BOOK
Pathogenic Mycobacteria in Water
Steve Pedley | Jamie Bartram | G. Rees | A. Dufour | J. A. Cotruvo
(2004)
Additional Information
Book Details
Abstract
Environmental mycobacteria can be found in diverse environments around the world and most appear to exhibit a saprophytic lifestyle. However, some have the ability to infect animals, birds and humans, and have evolved mechanisms by which they can invade and grow within host cells: the pathogenic environmental mycobacteria (PEM). Although the diseases caused by these organisms have been known for many years, it is only recently that the potential significance of PEM as a waterborne pathogen has been appreciated. Pathogenic Mycobacteria in Water describes the current knowledge of the distribution of PEM in water and other parts of the environment. The routes of transmission that lead to human infection are discussed and there is a detailed analysis of the most significant disease symptoms that can follow infection. Many species of PEM are difficult to isolate in culture and so detection and identification rely upon the use modern techniques such as those based on selective nucleic acid amplification (PCR). The classical and modern methods of analysis are described. The book concludes with a discussion of the issues surrounding the control of PEM in drinking-water and the assessment and management of risks. Pathogenic Mycobacteria in Water has been developed from an expert workshop convened by the World Health Organization and the US Environmental Protection Agency. Contents Natural ecology and survival in water of mycobacteria of potential public health significance Environmental sources of Mycobacterium avium linked to routes of exposure Biology of waterborne pathogenic mycobacteria Analytical methods for the detection of waterborne and environmental pathogenic mycobacteria The Mycobacterium avium subspecies paratuberculosis problem and its relation to the causation of Crohn disease Disseminated infection, cervical adenitis and other MAC infections Skin, Bone, and Soft Tissue Infections Pulmonary infection in non-HIV infected individuals Disease resulting from contaminated equipment and invasive procedures Control, Treatment and Disinfection of Mycobacterium avium Complex in Drinking Water Approaches to risk management in priority settings
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover\r | Cover | ||
| Contents | v | ||
| Preface | xi | ||
| Acknowledgements | xiii | ||
| Executive Summary | xv | ||
| List of acronyms and abbreviations | xxi | ||
| 1:\rIntroduction | 1 | ||
| 1.1 ENVIRONMENTAL MYCOBACTERIA | 1 | ||
| 1.2 NOMENCLATURE AND TYPING | 2 | ||
| 1.3 UNDERSTANDING THE DISEASE | 5 | ||
| 1.3.1 The epidemiology of environmental mycobacteria | 5 | ||
| 1.3.2 Risk factors | 7 | ||
| 1.4 PATHOGENIC MYCOBACTERIA IN WATER | 7 | ||
| 1.4.1 Water supply | 7 | ||
| 1.4.2 Recently reported cases of waterborne mycobacterialdisease | 8 | ||
| 1.5 GLOBAL BURDEN OF DISEASE | 8 | ||
| 1.5.1 Crohn disease and Johne disease | 11 | ||
| 1.6 CONTROL MEASURES | 12 | ||
| 1.7 GENOMIC AND EVOLUTIONARY PERSPECTIVES | 12 | ||
| 1.8 KEY RESEARCH ISSUES | 14 | ||
