to prevent and/or treat biofilm-based infections.

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Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: CAVEOLAE MEDIATED BACTERIAL UPTAKE BY MAST CELLS Principal Investigator & Institution: Abraham, Soman N.; Associate Professor; Pathology; Duke University Durham, Nc 27706 Timing: Fiscal Year 2002; Project Start 01-JUL-2001; Project End 31-MAY-2006 Summary: (provided by the applicant): Recently, we discovered that the bacterial receptor for FimH-expressing bacteria was localized in plasmalemmal caveolae of mast cells and that these caveolae were actively involved in the internalization of the bacteria. Caveolae are subcellular entities rich in glycolipid; and cholesterol and typically contain the scaffolding protein, caveolin. Caveolae mediated bacterial uptake is remarkable because intracellular bacteria remain viable and encased in membranes comprising of caveolar components. Although the significance and scope of caveolae-mediated bacterial uptake by mast cells is, as yet, unknown, this observation represents a novel activity for cellular caveolae in immune cells. To extend our observations, the following specific aims are proposed: (I), Define the scope and molecular basis for caveolaemediated uptake of bacteria (II), Elucidate the ultimate fate of bacteria internalized via caveolae and (III), Investigate the molecular basis for the caveolae-mediated uptake of FimH-expressing bacteria in human mast cells. Our observations highlighting the role of cellular caveolae in the uptake of bacteria represents an important and novel activity triggered by pathogens in immune cells. The proposed studies should provide new insights into the cellular response of mast cells and possibly other immune cells to infectious agents and provide new clues for devising effective strategies to combat bacterial infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

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Project Title: CONJUGATE VACCINE FOR THE PREVENTION OF TULAREMIA Principal Investigator & Institution: Tzianabos, Arthur O.; Associate Professor of Medicine; Harvard University (Medical School) Medical School Campus Boston, Ma 02115 Timing: Fiscal Year 2003; Project Start 01-AUG-2003; Project End 31-JUL-2008 Summary: Francisella tularensis is a highly infectious bacterium that poses a serious threat as an agent of bioterrorism. A live whole cell vaccine is currently available for atrisk populations, but it is associated with incomplete immunity and side-effects. Studies of humans and mice vaccinated with this preparation indicate that humoral and cellmediated immune responses are required for complete protection in the infected host. Currently, little is known concerning the virulence factors associated with F. tularensis that contribute to its ability to cause lethal disease. However, previous studies have identified the capsule and LPS as principle determinants of its pathogenic potential. Our analysis of the recently released genome of F. tularensis Schu S4 has shown that it possesses a single polysaccharide biosynthetic locus responsible for expression of one surface polysaccharide. Based on these data, we hypothesize that the previously described capsule and O-antigen of this organism actually represents a single Oantigen/capsule that has the same repeating unit structure, but is expressed as a distinct large molecular-weight polymer and smaller molecular-weight Lipid A-linked polysaccharide. We predict that this structure has a central role in the pathogenesis of this organism and can be used as the basis for novel glycoconjugate vaccines that will elicit complete protection against experimental tularemia. To address the structural nature of this virulence factor and its role in the pathogenesis and immunity to F.

