Medical Microbiology Introduction (MICR1010) 2023 PDF

MICR1010 INTRODUCTION TO MEDICAL MICROBIOLOGY DR. STACY STEPHENSON-CLARKE [email protected] INTRODUCTION Medical microbiology: study of collecting and identifying pathogenic organisms for medical management Numerous specialties (e.g., bacteriology, virology, mycology, parasitology) I...

MICR1010 INTRODUCTION TO MEDICAL MICROBIOLOGY DR. STACY STEPHENSON-CLARKE [email protected] INTRODUCTION Medical microbiology: study of collecting and identifying pathogenic organisms for medical management Numerous specialties (e.g., bacteriology, virology, mycology, parasitology) Insight into prevention of healthcare–associated infections 2-3 MODERN MEDICAL MICROBIOLOGY Bacteriology – the science of bacteria, the causative agents of a member of infectious diseases. Virology – the science of viruses, non-cellular living systems, capable of causing infectious diseases in man. Immunology – the science which concerned with mechanisms of body protection against pathogenic microorganisms and foreign cells and substances. Mycology – the study of fungi pathogenic for man. Protozoology – which deals with pathogenic unicellular animal organisms. TERMS USED IN MEDICAL MICROBIOLOGY Pathogens Microbial parasites Pathogenicity The ability of a parasite to inflict damage on the host Virulence Measure of pathogenicity Opportunistic pathogen Causes disease only in the absence of normal host resistance TERMS USED IN MEDICAL MICROBIOLOGY Infection Situation in which a microorganism is established and growing in a host, whether or not the host is harmed Disease Damage or injury to the host that impairs host function THE HUMAN MICROBIAL FLORA NORMAL HUMAN-MICROBIAL INTERACTIONS Most microorganisms are benign Few contribute to health, and fewer pose direct threats to health Normal microbial flora Microorganisms usually found associated with human body tissue Mammals develop in a microbially sterile environment in utero Colonization of tissues by numerous microbes occurs as mammals are exposed during the birth process The normal microflora grows on or in the human body NORMAL MICROBIOTA/FLORA Microorganisms that colonize the body but do not produce disease under normal conditions Region Examples of Microbiota Skin Staphylococcus, Propionibacterium, Micrococcus, Candida (fungus) Eyes Staphylococcus aureus, Micrococcus, Propionibacterium (causes acne) Upper Respiratory System (Nose & Throat) S. aureus, S. epidermidis, Streptococcus pneumoniae, Neisseria Oral Cavity (Mouth) Lactobacillus, Streptococcus, Staphylococcus, Bacteroides Large Intestine E. coli, Bacteroides, Enterococcus, Lactobacillus, Klebsiella, Candida (fungus) Urogenital Tract Staphylococcus, Lactobacillus, Candida albicans, Micrococcus, Streptococcus MICROFLORA OF THE GASTROINTESTINAL TRACT Major bacteria present Esophagus Organ Major physiological processes Prevotella Streptococcus Veillonella Esophagus Helicobacter Proteobacteria Bacteroidetes Actinobacteria Fusobacteria Stomach Secretion of acid (HCI) Digestion of macromolecules pH 2 Small intestine Continued digestion Absorption of monosaccharides, amino acids, fatty acids, water pH 4–5 Large intestine Absorption of bile acids, vitamin B12 pH 7 Duodenum Enterococci Lactobacilli Bacteroides Bifidobacterium Clostridium Enterobacteria Enterococcus Escherichia Eubacterium Klebsiella Lactobacillus Methanobrevibacter (Archaea) Peptococcus Peptostreptococcus Proteus Ruminococcus Staphylococcus Streptococcus Jejunum IIeum Colon Anus MEDICAL MICROBIOLOGY SAFETY IN THE MICROBIOLOGY LABORATORY BSL-1: lowest of the four, includes laboratory settings in which personnel work with low-risk microbes that pose little to no threat of infection in healthy adults. Example: nonpathogenic strain of E. coli. BSL-2: work with agents associated with human diseases (i.e. pathogenic) that pose a moderate health hazard. Examples: HIV, as well as Staphylococcus aureus (staph infections). BSL-3: work on microbes that are either indigenous or exotic, and can cause serious or potentially lethal disease through inhalation. Examples: yellow fever, West Nile virus, and the bacteria that causes tuberculosis. BSL-4: work with highly dangerous and exotic microbes. Infections are frequently fatal, and come without treatment or vaccines. Examples: Ebola virus HEALTHCARE-ASSOCIATED INFECTIONS Healthcare-associated infection (HAI) A local or systemic infection acquired at a healthcare facility Also called nosocomial infection Some HAI are acquired from patients Some HAI are