| 2:\rNatural ecology and survival inwater of mycobacteria of potentialpublic health significance | 15 | ||
| 2.1 THE ECOLOGY OF ENVIRONMENTAL\rMYCOBACTERIA | 16 | ||
| 2.1.1 Protozoa, helminths and insects | 16 | ||
| 2.1.2 Infections in birds and animals | 16 | ||
| 2.1.3 Infections in fish | 17 | ||
| 2.2 PHYSIOLOGIC CHARACTERISTICS OF M. AVIUM\rRELEVANT TO ITS ECOLOGY AND DISTRIBUTION | 18 | ||
| 2.2.1 Physiologic characteristics of M. avium that aredeterminants of its ecology | 18 | ||
| 2.2.1.1 Growth characteristics | 18 | ||
| 2.2.1.2 M. avium hydrophobicity | 19 | ||
| 2.2.1.3 M. avium response to temperature, oxygen, pH, and salinity | 19 | ||
| 2.2.1.4 M. avium metabolism | 20 | ||
| 2.2.2 M. avium physiologic ecology | 20 | ||
| 2.3 HETEROGENEITY OF ENVIRONMENTAL ISOLATES\rOF M. AVIUM | 21 | ||
| 2.3.1 Impact of heterogeneity on identifying sources of humaninfection | 21 | ||
| 2.3.2 M. avium fingerprinting methods | 21 | ||
| 2.4 CHANGES IN THE OCCURRENCE IN\rMYCOBACTERIAL SPECIES | 23 | ||
| 2.4.1 Shift of M. scrofulaceum to M. avium in cervical\rlymphadenitis in children | 23 | ||
| 2.4.2 Selection of mycobacteria by disinfectants | 23 | ||
| 2.5 KEY RESEARCH ISSUES | 24 | ||
| 3:\rEnvironmental sources ofMycobacterium avium linked toroutes of exposure | 26 | ||
| 3.1 ENVIRONMENTAL SAMPLE TYPES YIELDING\rM. AVIUM | 27 | ||
| 3.1.1 M. avium in water | 27 | ||
| 3.1.1.1 Methods of isolation | 27 | ||
| 3.1.1.2 M. avium in natural waters | 28 | ||
| 3.1.1.3 M. avium in drinking-waters | 28 | ||
| 3.1.1.4 Other water samples | 29 | ||
| 3.1.1.5 M. avium in biofilms | 29 | ||
| 3.1.2 M. avium in soils | 30 | ||
| 3.1.2.1 Methods of isolation | 30 | ||
| 3.1.2.2 M. avium in soils and peat | 30 | ||
| 3.1.3 M. avium in aerosols, ejected droplets and dust | 31 | ||
| 3.1.3.1 Methods of isolation | 31 | ||
| 3.1.3.2 M. avium in ejected droplets | 31 | ||
| 3.1.3.3 M. avium in aerosols | 32 | ||
| 3.1.4 M. avium in phagocytic protozoa and amoebae | 32 | ||
| 3.1.4.1 Intracellular growth and enumeration | 32 | ||
| 3.1.5 Other sources of M. avium | 33 | ||
| 3.2 IMPACT OF UNIDENTIFIED MYCOBACTERIAL\rISOLATES | 34 | ||
| 3.3 ENVIRONMENTS WITH HIGH NUMBERS OF M. AVIUM | 34 | ||
| 3.4 ROUTES OF EXPOSURE | 35 | ||
| 3.4.1 Ingestion | 35 | ||
| 3.4.2 Inhalation | 36 | ||
| 3.4.3 Trauma | 36 | ||
| 3.4.4 Biofilms | 36 | ||
| 3.5 OVERLAP OF HUMAN AND M. AVIUM ENVIRONMENTS | 37 | ||
| 3.6 KEY RESEARCH ISSUES | 37 | ||
| 4:\rBiology of waterborne pathogenic mycobacteria | 39 | ||
| 4.1 INTRODUCTION\r | 39 | ||
| 4.1.1 Taxonomy and terminology | 39 | ||
| 4.1.2 Evolution and diversity of MAC | 41 | ||
| 4.2 MYCOBACTERIAL GENOMES | 43 | ||
| 4.2.1 The MAA genome | 43 | ||
| 4.2.2 The MAP genome | 46 | ||
| 4.2.3 Genomes of other environmental mycobacteria | 47 | ||
| 4.3 BACTERIAL PHYSIOLOGY\r | 48 | ||
| 4.3.1 The cell envelope and its role in virulence and antimicrobial\rresistance | 48 | ||
| 4.3.2 Morphotypic switches | 48 | ||
| 4.3.3 Metabolism and catabolism | 50 | ||
| 4.4 BIOLOGY OF MAC IN HOST ENVIRONMENTS\r | 51 | ||
| 4.4.1 Entry and survival in host cells | 51 | ||
| 4.4.2 MAA genes involved in intracellular life | 51 | ||
| 4.4.3 MAP genes involved in intracellular life | 53 | ||
| 4.5 KEY RESEARCH ISSUES | 53 | ||