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tularensis, we propose to: 1) Characterize the structural and genetic nature of the Oantigen/capsule; 2) Determine the role of the O-antigen/capsule in virulence; 3) Determine the humoral and cell-mediated immune responses to the O-antigen/capsule and proteins of F. tularensis; and 4) Develop a conjugate vaccine for F. tularensis infections. These studies will employ a proteomics-based approach to identify new immunogenic proteins from F. tularensis that can be used as carriers in the development of novel acellular glycoconjugate vaccines. It is anticipated that these vaccines will activate both humoral and cell-mediated immune responses and elicit complete protection against tularemia. Glycoconjugate vaccines have been among the most effective biologics ever developed for the prevention of bacterial infections. It is expected that this approach can be applied successfully to the development of a vaccine that can ultimately be tested in clinical trials for the prevention of tularemia. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: CONTROL OF BACTERIAL TOXINS BY VIRUSES AND PLASMIDS Principal Investigator & Institution: Holmes, Randall K.; Professor and Chair; Microbiology; University of Colorado Hlth Sciences Ctr P.O. Box 6508, Grants and Contracts Aurora, Co 800450508 Timing: Fiscal Year 2002; Project Start 30-SEP-1976; Project End 31-MAR-2005 Summary: (Adapted from the Applicant's Abstract): The long term goals of this project are to determine molecular mechanisms for virulence regulation in pathogenic bacteria and to develop new methods to treat bacterial infections. The investigators will study Corynebacterium diphtheriae, a paradigm for toxin-mediated bacterial infections, and Mycobacterium tuberculosis, a prototype for intracellular bacterial infections. These very different bacterial pathogens produce closely related, iron-activated, global regulatory proteins that govern virulence: the diphtheria toxin repressor (DtxR) and the iron-dependent regulator (IdeR), respectively. The investigators will determine the molecular basis for function of DtxR, IdeR and the homologous regulator SirR from Staphylococcus epidermidis. The investigators will use structure-based design to develop new antimicrobial drugs called "super-activators" that will target DtxR, IdeR or their homologs; activate them by iron-independent mechanisms; and inhibit production of virulence factors that are negatively regulated by iron- and DtxR-related repressors. The development of IdeR as a novel target for antimicrobial therapy could address the urgent global need for improved treatment of tuberculosis. The investigators will characterize the genes and gene products that are iron-regulated and under control of DtxR and IdeR, both to provide new insights into the pathogenesis of diphtheria and tuberculosis and for development of additional classes of antimicrobial agents. Specific Aim I will analyze structure and function of DtxR, IdeR and SirR. The investigators will investigate the molecular basis for repressor-operator interactions, for iron-independent super-repressor activity, and for domain function in biological activity of these regulatory proteins. Specific Aim 2 will characterize the DtxR and IdeR regulons in C. diphtheriae and M. tuberculosis. The investigators will develop an allelic exchange system for C. diphtheriae, characterize the DtxR and IdeR regulons by proteomic and molecular genetic methods, assess physiological functions of DtxR and IdeR domain 3, and investigate atypical phenotypes among clinical isolates of C. diphtheriae. Specific Aim 3 will develop super-activators of DtxR and IdeR by structure-based design. The investigators will design combinatorial peptide libraries, test them for super-activator function, identify individual peptides with activity, determine the structural basis for that activity, and develop better super-activators by iterative application of these methods. The investigators will also use molecular genetic methods to identify novel

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mechanisms for super-repressor activity and new lead compounds for development as tools against these bacterial infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: CONTROL OF BIOFILMS BY NATURAL PRODUCTS Principal Investigator & Institution: Costerton, John William.; Professor & Director; Sequoia Sciences 11199 Sorrento Valley Rd, Ste H San Diego, Ca 92121 Timing: Fiscal Year 2003; Project Start 01-APR-2001; Project End 31-JAN-2005 Summary: (provided by applicant): Chronic bacterial infections are serious medical problems in the United States. In chronic bacterial infections, biofilms protect bacteria from antibiotics and immune response mechanisms, thus increasing the rates of reoccurring symptoms and resistance to antibiotics. We discovered four novel compounds in Phase I under this STTR project that prevent the formation and disrupt biofilms, and we expect to identify additional novel compounds in Phase II. We propose to use the strategies developed in Phase I to prioritize the other active samples that have been identified. We will elucidate the structures of the active compounds and characterize their biological activity as biofilm inhibitors or antibacterials. We will also continue the discovery process for additional active samples. This work will enable us to commercialize these compounds that regulate biofilms and to further optimize or methods and strategies by which to discover more novel compounds that regulate formation of biofilms that are needed for a wide range of applications. In the United States, the market for microbial biofilm inhibitors is contained within the $8.5 billion market for antibiotics. Biofilms are involved in 65% of human bacterial infections; accordingly, biofilm inhibitors could capture a $4 to $6-billion segment of the antibiotic market. Biofilm inhibitors will have the greatest medical impact by treating many chronic infections, reducing catheter- and medical device-related infections, and in treating cystic fibrosis patients. Research has clearly established that biofilms play a significant role in these areas, representing a large market whose needs are unmet. The potential market penetration for potent biofilm inhibitors is exemplified by the sheer number of cases in which biofilms cause medical problems. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

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Project Title: CRANBERRY JUICE AND URINARY TRACT INFECTIONS Principal Investigator & Institution: Barbosa-Cesnik, Cibele T.; Epidemiology; University of Michigan at Ann Arbor 3003 South State, Room 1040 Ann Arbor, Mi 481091274 Timing: Fiscal Year 2004; Project Start 15-JAN-2004; Project End 31-DEC-2007 Summary: (provided by applicant): Urinary tract infection (UTI) is one of the most commonly acquired bacterial infections in ambulatory and hospitalized populations and E.coli is the most common urinary pathogen, accounting for 90% of UTIs acquired in the community. Antimicrobial treatment and prophylaxis has resulted in increasing resistance to antimicrobials among uropathogenic bacteria both in the United States and worldwide. Several observational studies and a few randomized trials suggest that cranberry juice reduces the incidence of UTI. Reduced incidence of UTI could decrease antibiotic use and ultimately minimize prevalence of antibiotic resistance. Our overall goal is to determine the effect of cranberry on reducing the rate of recurrent UTI and duration of symptoms over antibiotics alone. We propose a randomized clinical trial of 600 college women presenting to the University Health Service with acute urinary tract infection. The study will have 3 arms and patients will be randomly assigned to taking 8

