Contents -- Preface -- Acknowledgements -- Executive Summary -- List of acronyms and abbreviations -- 1 Introduction -- 1.1 Environmental Mycobacteria -- 1.2 Nomenclature and typing -- 1.3 Understanding the disease -- 1.3.1 The epidemiology of environmental mycobacteria -- 1.3.2 Risk factors -- 1.4 Pathogenic mycobacteria in water -- 1.4.1 Water supply -- 1.4.2 Recently reported cases of waterborne mycobacterial disease -- 1.5 Global Burden of Disease -- 1.5.1 Crohn disease and Johne disease -- 1.6 Control measures -- 1.7 Genomic and evolutionary perspectives -- 1.8 Key research issues -- 2 Natural ecology and survival in water of mycobacteria of potential public health significance -- 2.1 The ecology of environmental mycobacteria -- 2.1.1 Protozoa, helminths and insects -- 2.1.2 Infections in birds and animals -- 2.1.3 Infections in fish -- 2.2 Physiologic characteristics of M. avium relevant to its ecology and distribution -- 2.2.1 Physiologic characteristics of M. avium that are determinants of its ecology -- 2.2.2 M. avium physiologic ecology -- 2.3 Heterogeneity of Environmental Isolates of M. avium -- 2.3.1 Impact of heterogeneity on identifying sources of human infection -- 2.3.2 M. avium fingerprinting methods -- 2.4 Changes in the Occurrence in Mycobacterial Species -- 2.4.1 Shift of M. scrofulaceum to M. avium in cervical lymphadenitis in children -- 2.4.2 Selection of mycobacteria by disinfectants -- 2.5 Key research issues -- 3 Environmental sources of Mycobacterium avium linked to routes of exposure -- 3.1 Environmental sample types yielding M. avium -- 3.1.1 M. avium in water -- 3.1.2 M. avium in soils -- 3.1.3 M. avium in aerosols, ejected droplets and dust -- 3.1.4 M. avium in phagocytic protozoa and amoebae -- 3.1.5 Other sources of M. avium -- 3.2 Impact of unidentified mycobacterial isolates.

3.3 Environments with high numbers of M. avium -- 3.4 Routes of exposure -- 3.4.1 Ingestion -- 3.4.2 Inhalation -- 3.4.3 Trauma -- 3.4.4 Biofilms -- 3.5 Overlap of human and M. avium environments -- 3.6 Key research issues -- 4 Biology of waterborne pathogenic mycobacteria -- 4.1 Introduction -- 4.1.1 Taxonomy and terminology -- 4.1.2 Evolution and diversity of MAC -- 4.2 Mycobacterial genomes -- 4.2.1 The MAA genome -- 4.2.2 The MAP genome -- 4.2.3 Genomes of other environmental mycobacteria -- 4.3 Bacterial physiology -- 4.3.1 The cell envelope and its role in virulence and antimicrobial resistance -- 4.3.2 Morphotypic switches -- 4.3.3 Metabolism and catabolism -- 4.4 Biology of MAC in host environments -- 4.4.1 Entry and survival in host cells -- 4.4.2 MAA genes involved in intracellular life -- 4.4.3 MAP genes involved in intracellular life -- 4.5 Key research issues -- 4.5.1 Diversity -- 4.5.2 Molecular markers of virulence -- 4.5.3 Taxonomy -- 4.5.4 Evolutionary context -- 4.5.5 Genomic analysis -- Acknowledgements -- 5 Analytical methods for the detection of waterborne and environmental pathogenic mycobacteria -- 5.1 Introduction -- 5.2 The analysis process -- 5.2.1 Sampling -- 5.2.2 Sample storage -- 5.2.3 Sample preparation -- 5.2.4 Detection -- 5.3 Key research issues -- 6 The Mycobacterium avium subspecies paratuberculosis problem and its relation to the causation of Crohn disease -- 6.1 Mycobacterium avium subspecies paratuberculosis -- 6.2 MAP infection and Johne disease in domestic livestock -- 6.3 Different strains of MAP -- 6.4 MAP in wildlife and in the environment -- 6.5 Transmission of MAP from animals to humans -- 6.5.1 In food -- 6.5.2 In water supplies and aerosols -- 6.6 Crohn disease -- 6.6.1 Definition -- 6.6.2 Epidemiology, environmental factors, and inherited susceptibility to CD -- 6.6.3 The isolated case of Iceland.

