Medical Microbiology Notes PDF

LECCTURE NOTE ON MEDICAL MICROBIOLOGY AND PARASITOLOGY Course code: NSC Course title: Medical Microbiology and Parasitology COURSE OUTLINE. INTRODUCTION 1. Definition of microbiological terms 2. History and development of Microbiology 3. Rel...

LECCTURE NOTE ON MEDICAL MICROBIOLOGY AND PARASITOLOGY Course code: NSC Course title: Medical Microbiology and Parasitology COURSE OUTLINE. INTRODUCTION 1. Definition of microbiological terms 2. History and development of Microbiology 3. Relevance of Microbiology to Nursing 4. Classification of Microorganisms. INFECTIOUS PROCESS AND INFECTIOUS DIESEASE CONTROL 1. Source, transmission, and course of infectious 2. Chain of spread of infectious disease (causative agent, reservoir, carriers, Portal of exit, mode of transmission, portal of entry and susceptible hosts) 3. Lesions produced by infective agents in the body 4. General signs and symptoms of infectious process 5. Principle of Control of infectious process ❖ Handwashing, waste disposal, handling and disposal of sharps ❖ Decontamination, disinfection and sterilization ❖ Principles of Asepsis and application to sterile procedures/operating theatre ❖ Disposal of infected Materials and specimens 6. Quarantine, Isolation, contact tracing, case control and notification 7. Standard precautionary measures 8. Functions of the infectious control units of the hospital INTRODUCTION TO IMMUNOLOGY AND IMMUNE RESPONSE ❖ General principles and practices of immunology ❖ Antigens and antibodies ❖ Body defense against microbes i. Specific ii. Non-specific ❖ Classification of immunity ❖ Abnormal immune response i. Autoimmune response ii. Anaphylaxis iii. Serum sickness iv. Acquired immune deficiencies. DEFINITION OF MICROBIOLOGY: Microbiology is defined as the scientific discipline that is saddled with the responsibility of studying biological agent(s) that are invisible to an unaided eye. Microorganisms are everywhere and they can be beneficial as well as harmful to humans. For instance, Escherichia coli that are found in the lower alimentary canal are harmless at this site (normal body flora) and harmful at another site like th e vagina (causing infection). DEFINITION OF MICROBIOLOGICAL TERMS 1. Culture: this term is used to describe growing microorganism in an artificial media called culture media. 2. Culture media: This term describes the substrate used to grow microorganisms in the laboratory. It is either solid or in broth form and contains nutrients needed for microbial nutrition and growth. 3. Inoculations: This term described the introduction of microbes onto a culture media for the purpose of incubation and thereafter studying the features. 4. Incubation: 5. Bacteriophage: This term describes viruses that infect bacteria. 6. Antibiotics: This are synthetic drugs design to eliminate disease causing organism. 7. Antiseptic: A chemical solution, which will reduce and prevent growth of microorganisms on skin 8. Normal flora: This are mivrobes living freely on or within a living host without causing disease to the host. 9. Opportunistic organisms: This is a group of organism that are initial non-pathogenic but however becomes pathogenic when the immune system is compromised.  10. Pathogen: A microorganism with potential of causing disease 11. Pathogenesis: This terms describes the process leading to the development of a disease condition. 12. SOURCE: This is the part of the reservoir which provides the organisms that have infected or colonized patients i.e. where the organisms have come from. 13. FOMITES: inanimate objects or material on which disease producing agents may be conveyed, for example bedding and clothes History and Development of Microbiology Microbiology as defined earlier is the study of microscopic organisms. Life as we know it would not exist without microorganisms, this is because plants depends on microorganisms to help them obtain the nitrogen they need for survival, animals such cows and sheep need microorganisms in order to digest the cellulose in their plant based diets, humans depends a lot on plants and these other animals for their nutritional needs. Our ecosystem relies on the activities of these minute but very important organisms to degrade waste, enrich the soil and support life. Microorganisms is used to make cheese, wine, and to develop vaccines and antibiotics. The human body is home to billions of microorganisms referred to as “Normal flora or microbial flora” many of which helps to keep us healthy. Some microorganisms cause disease (i.e pathogenic microorganisms), from the common cold to AIDS. The threat of bioterrorism and new or re-emerging infectious microorganisms. Highlighted below are scientist and their contribution to the development of Microbiology; Robert Hooke (1635 - 1703) was a “polymath’ he made many scientific discoveries in the 17th century, including making one of the first microscopes and also using a copy of one of Leeuwenhoek’s microscopes to see and draw details of the structure of plant cells and some microbes.  