Microbiology & Parasitology Lecture Notes PDF

MICROBIOLOGY PARASITOLOGY Adapted 1  Lesson 1 Outline Introduction What is microbiology? Why study microbiology? First microorganisms on Earth Earliest known infectious diseases Pioneers in the science of microbiology Careers in microbiology...

MICROBIOLOGY PARASITOLOGY Adapted 1  Lesson 1 Outline Introduction What is microbiology? Why study microbiology? First microorganisms on Earth Earliest known infectious diseases Pioneers in the science of microbiology Careers in microbiology 2  What is Microbiology? Biology is the study of living organisms Microbiology is an advanced biology course Microbiology is the study of microbes, which are extremely small (microscopic) living organisms and certain non-living entities Living microbes are known as cellular microbes or microorganisms; examples include bacteria, archaea, some algae, protozoa, and some fungi Non-living microbes are known as acellular microbes or infectious particles; examples include viroids, prions, and viruses Microorganisms are ubiquitous 3 Acellular and Cellular Microbes 4  What is Microbiology? The microbes that cause disease are sometimes referred to as “germs” The scientific term for disease-causing microbes is pathogens Microbes that do not cause disease are called nonpathogens; the vast majority of microbes are nonpathogens 5  What is Microbiology? Microbes that live on and in our bodies are referred to as our indigenous microflora Some members of our indigenous microflora are opportunistic pathogens Opportunistic pathogens are microbes that can cause disease, but usually do not; they can be thought of as microbes that are awaiting the opportunity to cause disease Pathogens cause two categories of diseases: infectious diseases and microbial intoxications 6 Categories of Diseases Caused by Pathogens GLBH 205 - Microbiology 7  Why Study Microbiology? Microorganisms play significant roles in our lives; they are essential for life on this planet Photosynthetic algae and bacteria (such as cyanobacteria) produce much of the oxygen in our atmosphere Microorganisms are involved in the decomposition of dead organisms and waste products Saprophytes are organisms that live on dead and/or decaying organic matter The use of microbes to clean up toxic wastes and other industrial waste products is known as bioremediation 8 Microbes as Saprophytes 9  Why Study Microbiology? Many microbes play essential roles in various elemental cycles; e.g., the carbon, nitrogen, oxygen, sulfur, and phosphorous cycles Algae and bacteria serve as food for tiny animals; they are important links in food chains Microbes that live in the intestinal tracts of animals aid in the digestion of food and produce beneficial substances For many years, microorganisms have been used as “cell models”; the more that scientists learned about microbial cells, the more they learned about cells in general 10 They are important links in food chains Humans are on the top of the food chain 11 12 Microbes and Nitrogen Fixation 13  Why Study Microbiology? Microbes are used in many industries; e.g., food, beverage, chemical, and antibiotic industries and in genetic engineering In genetic engineering, a gene or genes from one organism is/are inserted into a bacterial or yeast cell; the cell that receives the new gene(s) is then capable of producing the gene product(s) coded for by the new gene(s) The use of living organisms or their derivatives to make or modify useful products or processes is call biotechnology 14 Typical application of biodispersant to remediate an oil spill http://en.wikipedia.org/wiki/US_Microbics#George_Robinson 15 More on Why to Study Microbiology… Use of microbes as “cell models” – E. Coli is one of the most studied Microbes cause two categories of diseases: 1. Infectious disease – This is the leading cause of death in the world and the 3rd leading cause of death in the US (after heart disease and cancer). 2. Microbial intoxication 16 17  First Microorganisms on Earth Scientists tell us … Fossils of primitive microorganisms date back about 3.5 billion years ago. Candidates for the first microorganisms on Earth are archaea and cyanobacteria. Infectious diseases of humans and animals have existed for as long as humans and animals have inhabited the planet. Earliest known account of pestilence occurred in Egypt in about 3180 BC. 18  Earliest Observations Bacteria and protozoa were the first microbes to be observed by humans Earliest observations recorded in 1665 The earliest microbiologists: 1. Anton van Leeuwenhoek (1632 – 1723) 2. Louis Pasteur (1822 – 1895) 3. Robert Koch (1843 – 1910) 19  The First Observations 1665: Robert Hooke reported that living things were composed of little boxes, or cells – Ground for the cell theory 1858: Rudolf Virchow said cells arise from preexisting cells Cell theory: All living things are composed of cells and come from preexisting cells 20  Pioneers in the Science of Microbiology Anton van Leeuwenhoek (1632- 1723) – “Father of Microbiology” – Not a trained scientist! – Made many simple single-lens microscopes – Observed ”animalcules” (bacteria and protozoa) 21  Pioneers in the Science of Microbiology Louis Pasteur (1822-1895) – French chemist who made numerous contributions to microbiology – Investigated different fermentation products – Developed the pasteurization process – Discovered life forms that could exist without oxygen (anaerobes) – Developed several vaccines, including rabies and anthrax vaccines 22  Debate on Spontaneous Generation Francisco Redi (1668) demonstrated that maggots appear on decaying meat only when flies are able to lay eggs on the meat John Needham (1745) claimed microorganism arise spontaneously from heated nutrient broth Lazzaro Spallanzani (1765) repeated Needham’s experiments and suggested that it was due to air- microorganisms entering the broth. Rudolf Virchow (1858) introduced “biogenesis” concept where living cells arise only from preexisting cells. 23  Evidence Pro and Con 1668: Francesco Redi filled 6 jars with decaying meat Conditions Results Three jars covered with No maggots fine net Three open jars Maggots appeared From where did the maggots come? What was the purpose of the sealed jars? Spontaneous generation or biogenesis? 24  Evidence Pro and Con 1745: John Needham put boiled nutrient broth into covered flasks Conditions Results Nutrient broth heated, Microbial growth then placed in sealed flask From where did the microbes come? Spontaneous generation or biogenesis? 25  Evidence Pro and Con 1765: Lazzaro Spallanzani boiled nutrient solutions in flasks Conditions Results Nutrient broth placed in No microbial growth flask, heated, then sealed Spontaneous generation or biogenesis? 26  Evidence Pro and Con 1861: Louis Pasteur demonstrated that microorganisms are present in the air Conditions Results Nutrient broth placed in flask, Microbial growth heated, not sealed Nutrient broth placed in flask, No microbial growth heated, then sealed Spontaneous generation or biogenesis? 27  The Theory of Biogenesis Pasteur’s S-shaped flask kept microbes out but let air in 28 1.3 Figure Fermentation and Pasteurization Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not hot enough to evaporate the alcohol in wine Pasteurization is the application of a high heat for a short time Figure 1.4 29 Pioneers in the Science of Microbiology Robert Koch (1843-1910) – German physician who made numerous contributions to microbiology – Made significant contributions to the germ theory of disease – Discovered that Bacillus anthracis produced spores – Developed methods of fixing and staining bacteria – Developed methods to cultivate bacteria 30  Koch’s Postulates 1. A particular microbe must be found in all cases of the disease and must not be present in healthy animals or humans. 2. The microbe must be isolated from the diseased animal or human and grown in pure culture in the laboratory. 3. The same disease must be produced when microbes from the pure culture are inoculated into healthy susceptible laboratory animals. 4. The same microbe must be recovered from the experimentally infected animals and grown again in pure culture. 31 Koch’s Postulates 32  Koch’s Postulates, cont. If an organism fulfills Koch’s postulates, it has been proven to be the cause of that particular infectious disease Koch’s Postulates helped prove the germ theory of disease Koch gave a tremendous boost to the development of microbiology by stressing laboratory culture and identification of microorganisms Circumstances do exist in which Koch’s Postulates cannot be fulfilled 33  Exceptions to Koch’s Postulates Regarding in-vitro grow/culture of pathogen in or on artificial culture media – Some pathogens will not grow in this media Viruses, rickettsias, chlamydias that are obligate intracellular pathogens Bacteria causing leprosy and syphilis – Some fastidious microbes (with complex and demanding nutritional requirements) Some pathogens are species-specific Synergistic infections are caused by combined effects of two or more different microbes. Some diseases are not caused by microbes (e.g. nutritional deficiencies 34  Careers in Microbiology A microbiologist is a scientist who studies microbes. There are many career fields within the science of microbiology (e.g., bacteriology, phycology, protozoology, mycology, parasitology, and virology). Medical Microbiology – Involves the study of pathogens, the disease they cause and the body’s defenses against disease. – Concerned with epidemiology, transmission of pathogens, disease-prevention measures, aseptic techniques, treatment of infectious diseases, immunology, and production of vaccines. 