6.7 MAP causing Crohn disease -- 6.7.1 MAP in the inflamed gut of people with Crohn disease -- 6.7.2 Serological recognition of MAP proteins in Crohn disease -- 6.7.3 Response of Crohn disease to treatment with anti-MAP drugs -- 6.7.4 Pathogenic mechanisms of MAP in Crohn disease -- 6.8 Key research issues -- Acknowledgements -- 7 Disseminated infection, cervical adenitis and other MAC infections -- 7.1 Disseminated MAC infection -- 7.1.1 Clinical aspects -- 7.1.2 Microbiology -- 7.1.3 Epidemiology and risk factors -- 7.1.4 Burden of disease -- 7.1.5 Prevention and treatment -- 7.2 Cervical adenitis -- 7.2.1 Clinical aspects -- 7.2.2 Epidemiology and risk factors -- 7.2.3 Morbidity/mortality -- 7.2.4 Burden of disease -- 7.2.5 Prevention and treatment -- 7.3 Tenosynovitis -- 7.4 Osteomyelitis and septic arthritis -- 7.5 Meningitis -- 7.6 Pancreatic infection -- 7.7 Sarcoidosis -- 7.8 Key research issues -- 8 Skin, Bone and Soft Tissue Infections -- 8.1 Clinical aspects -- 8.1.1 M. marinum -- 8.1.2 Rapidly Growing Mycobacteria -- 8.1.3 Mycobacterium avium complex -- 8.1.4 M. haemophilum -- 8.1.5 M. ulcerans -- 8.1.6 M. terrae -- 8.2 Overall burden of disease -- 8.3 Distribution -- 8.4 Descriptive epidemiology -- 8.5 Risk factors -- 8.6 Causality and associated microbes -- 8.7 Key research issues -- 9 Pulmonary infection in non-HIV infected individuals -- 9.1 Clinical aspects -- 9.1.1 Primary and secondary pathogenic pulmonary environmental mycobacterial infection -- 9.1.2 Selected treatment issues -- 9.1.3 Selected microbiological issues -- 9.2 Overall burden of disease -- 9.3 Distribution -- 9.4 Descriptive epidemiology -- 9.5 Causality and associated microbes -- 9.6 Risk factors -- 9.7 Prevalence of asymptomatic disease -- 9.8 Key research issues -- 10 Disease Resulting From Contaminated Equipment and Invasive Procedures -- 10.1 Clinical aspects.

10.1.1 General comments -- 10.1.2 Specific infections -- 10.1.3 Selected microbial factors -- 10.2 Overall burden of disease -- 10.3 Distribution -- 10.4 Descriptive epidemiology -- 10.5 Risk factors -- 10.6 Causality and associated microbes -- 10.7 Key research issues -- 11 Control, Treatment and Disinfection of Mycobacterium avium Complex in Drinking Water -- 11.1 Introduction -- 11.2 Removal of mycobacteria by water treatment processes -- 11.2.1 Physical removal by coagulation and filtration -- 11.2.2 Disinfection -- 11.3 Regrowth of mycobacteria in drinking water -- 11.3.1 Biodegradable organic matter -- 11.3.2 Impact of water contact materials -- 11.4 Other environmental and control factors -- 11.4.1 Temperature -- 11.4.2 Control of free living amoebae -- 11.5 Role of distribution system recontamination -- 11.6 Key research issues -- Acknowledgements -- 12 Approaches to risk management in priority setting -- 12.1 Introduction -- 12.2 Public health response -- 12.3 Management options -- 12.3.1 Drinking/bathing water -- 12.3.2 Recreational water -- 12.3.3 Industrial exposure -- 12.3.4 Institutional exposure -- 12.3.5 The high risk groups -- 12.4 The HACCP approach to management -- 12.5 Key research issues -- References -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- L -- M -- N -- O -- P -- R -- S -- T -- U -- V -- W.