Antony van Leeuwenhoek (1632-1723) made the first useful microscopes in the 19th century, they were fiendishly difficult to make and use, they were essentially a lens held in a metal clip, the lens was made from a tiny drop of molten glass, and he used such a microscope to see the first microscopic cells. Ilya Metchnikoff (1845-1916) was the first to realize that animals such as us had a defence system against infection, what we now call the immune system Paul Ehrlich (1854-1915), searched for the “magic bullet” against infectious disease, he synthesized the first successful (but very toxic) drug against a disease – syphilis, it was an arsenic derivative he called salvarsan. Gerhardt Domagk (1895-1964) developed the first useful drug against a variety of bacterial infections, the first sulfa drug –prontosil. Ironically, he died of an infection! Sir Alexander Fleming (1881-1955) and Selman Waksman (1888-1973) discovered the first relatively safe and effective antibiotics (of natural origin) – isolated from microorganisms. Fleming discovered penicillin, Waksman discovered streptomycin and a number of other antibiotics. Louis Pasteur (1822-1895) was a chemist, he made many great discoveries, and he performed a crucial experiment using a swan necked flask that proved that new life did not just spontaneously arise from substances like rotting meat. For centuries before Pasteur, many people believed in Spontaneous Generation- the belief that life is generated spontaneously from dead organic matter. Robert Koch (1843-1910) and his colleagues made many important discoveries in microbiology, Koch initiated the use of the seaweed polysaccharide gel called agar as a stable material for the formation of a gel on which separated and pure (single species) colonies of bacteria and fungi could be grown (actually it was the wife of a colleague of his who suggested it), this was a critical advance, and he also stated and used his Koch’s postulates required to prove that a given organism caused a given disease. They are popularly known as Koch’s postulates (Henle-Koch’s Postulates); 1. A specific organism should be found constantly in association with the disease. 2. The organism should be isolated and grown in a pure culture in the laboratory. 3. The pure culture when inoculated into a healthy susceptible animal should produce symptoms/ lesions of the same disease. 4. From the inoculated animal, the microorganism should be isolated in pure culture. 5. An additional criterion introduced is that specific antibodies to the causative organism should be demonstrable in patient’s serum. RELEVANCE OF MICROBIOLOGY TO NURSING Everyday nurses’ encounter with microbial world while working in medical health care settings/hospitals. They are engaged in managing all aspects of out-patient’s health and infection control in the hospitals. The microbial world is integral part of the healthcare settings. We all are aware of the fact that microbiology is a science of microscopic organisms which are invisible to our naked eyes. These microorganisms are present on and around human body and they maybe pathogenic (i.e disease causing potential) which gives rise to various diseases and commensals which help a person in remaining disease free. The study of microbiology is relevant to nurse in understanding vast world of these microscopic organisms, their disease-causing mechanism (i.e pathogenesis), control and also to establish a fact that they are connected with human world in many ways. Medical microbiology deals with the study of microorganisms responsible for various diseases of low to high intensity and it can be divided into: 1. Bacteriology, which deals with study of unicellular bacteria. 2. Virology, which facilitates study of viruses. 3. Parasitology, which involves unicellular to multicellular parasites. 