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ounces of juice twice a day containing either 27% cranberry juice, 13.5% cranberry juice, or placebo juice. In addition, we will determine whether regularly taking cranberry juice changes the 3 and 6 month prevalence of bladder, rectal, vaginal and periurethral colonization with E coli containing known uropathogenic virulence factors relative to placebo controls. The results of this study will increase our understanding of the cranberry juice effect on reducing the symptoms of acute UTI, and on preventing recurring UTIs. We will be able to understand the dose-response effects on the outcomes of interest, including on side effects and compliance. We will also be able to evaluate if the bacterial population in the vagina, periurethra and stool is different after regularly drinking cranberry juice compared to placebo. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: DETERMINANTS OF INNATE IMMUNITY TO GROUP B STREPTOCOCCI Principal Investigator & Institution: Levy, Ofer; Brigham and Women's Hospital 75 Francis Street Boston, Ma 02115 Timing: Fiscal Year 2002; Project Start 01-MAR-2002; Project End 28-FEB-2006 Summary: (provided by applicant): The central goal of this project is to understand the role of innate immunity in infections caused by Group B streptococci (S. agalactiae or GBS). GBS are the major cause of neonatal sepsis and meningitis and thus a leading cause of neonatal morbidity and mortality. GBS-induced inflammatory mediators include tumor necrosis factor (TNF) that, when excessive, can contribute to host morbidity and mortality. Recent evidence suggests that a variety of Gram-positive bacterial surface molecules activate the innate immune system via phagocyte innate immune receptors including cellular differentiation antigen-14 (CD14), complement receptors-3 and -4 (CR3/4), and Toll-like receptor 2 (TLR2). The candidate will further characterize bacterial and host determinants of innate immunity to GBS and test the following hypotheses: Specific molecular interactions between GBS surface components and phagocyte innate immune receptors mediate the host inflammatory response to GBS infection, that such responses are down-regulated by neutrophil-derived antimicrobial peptides that bind and neutralize inflammatory GBS surface molecules, and that these pro- and anti-inflammatory innate immune responses differ between newborns and adults. In Aim 1, GBS surface components that activate host phagocytes (i.e., neutrophils and monocytes) will be identified and characterized. In Aim 2, newborn and adult phagocytes will be compared with respect to expression and function of CR3/4, CD14, and TLR2. In Aim 3, putative neutrophil-derived peptides with anti-inflammatory activity against GBS will be isolated and characterized. The candidate seeks an intensive, formal, mentored training as preparation for becoming an independent scientist. As a specialist in pediatric infectious diseases, his long-term goal is to identify molecular pathways of innate immunity that might someday be modulated to improve outcomes of GBS and other bacterial infections in neonates. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

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Project Title: DEVELOPMENT EXPRESSION OF CHEMOKINES AND THEIR RECEPTORS Principal Investigator & Institution: Calhoun, Darlene A.; Pediatrics; University of South Florida 4202 E Fowler Ave Tampa, Fl 33620 Timing: Fiscal Year 2002; Project Start 13-AUG-2001; Project End 31-JUL-2003