| 4.5.1 Diversity | 53 | ||
| 4.5.2 Molecular markers of virulence | 54 | ||
| 4.5.3 Taxonomy | 54 | ||
| 4.5.4 Evolutionary context | 54 | ||
| 4.5.5 Genomic analysis | 54 | ||
| Acknowledgements | 54 | ||
| 5: Analytical methods for the detection of waterborne and environmental\rpathogenic mycobacteria | 55 | ||
| 5.1 INTRODUCTION | 55 | ||
| 5.2 THE ANALYSIS PROCESS | 58 | ||
| 5.2.1 Sampling | 60 | ||
| 5.2.2 Sample storage | 61 | ||
| 5.2.3 Sample preparation | 61 | ||
| 5.2.4 Detection | 63 | ||
| 5.2.4.1 Detection (first level) | 63 | ||
| 5.2.4.2 Detection (second level) | 66 | ||
| 5.2.4.2.1 Genus and species identification | 67 | ||
| 5.2.4.2.2 Commercial tests for genus and species identification | 69 | ||
| 5.2.4.2.3 Pathogen-specific PCR tests | 69 | ||
| 5.2.4.3 Detection (third level) | 70 | ||
| 5.2.4.3.1. IS restriction fragment length polymorphism | 70 | ||
| 5.2.4.3.2 Pulsed-field gel electrophoresis | 71 | ||
| 5.2.4.3.3 Inter-insertion sequence polymerase chain reaction | 71 | ||
| 5.2.4.3.4 Random amplified polymorphic DNA (RAPD) | 72 | ||
| 5.2.4.3.5 Multi-locus sequence typing | 72 | ||
| 5.3 KEY RESEARCH ISSUES | 73 | ||
| 6: The Mycobacterium avium subspecies paratuberculosis problem and its relation to the\rcausation of Crohn disease | 74 | ||
| 6.1 MYCOBACTERIUM AVIUM SUBSPECIES PARATUBERCULOSIS\r | 74 | ||
| 6.2 MAP INFECTION AND JOHNE DISEASE IN DOMESTIC LIVESTOCK | 75 | ||
| 6.3 DIFFERENT STRAINS OF MAP | 78 | ||
| 6.4 MAP IN WILDLIFE AND IN THE ENVIRONMENT | 79 | ||
| 6.5 TRANSMISSION OF MAP FROM ANIMALS TO HUMANS | 80 | ||
| 6.5.1 In food | 81 | ||
| 6.5.2 In water supplies and aerosols | 82 | ||
| 6.6 CROHN DISEASE\r | 83 | ||
| 6.6.1 Definition | 83 | ||
| 6.6.2 Epidemiology, environmental factors, and inherited susceptibility to CD | 85 | ||
| 6.6.3 The isolated case of Iceland | 87 | ||
| 6.7 MAP CAUSING CROHN DISEASE | 88 | ||
| 6.7.1 MAP in the inflamed gut of people with Crohn disease | 89 | ||
| 6.7.2 Serological recognition of MAP proteins in Crohn disease | 91 | ||
| 6.7.3 Response of Crohn disease to treatment with anti-MAP drugs | 92 | ||
| 6.7.4 Pathogenic mechanisms of MAP in Crohn disease | 93 | ||
| 6.8 KEY RESEARCH ISSUES | 94 | ||
| Acknowledgements | 94 | ||
| 7: Disseminated infection, cervical\radenitis and other MAC infections | 95 | ||
| 7.1 DISSEMINATED MAC INFECTION | 95 | ||
| 7.1.1 Clinical aspects | 95 | ||
| 7.1.2 Microbiology | 96 | ||
| 7.1.3 Epidemiology and risk factors | 96 | ||
| 7.1.4 Burden of disease | 98 | ||
| 7.1.5 Prevention and treatment | 98 | ||
| 7.2 CERVICAL ADENITIS | 99 | ||
| 7.2.1 Clinical aspects | 99 | ||
| 7.2.2 Epidemiology and risk factors | 100 | ||
| 7.2.3 Morbidity/mortality | 101 | ||
| 7.2.4 Burden of disease | 101 | ||
| 7.2.5 Prevention and treatment | 101 | ||
| 7.3 TENOSYNOVITIS | 102 | ||
| 7.4 OSTEOMYELITIS AND SEPTIC ARTHRITIS | 102 | ||
| 7.5 MENINGITIS | 103 | ||
| 7.6 PANCREATIC INFECTION | 103 | ||
| 7.7 SARCOIDOSIS | 103 | ||
| 7.8 KEY RESEARCH ISSUES | 103 | ||
| 8:\rSkin, bone and soft tissue infections | 104 | ||
| 8.1 CLINICAL ASPECTS | 105 | ||
| 8.1.1 M. marinum | 105 | ||
| 8.1.2 Rapidly Growing Mycobacteria | 107 | ||
