Infectious and Host Defence PDF

[IASM] Module 3: Infectious and Host Defence [IAS 51-70] Infectious and Host Defence [IAS51] How Are Healthcare Systems Organised.......................................................................................5 [IAS52,53,54] Microbes and Disease...........

[IASM] Module 3: Infectious and Host Defence [IAS 51-70] Infectious and Host Defence [IAS51] How Are Healthcare Systems Organised.......................................................................................5 [IAS52,53,54] Microbes and Disease..........................................................................................................12 Glossary...................................................................................................................................................13 Clinical Microbiology................................................................................................................................ 16 Scope of Study.............................................................................................................................16 Clinical Significance of Knowledge on Infectious Agents.............................................................16 Host Microbe Relationship....................................................................................................................... 17 Host-microbe Interactions............................................................................................................ 18 The Human Microbiome - Commensals.......................................................................................19 Microbial Pathogenesis of Human Diseases........................................................................................... 20 Transmission Triangle.................................................................................................................. 20 The Chain of an Infection............................................................................................................. 21 Stages of an Infection.................................................................................................................. 22 Pathogenesis of an Infection - 6 Basic Steps...............................................................................24 Diagnosis of Infectious Disease...............................................................................................................25 [IAS55-56] Medically Important Gram-Positive, Negative Bacteria.........................................................26 Bacteria....................................................................................................................................................27 Bacterial Structure........................................................................................................................27 Bacterial Mode of Existence.........................................................................................................30 Bacterial Growth and Nutritions................................................................................................... 30 Bacterial Genetics........................................................................................................................ 31 Classification of Bacteria Based on Phenotypic Characteristics.................................................. 31 Management of Bacterial Infection...............................................................................................34 Classification of Gram Positive Bacteria.................................................................................................. 34 I. Based on Gram Staining........................................................................................................... 36 II. Based on Morphology.............................................................................................................. 36 III. Based on Catalase Reaction (Positive)..................................................................................37 IV. Based on Atmospheric Requirement...................................................................................... 38 Classification of Gram Negative Bacteria................................................................................................ 39 [IAS57] Medically Important Fungal Pathogens....................................................................................... 40 Mycology (Study of Fungi)....................................................................................................................... 41 Structure of Fungi.........................................................................................................................41 Classification of Fungi.................................................................................................................. 41 Epidemiology of Fungal Infection.............................................................................................................42 Clinical Diseases of Fungal Infection....................................................................................................... 42 A. Superficial Infections................................................................................................................42 B. Systemic Infections..................................................................................................................43 C. Mycetoma................................................................................................................................ 43 Laboratory Diagnosis of Fungal Infections...............................................................................................44 A. Detection of Fungus or Its Components.................................................................................. 44 B. Detection of Patients’ Responses............................................................................................44 Treatment : Antifungal Agents................................................................................................................. 45 Types of Antifungal.......................................................................................................................45 1  [IASM] Module 3: Infectious and Host Defence Antifungal Susceptibility Testing...................................................................................................45 Case Study : Candida albicans................................................................................................................46 [IAS58] Principles of Disinfection, Sterilisation and Infection Control.................................................. 48 Infection Prevention Control on Nosocomial Infections........................................................................... 49 Significance Of Controlling HAIs.................................................................................................. 49 Nosocomial Transmission Route................................................................................................. 49 Two-tier System (Breaking Nosocomial Transmission)................................................................49 Other Aspects of Prevention and Control................................................................................................ 52 Killing Microbes............................................................................................................................ 52 [IAS59,65] Viruses and Prions / Medically Important Viruses................................................................. 