35  Types of symbiotic microbe-host relationships Mutualism * Commensalism * Parasitism What are the benefits of normal flora? Benefit to the bacteria = They have a place to eat, survive and multiply. Benefits to the human = Bacteria may produce vitamins (such as B and K), and break down food that host cant normally digest. Normal flora protect host against infection by pathogenic organisms: - take up space, so pathogen has nowhere to set up shop - may out-compete the invader for available nutrients - may produce anti-bacterial chemicals (bacteriocins) - long-term relationship with the human immune system 36  Types of symbiotic microbe-host relationships Mutualism * Commensalism * Parasitism - One partner in the relationship – Pathogens that harm benefits.The other neither their host. benefits nor is harmed. – Cost to the host can vary from slight to Streptococcus fatal. pyogenes, a pathogen that – External parasites can cause Strep throat, post- (ectoparasite) cause partum fever, infestation. – Internal parasites pneumonia and necrotizing fasciitis. (endoparasite) cause infection.  Q: Why are you in this class? “Because it is a requirement to get into my program of study. Why else?  Impact of Infectious Disease Average life span: - Bronze age 26 yrs - Medieval Europe (400 – 1500 ad) 30 yrs - Early 20th century 50 – 64 yrs - Now world average 71 years (USA., 78.7) Q: Why? From the Virtual Microbiology Classroom on ScienceProfOnline.com Impact of Infectious Disease Bubonic Plague a.k.a. Black Plague & Black Death Caused by bacteria Yersinia pestis. Several pandemics of plague have occurred throughout history. Doctor beak from Roman engraving, 1656 Physician attire for protection from 50 million deaths between the Bubonic plague (a.k.a years 1346 – 50. Black death). Nearly 1/2 of Europe perished in this plague  Impact of Infectious Disease The Sedlec Ossuary, small Roman Catholic chapel, located in the Czech Republic. Contains ~ 40,000-70,000 human skeletons which have been artistically arranged to form decorations and furnishings for the chapel. Many of these bones were from bubonic plague victims. “Bring out your dead!” plague scene from Monty Python & Holy Grail.  Impact of Infectious Disease Bubonic Plague  Impact of Infectious Disease Smallpox Caused two airborne virus variants, Variola major and Variola minor. Deadly disease that, in survivors, can cause disfigurement and blindness. Killed Queen Mary II of England, Emperor Joseph I of Austria, King Luis I of Spain, Tsar Peter II and King Louis XV of France. Approx 300 million deaths worldwide just in the 20th century. Eradicated in 1980 though widespread vaccination. Now still possible weapon of bioterrorism. Watch this short National Geographic video on Smallpox.  Impact of Infectious Disease Influenza Infectious disease caused by RNA viruses in the family Orthomyxoviridae. Spanish flu pandemic 1918; more than 50 million deaths. In the U.S. seasonal flu kills thousands of people every year (mainly very young and old). Q: How is pandemic influenza different from seasonal flu? Watch this short National Geographic video “How Flu Viruses Attack”.  Impact of Infectious Disease AIDS - Acquired immune deficiency syndrome (AIDS). - Caused by HIV (human immunodeficiency) virus, a retrovirus that infects T-cells of the immune system. - AIDS fatalities typically die of opportunistic infections and tumors. Everything comes - More than 39 million people have from died from HIV since it was recognized somewhere… in 1981. Where did HIV come from? - With anti-retroviral drug therapy, This semester more, and more people are living with we will listen to aids. the RADIOLAB - New breakthroughs in anti-retroviral podcast drugs can reduce contagiousness and “Patient 0” to transmission of HIV. find out. - Recent HIV News:“New Insights into HIV Vaccines Will Improve Drug Development”, Science News 2013  Impact of Infectious Disease HBV Hepatitis B = infectious inflammatory illness of the liver caused by hepatitis B virus (HBV). Virus transmitted by exposure to infectious blood or body fluids. Risk of HBV transmission from carrier 10 – 35%. Health care workers high risk group. The hepatitis B virus is 50 to 100 times more infectious than HIV. HBV infection may be either acute (self-limiting) or chronic (long- standing). Persons with self-limiting infection clear the infection spontaneously within weeks to months. Watch this video on Hepatitis A & B and how they can damage the liver. Get vaccinated!  