4. Mycology, that deals with various fungal microorganisms Medical microbiology is an integral part of nursing and significant part of nursing profession. It provides the basic foundation to the nursing profession. Nurses take care of various groups of patients, including those with contagious infections so it is necessary for nurses to have good knowledge of microorganisms. In this case knowledge of medical microbiology would help them to understand the causative organism of disease and patient’s normal flora as some of them may turn pathogenic under specific conditions. For example, E coli which is a microorganism which is found in intestine and helps in absorption of Vitamin K, but it turns pathogenic in certain situations like when the immune system is weak due to certain diseases condition or in post-surgery this microbe may get transplanted at different place in the body. In such situation it would turn harmful (i.e becomes an opportunistic pathogen) to the body and produce symptoms of disease like, urinary tract infection. A nurse must learn to identify these bacteria so that appropriate medicines could be given to the patient and treatment is done accordingly. Bacteria usually tend to adapt themselves with the change in environment and resist some antibiotics or may be sensitive to other antibiotics. The knowledge of microbiology helps in treatment with suitable antibiotics. At times when an individual is not responding to chemotherapeutic agent given for treatment, antibiotic sensitivity test is performed to know the specific antibiotic which could be used in treatment. Microbiology helps a nursing professional to understand the basic concepts of reproduction, morphology, biochemical characteristics and genetics. Microbiology creates awareness about new diseases and modern molecular identification methods. The role of microorganism in development of certain medications and vaccinations cannot be ignored either. IMPORTANCE OF MEDICAL MICROBIOLOGY TO NURSING Below are some of the importance of having a sound knowledge of medical microbiology to a nursing professional: 1. Nurses are involved in managing all aspects of patient’s health and infection control in the hospitals. Nurse must know microbiology to take care of patient and to protect oneself from pathogenic microorganisms. Nurses utilise concepts of microbiology while giving patient care or doing procedures. 2. To prevent spread of infection: Nurses should have knowledge about the mode of spread of infection. Some of the infections are spread by contact (touch), air (air- borne), droplets (sneezing, coughing), some by eating contaminated food or drink (food borne), sexual contact (STDs), by arthropod bite (vector born) and others by contaminated blood transfusion, etc. This knowledge would help a nurse to look for specific control of spread of infection. If a nurse knows how the disease producing organism enters into the body, how they are discharged from the body and how they spread from person to person, the knowledge would help a nurse to use particular measures to save community and hospital spread of infection. 3. To maintain sterile field: A nurse must know procedures used to create and maintain a sterile field in the hospitals and these are based on the knowledge of microbiology. For instance, in operation theatres sterile field is very necessary, so a nurse must know how to create it and maintain it so that the post-operative infections could be avoided. One of the most important things is handwashing. This simple yet over looked act can prevent or reduce the chances of spreading infections. Hand washing technique reduces  load of microorganisms on hands of a nurse which further helps in restricting risk of hospital acquired infection. The knowledge of microbiology can further help a nurse to use sterile equipment which are a necessary part of invasive procedures done on patients. The principles of asepsis are based on microbiology. The knowledge of sterilisation techniques is mandatory for a nurse. The proper disposal of biomedical waste is equally important and knowledge of microbiology helps in this field also. The segregation of waste in different bins according to their origin is very important step before sending for disposal in order to avoid environmental pollution. 4. To collect specimens: Nurse must recognise the importance of proper collection of specimens to be sent for bacteriological examination to obtain accurate results. For instance, nurses need to be familiar with the various infectious disease and their route of infection so as to collect clinical specimen from a proper site like, pustule or blood or stool etc. Nurse must recognise the importance of proper collection of specimens to be sent for bacteriological examination to obtain accurate results. 