acquired from hospital personnel LABORATORY DIAGNOSIS 1. Bacterioscopical 2. Bacteriological 3. Detection sensitivity of bacteria to antibiotics 4. Serological 5. Biological 6. DNA-technology test (PCR) DIRECT DETECTION OF PATHOGENS If a physician suspects a disease is caused by an infectious agent Samples of tissues or fluids are collected for microbiological, immunological, and molecular biological analyses Samples may include blood, urine, faeces, sputum, cerebrospinal fluid, or pus DIRECT DETECTION OF PATHOGENS Specimens must be obtained and handled properly Specimen should be obtained from site of infection and not surrounding tissue Sample must be taken aseptically Sample size must be large enough Metabolic requirements for the organism must be maintained during sampling, storage, and transport Collect before administration of antibiotics Label each specimen properly Transport to lab within allotted time Safe collection and handling lead to Accurate results Prevention of spread of disease to other health care workers or patients DIRECT DETECTION OF PATHOGENS Most microbes of clinical importance can be grown, isolated, and identified with specialized growth media Selective media Allow some organisms to grow while inhibiting others E.g. MSA (mannitol salt agar) contains mannitol, a phenol red indicator, and 7.5% sodium chloride. The high salt concentration inhibits the growth of most bacteria other than staphylococci Differential media Allow identification of organisms based on their growth and appearance on the medium E.g. EMB (eosin methylene blue agar) is used for the detection and isolation of Gramnegative intestinal pathogens. Eosin and methylene blue is used as an indicator and allows differentiation between organisms that ferment lactose and those that do not. Methylene blue inhibits Gram-positive organisms Blood agar Chocolate agar EMB agar ANTIMICROBIAL DRUG SUSCEPTIBILITY TESTING Minimum inhibitory concentration (MIC) procedure for antibiotic susceptibility testing employs an antibiotic dilution assay. Wells containing serial dilutions of antibiotics are inoculated with a standard amount of a test organism Look for inhibited growth Laboratory observation of antibiosis. ANTIMICROBIAL DRUG SUSCEPTIBILITY TESTING Disc diffusion test Standard procedure for assessing antimicrobial activity Agar media is spread evenly with culture of bacteria Inhibition zones Used to determine an organism's susceptibility to an antimicrobial agent Antibiotic susceptibility testing ANTIMICROBIAL DRUG SUSCEPTIBILITY TESTING E test is a non-diffusionbased technique that employs a preformed and predefined gradient of an antimicrobial agent immobilized on a plastic strip E test (for epsilometer), a gradient diffusion method that determines antibiotic sensitivity and estimates minimal inhibitory concentration (MIC). Figure 20.18 The E test (for epsilometer), a gradient diffusion method that determines antibiotic sensitivity and estimates minimal inhibitory concentration (MIC). MIC MIC GROWTH-INDEPENDENT DIAGNOSTIC METHODS Immunoassays for Infectious Disease Agglutination Immunofluorescence Enzyme Immunoassays, Rapid Tests, and Immunoblots Nucleic Acid Amplification ANTIMICROBIAL DRUGS Antimicrobial drugs are classified on the basis of: Molecular structure Mechanism of action Spectrum of antimicrobial activity Two categories of antimicrobial drugs Synthetic antimicrobial drugs Antibiotics 1. Inhibition of cell wall synthesis: penicillins, 2. Inhibition of protein synthesis: chloramphenicol, cephalosporins, bacitracin, vancomycin erythryomycin, tetracyclines, streptomycin DNA mRNA Transcription Protein Translation Replication Enzyme 4. Injury to plasma membrane: polymyxin B 5. Inhibition of essential metabolite synthesis: sulfanimide, trimethoprim 3. Inhibition of nucleic acid replication and transcription: quinolones, rifampin Major Action Modes of Antimicrobial Drugs RESISTANCE MECHANISMS AND SPREAD A variety of mutations can lead to antibiotic resistance Resistance genes are often on plasmids or transposons that can be horizontally transferred between bacteria Misuse of antibiotics selects for resistance mutants Misuse includes: Using outdated or weakened antibiotics Using antibiotics for the common cold and other inappropriate conditions Using antibiotics in animal feed Failing to complete the prescribed regimen Using someone else’s leftover prescription RESISTANCE MECHANISMS AND SPREAD Almost all pathogenic microbes have acquired resistance to some chemotherapeutic agents A few pathogens have developed resistance to all known antimicrobial agents (multiple-drug resistant) Methicillin-resistant S. aureus (MRSA) Resistance can be minimized by using antibiotics correctly and only when needed Resistance to a certain antibiotic can be lost if antibiotic is not used for several years PATHOGENICITY OF MICROORGANISMS KOCH’S POSTULATES 1. The same pathogen must be present in every case of the disease. 