Impact of Infectious Disease SARS Severe acute respiratory syndrome caused by the SARS coronavirus, an enveloped RNA virus. One near pandemic to date, with 8,096 known infected cases and 774 deaths (fatality rate of 9.6%). Within a matter of weeks in early 2003, SARS spread from a province of China to infect individuals in 37 countries. Majority of those who became sick were household contacts and health care workers.  Where does the Ebola virus hide? Ebola Virus Disease May be present in more animals than previously thought, including chimpanzees, gorillas, fruit (a.k.a. Ebola Hemorrhagic Fever) bats, monkeys, antelopes, porcupines, rodents, dogs, pigs and humans. Caused by ssRNA animal viruses, a filovirus Ebola viruses, and their relative Marbug viruses cause severe and often fatal hemorrhagic fever in humans and other mammals. EVD first appeared in 1976 in 2 simultaneous African outbreaks, one in Sudan, and the other in Democratic Republic of Congo. The 2014 Ebola epidemic is the largest in history, affecting multiple countries in West Africa, causing more than 8,000 deaths. Transmission Transmitted from wild animals and spreads in the human population through human-to-human transmission. Spreads through direct contact with bodily fluids of infected people and animals, as well as from contaminated surfaces. Health-care workers frequently infected when infection control precautions not strictly practiced. Burial ceremonies where mourners have direct contact with body of deceased Ebola victim can also play a role in transmission. People remain infectious as long as their body fluids contain the virus. Recovered males can transmit through semen for up to 7 weeks after recovery.  Coronavirus disease 2019 (COVID-19) is a contagious disease caused by the virus SARS-CoV-2. The first known case was identified in Wuhan, China, in December 2019.The disease quickly spread worldwide, resulting in the COVID-19 pandemic. Symptoms: Fever, cough, fatigue, shortness of breath, vomiting, loss of taste or smell; some cases are asymptomatic Complications: Pneumonia, sepsis, ARDS, kidney failure, respiratory failure, pulmonary fibrosis, MIS-C, long COVID Usual onset: 2–14 days (typically 5) after infection Duration: 5 days to chronic Causes: SARS-CoV-2 Diagnostic method: RT-PCR testing, CT scan, rapid antigen test Prevention: Vaccination, face coverings, quarantine, social distancing, ventilation, hand washing Treatment: Symptomatic and supportive Frequency: 712,626,736 confirmed cases Deaths: 6,202,362 (reported) 17.6–31.4 million (estimated) 49  What is a nosocomial infection? There are many different 2011 HAI Prevalence Survey found that on any given day, about 1 in 25 types of microbes that cause hospital patients has at least one HAIs. Many are bacteria healthcare-associated infection. resistant to antibiotics. There were an estimated 722,000 A majority of HAIs include: HAIs in U.S acute care hospitals in 2011. Urinary tract infections Surgical site infections About 75,000 hospital patients with Bloodstream infections HAIs died during their Pneumonia hospitalizations. Most of these HAI infections are preventable..  Q: What is the single most important thing that you can do to prevent the spread of infectious disease? Find out by watching this CDC (Centers for Disease Control) video: Put Your Hands Together.  Confused? Sm Here are links to fun resources that further explain ar t what we discussed in this lecture: Li ksn Intro to Microbiology Main Page on the Virtual Microbiology Classroom of Science Prof Online. Play Pandemic 2 a video game of strategy, where you try to become a successful pandemic microbe and infect the world. My 14-year old, daughter and I recommend this one to you. “Quarantine” a scary movie about a new infectious disease. “Contagion” great dramatic movie that realistically depicts what could happen in outbreak of a novel, virulent infectious disease. Play Disease Defenders educational video game, Rice University. Normal Flora webpage, by Douglas F. Fix. Interactive page where you can select an area of the body and learn which normal flora typically colonize that location. “Catch My Disease” song by Ben Lee. Bacterial Pathogen Pronunciation Station, a webpage with links to audio files containing the pronunciation of the bacterial names, created by Neal R. Chamberlain, Ph.D. Giant Microbes, a company that sells adorable stuffed microbes. (You must be in PPT slideshow view to click on links.) END OF PRESENTATION 53