Introduction To Microbial Biodiversity PDF

INTRODUCTION TO MICROBIAL BIODIVERSITY Biodiversity: All the different forms of life forms (plants, animals, microorganisms) Our world is a microbial one.  Earth formed 4.5 billion years ago. Within the next billion years, the first cellular life forms-microbes-appeared. Since that time,...

INTRODUCTION TO MICROBIAL BIODIVERSITY Biodiversity: All the different forms of life forms (plants, animals, microorganisms) Our world is a microbial one.  Earth formed 4.5 billion years ago. Within the next billion years, the first cellular life forms-microbes-appeared. Since that time, microorganisms have evolved and diversified to occupy virtually every habitat on Earth: from oceanic geothermal vents to the coldest Arctic ice.  Microorganisms are defined as those organisms too small to be seen clearly by the unaided eye. The diversity of microorganisms has always presented a challenge to microbial taxonomists. Five kingdom classification + Virus (Example. Corona virus, HIV) INFECTION The first step, occurs when bacteria, viruses or other microbes that cause disease enter your body and begin to multiply. DISEASE Occurs when the cells in your body are damaged — as a result of the infection — and signs and symptoms of an illness appear. Localized infection: An infection that affects only one body part or organ. Generalized infection: An infection that has entered the bloodstream and has general systemic symptoms such as fever, chills, and low blood pressure. Endemic: A disease outbreak is endemic when it is consistently present but limited to a particular region. This makes the disease spread and rates predictable. Eg. Malaria, is considered endemic in certain countries and regions. Epidemic: an unexpected increase in the number of disease cases in a specific geographical area. Eg. Yellow fever, smallpox, measles, and polio. An epidemic disease doesn't necessarily have to be contagious. West Nile fever and the rapid increase in obesity rates are also considered epidemics. Pandemic: When a disease’s growth is exponential. This means the growth rate skyrockets, and each day cases grow more than the day prior. In being declared a pandemic, the virus has nothing to do with virology, population immunity, or disease severity. It means a virus covers a wide area, affecting several countries and populations. Sporadic: disease which occurs only infrequently, haphazardly, irregularly or occasionally from time to time in a few isolated places with no discernible temporal or spatial pattern, as opposed to a recognizable epidemic or endemic pattern. In the United States, tetanus, rabies, and plague are considered examples of sporadic diseases. Infection may be classified in various ways 1. Primary infection 2. Reinfection 3. Secondary infection 4. Focal infection 5. Cross infection 6. Nosocomial infection 7. Iatrogenic infection 8. Inapparent infection 9. Atypical infection 10.Latent infection COMMUNICABLE DISEASES NON COMMUNICABLE DISEASES Causes 1. Sedentary lifestyle: Insufficient or no physical activity, no outdoor games, lack of exercise, excessive use of vehicles. 2. Eating habits: Fast food that is high in fat and sugar (burgers, cakes, aerated drinks) lead to obesity at a young age. Can never replace the balanced nutrition provided by the Indian meal of chapattis or rice, pulses and vegetables. 3. Type “A” personality: People who are always focused on doing better than others rather than doing their best, those who get angry and frustrated easily and are intolerant towards others are more susceptible to lifestyle diseases. 4. Family history of heart disease and diabetes also predispose people to these diseases. Prevention Increased awareness of the reasons for lifestyle-related disorders Regular exercise, yoga, meditation Avoiding junk food, and increasing intake of vegetables and water Stress management, increased tolerance for others, and positive attitude Setting one’s own goals for improvement rather than blindly copying others Motivating people around you for practicing the above mentioned healthy habits. Identify the following diseases as communicable and non-communicable with justification Malaria HIV Hepatitis Dengue Diabetes Tuberculosis Influenza Obesity Hypertension COVID 19 How Do Infections Occur? An infection occurs when germs enter the body, increase in number, and cause a reaction of the body. Three things are necessary for an infection to occur: 1. Source: Places where infectious agents (germs) live (e.g., sinks, surfaces, human skin) 2. Susceptible Person with a way for germs to enter the body 3. Transmission: a way germs are moved to the susceptible person  SOURCES OF INFECTION Human Animals Insects Soil and Water 1. HUMAN: People are one source of germs including: Patients Healthcare workers Visitors and household members People can be sick with symptoms of an infection or colonized with germs (not have symptoms of an infection but able to pass the germs to others). Germs are also found in the healthcare environment. Examples of environmental sources of germs include: Dry surfaces in patient care areas (e.g., bed rails, medical equipment, countertops, and tables) Wet surfaces, moist