56 Introduction to Viruses............................................................................................................................. 57 Structure of Viruses......................................................................................................................57 Classification of Viruses............................................................................................................... 58 Size of Viruses............................................................................................................................. 59 The Virus Replication Cycle (Lytic Cycle).................................................................................... 59 Viral Diseases.......................................................................................................................................... 61 Transmission of Viral Diseases.................................................................................................... 61 Development of Viral Diseases.................................................................................................... 61 Pathogenesis of Viral Diseases................................................................................................... 62 Diagnosis For Viral Diseases....................................................................................................... 63 Examples of Medically Important Viral Diseases......................................................................... 66 Causal Relationship Between Specific Microorganism and Disease.......................................................77 Koch’s Postulations......................................................................................................................77 Fredricks & Relman......................................................................................................................77 Other Types of Agents............................................................................................................................. 78 Defective Viruses......................................................................................................................... 78 Prions (Protein Infectious)............................................................................................................78 [IAS60] Social Determinants of Health...................................................................................................... 79 [IAS61] Medically Important Parasites.......................................................................................................86 Significance of Parasitology.....................................................................................................................87 Introduction to Parasitism........................................................................................................................ 87 Glossary....................................................................................................................................... 87 Life Cycle of Parasites................................................................................................................. 87 Prevention of Parasitic Infections.................................................................................................88 Parasitic Infection and Classification....................................................................................................... 89 Protozoa (Unicellular)...................................................................................................................89 Helminths..................................................................................................................................... 93 Arthropods..................................................................................................................................100 [IAS62] Health, Illness and Disease......................................................................................................... 103 [IAS63] One Health and Planetary Health................................................................................................ 110 [IAS64] Immune Defense Mechanisms.................................................................................................... 114 Types and Features of Immunity............................................................................................................115 Triggering Immune Response.................................................................................................... 115 Innate Immunity......................................................................................................................................117 A. Defence Barriers.................................................................................................................... 117 B. Phagocytosis..........................................................................................................................118 2  [IASM] Module 3: Infectious and Host Defence C. Humoural - Soluble Factors...................................................................................................120 Natural Killer Cells (NK Cells) in Innate Immunity......................................................................122 [IAS66] The Immune System in Health and Disease.............................................................................. 123 Immunity against infectious agents........................................................................................................124 Immunity against “non-self” (allergy, transplantation immunity).............................................................124 Immunity against “self” (autoimmunity, anti-tumour immunity)...............................................................124 Anti-Tumour Immunity................................................................................................................ 124 AutoImmunity............................................................................................................................. 125 [IAS70] Adaptive Immune Reactivity : Antibodies and Lymphocytes.................................................. 126 Cells of Adaptive Immunity.................................................................................................................... 127 Detection of Pathogen by Adaptive Immunity........................................................................................ 129 Recognition of Antigen............................................................................................................... 129 Antigen Presenting Cells (APCs)............................................................................................... 129 Mechanisms of Adaptive Immunity........................................................................................................ 131 A. Specific Humoral Immunity by Immunoglobulins (Antibodies)...............................................131 B. Cell-Mediated Immunity (CMI) by T Cells.............................................................................. 140 Secondary Immune Response (Memory) In Adaptive Immunity................................................145 Immunodeficiencies............................................................................................................................... 147 [IAS67] Chronic Inflammation.................................................................................................................. 148 Causes of Chronic Inflammation............................................................................................................149 HIstological Hallmarks of Chronic Inflammation.................................................................................... 