2. The pathogen must be isolated from the diseased host and grown in pure culture. 3. The pathogen from the pure culture must cause the disease when it is inoculated into a healthy, susceptible laboratory animal. 4. The pathogen must be isolated from the inoculated animal and must be shown to be the original organism. Koch’s Postulates: Understanding Disease. 1 Microorganisms are isolated from a diseased or dead animal. 2a The microorganisms are grown in pure culture. 3 The microorganisms are injected into a healthy laboratory animal. Colony 2b The microorganisms are identified. 4 Disease is reproduced in a laboratory animal. 5a The microorganisms are isolated from this animal and grown in pure culture. 5b Microorganisms are identified. The microorganism from the diseased host caused the same disease in a laboratory host. PATHOGENICITY AND VIRULENCE Pathogens use various strategies to establish virulence Virulence is the relative ability of a pathogen to cause disease ADHERENCE Bacteria and viruses that initiate infection often adhere specifically to epithelial cells through interactions between molecules on the surfaces of the pathogen and the host cell ADHERENCE E. coli bacteria (yellow-green) on human urinary bladder cells Bacteria (purple) adhering to human skin ADHERENCE Adhesins/ ligands bind to receptors on host cells Glycocalyx: Streptococcus mutans Fimbriae: Escherichia coli M protein: Streptococcus pyogenes Form biofilms Bacterial adherence can be facilitated by Extracellular macromolecules that are not covalently attached to the bacterial cell surface. Examples: slime layer, capsule Fimbriae and pili Fimbriae CAPSULES Aid attachment Aid antimicrobial resistance Prevent phagocytosis ▪ Streptococcus pneumoniae ▪ Haemophilus influenzae ▪ Bacillus anthracis Capsules and colonies in Streptococcus pneumoniae Mechanisms of Exotoxins and Endotoxins. exotoxins endotoxins Exotoxins are proteins produced inside pathogenic bacteria, most commonly grampositive bacteria, as part of their growth and metabolism. The exotoxins are then secreted into the surrounding medium during log phase. Endotoxins are the lipid portions of lipopolysaccharides (LPS) that are part of the outer membrane of the cell wall of gramnegative bacteria (lipid A). The endotoxins are liberated when the bacteria die and the cell wall breaks apart. Cell wall Exotoxin: toxic substances released outside the cell Clostridium botulinum, an example of a grampositive bacterium that produces exotoxins Salmonella typhimurium, an example of a gramnegative bacterium that produces endotoxins Endotoxins: toxins composed of lipids that are part of the cell membrane Microbial Mechanisms of Pathogenicity. When the balance between host and microbe is tipped in favor of the microbe, an infection or disease results. Learning these mechanisms of microbial pathogenicity is fundamental to understanding how pathogens are able to overcome the host’s defenses. H1N1 flu virus portals of entry Mucous membranes Respiratory tract Gastrointestinal tract Genitourinary tract Conjunctiva Skin Parenteral route Number of invading microbes penetration or evasion of host defenses Capsules Cell wall components Enzymes Antigenic variation Invasins Intracellular growth Adherence Mycobacterium intracellulare Clostridium tetani Micrographs are not shown to scale. damage to host cells Siderophores Direct damage Toxins Exotoxins Endotoxins Lysogenic conversion Cytopathic effects portals of exit Generally the same as the portals of entry for a given microbe: Mucous membranes Skin Parenteral route IMMUNITY INNATE RESISTANCE TO INFECTION Hosts have innate resistance to most pathogens Natural host resistance Tissue specificity Physical and chemical barriers ANTIBODIES Antibodies (immunoglobulins) are soluble proteins made by B cells in response to exposure to nonself antigens B cells display antibodies on their cell surfaces that directly interact with antigens to cause B cells to ingest pathogen via phagocytosis B cells then produce many pathogen-derived peptide antigens that are presented to antigen-specific helper T cells