environments, and biofilms (e.g., cooling towers, faucets and sinks, and equipment such as ventilators) In dwelling medical devices (e.g., catheters and IV lines) Dust or decaying debris (e.g., construction dust or wet materials from water leaks) 2. ANIMALS Animals sometimes carry harmful germs that can spread to people and cause illness – these are known as zoonotic diseases or zoonoses. Caused by harmful germs like viruses, bacteria, parasites, and fungi. These germs can cause many different types of illnesses in people and animals, ranging from mild to serious illness and even death. Animals can sometimes appear healthy even when they are carrying germs that can make people sick, depending on the zoonotic disease. HOW DO GERMS SPREAD BETWEEN ANIMALS AND PEOPLE? Direct contact: Coming into contact with the saliva, blood, urine, mucous, feces, or other body fluids of an infected animal. Examples include petting or touching animals, and bites or scratches. Indirect contact: Coming into contact with areas where animals live and roam, or objects or surfaces that have been contaminated with germs. Examples include aquarium tank water, pet habitats, chicken coops, barns, plants, and soil, as well as pet food and water dishes. Vector-borne: Being bitten by a tick, or an insect-like a mosquito or a flea. Foodborne: Eating or drinking something unsafe, such as unpasteurized (raw) milk, undercooked meat or eggs, or raw fruits and vegetables that are contaminated with feces from an infected animal. Contaminated food can cause illness in people and animals, including pets. Waterborne: Drinking or coming in contact with water that has been contaminated with feces from an infected animal. What can you do to protect yourself and your family from zoonotic diseases? People can come in contact with animals in many places - zoos, schools, stores, and parks. Insects, like mosquitoes and fleas, and ticks bite people and animals day and night. Keep hands clean. Always wash your hands after being around animals, even if you didn’t touch the animals. Know the simple things you can do to stay safe around your pets. Prevent bites from mosquitoes, ticks, and fleas. Learn more about ways to handle food safely Be aware of zoonotic diseases both at home, away from home, in childcare settings or schools and when you travel. Avoid bites and scratches from animals. 3. INSECTS The diseases occur because of the transmission of pathogens by insects to human beings- Arthropod-borne disease. Mosquitoes, ticks, mites, flies, fleas, and lice – vectors. There are two methods of transmission of a pathogen by insects: mechanical and biological. Examples : i. MALARIA: involved a Plasmodium protozoan that is transmitted by mosquitoes of the genus Anopheles. Malaria is the most deadly Arthropod-borne disease in the world, affecting some 250 million people in the world, with as many as 2 million deaths annually. ii. Plague: Fleas are the vector for the plague (or black death), which infects man as well as rats and other rodents. The plague has killed millions of people in history, especially in the 14th and 17th centuries. In 14th century Europe, the great pandemic resulted in twenty-five million deaths. iii. Enteric diseases: There are many bacterial diseases that are transmitted by some form of fecal contamination of food or water, either directly or indirectly. House flies are a primary agent in transmitting these diseases, and do so mechanically. Typhoid Fever (Salmonella typhi) is a well-known enteric disease, and affects humans worldwide. Cholera is another enteric disease of great importance. Shigella, causing dysentery and diarrhea, and Escherichia coli, causing urogenital and intestinal infections, are widespread enteric diseases. 4. SOIL AND WATER Soil-transmitted helminth infections are among the most common infections worldwide and affect the poorest and most deprived communities. They are transmitted by eggs present in human feces which in turn contaminate soil in areas where sanitation is poor. The main species that infect people are the roundworm (Ascaris lumbricoides), the whipworm (Trichuris trichiura) and hookworms (Necator americanus and Ancylostoma duodenale). Some pathogens can survive in the soil for very long periods. 5. FOOD Foodborne illnesses are usually infectious or toxic in nature and caused by bacteria, viruses, parasites or chemical substances entering the body through contaminated food. Chemical contamination can lead to acute poisoning or long-term diseases, such as cancer. Many foodborne diseases may lead to long-lasting disability and death. Bacteria Salmonella, Campylobacter, and enterohaemorrhagic Escherichia coli are some of the most common foodborne pathogens. Symptoms can be fever, headache, nausea, vomiting, abdominal pain, and diarrhea. Foods involved in outbreaks of salmonellosis include eggs, poultry, and other products of animal origin. Foodborne cases with Campylobacter are mainly caused by raw milk, raw or undercooked poultry and drinking water. Enterohaemorrhagic Escherichia coli is associated with unpasteurized milk, undercooked meat and contaminated fresh fruits and vegetables.  