150 A. Mononuclear Inflammatory Cell Infiltrate............................................................................... 150 B. Granulation Tissue.................................................................................................................152 C. Tissue Destruction and Fibrosis (Scarring)........................................................................... 152 D. Regeneration......................................................................................................................... 153 Effects of Chronic Inflammation............................................................................................................. 153 Granulomatous Inflammation.................................................................................................................154 Formation................................................................................................................................... 154 Structure of Granuloma..............................................................................................................154 Types of Granuloma...................................................................................................................155 Chronic VS Acute Inflammation............................................................................................................. 156 [IAS69] Acute Inflammation...................................................................................................................... 157 Process of Acute Inflammation.............................................................................................................. 158 Hallmarks and Pathological Basis of Acute Inflammation......................................................................158 Clinical Features of Acute inflammation.....................................................................................158 Pathological Features of Acute inflammation.............................................................................159 The Outcomes of Acute Inflammation........................................................................................167 Example of Acute Inflammation............................................................................................................. 168 Clinical Significance of Acute Inflammation........................................................................................... 169 [IAS68] Antimicrobials and Immunization...............................................................................................170 Antimicrobials.........................................................................................................................................171 Discovery Of Antimicrobials....................................................................................................... 171 Classification of Antibacterial Agents......................................................................................... 172 Antibacterial Activity (Bactericidal / Bacteriostatic).................................................................... 176 Antimicrobial Resistance Mechanisms.......................................................................................178 Immunisation..........................................................................................................................................179 3  [IASM] Module 3: Infectious and Host Defence Active Immunity (Acquired Immunity) - Vaccination................................................................... 179 Passive Immunity....................................................................................................................... 182 Active Immunity VS Passive Immunity.......................................................................................183 4  [IASM] Module 3: Infectious and Host Defence [IAS51] How Are Healthcare Systems Organised Learning Outcomes Describe the functional anatomy of healthcare systems with reference to Hong Kong and GBA development. Discuss the macro-organisation and investment in a health care system to achieve health coverage. Outline the generic functions and 'control knobs' for health system reform. 5 [IASM] Module 3: Infectious and Host Defence 6 [IASM] Module 3: Infectious and Host Defence 7 [IASM] Module 3: Infectious and Host Defence 8 [IASM] Module 3: Infectious and Host Defence 9 [IASM] Module 3: Infectious and Host Defence 10 [IASM] Module 3: Infectious and Host Defence 11  [IASM] Module 3: Infectious and Host Defence [IAS52,53,54] Microbes and Disease Learning Outcomes Identify and diagram the stages of an infection Explain how microbial and host factors affect the outcome of an infection 12  [IASM] Module 3: Infectious and Host Defence Glossary Microbiology The study of organisms which are usually small in size, simple in structure, neither plants nor animals (except in the case of algae and parasites) Clinical microbiology The study of the effects of microbes on humans as pathogen or/and commensal at the laboratory and the bedside. Concerns with the diagnosis, management and control of infectious disease Epidemiology The study of the rate of occurrence of a particular disease caused by microorganisms, with respect to time, place and the person Microbes Micro-organisms Virus Bacteria Fungus Protozoa (parasites) Prions Pathogens Disease causing organisms Commensal Colonising organisms Infectious disease Diseases caused by microbes and are often communicable / spread by direct or indirect contact and other ways of exposure Infectivity The characteristics of the disease agent that embodies capability to enter, survive, and multiply in the host Pathogenicity The degree or ability of a pathogenic organism to cause disease Virulence factors Microbial factors that enhance the organism’s ability to Colonise Invade and multiply inside host Evade the host’s defence mechanism Communicable A disease whose causal agent can be transmitted from successive hosts to disease healthy subjects, from one individual to another 13  [IASM] Module 3: Infectious and Host Defence Cluster An aggregation of cases of a disease or health condition that are grouped together in terms of time and place. May not necessarily exceed the expected number of cases but indicates a spatial or temporal concentration that may warrant investigation Outbreak The occurrence of cases of a particular disease or health condition in a population or geographic area that is greater than what is normally expected. It represents a noticeable increase in the number of cases, usually within a specific time frame and location. Outbreaks can vary in scale From localised outbreaks within a specific community or institution to larger-scale outbreaks that can affect multiple regions. Epidemics An epidemic occurs when there is a sudden increase in the number of cases of a disease within a specific population, geographic area, or community. It represents a significant rise in the occurrence of a disease beyond what is normally expected The term "epidemic" is typically used when the disease spreads within a defined region or population. Pandemics A pandemic refers to a global outbreak of a disease, affecting multiple countries or continents and spreading across a large population. Unlike an epidemic, which is limited to a specific geographic area, a pandemic involves the worldwide spread of a disease. The term "pandemic" is used when a disease reaches a global level of spread and impact. Zoonoses Infectious diseases that can be transmitted between animals and humans Immunopathological