Antibodies can bind to pathogens Antibodies can bind to and inactivate toxins Antibodies provide targets for interaction with proteins of the complement system, resulting in destruction of antigens through lysis ANTIBODIES Several different classes of antibodies exist and are distinguished from one another by their amino acid sequence Each antibody class has a specific function: IgM are found in the blood, lymph & B cells; agglutinate microbes; first Ab produced in response to infection IgG - found in blood, lymph and intestine; cross placenta to protect fetus and newborn; enhance phagocytosis; neutralize toxins and viruses IgA is found in secretions from mucous membranes; mucosal protection IgE is found on blood, mast cells & basophils; allergic reactions; lysis of parasitic worms IgD is found on surface of B cell; initiate immune response TYPES OF ADAPTIVE IMMUNITY Naturally acquired active immunity Resulting from infection By acquiring an infection that initiates an adaptive immune response Naturally acquired passive immunity Transplacental or via colostrum Through antibody transfer across the placenta or in breast milk Artificially acquired active immunity Injection of Ag (vaccination) Exposure to a controlled dose of a harmless antigen to induce formation of antibodies Artificially acquired passive immunity Injection of Ab Injection of an antiserum derived from an immune individual RISK FACTORS FOR INFECTION Compromised host One or more resistance mechanisms are inactive (immunocompromised) The probability of infection is increased Age is an important factor Very young and very old individuals are more susceptible Stress can predispose a healthy individual to disease Diet plays a role in host susceptibility to infection Certain genetic conditions can compromise a host Degree of virulence exhibited by pathogenic microorganism EPIDEMIOLOGY EPIDEMIOLOGY BASICS A disease is an epidemic when it occurs in a large number of people in a population in a given area in a short time A pandemic is widespread, usually worldwide An endemic disease is constantly present in a population, usually at low incidences The incidence of a disease is the number of new cases of the disease in a given period of time The prevalence of a disease is the total number of new and existing cases in a population in a given time INFECTIOUS DISEASE TRANSMISSION Epidemiologists follow transmission of a disease by correlating geographic, climatic, social, and demographic data Used to identify possible modes of transmission For example, a disease limited to a tropical area may suggest something about its vector (e.g. Dengue fever) Direct host-to-host transmission Infected individual transmits a disease directly to a susceptible host without the assistance of an intermediary (e.g., flu, common cold, STDs, ringworm) Indirect host-to-host transmission Occurs when transmission is facilitated by a living or nonliving agent Living agents are called vectors Nonliving agents are called fomites VEHICLE TRANSMISSION Transmission by an inanimate reservoir (food e.g. botulism, water e.g. cholera, air e.g. influenza) DISEASE RESERVOIRS AND EPIDEMICS Reservoirs are sites in which infectious agents remain viable and from which individuals can become infected A number of infectious diseases are caused by pathogens that propagate in humans and animals For other pathogens, nonliving matter serves as reservoirs For example, soil is a reservoir for Clostridium tetani, the cause of tetanus Zoonosis is any disease that primarily infects animals but is occasionally transmitted to humans Control of a zoonotic disease in the human population may not eliminate the disease as a potential public health problem Certain infectious diseases have complex life cycles involving an obligate transfer from a nonhuman host to humans followed by transfer back to the nonhuman host DISEASE RESERVOIRS AND EPIDEMICS Carriers Pathogen-infected individuals showing no signs of clinical disease Potential sources of infections May be individuals in the incubation period of the disease Can be identified using diagnostic techniques, including culture MICROBIAL DISEASES OF THE SKIN: MACULAR RASH MICROBIAL DISEASES OF THE SKIN: PUSTULAR RASH MICROBIAL DISEASES OF THE EYE MICROBIAL DISEASES OF THE CNS: PART I MICROBIAL DISEASES OF THE CNS: PART II MICROBIAL DISEASES OF THE CIRCULATORY SYSTEM MICROBIAL DISEASES TRANSMITTED BY VECTORS MICROBIAL DISEASES OF RESPIRATORY SYSTEM MICROBIAL DISEASES OF DIGESTIVE SYSTEM MICROBIAL DISEASES OF GENITOURINARY SYSTEM