Listeria infections can lead to miscarriage in pregnant women or death of newborn babies. Listeria is found in unpasteurised dairy products and various ready-to-eat foods and can grow at refrigeration temperatures. Vibrio cholerae can infect people through contaminated water or food. Symptoms may include abdominal pain, vomiting and profuse watery diarrhoea, which quickly lead to severe dehydration and possibly death. Rice, vegetables, millet gruel and various types of seafood have been implicated in cholera outbreaks. Antibiotics, are essential to treat infections caused by bacteria, including foodborne pathogens. Viruses Although food is not a host for viruses, i.e. they cannot multiply in food, they can get onto the food via infected persons (e.g. food retailers or cooks) and survive there. Norovirus is a common cause of foodborne infections that is characterized by nausea, explosive vomiting, watery diarrhoea and abdominal pain. Hepatitis A virus can also be transmitted by food and can cause long-lasting liver disease and spreads typically through raw or undercooked seafood or contaminated raw produce. Parasites Some parasites, such as fish-borne trematodes, are only transmitted through food. Others, for example tapeworms like Echinococcus spp, or Taenia spp, may infect people through food or direct contact with animals. Other parasites, such as Ascaris, Cryptosporidium, Entamoeba histolytica or Giardia, enter the food chain via water or soil and can contaminate fresh produce. METHODS OF TRANSMISSION OF INFECTION  An infectious agent may be transmitted from its natural reservoir to a susceptible host in different ways. There are different classifications for modes of transmission. Here is one classification: 1. Direct Direct contact Droplet spread 2. Indirect Airborne Vehicleborne Vectorborne (mechanical or biologic)  Direct contact occurs through physical contact. Direct contact also refers to contact with soil or vegetation harboring infectious organisms. Droplet spread - to spray with relatively large, short-range aerosols produced by sneezing, coughing, or even talking. Droplet spread is classified as direct because transmission is by direct spray over a few feet, before the droplets fall to the ground. Pertussis and meningococcal infection are examples of diseases transmitted from an infectious patient to a susceptible host by droplet spread.  Indirect transmission refers to the transfer of an infectious agent from a reservoir to a host by suspended air particles, inanimate objects (vehicles), or animate intermediaries (vectors). Airborne transmission occurs when infectious agents are carried by dust or droplet nuclei suspended in air. Airborne dust includes material that has settled on surfaces and become resuspended by air currents as well as infectious particles blown from the soil by the wind. Droplet nuclei may remain suspended in the air for long periods of time and maybe blown over great distances. Measles, for example, has occurred in children who came into a physician’s office after a child with measles had left, because the measles virus remained suspended in the air. Vehicles that may indirectly transmit an infectious agent include food, water, biologic products (blood), and fomites (inanimate objects such as handkerchiefs, bedding, or surgical scalpels). A vehicle may passively carry a pathogen — as food or water may carry hepatitis A virus. Alternatively, the vehicle may provide an environment in which the agent grows, multiplies, or produces toxin — as improperly canned foods provide an environment that supports production of botulinum toxin by Clostridium botulinum. Vectors such as mosquitoes, fleas, and ticks may carry an infectious agent through purely mechanical means or may support growth or changes in the agent. Examples of mechanical transmission are flies carrying Shigella on their appendages and fleas carrying Yersinia pestis, the causative agent of plague, in their gut. In contrast, in biologic transmission, the causative agent of malaria or guinea worm disease undergoes maturation in an intermediate host before it can be transmitted to humans (Figure 1.20). Disinfection – Types of disinfection procedures  Disinfection describes a process that eliminates many or all pathogenic microorganisms on inanimate objects, with the exception of bacterial spores. It is usually accomplished by the use of liquid chemicals or wet pasteurization in health care settings. Sterilization is the complete elimination or destruction of all forms of microbial life and is accomplished in health care facilities by either physical or chemical processes. Disinfection and sterilization are essential for ensuring that medical and surgical instruments do not transmit infectious pathogens to patients.  Multiple studies in many countries have documented lack of compliance with established guidelines for disinfection and sterilization. Failure to comply with scientifically-based guidelines has led to numerous outbreaks. CDC: This guideline presents a pragmatic approach to the selection and proper use of disinfection and sterilization processes; the approach is based on well-designed studies assessing the efficacy (through laboratory investigations) and effectiveness (through clinical studies) of disinfection and sterilization procedures.  