5. To implement immunisation schedule in hospitals: A nurse also plays an important role in immunization to control threats of various diseases like diphtheria or MMR, polio etc. Thus, they must have knowledge of various antisera and vaccines used in preventing the dreadful diseases. The immunisation schedules and the cold chain (i.e a system of storing and transporting vaccines at the recommended temperature range from point of manufacture to point of use) used to deliver the vaccines from the production to the administration should be known to a nurse. The knowledge of immunology that is a part of microbiology, helps a nurse in this respect. Knowledge of immunology makes a nurse well prepared for vaccination and protection of vaccines by using cold chain.  Classification of Microorganism. Classification is the process by which organisms are grouped into various categories based on morphological, physiological, cellular, molecular characteristics and also on evolutionary relationships (i.e. phylogenetic relationships). Based on the listed characteristics, microorganisms are classified into the following five (5) kingdom: 1. Monera – Unicellular prokaryotes 2. Protista – Unicellular eukaryotes 3. Fungi – Eukaryotic, heterotrophic (saprophytic/ parasitic) and with a cell wall (chitin) 4. Plantae – Eukaryotic, autotrophic (photosynthetic) and with a cell wall (cellulose) 5. Animalia – Eukaryotic, heterotrophic (holozoic/ saprophytic etc.) and without a cell wall NOTE: Microorganisms except for viruses, which are non-cellular and have their own classification system, were placed in the first three kingdoms. The Three Domains System of Classification Presently, through advances in cell biology, biochemistry and genetics, microorganisms are now placed into three domains, each of which comprises of various kingdoms. The domains are: 1. Bacteria (prokaryotic – “true bacteria”) 2. Archaea (prokaryotic – “ancient bacteria”) 3. Eucarya (eukaryotic) Characteristics domain Bacteria: a. They are prokaryotic. b. They are single-celled organisms. c. They lack membrane bound nucleus and organelles. d. Most have cell wall that contains peptidoglycan. e. They are found in the soil, water and air and on other living organisms. f. Some are harmful while others are beneficial to man. Characteristics of domain Archaea a. They are prokaryotic. b. They are single-celled organisms. c. They lack membrane bound nucleus and organelles. d. They lack peptidoglycan in their cell walls. e. They have unique membrane lipids. f. Some have unusual metabolic characteristics, e.g. methanogens. g. Many are found in extreme environments. Domain Eucarya The major groups of microorganisms in this domain are fungi and protists that is consist of unicellular algae, protozoa, slime moulds. Fungi however is a group of microorganisms that range from unicellular forms like yeasts to moulds and mushrooms which are multicellular, it has characteristic thread like structures called hyphae. Many fungi play beneficial roles while others cause diseases in plants, animals and human. INFECTIOUS PROCESS AND INFECTIOUS DIESEASE CONTROL Source, Transmission and Course of infectious Infectious Agents (Bacteria,Viruses,Helminths,Protozoa) Susceptible Host Reservoir/Source Immunosuppressed individuals People Neonates Equipment Elderly water, food etc Portal of Entry Portal of Exit Urinary tract Excretion Mucous membrane Secretion Broken skin Skin contact Respiratory tract Respiratory droplet Means of transmission Airborne Waterborne Vector borne INFECTIOUS CYCLE Source/Reservoir of infectious agents: This simply is where microorganisms can be found. This may include: The environment e.g. dust, bedding, equipment, furniture, sinks or washbowls, bedpans, surfaces) Humans, including patients, staff and visitors, especially from hands. Portals of exit: This are required for microorganisms to be transmitted from human sources. Within hospital settings, portals of exit include: intravenous lines, urinary catheters, wound sites, open skin lesions, invasive devices, the respiratory system, skin, and mucous membranes Means of Transmission: - Infectious agents/pathogens are transmitted through the following listed means/ways: 1. Bloodborne: Through sexual transmission, injury or inoculation. The main concerns in hospitals are the transmission of HIV, Hepatitis B and C through sharp injuries or blood splashes. 2. Airborne: Through inhalation of small particles that remain suspended in the air for long periods of time and can be widely dispersed by air currents. 3. Respiratory Droplet: This also occurs through inhalation. Droplet transmission differs as the particles are larger and therefore do not remain suspended in the air. Spread is therefore through close contact with infected persons who may be sneezing, coughing, talking, or undergoing airway procedures such as intubation or bronchoscopy. 