The damage caused to an organism by its own immune system damage Disease association The observed relationship between two or more factors, such as a specific disease and certain risk factors or co-occurring conditions. Disease The signs, symptoms, or characteristics that are displayed by an individual who manifestation has a particular disease. It refers to how the disease presents or appears in the affected person. Infection Deposition and multiplication of microbes (synonyms accepted: Microbes, pathogens, microorganisms, etc) in tissue or on surfaces of body (just the word ‘body’, ‘human’, ‘living being’, etc. also accepted) with associated tissue reaction (accepted – harmful effects, adverse reactions, tissue destruction, etc.) HAI An infection originating in a medical facility; e.g., occurring in a patient in a hospital or other health care facility in whom the infection was not present or incubating at the time of admission. Includes infections acquired in the hospital but appearing after discharge and such infections among staff. Hospital acquired infections Healthcare associated infections Nosocomial infections Infection Prevention Evidence-based practices and procedures that, when applied consistently in Control health care settings, can prevent or reduce the risk of transmission of microorganisms to health care providers, clients, patients, residents and visitors. Opportunistic Infections that occur more frequently and are more severe in people with infection weakened immune systems 14  [IASM] Module 3: Infectious and Host Defence Endogenous An infection caused by an infectious agent that is present on or in the host prior to infection the start of the infection Disseminated A localised infection spreads (disseminates) from one area of the body to other infection organ systems Invasive infection When pathogens invade parts of the body that are normally sterile Disease syndrome The illness during an infection or a specific group of symptoms and signs Colonisation Presence of microbes with little or no host response (1 mark) Contamination Soiling of living or inanimate materials by potentially infectious or harmful matter (full marks should be given only if students mention both living and non-living objects / materials) 15  [IASM] Module 3: Infectious and Host Defence Clinical Microbiology Scope of Study Basic morphology Infectious diseases Antimicrobials and resistance Immunisation and vaccination Infection control in health care and community settings Infectious disease epidemiology Treatment Prevention Clinical Significance of Knowledge on Infectious Agents Understand pathogenic mechanisms to determine potential targets of prevention and treatment ○ Immunisation ○ Neutralisation of toxins Clinical significance of the results Understand the most likely pathogens in a particular clinical setting Understand the most likely source and cause of the infection Decide what tests to be done to look for microbes Decision making in treatment plans ○ To treat or not to treat ○ Methods of treatment ○ Choosing the most appropriate antimicrobials 16  [IASM] Module 3: Infectious and Host Defence Host Microbe Relationship Type Role Microbe Pathogen Ability to Defend ○ Disease producing ○ Virulent Commensal ○ Non disease producing ○ Non virulent Host Normal host Ability to Invade ○ Normal innate and Low infective dose acquired immune High attack rate defences Number and potency of virulence factors Abnormal host ○ Abnormal innate and/or High morbidity and mortality acquired immune High ability to cause disease responses ○ Immunocompromised 17  [IASM] Module 3: Infectious and Host Defence Host-microbe Interactions Normal host VS Pathogen Normal host VS Non-pathogen Abnormal host VS Pathogen Abnormal host VS Non-pathogen Opportunistic infection 18  [IASM] Module 3: Infectious and Host Defence The Human Microbiome - Commensals Types ○ Resident flora Permanent residents of the associated body site under normal circumferences ○ Transient flora Carrier state Generally not part of the normal microbiota Often asymptomatic Can serve as a reservoir for further transmission or environmental contamination Functions ○ Development of the normal immune system ○ Colonisation resistance Prevents the invasion by potentially pathogens ○ Diverse associations with various metabolic and immunological functions Clinical relevance ○ Altered microbiota could be associated with various disease states Examples 19  [IASM] Module 3: Infectious and Host Defence Microbial Pathogenesis of Human Diseases Transmission Triangle Agent ○ Infecting microbes Environment ○ A source of infecting microbes A susceptible host 20  [IASM] Module 3: Infectious and Host Defence The Chain of an Infection A. Infectious Agents Virus Bacteria Fungi Parasite B. Reservoirs Exogenous (outside host) Endogenous Human contacts Normal microbiota on skin and mucosa Animal contracts Environment C. Portal of Exit (Object) D. Mode of Transmission (Route) E. Entry Portals (Object) From the respiratory tract Via inhalation of droplets / aerosol Skin Coughing Tuberculosis Mucosa Sneezing Measles ○ Eye, nose, mouth, Severe acute respiratory airway, gut, genital Talking syndrome tract From contaminated Via ingestion environment or food items From arthropods, insects Via bites, cuts wounds Soft tissue, blood vessels From excreta of animals Via contact (indirect / direct) Saliva Urine Faeces From donated organs Via transplantation , transfusion Organ, tissue, faecal (iatrogenic) F. Host Outcome Carry out medical treatment 21  [IASM] Module 3: Infectious and Host Defence Stages of an Infection Period Event Example : Dengue Fever 1. Incubation Time interval between exposure and Day -4 - 0 (Last 3-10 days) period appearance of symptoms Infected by mosquito bite Factors Affecting Incubation Period Microbial inoculum (dose) Route of inoculation Rate of replication of the microbe Host susceptibility Host immune response 2. Prodromal The period when nonspecific No prodromal period period symptoms occur Not all infections have prodromal period 3. Specific illness The period when characteristic Day 0 - 6 period features of an infectious disease occur Day 0 Immunity starts to kick in ○ Detection of virus By PCR By NS1 antigen Day 3 ○ Detection of antibody IgM IgG ELISA Symptoms : ○ Fever ○ Viraemia Entering blood ○ Eye, muscle, bone, joint pain ○ Rash ○ Risk of shock and haemorrhage Day 4-6 22  [IASM] Module 3: Infectious and Host Defence 4. Decline period The period when symptoms are resolving due to action of immune system 5. Convalescence The stage when the patient has recovered from the illness Some microorganisms can cause latent infection or chronic infection 6. Normally : Infectious virus is completely eliminated Latent infection The phase during the course of an infection during which the pathogen is dormant or inactive Latent period -> reactivation when immune system declines Can occur in different tissues and locations Chronic infection Persistent replication of microorganisms -> causing slow damage Specific chronic infection Disease manifested after many years E.g. Persistent measles leads to subacute sclerosing panencephalitis ○ Progressive brain disorder 23  [IASM] Module 3: Infectious and Host Defence Pathogenesis of an Infection - 6 Basic Steps 1. Encounter Surface contact 2. Invasion Local and beyond 3. Spread 4. Multiplication Increase in number 5. Damage Pathogenic mechanism of the microbe overcome the defence mechanism of the host Direct cytolysis ○ Intracellular replication of microbes in host cells / Secretion of toxins Indirect immunopathological damage by non-specific upregulation of inflammation through ○ Activation of host’s pathogen associated