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Summary: (provided by applicant) Despite the development of newer and more effective antibiotic therapies, sepsis related mortality in neonates undergoing intensive care has remained constant for nearly two decades. The rate of infection among these neonates ranges from 25% to 50%, with bacterial infection remaining a major cause of death and long-term morbidity. The cost of caring for premature neonates, who are the most susceptible to infection, represents over 50% of the total dollars expended for neonatal intensive care unit (NICU) services. The unique susceptibility of the human neonate to serious and overwhelming bacterial infections relates in part to deficiencies of antibody, complement, and T lymphocytes. However, while deficiencies in these contribute to the neonate s susceptibility, neutrophil defects appear to be the major host defense abnormality. Functional defects in neonatal polymorphonuclear leukocyte adherence, aggregation, chemotaxis, phagocytosis, and intracellular killing have been described in both the term and preterm infant. Of these defects, neutrophil chemotaxis, as assessed by in vitro assays, is abnormal at birth. While term infants rapidly establish normal chemotactic function, the process of postnatal maturation begins two to three weeks after birth in the preterm infant and proceeds very slowly. Neutrophils follow a concentration gradient of chemotactic factors in their movement from the vascular compartment to the site of microbial invasion. Chemokines are chemotactic cytokines that largely control leukocyte migration. While considerable information has emerged in the past ten years related to the role of chemokines in the adult, very little information exists as to the physiologic significance of chemokines in the neonate. Candidate chemokine/chemokine receptors for influencing neutrophil chemotaxis include members of the CXC chemokines. We propose that understanding the gene regulation for the expression of specific chemokine receptors (CXCR) during development would enhance our understanding of chemotaxis in the neonate. We further propose that defining circulating concentrations of chemokines critical for neutrophil migration would be essential to understanding their role in both health and disease. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: DNA GYRASE AND QUINOLONE RESISTANCE IN TUBERCULOSIS Principal Investigator & Institution: Drlica, Karl A.; Associate Professor; Public Health Research Institute 225 Warren St Newark, Nj 07103 Timing: Fiscal Year 2003; Project Start 30-SEP-1993; Project End 31-DEC-2007 Summary: (provided by applicant): The goals of this program are to understand how the quinolones act in mycobacteria and to discover ways to protect the compounds from the development of resistance. Previous work showed that structure modifications at the C8 position of fluoroquinolones increase antibacterial activity, particularly with fluoroquinolone-resistant mutants. This feature, plus other variations in fluoroquinolone structure, will be examined to explore the hypothesis that lethal activity arises in part from the dissociation of gyrase subunits attached to cleaved DNA. Since gyrase subunit dissociation is assayed as lethal activity in the absence of protein synthesis, this work may reveal ways to improve action against nongrowing bacteria. To define how low fluoroquinolone concentrations affect the development of resistance, non-gyrase resistance mutants of Mycobacterium tuberculosis, obtained through selective growth at low drug concentration, will be examined for their ability to increase the frequency at which subsequent gyrase mutants are selectively enriched. This portion of the study is expected to influence fluoroquinolone dosing strategies. In patients, M. tuberculosis develops resistance so readily that anti-tuberculosis agents are administered as combination therapies; consequently, the lethal activity of new fluoroquinolones will be examined in combination with traditional agents to identify combinations of

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compounds that are unlikely to have intrinsic interfering activities. Traditional agents will also be combined with C-8-methoxy fluoroquinolones in a dynamic in vitro model to examine the effect of pharmacodynamic mismatch on the development of resistance. These two aspects of the program will help optimize the use of new fluoroquinolones. To provide a clinical context for the work, isolates from New York City will be examined for susceptibility to fluoroquinolones. Comparison of isolates obtained in the early 1990s with those obtained recently will indicate whether susceptibility is being lost. Principles emerging from these in vitro studies may be generally applicable to bacterial infections for which fluoroquinolone treatment is indicated; ideas concerning resistance may also extend to other compounds in which de novo antimicrobial resistance develops in a gradual, stepwise manner. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: EFFECTS OF TOBACCO SMOKE ON AIRWAY BACTERICIDAL ACTIVITY Principal Investigator & Institution: Di, Yuan-Pu P.; Environ & Occupational Health; University of Pittsburgh at Pittsburgh 350 Thackeray Hall Pittsburgh, Pa 15260 Timing: Fiscal Year 2002; Project Start 18-SEP-2002; Project End 31-JUL-2005 Summary: (Taken from the Investigator's Abstract) Environmental stresses such as microorganisms and toxic chemicals have profound effects on lung injury and pulmonary disease. Airway bacterial infection has been associated with various lung diseases such as pneumonia, cystic fibrosis, and tuberculosis. Tobacco smoke (TS) is known to induce pulmonary diseases such as emphysema and lung cancer and has effects on the host defense mechanism against pathogens, but the molecular mechanisms by which this occurs is not completely understood. The long-term goal of this proposal is to investigate the functional characteristics of a novel airway specific gene, DD4, its regulation and its potential role in health and human lung diseases that relate to tobacco smoke. The human DD4 gene is specifically expressed in serous cells of submucosal glands where bactericidal proteins such as lysozyme and lactoferrin are secreted. This novel gene has exhibited significant response to promoting agents of mucous cell differentiation such as UTP and retinoids, as well as to several mediators of inflammation and proliferation such as tumor necrosis factor-alpha (TNF-alpha) and epidermal growth factor (EGF). Of potential significance, the candidate?s preliminary studies revealed that DD4 has antibacterial properties and that its secretion varied dramatically between different lung diseases. In addition, the candidate?s laboratory also observed that human DD4 MRNA expression is elevated upon TS stimulations in both time and dose dependent manner. The objective of this application is to elucidate effects of TS on the regulatory mechanism of DD4?s gene expression and to examine DD4?s function after TS exposure both in vitro and in vivo. The central hypothesis to be tested is that DD4 is a secreted bactericidal protein that plays a role in airway defense mechanisms against pathogens. The rationale behind this research is that modulation (such as TS exposure) of the secretary DD4 protein is one means of directly affecting host defense response against human airway infection. Therefore, regulation of DD4 gene expression and protein secretion in response to pathological stimuli must be understood before the mobilization of host defenses and the pathogenesis of airway diseases that are related to DD4 can be fully appreciated. To accomplish the objectives of this application, they will pursue three specific aims: (1) to characterize the bactericidal activity of DD4; (2) to elucidate the regulatory mechanism of TS exposure on DD4?s bactericidal function; (3) to evaluate DD4?s antibacterial effect in vivo. At the completion of this research, the candidate expects to have determined the bactericidal