4. Contact: Through direct or indirect contact. Direct is the transfer of organisms by contact with contaminated hands. Indirect is the transfer of organisms through contact with contaminated fomites 5. Common vehicle: Through contaminated food, water, drugs, blood or other solutions 6. Vector borne: this occurs usually through arthropods such as mosquitoes and ticks but cockroaches, ants and flies can also transmit infection. Portals of entry: This is the route through which infectious agent gain access/entry into a susceptible host, they are the same as the portals of exit and are either natural or artificial. Susceptible host: An individual’s immune system ability to fight infection is often incapacitated/suppressed due to a number of factors itemised below, this makes an individual vulnerable/susceptible to infection. 1. Presence of underlying disease (diabetes) 2. Immune-compromised state resulting from HIV or chemotherapy treatment etc 3. Nutritional status 4. Age (the very young and the very old). Prevent and control infectious Agent: This is achieved by altering the disease circle by either of the following; 1. Limiting reservoirs/sources of infectious agents. 2. Preventing the routes of transmission. 3. Minimising portals of entry, and 4. Protecting susceptible patients. Principle of Control of infectious process Control of infectious diseases is designed to be archived by adherence to: A. Universal precautions and other standard precautions designed and intended to reduce the risk of transmission of bloodborne viruses and other common pathogens found within the healthcare setting. This includes the following: 1. Use of Gloves, which should be well-fitting and available for use wherever contact with blood or body fluids is anticipated. Although gloves cannot prevent penetrating injuries from sharp instruments and equipment, they can reduce the incidence of hand contamination from blood and body fluids. 2. Use of Glasses and masks to protect the Mucous membranes of healthcare workers (for example, eyes and mouth) against blood or body fluid splashes. Glasses, visors or shields can be used for the eyes and should be available for use, especially during procedures with increased risk of splashes, for example, surgical procedures, intravenous line insertions, irrigation, airway suctioning or bronchoscopy. Masks should also be worn during any procedures with an increased risk of splashes. Masks must be changed if they become contaminated or if they are not intact. Decontamination of reusable visors should be carried out frequently. 3. Protective clothing such as; impermeable plastic aprons or gowns should be worn where there is a risk of blood or other body fluids splashing onto clothing or bare skin.  4. Proper handling of contaminated instruments: such as needles, scalpel, blades. Such sharps should be kept minimal when in use and should be kept on sight too when in use. 5. Handling and Disposal of Linen: The use of protective clothing is advised. Contaminated linen (for example, bed sheets, pajamas, and towels) is usually described as infected or soiled. Such linen should be disposed of immediately, normally into a water-soluble bag, and clearly identified as contaminated. 6. Handling of clinical wastes: Clinical waste such as soiled dressings, cotton swabs and catheter bags. Disposal of clinical waste, including waste contaminated with blood or body fluids, should be carried out immediately, with the wastes put into clearly marked bags. Gloves and protective clothing should always be used when handling clinical waste. If bags are not available and non-disposable buckets are used, the buckets must be disinfected frequently, as they could be a source of infectious material. Bags or buckets should have a covering lid, and should be kept close to where contaminated waste will be generated. Bags and buckets should never be overfilled and should be closed securely as soon as they are full. They should be sent for incineration, and stored until they are out of the hospital. 7. Cleaning of spillages of blood and body fluids Spillages of blood and potentially infected body fluids onto the floor, on equipment, or other surfaces must be cleaned as soon as they occur, in order to prevent further unnecessary exposure. NOTE: To avoid cross contamination, additional precautionary measures needs to be ensured these measures includes; Handwashing, asepsis and decontamination. Handwashing: Proper handwashing can limit both cross infection of microorganisms and contamination from bloodborne pathogens. When procedures or tasks are finished, it is essential that healthcare staff go directly to available handwashing facilities with running water, preferably hot. Running water from a tap or pitcher is preferred, as microorganisms can breed in stagnant water. Hands should never be dipped into bowls of water, as this may re-contaminate the bowls. Steps to effective hand washing technique. 