molecular pattern (PAMP) receptors ○ Molecular mimicry Oncogenesis ○ Due to integration of viral genome into host chromosome ○ Due to chronic inflammation 6. Outcome Causing significant physiological disturbance Symptoms 24  [IASM] Module 3: Infectious and Host Defence Diagnosis of Infectious Disease 1. Clinical assessment 2. Appropriate specimen collection 3. Laboratory diagnosis Use of microbial factors Use Of host factors Visualisation of the characteristic morphology of the Specific antibody responses of the microbe in clinical specimen host towards microbial component ○ Bacteria : ○ Especially during convalescent By Gram stain and light microscope phase ○ Virus : Cell structure system Cellular immune response of the host ○ Mantous test Culture of microbe ○ T and B lymphocyte ○ Bacteria and fungi : highly variable proliferation and activation Atmospheric condition towards specific antigens Type of nutritional supplement Temperature ○ Virus Cell structure system Detection of specific microbial components ○ Enzyme immunoassay ○ Specific conformation of the protein, lipid or polysaccharide antigens ○ Specific volatile fatty acid profile Generated by gas liquid chromatography in anaerobes and mycobacteria ○ Specific DNA and RNA sequences detected by : Polymerase Chain Reaction (PCR) Reversetranscription polymerase reaction (RT-PCR) Probe hybridisation Mass spectrometry 4. Antibiotic susceptibility testing 25  [IASM] Module 3: Infectious and Host Defence [IAS55-56] Medically Important Gram-Positive, Negative Bacteria Learning Outcomes Describe how medically important Gram-positive bacteria are classified. Describe the virulence factors and diseases caused by Staphylococcus aureus and medically important coagulase-negative staphylococci. Briefly describe the microbiology and disease association of medically important Gram-positive bacilli Briefly describe the virulence factors, diseases, and prevention of pathogenic neisseriae Briefly describe the microbiology and disease association of medically important Gram-positive bacilli Briefly describe the virulence factors, diseases, and prevention of pathogenic neisseriae. 26  [IASM] Module 3: Infectious and Host Defence Bacteria Bacterial Structure Structure Description Cytoplasm Contains many ribosomes as protein synthetic factories which allow the bacteria to multiply rapidly Cytoplasmic Contains phospholipids membrane ○ Also cholesterol in mycoplasma Contains proteins ○ For nutrient import ○ Secretion of virulence factors & signal molecules Contains enzyme system ○ For oxidative phosphorylation ○ Ion transport ○ Electron transfer 27  [IASM] Module 3: Infectious and Host Defence Structure Description Cell wall Made up of peptidoglycan ○ A polymer of repeating sugar subunits of 1-4 linked N-acetylglucosamine (NAG) and N-acetyl muramic acid (NAMA) ○ The sugar polymers are cross linked via the peptide bridges on N-acetyl muramic acid ○ The enzymes cross-linking these peptides can be inhibited by antibiotics such as penicillins and vancomycin. Provides structural integrity and provide support A key target of action by some antibiotics Capsule An additional covering of polysaccharides or polypeptide on the surface of the cell wall of some bacteria Can be a virulence factor ○ Conferring antiphagocytic function against white blood cells ○ Adhesion onto host cells to start infection. Some bacteria have a prominent capsule which prevent their recognition by host immune system 28  [IASM] Module 3: Infectious and Host Defence Structure Description Ribosomes Made up of the smaller 30S and the 50S subunits Antibiotics have a high affinity to bind to bacterial ribosomes ○ such as gentamicin (aminoglycosides), tetracyclines and erythromycin (macrolides) ○ To stop bacterial protein synthesis with little effect on eukaryotic ribosomes. Flagella Propels bacteria through liquid Allowing them to spread and find new source of nutrients Pili and Facilitate bacteria to adhere to mucosa fimbriae Serve as colonising factors for enteric pathogens Sex pili ○ Serve as receptors for phages or a conduit for transfer of genes from one bacterium to another through the genetic process of conjugation Spores Structure (endospores) ○ Contain bacterial DNA, small amount of cytoplasm, cell membrane ○ Protected by a thick spore coat made of peptidoglycan and protein coat Significance ○ Survival advantages Highly resistant to heat, chemical and radiations Environmental persistence ○ Clinical relevance Contaminate food Killed by disinfection and sterilisation Can result to infection control implications Metabolic inert Biofilm Slimy adherent extracellular matrix secreted by some bacteria On surfaces and medical device which Allows them to persist despite exposure to antimicrobials. Plasmids Additional genetic material harboured by bacteria and other organisms Double stranded circular coiled DNA Replicate independently of the bacterial chromosome Some plasmid can be transferred to other bacteria via sex pili by a process called conjugation 29  [IASM] Module 3: Infectious and Host Defence Bacterial Mode of Existence Intracellular Extracellular Exist and multiply within the host cell Exist outside the human cell Protected against the defence Greater opportunities for growth, reproduction and mechanism of the host dissemination Face the onslaught by host immune system and harsh environmental conditions Bacterial Growth and Nutritions Phase Event Lag phase The initial period when the newly introduced bacteria are slowly adapting to the utilisation of nutrient in the medium There is no change in cell number Log phase The number of bacteria increases exponentially Bacteria multiply by binary fission About 30 min for rapidly growing bacteria like Escherichia coli Stationary phase No increase in cell number as the amount of nutrients becomes exhausted 30  [IASM] Module 3: Infectious and Host Defence Bacterial Genetics Methods of genetic changes Process Bacterial viruses (Phages) Transduction in elaboration of exotoxins Lysogeny ○ Toxin gene in phage genome is integrated into the bacterial chromosome One gene (the suppressor gene) is expressed The product will prevent the expression of other phage genes Plasmids Conjugation Allow bacteria to acquire several new genes simultaneously Cause outbreaks of infection by bacteria with multiple antibiotic resistance Point mutations Brings about mutations ○ Occurs randomly Leads to changes in ○ Antigenicity ○ Virulence ○ Transmissibility ○ Antimicrobial susceptibility Classification of Bacteria Based on Phenotypic Characteristics Staphylo Clusters of grapes Strepto Chains Entero Gut Haemo Blood Helico Spiral Based on Staining Properties Acid Fast E.g. Ziehl-Neelsen Stain Used particularly to identify mycobacterium Has a blue background Cell wall-deficient bacteria Cannot be stained by gram stain due to the lack of cell wall 31  [IASM] Module 3: Infectious and Host Defence Gram Staining Using stain colour complex - crystal violet and iodine Gram-positive Gram-negative bacteria bacteria Staining results Deep purplish blue Light pink Peptidoglycan cell wall Thick (traps stain) Thin Outer Membrane Absent Present Lipopolysaccharides (LPS) / Endotoxins Structure ○ Core oligosaccharide ○ O-specific side chain ○ Lipid A carries all the physiological properties Biological effect ○ A potent stimulus of host pro-inflammatory cytokine production ○ Activates the host’s Toll-like receptor 4 (TLR4) Clinical relevance ○ Can cause sepsis and shock Endospores More common Less common Infections Lower mortality High mortality in severe infections Cause sepsis > 25-30% mortality 32  [IASM] Module 3: Infectious and Host Defence Based on Morphology Cocci ○ Clusters ○ Diplococci Bacilli (rod) ○ Curved rods ○ Straight Spirochaetes Based on Oxygen Requirement for Growth Strict aerobes Exclusively use oxygen as the final electron acceptor Strict anaerobes Use other inorganic substances as final electron acceptor ○ NO2 ○ SO4 Oxygen radicals generated from aerobic respiration are toxic to these bacteria ○ As they dont have required detoxification enzymes such as catalase Produce foul smelling volatile fatty acid as by products of metabolism Facultative anaerobes Grow in presence ○ Uses oxygen as final electron acceptor Grow in absence of air ○ Uses organic substances (Pyruvic acid) as final electron acceptor Most medically important Microaerophilic bacteria Grow under Low oxygen tension Presence of carbon dioxide 33  [IASM] Module 3: Infectious and Host Defence Management of Bacterial Infection 1. Treatment Supportive treatment Specific antimicrobial treatment (antibiotics) ○ Mechanism of actions : Immunological therapy ○ Neutralisatin of toxins ○ Modification of immune system 2. Prevention Understanding the routes of infection ○ To prevent exposure ○ To interrupt the chain of transmission Passive immunisation ○ Immunoglobulins ○ Antibodies Active immunisation ○ Vaccines Chemoprophylaxis ○ Using antimicrobial agents to prevent the development of disease 34  [IASM] Module 3: Infectious and Host Defence Classification of Gram Positive Bacteria 35  [IASM] Module 3: Infectious and Host Defence I. Based on Gram Staining Gram positive Gram negative Gram variable Cell-wall deficient (no gram staining) II. Based on Morphology Cocci (round) Bacilli (rod) Coccobacilli (short rod) Spirochete 36  [IASM] Module 3: Infectious and Host Defence III. Based on Catalase Reaction (Positive) Oxygen produced act as a parameter to determine whether there is a catalase reaction A. Based on Coagulase Activity 1. Positive 2. Negative Function of coagulase Mannitol Salt Agar Test (MSA) Converts fibrinogen to fibrin ○ A selective agar test for isolation of S. ○ Clot plasma aureus ○ Fibrin deposited on the surface of S. ○ Mannitol aureus Differential utilisation, creating Hinder phagocytosis different colours Types of coagulase ○ High salt concentration To inhibit growth of other Bound / clumping factor organisms except for ○ Tested by slide coagulase test staphylococci Extracellular ○ Tested by tube coagulase test 37  [IASM] Module 3: Infectious and Host Defence III. Based on Catalase Reaction (Negative) B. Based on different hemolytic profile on blood agar Beta-hemolytic ○ Complete haemolysis Alpha-hemolytic ○ Partial haemolysis Non(gamma)-hemolytic ○ No haemolysis IV. Based on Atmospheric Requirement A. Aerobic ○ Uses oxygen B. Anaerobic ○ No oxygen Based on Spore Formation 1. Spore-forming 2. Non-spore forming 38  [IASM] Module 3: Infectious and Host Defence Classification of Gram Negative Bacteria 39  [IASM] Module 3: Infectious and Host Defence [IAS57] Medically Important Fungal Pathogens Learning Outcomes Describe the biology of fungi and the morphological characteristics of medically important fungal pathogens. Describe the classification of medically important fungi. Describe the classification of fungal diseases. Describe major routes of transmission, epidemiology and pathogenesis of fungal diseases. Describe the common clinical manifestations and laboratory diagnosis of fungal diseases. Describe the management for patients with fungal infections and the prevention of fungal diseases in hospitals. 40  [IASM] Module 3: Infectious and Host Defence Mycology (Study of Fungi) Structure of Fungi Eukaryotic Cell ○ 60% glucan Not present in human Target for antifungal ○ 30% protein ○ 10% chitin Cell membrane ○ Ergosterol Not present in human Target for antifungal Cytoplasm Nucleus Classification of Fungi Type Yeasts Moulds Thermodimorphic fungi Features Unicellular Multicellular At 25℃ (environment) 5 um in diameter Forms hyphae ○ Mould Reproduce by budding ○ Long branching filaments At 37 ℃ (body) ○ 2-4 umwide ○ Yeast ○ Mapped together to form mycelium Spore forming ○ For asexual or sexual reproduction Examples Candida albicans Aspergillus fumigatus Talaromyces (Penicillium) marneffei 25℃ Cryptococcus neoformans Dermatophytes 37℃ Infect skin - tinea infections Trichophyton Epidermophyton Microsporum Indian ink staining Negative staining 41  [IASM] Module 3: Infectious and Host Defence ○ Stains background Epidemiology of Fungal Infection Geographical distribution Risk factors Globally Neutropenia ○ Candida ○ Low neutrophil count ○ Aspergillus HIV infections ○ Dermatophytes Locally ○ T. marneffei ○ Other dimorphic fungi Clinical Diseases of Fungal Infection A. Superficial Infections Infection Candidiasis Dermatophytosis (ringworm/ skin infection) Manifestation Vaginal thrush Tinea pedis (athlete’s foot) Oral thrush Tinea capitum (head) Tinea unguium (nails) 42  [IASM] Module 3: Infectious and Host Defence B. Systemic Infections Infected Immunocompetent Immunocompromised population Infection is Opportunistic infection uncommon Neutropenia HIV infections Infections Mostly allergic reactions Systemic candidiasis by / As body is C. neoformans Manifestation hypersensitive to A. fumigatus spores ○ Invasive aspergillosis by A. fumigatus Sputum analysis X-ray of lungs On skin (in HIV patients) T. marneffei C. Mycetoma Locally invasive infection Affects the skin, subcutaneous tissues, and sometimes bones 43  [IASM] Module 3: Infectious and Host Defence Laboratory Diagnosis of Fungal Infections A. Detection of Fungus or Its Components Direct visualisation Culturing Potassium hydroxide smear Agar plates ○ Identities mould Broth culture Gram smear ○ From oral swab ○ Identifies Candida Indian ink smear ○ Identifies C. neoformans Biopsy and histopathology Antigen detection Nucleic acid detection beta-D-glucan For Aspergillus Capsular polysaccharides in C. neoformans Galactomannan in Aspergillus B. Detection of Patients’ Responses Antibody detection ○ For T. marneffei Biopsy and histopathology 44  [IASM] Module 3: Infectious and Host Defence Treatment : Antifungal Agents Types of Antifungal Action on cell membrane Polyenes ○ Complex with ergosterol Disrupts fungal plasma membrane ○ Examples Nystatin Amphotericin B Azoles ○ Inhibit ergosterol synthesis ○ Examples Fluconazole Itraconazole Voriconazole Nucleoside analogues 5-flucytosine Cell wall synthesis inhibitor Echinocandins Examples ○ Caspofungin ○ Micafungin ○ Anidulafungin Antifungal Susceptibility Testing Not performed Proper identification of the fungus is the cornerstone to guide treatment 45  [IASM] Module 3: Infectious and Host Defence Case Study : Candida albicans Mycology Yeast Other species under family Candia ○ C. parapsilosis ○ C. tropicalis ○ C. krusei Host defence against infection ○ Intact skin ○ Neutrophils ○ Monocytes Epidemiology Reservoir ○ Normal commensals of human In skin In GI tract In female genital tract Distribution ○ Globally Risk factors ○ Use of broad spectrum antibiotics (acts as selection pressure) ○ Hospitalisation ○ Intravenous illness ○ HIV ○ Neutropenia ○ Organ transplant patients ○ Use of steroids Clinical disease Endogenous infection Disease manifestation Immunocompetent hosts ○ Vaginal thrush Immunocompromised hosts Refractory (difficult to treat) superficial infections ○ Oral thrush ○ Mucocutaneous superficial infections Systemic candidiasis ○ Candidemia (can cause bloodstream infections) 46  [IASM] Module 3: Infectious and Host Defence ○ Disseminated infections in eye, skin, kidney ○ Hepatosplenic candidiasis involves liver and spleen Laboratory By detecting C. albicans or its components diagnosis Direct visualisation ○ Gram smear Culture ○ Agar plates to culture from pus ○ Broth culture to culture from blood ○ Germ tube formation