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potency of DD4 and the regulation by TS of the antibacterial defense mechanism of DD4. The candidate expects that regulation of DD4 will prove to be related, at least in part, to the inflammatory response and tobacco smoke exposure. Finally, the candidate may obtain a better understanding of the pathogenesis of bacterial infections in certain lung diseases under effects of tobacco smoke, and the development of new therapeutic strategies. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: ELR-CXC CHEMOKINES IN LUNG ANTIBACTERIAL HOST DEFENSE Principal Investigator & Institution: Standiford, Theodore J.; Professor; Internal Medicine; University of Michigan at Ann Arbor 3003 South State, Room 1040 Ann Arbor, Mi 481091274 Timing: Fiscal Year 2002; Project Start 01-DEC-1996; Project End 30-NOV-2005 Summary: (provided by applicant): Bacterial pneumonia is the second most common cause of hospital-acquired infection, and is leading cause of death among all nosocomial infections. Innate, or natural immunity, is the principal pathway for effective elimination of bacterial organisms from the lung. While ELR-CXC chemokines have been shown to be expressed during the generation of Th1 cell-mediated immune responses against intracellular microbial pathogens, the contribution of this family of chemokines to innate immunity against common gram-positive and gram-negative bacterial pathogens is unknown. We have focused this competitive renewal on ELRCXC chemokines, as our preliminary observations indicate that the in-vivo depletion of selected ELR-CXC chemokines substantially impairs bacterial clearance and survival of mice with pneumonia due to Klebsiella pneumoniae. It is the hypothesis of this proposal that ELR-CXC chemokines are integral components of the innate neutrophil-dependent immune response against gram-negative bacterial infection of the lung. A murine model of Klebsiella pneumonia will be employed to achieve the following specific aims: 1) to determine the time course of expression and cellular sources of ELR-CXC chemokines and their common receptor (CXCR3) during the evolution of gram-negative bacterial pneumonia; 2) to determine the contribution of ELR-CXC chemokines and their receptor to leukocyte recruitment, proinflammatory cytokine expression, bacterial clearance, survival in Klebsiella pneumonia using specific neutralizing antibodies or knockout mice; 3) to determine the effect of IP-10 or MIG administration/transgenic expression on proinflammatory cytokine expression, bacterial clearance, and survival in murine Klebsiella pneumonia in-vivo and on alveolar macrophage effector cell function in-vitro; and 4) to identify endogenous signals that regulate the expression of ELR-CXC chemokines during the evolution of Klebsiella pneumonia in-vivo and in isolated lung cells in-vitro. Elucidation of specific cellular and molecular mechanisms of lung antibacterial host defense, in conjunction with the use of novel gene therapy approaches will provide important insights into the treatment of patients with serious multi-drug resistant bacterial infections of the lung. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

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Project Title: EMERGING DRUG-RESISTANT INFECTIONS Principal Investigator & Institution: Riley, Lee W.; Professor; None; University of California Berkeley Berkeley, Ca 94720 Timing: Fiscal Year 2003; Project Start 04-SEP-2003; Project End 31-MAR-2008