Many disinfectants are used alone or in combinations in the health care setting. These include alcohols, chlorine and chlorine compounds, formaldehyde, glutaraldehyde, ortho-phthalaldehyde, standard and improved hydrogen peroxide, iodophors, peracetic acid, phenolics, and quaternary ammonium compounds. Terms with the suffix cide or cidal for killing action also are commonly used. For example, a germicide is an agent that can kill microorganisms, particularly pathogenic organisms (“germs”). The term germicide includes both antiseptics and disinfectants. Antiseptics are germicides applied to living tissue and skin; disinfectants are antimicrobials applied only to inanimate objects.  Alcohols (60% to 90%): Alcohols are not recommended for sterilizing medical and surgical materials, principally because of their lack of sporicidal action and their inability to penetrate protein-rich materials. It’s used to disinfect oral and rectal thermometers, computers, hospital pagers, scissors, external surfaces of equipment (e.g., ventilators), and stethoscopes. Alcohol towelettes have been used for years to disinfect small surfaces such as rubber stoppers of multiple-dose medication vials or vaccine bottles. Alcohols are flammable and consequently must be stored in a cool, well-ventilated area. They also evaporate rapidly, and this makes extended exposure time difficult to achieve unless the items are immersed  Chlorine and Chlorine Compounds: Hypochlorites are the most widely used of the chlorine disinfectants and are available in liquid (e.g., sodium hypochlorite) or solid (e.g., calcium hypochlorite) forms. The most prevalent chlorine products are aqueous solutions of 5.25% to 6.15% sodium hypochlorite, which usually are called household bleach. They have a broad spectrum of antimicrobial activity.  Glutaraldehyde has gained wide acceptance as a high-level disinfectant and chemical sterilant. Hydrogen peroxide: good germicidal activity Hospital-acquired infections/ healthcare-associated infections (HAI)/ Nosocomial infections  A hospital-acquired infection (HAI) is an infection whose development is favored by a hospital environment, such as one acquired by a patient during a hospital visit. Modern healthcare employs many types of devices and procedures to treat patients and to help them recover. Infections can be associated with the devices used in medical procedures, such as catheters or ventilators.  These HAIs include 1. central line-associated bloodstream infection, 2. catheter-associated urinary tract infections, 3. ventilator-associated pneumonia, and 4. surgical site infection Infections may also occur at surgery sites, known as surgical site infections. CDC works to monitor and prevent these infections because they are an important threat to patient safety. 1. Central line-associated bloodstream infection (CLABSI) occurs when bacteria or other germs enter the patient’s central line and then enter their bloodstream. 2. Catheter-associated urinary tract infections: A urinary tract infection (UTI) is an infection involving any part of the urinary system, including the urethra, bladder, ureters, and kidney. UTIs are the most common type of healthcare-associated infection. Among UTIs acquired in the hospital, approximately 75% are associated with a urinary catheter, which is a tube inserted into the bladder through the urethra to drain urine. 3. Ventilator-associated pneumonia: is a lung infection that develops in a person who is on a ventilator. A ventilator is a machine that is used to help a patient breathe by giving oxygen through a tube placed in a patient’s mouth or nose, or through a hole in the front of the neck. An infection may occur if germs enter through the tube and get into the patient’s lungs. CDC provides guidelines and tools to the healthcare community to help end ventilator- associated pneumonia and resources to help the public understand these infections and take measures to safeguard their own health when possible. 4. Surgical site infection: is an infection that occurs after surgery in the part of the body where the surgery took place. Surgical site infections can sometimes be superficial infections involving the skin only. Other surgical site infections are more serious and can involve tissues under the skin, organs, or implanted material. CDC provides guidelines and tools to the healthcare community to help end surgical site infections and resources to help the public understand these infections and take measures to safeguard their own health when possible. Preventing Healthcare-associated Infections HAI are a threat to patient safety. CDC provides national leadership in surveillance, outbreak investigations, laboratory research, and prevention of healthcare-associated infections. CDC uses knowledge gained through these activities to detect infections and develop new strategies to prevent healthcare-associated infections. Public health action by CDC and other healthcare partners has led to improvements in clinical practice, medical procedures, and the ongoing development of evidence-based infection control guidance and prevention successes.