in serum ○ Biochemical tests Antigen detection ○ beta-D-glucan from serum (blood) Treatment Treating superficial candidiasis ○ Topical treatment E.g. nystatin Treating refractory superficial candidiasis ○ Systemic treatment E.g. Fluconazole Treating systemic candidiasis ○ Systemic treatment Orally or intravenously E.g. Fluconazole, amphotericin B Prevention Impossible to avoid exposure due to endogenous nature Avoid antibiotic overuse ○ Prevents overgrowth Prescribe Fluconazole prophylaxis fort transplant recipients No vaccine available currently 47  [IASM] Module 3: Infectious and Host Defence [IAS58] Principles of Disinfection, Sterilisation and Infection Control Learning Outcomes Recognize the importance of infection control in healthcare settings Describe the rationale of basic infection control including standard and transmission-based precautions Understand the specific definitions of disinfection and sterilisation Give examples of how we achieve disinfection and sterilisation in healthcare settings 48  [IASM] Module 3: Infectious and Host Defence Infection Prevention Control on Nosocomial Infections Evidence-based practices and procedures that, when applied consistently in health care settings, can prevent or reduce the risk of transmission of microorganisms to health care providers, clients, patients, residents and visitors. Significance Of Controlling HAIs In patients’ perspectives ○ Prevents outbreaks and cross infection ○ Reduce morbidity ○ Reduce mortality ○ Reduce costs In staff’s perspectives ○ Provides a safe working environment ○ Ensures safety and health Nosocomial Transmission Route Between workers and patients Between contaminated equipments and patients Refer to table below Two-tier System (Breaking Nosocomial Transmission) Tier When / who Application Procedures 1. Standard Designed for the care of Blood Hang hygiene precautions all patients in hospital All body fluids, ○ Handwashing (1996) Regardless of their secretion and ○ Hygienic handwash diagnosis or presumed excretions (except ○ Hegemonic handrub Premise : infection status sweat) ○ surgical hand Anticipate a Non-intact skin antisepsis potential source ○ Wounds Gloves of exposure ○ Mucous PPE (personal membrane protective equipment) ○ Mask, eye protection, face shield, gown ○ When splashing is likely Needles ○ Never recapped, bent, broken ○ Proper disposal 2. Transmission For the care of specific In addition to standard Refer to table below -based patients precautions precautions ○ With known or suspected infection with epidemiologically important pathogens that can be transmitted Documented patients 49 [IASM] Module 3: Infectious and Host Defence 50  [IASM] Module 3: Infectious and Host Defence Route Descriptions Example Transmission-based precautions Contact Direct contact Streptococcus pyogenes Prevent direct contact Body surface to body surface Staphylococcus aureus ○ PPE Through skin / mucosa Respiratory viruses ○ Person to person Rotavirus Indirect Through inanimate objects ○ Gowns ○ Gloves Prevent contact with items in patient’s environment Droplet Large particle aerosols depositing on mucous membrane Most respiratory pathogens Masks Sources Neisseria meningitidis Shields ○ Coughing ○ Sneezing ○ Talking ○ Aerosol generating procedures (AGP) : Suctioning Bronchoscopy Airborne for a short period of time ○ Drop onto floor ○ Do not travel far Airborne Droplet nuclei of evaporated aerosols Mycobacterium tuberculosis N95 respirator ○ Residue of large aerosols Measle virus Respirator with HEPA filter ○ Small : < 5 um diameter Varicella-zoster virus (chicken Powered air purifying respirator Bypass filter mechanisms pox) systems ○ Deposit in lower respiratory tract and lungs Source : AGP in hospitals Remains airborne for prolonged periods 51  [IASM] Module 3: Infectious and Host Defence Other Aspects of Prevention and Control Killing Microbes Principles Sterilisation ○ The use of physical of chemical procedures to destroy all microbial life (including spores) Disinfection ○ A physical or chemical produces performed on inanimate objects that destroy most pathogenic microbes Antisepsis ○ Use of a germicide on skin or living tissue for the purpose of inhibiting or destroying microbes 52  [IASM] Module 3: Infectious and Host Defence Methods of Sterilisation and Disinfection Physical Heat Sterilisation (most effective) ○ Dry heat Flaming (open flame) Hot air oven ○ Moist heat : autoclave (pressure steam steriliser) Producing steam in high temperature > 100 degrees 121 degrees , 15 minutes Disinfection : moist heat ○ Boilers (can cause injuries) ○ Thermal washer disinfectors Radiation Ionising radiation (commercial use) ○ Electron beams (beta rays) ○ Gamma rays Ultraviolet radiations for surface ○ 253 nm wavelength ○ Poor penetrating power Filtration Membrane filters ○ 1.2 um ○ 0.45 um ○ 0.22 um Chemical Aldehydes Glutaraldehyde ○ Forms Cidex 2% glutaraldehyde activated alkaline solutions ○ Target Bactericidal, fungicidal, virucidal, tuberculocidal, sporicidal ○ Hazard Irritating (non-corrosive) ○ Level of disinfection 3 hours - sterilisation 20 mins - high level disinfection Formaldehyde ○ Hazard Very toxic ○ Level of disinfection 37% - sterilisation 3-8% - disinfection Halogens Chlorine ○ Forms releasing Clorox (strong alkaline hypochlorite solutions) agents Hypochlorite solutions (1-5% NaOCl) (bleach) Hypochlorite powders Presept (tablet) dissolving in water ○ Disadvantage Inactivated by proteins 53  [IASM] Module 3: Infectious and Host Defence Iodine ○ 1% iodine in 70% alcohol ○ Povidone-iodine Iodophors ○ Composition Complexes of iodine and solubilizers Same activity as iodine ○ Use Disinfection of skin Wound disinfectant Hand hygiene, hand washing ○ Hazard Not irritant Do not stain skin Chlorhexidine ○ Form Hibitane Hibiscrub (4% chlorhexidine gluconate) Savlon (cetrimide + chlorhexidine) ○ Target Highly active against Gram positive bacteria Less active against Gram negative bacteria Fungicidal Little or no activity against Mycobacterium tuberculosis, bacterial spores, enveloped viruses ○ Use Skin infectant ○ Special effect Hibiscrub has residual effect that stays on disinfected surface Alcohols Form ○ 70% ethanol ○ 60% isopropanol Target ○ Bactericidal, fungicidal, tuberculocidal, virucidal ○ Not sporicidal ○ Poor penetrating powers Use ○ For rapid disinfection of clean surfaces ○ Skin disinfection ○ For skin preparation Chlorhexidine in alcohol 2% chlorhexidine gluconate + 70% isopropanol Hazard ○ Flammable ○ Rapid evaporation 54  [IASM] Module 3: Infectious and Host Defence Microbes’ Resistance to Disinfectants *Lipids in enveloped viruses can be destroyed by soap Spaulding Classification The Spaulding Classification is the fundamental framework that determines the minimum level of disinfection/sterilisation required to mitigate infection Class of device Description Example Requirement Critical Instruments that have Catheters Sterilisation contact with the Imopants bloodstream or sterile Needles body areas Semi-critical Devices that come into Endoscopes Sterilisation contact with the mucous Respiratory therapy equipment High-level disinfection membrane Non-critical Devise that come into Stethoscope Low level disinfection contact with intact skin Sphygmomanometer cuffs Simple cleaning Environmental surfaces 55  [IASM] Module 3: Infectious and Host Defence [IAS59,65] Viruses and Prions / Medically Important Viruses Learning Outcomes What diseases do viruses cause ? What is a virus? How does a virus differ from a bacterium? How do viruses replicate and cause disease? How do you grow a virus in the laboratory? How do you diagnose virus infections? Other types of agents 56  [IASM] Module 3: Infectious and Host Defence