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Summary: (provided by applicant): Drug-resistant bacterial infections that occur in both hospital and community settings are an emerging infectious disease problem in large urban centers of middle-income developing countries, such as Brazil. This training program will build on the last 5 years of a training program supported under the Fogarty International Training and Research in Emerging Infectious Diseases (ITREID) to create a sustainable research training infrastructure in Brazil to address the problem of drug-resistant bacterial infections that occur in both hospital and community settings. This infrastructure will be established at the Federal University of Rio de Janeiro (FUR J), involving faculty members at FURJ and in the US who have already been collaborating over the last 5 years. Specifically, the new program will build a training program structured around three areas of research: 1) field epidemiology, 2) molecular epidemiology, and 3) molecular biology of bacterial drug resistance. The training sites in the US will include the Infectious Disease and Epidemiology programs of the School of Public Health at University of California at Berkeley (UCB), the Infectious Disease program at the University of California at San Francisco (UCSF), and Department of Medicine at Weill Medical College of Cornell University in New York City. On-site training at FURJ will be provided for MD, master's and PhD-level students, while a select set of master's, PhD, and postdoctoral students, as well as junior faculty members will be trained short- (3-6 months), intermediate-(6-12 months), or long- (>12 months) term at the US sites. The field epidemiology activities will include on-the-job training in research study design, outbreak investigations, data collection and analyses, disease surveillance, and biostatistics. The molecular epidemiology training will focus on the development, validation, and application of new molecular strain typing methods and computer-based analysis of strain subtyping database to address specific epidemiologic questions. Training in molecular biology of drug-resistance mechanisms will include the analysis of genetic elements (integrons, cassettes, plasmids) that mediate drug resistance. Through these training activities, the program hopes to create a cadre of researchers who will not only become future trainers themselves, but who can generate and provide quality information that will assure evidence-based decision-making by clinicians, nosocomial infection control services, metropolitan public health authorities, and state and national government policy makers in Brazil. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: EXPRESSION AND FUNCTION OF MSP HOMOLOGUES IN T PALLIDUM Principal Investigator & Institution: Centurion-Lara, Arturo; University of Washington Grant & Contract Services Seattle, Wa 98105 Timing: Fiscal Year 2002 Summary: As primary syphilis resolves, most treponemes are cleared from the chancre. However, a few organisms escape the immune response to cause secondary syphilis and ultimately to establish chronic infection. May theories have been proposed to explain Treponema pallidum's capacity for immune evasion, yet none has convincing experimental support. Antigen variation is one of the most intriguing theories, but not candidate antigens have been identified until now. The recent identification of a polymorphic multicopy gene family in T. pallidum that encodes for proteins with predicated amino acid homology to the major sheath protein (msp) of Treponema denticola provides a family of likely candidates. We call these T. pallidum proteins the msp-homologues. The broad goal of this proposal is to determine the cellular location and the function of the msp-homologue proteins. The specific aims of the project are the following: 1. Determine whether msp-homologues are surface exposed antigens in T.

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pallidum Nichols strain. This aim will test the hypothesis that some of the msphomologues are surface exposed in living organisms. 2. Determine whether msphomologues are involved in cell attachment and function as porins. This aim will determine whether the msp-homologue family has a role in two well-recognized mechanisms of pathogenesis of bacterial infections. 3. Determine whether T. pallidum Nichols strain represents a colonal bacterial population or is comprised of subpopulations of treponemes. This aim will test the hypothesis that, like other spirochetes, T. pallidum strains contain subpopulations that express heterogeneous msp- homologues. 4. Determine whether the msp-homologues undergo antigen variation or phase variation. Antigenic variation is common other pathogenic treponemes and the msp-homologue gene family has characteristics highly suggestive of genetic recombination and reassortment. This aim will test the hypothesis that individual msp-homologues either change (antigenic variation) or are no longer expressed (phase variation) during the course of infection. The studies proposed in this application will define the role of the msp- homologues in immune evasion and in the pathogenesis of syphilis. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: GAMMA DELTA T CELLS IN ANTI-BACTERIAL HOST DEFENSE Principal Investigator & Institution: Moore, Thomas A.; Internal Medicine; University of Michigan at Ann Arbor 3003 South State, Room 1040 Ann Arbor, Mi 481091274 Timing: Fiscal Year 2002; Project Start 01-APR-2001; Project End 28-FEB-2006 Summary: (provided by applicant): Klebsiella pneumoniae is a leading cause of community-acquired and nosocomial infections. Moreover, K pneumoniae is the second leading cause of nosocomial gram negative bacteremia. The recent emergence of multiantibiotic resistant strains of K pneumoniae due to extended-spectrum B-lactamase (ESBL) production is cause for significant clinical concern. Interestingly, antibiotic resistance appears to be more prevalent in blood isolates than from other sources. While the innate host response towards gram-negative bacterial infections has been characterized, little is known about gamma delta-T cells and their role in these infections. Our preliminary studies indicate that gamma delta-T cell knockout (KO) mice have significantly impaired early expression of pulmonary and hepatic IFN-gamma and TNF-alpha mRNA following intratracheal K. pneumoniae infection, increased blood bacterial dissemination, and increased hepatic bacterial burden subsequent to the initial pulmonary infection. Additional studies indicate increased mortality following intravenous bacterial inoculation in gamma delta-T cell KO mice and uncontrolled blood bacterial growth. Combined, our preliminary data suggest gamma delta-T cell KO mice succumb from an impaired ability to clear disseminated bacteria rather than from an inability to clear the organism from the primary pulmonary infection. The hypothesis of this proposal is that gamma delta T cells play a critical role in the host acute inflammatory response during gram-negative bacteremia via recognition of heat shock protein 60 expression in the liver following infection. A murine model of blood-borne K pneumoniae infection will be used to perform the following Specific Aims: 1)To contrast the host response in gamma delta T cell knockout and wildtype mice during K pneumoniae bacteremia, 2) To assess the kinetics of gamma delta T cell A) recruitment and activation and B) cytokine production during K pneumonia bacteremia, 3) To reconstitute resistance to K pneumoniae in gamma delta T cell knockout mice by adoptive transfer of gamma delta T cells from wildtype and cytokine deficient (IFNgamma or TNF-alpha) mice, 4) To confer resistance to K. pneumoniae in gamma delta T cell knockout mice by TNF-alpha or IFN-gamma reconstitution using systemic