1. Palm to palm 2. Right palm over left dorsum and left palm over right dorsum 3. Palm to palm with fingers interlaced 4. Backs of fingers to opposing palms with fingers interlocked 5. Rotational rubbing of right thumb clasped in left palm and vice versa 6. Rotational rubbing backwards and forwards with clasped fingers of right hand in left finger and vice versa. SIGNIFICANCE OF HANDWASHING Effective handwashing helps to remove visible soilings Effective handwashing helps to remove transients’ organisms picked up during procedures or tasked within the hospital  It helps to reduce resident organisms that live on healthcare workers hands. This is especially important during surgical scrub for which the same hand washing technique is used, with the addition of the wrists and forearms. A surgical scrub should be carried out for 3–5 minutes and there should be utilization of a sterile disposable nailbrush and sterile towel for drying. Resident organisms can never be permanently removed and therefore no- touch techniques and sterile gloves are essential in surgical situations. When to perform hand wash: Hands should be washed: Before and after any aseptic technique or invasive procedure; Before contact with any susceptible patient or site, for example, intravenous sites or wounds; After contact with any body fluids, this also includes contact with toileting facilities; After handling contaminated equipment, waste or laundry; Before and after contact with any patient being nursed under isolation or transmission – based precautions; Before serving meals or drinks; After using the toilet; and At the start and end of work. Antiseptic hand cleansers should be used: 1. Before and after touching mucous membranes; for contact with skin that is not intact, including wounds 2. Before invasive procedures 3. When caring for high risk patients, for example, patients in critical care areas 4. When no water or soap is available. B. The use of isolation, or transmission-based precaution: This approach is employed in cases of highly infectious disease, it entails preventing  transmission of the infectious disease by isolating the infected individual in a treatment facility away from other patients in the health care facility while providing treatment and management. Decontamination: Decontamination procedures, when carried out appropriately, play an important part in preventing and controlling nosocomial infections. Unfortunately, the consequences of failed decontamination in the hospital setting can lead to outbreak of infection. Decontamination involves cleaning; which entails the removal of all visible dust, soil, other foreign material and removal of sufficient numbers of microorganisms to reduce risks for those who handle the object or an area. Effective methods of cleaning and drying have been proven to limit cross infection in all hospitals and should be performed on all items before disinfection and sterilization. Disinfection: This is a process that eliminates many or all, microorganisms on inanimate objects. Disinfectants may damage living tissue and are not intended for use as antiseptics. Some disinfectants may be inactivated by soilage found on objects and therefore, soilage must be cleaned off first. Disinfection is of three types: chemical, moist heat, and pasteurization. Sterilization: This is the complete elimination or destruction of all types of microbial life, sterilization is an absolute term, i.e. the article must be sterile meaning the absence of all microorganism, it effectively kills or eliminates transmissible agents such as fungi, bacteria, viruses and prions (Prions are infectious agents composed entirely of protein material which causes disease that is similar to viral infection) from equipment, foods, medications or biological culture medium. Sterilization is accomplished by a variety of methods, including: steam under pressure or moist heat (autoclaving); gas (ethylene oxide); dry heat (hot air oven), low temperature steam and formaldehyde and sterile filtration used for heat labile fluids or substances that can be damaged by irradiation and chemical sterilization such as injections and ophthalmic solutions, biological products, air and other gases for supply to aseptic areas. PRINCIPLES OF ASEPSIS AND APPLICATION TO STERILE PROCEDURES/OPERATING THEATRE