Introduction to Viruses Structure of Viruses Viral genes / viral nucleic acid ○ DNA / RNA Viral genome ○ < 10 genes Capsid ○ Protein covering Denatured by heat, bleach NaOCl ○ For protection Envelope (not always present) ○ Derived from the lipid bilayer membrane of the host cell ○ Only in enveloped viruses ○ Dissolved by detergents or alcohol 57  [IASM] Module 3: Infectious and Host Defence Classification of Viruses 58  [IASM] Module 3: Infectious and Host Defence Size of Viruses Sizes of Different Organisms Visualising Viruses Using electron microscope ○ Wavelengths 100,000 times shorter than light ○ Can magnify objects over 2,000,000 times Using light (not yet in clinical diagnosis) ○ Super-resolution microscopy ○ Expansion microscopy 1. Embed object into matrix 2. Expand object 3. Observe structure The Virus Replication Cycle (Lytic Cycle) Host cell is required Follows specificity ○ Only specific types of cell Invasion of Host Cell 1. Viral entry via receptor binding Receptor induced endocytosis 2. Attachment / adsorption 3. Penetration (entering host cell) 4. Uncoating genetic content in cytoplasm By fusion of envelope 5. Taking over host metabolic machinery 6. Viral protein (transcription and translation) synthesis 7. Viral nucleic acid replication 8. Virus assembly when materials are sufficient 9. Viral release (with / without cell death) 59  [IASM] Module 3: Infectious and Host Defence Viral Genetic Replication Host cell DNA replication DNA Virus replication Replicates the cell’s action RNA Virus replication 1. Viral RNA replicates 2. Two fates Follows Central Dogma a. -ve sense RNA Replicates to form +ve sense RNA b. +ve sense RNA Translate into viral protein Retroviral Replication (e.g. HIV) 60  [IASM] Module 3: Infectious and Host Defence Viral Diseases Transmission of Viral Diseases Contact Droplet Aerosol ○ TB, Measles, Varicella-zoster virus (VZV) Parenteral ○ Arthropod bites ○ Needlestick ○ Surgery ○ Transfusion ○ Tissue transplant Development of Viral Diseases Incubation period Viral reproduction Clinical disease phase Immune response triggered Symptoms developed Viral shedding Host is infectious Pre Symptoms appear Have different lengths ○ Longer for immunocompromised individuals (AIDs) Convalescence / (death) Immune system controls infection Development of antibiotics Symptoms subside 61  [IASM] Module 3: Infectious and Host Defence Pathogenesis of Viral Diseases Pathogenesis is a series of events and processes that combine to produce disease : Ecology of virus and host Population dynamics of virus and host Transmission route Virus virulence Pathogenic Mechanisms of Virus Cytolysis (cytopathic effect) ○ Uncontrolled viral replication ○ Switch off host cell function ○ Induce apoptosis Immunopathological ○ Induce immune system to kill viral infected cells ○ E.g. Hepatitis B Oncogenesis ○ Induction of tumours ○ E.g. Hepatitis B leads to Hepatocellular carcinoma Types of Infection Localised infections Systemic infections Viral replication Viral replication ○ Virus multiplies at the epithelial ○ Initially at site of entry surface or near site of entry ○ Viraemia Manifestations Virus enters and spreads by bloodstream ○ Local disease (restricted to 1 Acute (short) viraemia in early phase of organ) many disseminated virus infections Respiratory infections Chronic (prolonged) viraemia in hepatitis Viral diarrhoea B and HIV ○ Enters distant sites Manifestations ○ Tissue tropism in localised organs ○ Organ damage is the major disease 62  [IASM] Module 3: Infectious and Host Defence Diagnosis For Viral Diseases A. Using Host Factors a. Detection of Antibody Response Detect IgG (Immunoglobulin G) A. Qualitative : No specific time indicated B. Quantitative : Paired sera 10-14 days apart, tested for antibody titre Rising antibody titre : Infection can be at some time during ○ > 4 fold increase at intervals lifetime Able to investigate date from infection Further paired samples are needed Detect IgM (Immunoglobulin M) ○ For recent infection within recent 1-3 months ○ One off b. Cellular Immune Response Cytokine expressions in lymphocytes stimulated by viral specific antigen ○ IFN-g ○ TNF ○ IL-6 63  [IASM] Module 3: Infectious and Host Defence A. Using Viral Factors Method Time Features Electron microscopy Hours > 106 virus particles per mL needed Viral antigen detection Hours By immunofluorescence Viral protein recognised by antibody to send antigen signals Viral nucleic acid Hours / PCR amplifies target DNA detection days ○ Use of fluorescent signal emitting compounds to show real time PCR In RNA virus ○ Reverse transcription step to convert virus RNA to complementary DNA before PCR Viral inclusion bodies Days E.g. Negri bodies in rabies (histology) Virus culture in cell line Days / Requirements (TBC by above weeks ○ Viruses do not grow on simple methods) acellular media as they need a host ○ Living cells are required Injected into live animals Embryonated egg inoculation Procedure : transported in virus transport medium ○ Buffer Indicates if the pH of the culture is usable Right pH prevents change in viral conformation that can affect infectivity ○ Protein Maintain virus stability and osmolarity 64  [IASM] Module 3: Infectious and Host Defence ○ Antibiotics Prevent contamination by bacterial growth Appearance : Virus cytopathic effect (CPE) ○ Roundup cell, giant cells with multiple nucleus ○ Cell detachment Serum dilution ○ CPE in cell line fixed and stained ○ Count plaque forming units (PFU) ○ Serum neutralising antibody (nAb) titre: The dilution needed to reduce the number of PFU by 50% 65  [IASM] Module 3: Infectious and Host Defence Examples of Medically Important Viral Diseases I. Skin Rash and Systemic Viral Infections a. Herpes Simplex Virus (HSV) Infections Virus Primary infection Site of latency Reactivated diseases / cancer HSV1 Orofacial lesions Sensory nerve Orofacial lesions Oral pain, fever ganglion Herpes labialis (cold sores) Blisters and ulcers in oral cavity Rash around lips, nose and eyes Induced by stress Enveloped virus 200 nm diameter HSV2 Anogenital lesions Sensory nerve Anogenital lesions Sexually transmitted Painful genital vesicles and ulcers ganglion VZV Chickenpox Sensory nerve Herpes zoster Aerosol transmission Fever ganglion Painful vesicles along a belt from back to front (highly infectious) Vesicular and pustular rash over face and Over right upper chest wall trunk Due to stress 66  [IASM] Module 3: Infectious and Host Defence Virus Primary infection Site of latency Reactivated diseases / cancer Mechanism of reactivation in sensory nerve ganglion Primary infection ○ Enters latent cycle ○ Remains within the trigeminal and dorsal root sensory ganglia of Cervical, thoracic and lumbosacral nerve roots Recurrence ○ Re Enter lytic cycle ○ Lytic infection in brain, skin ○ During stress and immunosuppression ○ Can be fatal to organ transplant recipient Cytomegalovirus Infectious mononucleosis like syndrome Hematopoietic Asymptomatic (CMV) ○ Fever, sore throat, enlarged lymph nodes progenitor cells Severe or disseminated if immunocompromised ○ Skin rash after antibiotic treatment Congenital CMV disease ○ Baby can be born with impaired hearing, microcephaly (small brain) Human herpes virus 6 Roseola infantum CD4 T Asymptomatic (HHV6) lymphocytes Severe or disseminated if immunocompromised HHV7 Roseola infantum CD4 T Asymptomatic lymphocytes Severe or disseminated if immunocompromised Epstein - Barr virus Infectious mononucleosis B lymphocytes Nasopharyngeal cancer (EBV) Lymphoma, lymphoproliferative disease HHV8 (/ KSHV) Non-specific symptoms Monocytes, Kaposi’s sarcoma (KS..) in HIV patients dendrites ,B cells, Castleman’s disease endothelial cells Primary effusion lymphoma