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adenovirus gene therapy, and 5) To assess the requirement of heat shock protein 60 for gamma delta T cell activation during K. pneumoniae bacteremia. These studies will provide insights for the development of therapeutic modalities aimed at augmenting host responses, resulting in enhanced resolution of bacterial infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: GENOME ANALYSIS OF STREPTOCOCCUS AGALACTIAE Principal Investigator & Institution: Tettelin, Herve S.; Associate Investigator; Institute for Genomic Research Rockville, Md 20850 Timing: Fiscal Year 2002; Project Start 30-SEP-2001; Project End 29-SEP-2004 Summary: (provided by applicant): Group B streptococci (GBS) or Streptococcus agalactiae are weakly beta-hemolytic, facultatively anaerobic Gram-positive cocci, which have emerged over the past 50 years as the most significant bacterial cause of neonatal sepsis, pneumonia, and meningitis. GBS account for 30-50 percent of neonatal bacterial infections and increases in adult GBS infections have also been noted. This demonstrates that GBS infections remain an important public health problem. We propose to sequence the 2.1 Mb genome of S. agalactiae serotype Ia strain A909 using a genome-wide random shotgun approach. We will then use the final assembled sequence and its complete annotation to perform detailed comparative genomics analyses between serotype Ia and other organisms causing pneumonia and meningitis. These analyses will allow to identify virulence determinants shared by all organisms or specific to individual ones. These determinants will be related to Drs. Jones and Rubens? experiments on signature tagged mutagenesis and TnphoZ translational fusion (identification of secreted proteins) mutant libraries constructed through transposon insertions in strain A909. Regions where transposons inserted will be aligned to the genome sequence to identify the genes affected. A subset of the mutants conserved across serotypes will be analyzed in the rat sepsis model to evaluate their virulence. This collaborative effort will provide extensive preliminary data for future proposals relevant to understanding the pathogenesis of S. agalactiae infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen

•

Project Title: HIV SURVEILLANCE AFFECTS MACROPHAGE FUNCTION Principal Investigator & Institution: Wewers, Mark D.; Professor; Internal Medicine; Ohio State University 1960 Kenny Road Columbus, Oh 43210 Timing: Fiscal Year 2002; Project Start 30-SEP-1998; Project End 31-AUG-2003 Summary: Bacterial pneumonia remains one of the most common complications of HIV infections. In spite of our growing understanding of the pathogenesis of the immune deficiency associated with HIV infection, the factors that predispose HIV+ individuals to pneumonia remain obscure. For example, the risk of pneumonia for HIV infected individuals is 6 fold higher than for HIV-individuals. This risk can only partially be explained by lower blood CD4 counts. Our preliminary experiments demonstrate that the lung CD4 counts remain normal in the face of falling peripheral counts when compared to HIV uninfected subjects. However, CD8+ lymphocytes are markedly increased in the lung, a hallmark of HIV infection. These cytotoxic CD8+ lymphocytes (CTLs) are believed to function to suppress viral replication. In this context, the primary defense against bacterial infections in the lung is provided by alveolar macrophages which are also the prime source of HIV in the lung. Since macrophage HIV infection is enhanced by inflammatory events, we have hypothesized that 1) initiation of antibacterial function by lung macrophages induces local HIV replication, and 2) as a