| 8.1.3 Mycobacterium avium complex | 108 | ||
| 8.1.4 M. haemophilum | 109 | ||
| 8.1.5 M. ulcerans | 110 | ||
| 8.1.6 M. terrae | 110 | ||
| 8.2 OVERALL BURDEN OF DISEASE | 110 | ||
| 8.3 DISTRIBUTION | 111 | ||
| 8.4 DESCRIPTIVE EPIDEMIOLOGY | 112 | ||
| 8.5 RISK FACTORS | 112 | ||
| 8.6 CAUSALITY AND ASSOCIATED MICROBES | 113 | ||
| 8.7 KEY RESEARCH ISSUES | 114 | ||
| 9: Pulmonary infection in non-HIV\rinfected individuals | 115 | ||
| 9.1 CLINICAL ASPECTS | 116 | ||
| 9.1.1 Primary and Secondary Pathogenic Pulmonary\rEnvironmental Mycobacterial Infection | 118 | ||
| 9.1.1.1 Primary PEM | 118 | ||
| 9.1.1.2 Secondary PEM | 120 | ||
| 9.1.1.3 Hypersensitivity pneumonitis | 122 | ||
| 9.1.2 Selected treatment issues | 124 | ||
| 9.1.3 Selected microbiological issues | 126 | ||
| 9.2 OVERALL BURDEN OF DISEASE | 126 | ||
| 9.3 DISTRIBUTION | 127 | ||
| 9.4 DESCRIPTIVE EPIDEMIOLOGY | 127 | ||
| 9.5 CAUSALITY AND ASSOCIATED MICROBES | 128 | ||
| 9.6 RISK FACTORS | 128 | ||
| 9.7 PREVALENCE OF ASYMPTOMATIC DISEASE | 129 | ||
| 9.8 KEY RESEARCH ISSUES | 130 | ||
| 10: Disease resulting from contaminated equipment and\rinvasive procedures | 131 | ||
| 10.1 CLINICAL ASPECTS\r | 132 | ||
| 10.1.1 General Comments | 132 | ||
| 10.1.2 Specific infections | 135 | ||
| 10.1.2.1 Infection of intravascular catheters, pacemakers | 135 | ||
| 10.1.2.2 Dialysis related infection | 135 | ||
| 10.1.2.3 Injection abscesses | 136 | ||
| 10.1.2.4 Cosmetic industry | 136 | ||
| 10.1.2.5 Miscellaneous medical and surgical procedures | 137 | ||
| 10.1.3 Selected microbial factors | 139 | ||
| 10.1.3.1 The role of disinfectant resistance | 139 | ||
| 10.1.3.2 The role of biofilms | 139 | ||
| 10.1.3.3 Role of water temperature | 140 | ||
| 10.2 OVERALL BURDEN OF DISEASE | 140 | ||
| 10.3 DISTRIBUTION | 141 | ||
| 10.4 DESCRIPTIVE EPIDEMIOLOGY | 141 | ||
| 10.5 RISK FACTORS | 141 | ||
| 10.6 CAUSALITY AND ASSOCIATED MICROBES | 141 | ||
| 10.7 KEY RESEARCH ISSUES | 142 | ||
| 11: Control, treatment and disinfection\rof Mycobacterium avium complex in drinking water | 143 | ||
| 11.1 INTRODUCTION | 143 | ||
| 11.2 REMOVAL OF MYCOBACTERIA BY WATERTREATMENT PROCESSES | 145 | ||
| 11.2.1 Physical removal by coagulation and filtration | 145 | ||
| 11.2.2 Disinfection | 149 | ||
| 11.3 REGROWTH OF MYCOBACTERIA IN DRINKING\rWATER | 160 | ||
| 11.3.1 Biodegradable organic matter | 160 | ||
| 11.3.2 Impact of water contact materials | 162 | ||
| 11.4 OTHER ENVIRONMENTAL AND CONTROL FACTORS | 164 | ||
| 11.4.1 Temperature | 164 | ||
| 11.4.2 Control of free living amoebae | 165 | ||
| 11.5 ROLE OF DISTRIBUTION SYSTEM\rRECONTAMINATION | 166 | ||
| 11.6 KEY RESEARCH ISSUES | 167 | ||
| Acknowledgements | 168 | ||
| 12: Approaches to risk management in\rpriority setting | 169 | ||
| 12.1 INTRODUCTION | 169 | ||
| 12.2 PUBLIC HEALTH RESPONSE | 170 | ||
| 12.3 MANAGEMENT OPTIONS | 172 | ||
| 12.3.1 Drinking/bathing water | 172 | ||
| 12.3.2 Recreational water | 174 | ||
| 12.3.3 Industrial exposure | 174 | ||
| 12.3.4 Institutional exposure | 175 | ||
| 12.3.5 The high risk groups | 175 | ||
| 12.4 THE HACCP APPROACH TO MANAGEMENT | 176 | ||
| 12.5 KEY RESEARCH ISSUES | 178 | ||
| References | 179 | ||
| Index | 229 |