Studies

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consequence of this increase in viral burden, lung CTLs may be signaled to suppress this viral replication. This suppression of virus may in the process suppress macrophage antibacterial function. We therefore, propose to test these hypotheses by studying the macrophage's ability to phagocytose opsonized particles. We will evaluate lung macrophages from HIV infected individuals and normal controls to test whether opsonized phagocytosis induces viral replication in the macrophage. As a corollary we will determine whether CTLs can impair macrophage phagocytosis. These in vitro experiments will be corroborated by studies of lung macrophages taken at the time of bacterial pneumonia. Together these experiments will improve our understanding of how the innate immune defense against bacteria is affected by attempts to suppress HIV in macrophages. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: HOST-PATHOGEN INTERACTIONS IN THE MAMMALIAN AIRWAY Principal Investigator & Institution: Diamond, Gill; Associate Professor; Biochem and Molecular Biology; Univ of Med/Dent Nj Newark Newark, Nj 07103 Timing: Fiscal Year 2003; Project Start 01-APR-2003; Project End 31-MAR-2007 Summary: (provided by applicant): Epithelial cells lining the mammalian trachea form a crucial site in the host defense against airborne microbial pathogens, releasing numerous antimicrobial factors. Deficiencies in these defenses may result in recurrent airway infections. One of these defense mechanisms is the inducible production of betadefensins, a class of homologous antibiotic peptides highly abundant in mammalian epithelial cells. The genes encoding beta-defensins are expressed at high levels in the respiratory epithelium, and are induced by bacterial products and inflammatory mediators. Preliminary and published data support the hypothesis that some pathogenic strains of bacteria can evade the innate immune system in the airway by inhibiting beta-defensin gene expression, which can in turn diminish the antimicrobial defense of the airway. The mechanisms by which the specific bacterial virulence factors allow evasion of the first lines of host defense to colonize the airway are not yet defined. Elucidation of these mechanisms will aid in the development of therapeutic strategies for airway infections. The long-range goal of our research is to better understand the dynamic host defense systems in the airway. In this proposal we focus on the interactions of the airway pathogen, Bordetella bronchiseptica with its target cells in the respiratory epithelium. B. bronchiseptica is associated with respiratory infections in animals, and is closely related to B. pertussis, the causative agent of whooping cough in humans. We hypothesize that airway epithelial cells respond to bacteria by recognition of molecular patterns by specific receptors, resulting in the activation of NF-kappaB and induction of beta-defensin gene expression in order to prevent colonization. Pathogenic strains of B. bronchiseptica can prevent the increased production of antimicrobial peptides by interfering with the upregulation of the antimicrobial peptide genes through a type III secretion factor which interferes with the innate immune response. To test these hypotheses, the following aims are proposed: 1. Define the interaction of B. bronchiseptica with airway epithelial cells and the resultant induction of an innate immune response. 2. Define the mechanism of inhibition of innate immune induction by virulent B. bronchiseptica. The objective of these studies is to define how the airway epithelium responds to this model pathogen by the initiation of a host defense response. The second aim will determine how the bacterium circumvents this response utilizing proteomics to identify the bacterial factor responsible for this action, as well as a comprehensive characterization of the interaction of this factor and the defense

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response. The information will serve as a foundation for the development of novel therapies designed to work in the respiratory tract. This would include strategies to modulate the endogenous antimicrobial peptide expression to prevent serious bacterial infections. Website: http://crisp.cit.nih.gov/crisp/Crisp_Query.Generate_Screen •

Project Title: IMMUNOPATHOGENESIS OF GROUP A STREPTOCOCCAL INFECTION Principal Investigator & Institution: Kotb, Malak; Professor; Surgery; University of Tennessee Health Sci Ctr Memphis, Tn 38163 Timing: Fiscal Year 2003; Project Start 15-AUG-2003; Project End 29-FEB-2008 Summary: (provided by applicant): The overall goal of the present application is to explore the way specific host genetic factors and specific bacterial virulence determinants interact together to influence the outcome of an important infectious disease. This paradigm is critical to explain the wide variety of potential outcomes that occur when a human host encounters a potentially pathogenic organism like Group A streptococcus (GAS), from asymptomatic colonization to mild infection to severe morbidity or mortality. The model we have developed studies GAS-induced severe systemic disease (SSD; the bacterial superantigens (SAgs) that are key players in eliciting SSD; and the host factors involved are the HLA class II molecules that present the SAgs to T cells. The pathogenic link of the host genetic and bacterial virulence factors is clear, since the HLA molecules are receptors for SAgs, presenting them to the TCR and transmitting biochemical signals into APCs. We found that the host immunogenetic makeup influences the clinical outcome of invasive GAS disease. Specific HLA class II haplotypes conferred strong protection from the severe forms of the invasive disease, while others increased the risk for SSD. We also determined the underlying mechanism for these genetic associations by demonstrating that the presentation of Strep SAgs by the class II DRB1( 1501/DQB1*0602 haplotype, which was strongly associated with protection from SSD (P=0.0007), elicited significantly lower inflammatory responses as compared to their presentation by either risk or neutral haplotypes (P

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