Medical Microbiology MICR433/533 Spring 2025 Lecture Notes PDF

Medical Microbiology MICR433/533 Spring 2025 Classroom: SDS 100 Class Time: 10.00-10.50 AM. Instructor: Radhey Kaushik. Office Hours: Tuesday, 1pm-2pm. Office: McFadden Biostress Building-SNP 252B Tel: 605-688-5501 E-mail: [email protected] Co...

Medical Microbiology MICR433/533 Spring 2025 Classroom: SDS 100 Class Time: 10.00-10.50 AM. Instructor: Radhey Kaushik. Office Hours: Tuesday, 1pm-2pm. Office: McFadden Biostress Building-SNP 252B Tel: 605-688-5501 E-mail: [email protected] Course URL: https://d2l.sdbor.edu/ Textbook: Nester’s Microbiology: A Human Perspective by Anderson, Salm, and Beins; 10th edition, 2022.  MICR433/533 Grading scheme (undergraduates) 3 Term tests (40 points each) = 120 points 1 Final Exam = 80 points Quizzes, take home assignments & in-class activities (This may include specified readings, videos, lectures or written assignments) = 50 points TOTAL = 250 points The final course grade will be out of 250 points, converted to 100%. Graduate students: 50 points additional essay assignment TOTAL = 300 points Both announced and/or unannounced quizzes and in- class activities may be given any day of the class.  MICR433/533 Basis for letter grade: 89.6-100% = A 79.6-89.5 % = B 69.6-79.5% = C 55-69.5% = D < 55.0% = F Term tests: on Monday, Feb 3; Friday, Feb 28; and Wed, April 2, 2025. Each test will be of 40 points. Final Exam: on Monday, May 5, 2025, from 9.15-11:15 AM, and will include material since the 3rd exam (~55-65 points) plus comprehensive questions from material covered earlier (~15-25 points).  Tests and Exams Written tests will be single type and/or a combination of any of essay, case study, short answers, multiple choices, fill-in the blanks, matching and true-false questions etc. All quizzes, term tests and final examination will be conducted in class during assigned class time/final exam time.  Format for the Course The course material is broadly divided into 3 sections 1. Review of basic concepts in microbiology. 2. Review of host responses to infection. 3. System by system study of infectious diseases.  Microbiology and microorganisms Microbiology: study of the microbial world. Microorganisms and microbes (microbial world): Existed for several billion years. All higher forms of life evolved from microscopic forms, so microbes are the foundation of all life. All organisms including humans require the activities of microorganisms to survive.  Microbiology and microorganisms Microorganisms (cellular/living) & other infectious agents (acellular/non-living) are collectively called ‘microbes’. Microbes Can change their properties. are capable of rapid adaptation/evolution due to their rapid & short generation time & relatively simple genome. are very biodiverse. are both beneficial and harmful in nature.  The Human microbiome Skin & mucosa are populated with characteristic communities of microorganisms collectively called ‘normal microbiota’ or ‘normal flora’. Many sources claim that human body carries 10 times as many microbial cells as human cells. However, more recent and accurate estimates indicate that the ratio is closer to 3:1 or even 1:1.  The Human Microbiome Project Started in 2007. Used DNA sequencing technologies to characterize the microbial communities that inhabit the human body. The term ‘microbiome’ has two overlapping meanings: 1. The total genetic content of a microbial community. 2. The microbial community itself. Only less than 1% of the microorganisms can be currently cultured in the laboratory and, thus, they are mainly characterized using DNA technologies.  Human microbiome Normal microbiota play several essential roles: – Preventing disease by competing with pathogens. – Help in degradation of foods. – Promote the development of immune system. – Early exposure to certain microbes lessens the likelihood of allergies, asthma & other diseases. – Effect the brain chemistry and behavior and weight gain. Disturbances in a microbial population at body surfaces can create an imbalance which can harm a person’s health. The human microbiome’s effect on health and disease is an exciting area of active research.  Microorganisms in the environment Are the masters of recycling. Production of oxygen by various photosynthetic microorganisms. Microorganisms can recycle and use atmospheric nitrogen. They convert nitrogen in the form which other organisms can use through a process called nitrogen fixation.  Microorganisms in the environment Microorganisms can degrade variety of materials that other organisms cannot degrade. External: – Cellulose in plants is degraded (leaves and fallen trees). – Used for sewage & waste-water treatment. Internal: – Cellulose degradation in digestive tract of animals (cattle, sheep & deer).  Commercial benefits of microbes Food production: bread, beer, fermented drinks, yoghurt, buttermilk, cheese and probiotics (live organisms that provide health benefits). Bioremediation: degradation of toxic materials and environmental pollutants by microbes: – sewage and waste-water, – petroleum, – polychlorinated biphenyls (PCBs), – DDT, – trichloroethylene (toxic solvent used in dry cleaning), – oil spills, and – radioisotopes. Degradation of plastics by microorganisms.  Commercial benefits of microbes Synthesis of commercial products: Cellulose, amino acids, hydroxybutyric acid, hydrogen gas, ethanol, oils, insect toxins, and antibiotics. Biotechnology (the use of microbiological and biochemical techniques to solve practical problems): medically important products (insulin), recombinant proteins, vaccines, resistant plants and uses in gene therapy.  Microbes as research tools Microorganisms are wonderful model organism to study as they have same fundamental metabolic and genetic properties as higher life forms. All cells are composed of same chemical elements & they synthesize their cell structures by similar mechanisms. What is true of elephants is also true of bacteria, and bacteria are much easier to study! Bacteria can be used to obtain results quickly as they grow rapidly & can be grown in simple, inexpensive media. Most major advances towards understanding life have come through study of bacteria and yeast.  Microbes and disease Most microbes are beneficial (~87%) and not harmful. Only a very small minority (~3%) of microbes cause disease (pathogens). 10% are opportunistic microbes. Medical Microbiology: Study of disease-causing microbes (pathogens)-Viruses, bacteria, prions, fungi, protozoa etc. Infectious diseases have existed for many years, and affect humans, animals, plants, and microbes. More Americans died of influenza in 1918-19 than killed in World war I, II, Korean, Vietnam and Iraq wars combined.  Microbes and disease Smallpox virus killed many million people in the past. Worldwide vaccination program eliminated the smallpox since 1977 & WHO declared its eradication in 1980. Plague (1347-51)killed 25 million people & discovery of antibiotics made the plague treatment possible. Because of Foot & mouth disease outbreak 4 million pigs, sheep and cattle were killed in England in 2001. Recently over a million pigs in China either died from African swine fever or were killed to control the disease. Recently, SARS-CoV-2 (COVID-19) has killed over 6 million people worldwide during 2019-23.  Microbes and disease Modern sanitation, vaccination, quarantine methods and effective use of antibiotics has reduced the incidence of infectious diseases. The death rate due to infectious diseases decreased dramatically over the last 100 years. However, on a worldwide basis, infectious diseases remain too common, particularly in developing countries.  Remaining major challenges Emerging infectious disease (EID) is an infectious disease that has become more common in the last several decades. Many of EIDs are new or newly recognized such as: – COVID-19 (for Coronavirus disease 2019) – Ebola virus disease – Congenital Zika syndrome – Severe Acute Respiratory Syndrome (SARS) – Middle East respiratory syndrome (MERS) – Hepatitis C – Certain types of influenza including Swine flu – Lyme disease – Acquired Immunodeficiency syndrome (AIDS) – Hanta virus pulmonary syndrome – Mad-cow disease (bovine spongiform encephalopathy) Long-established diseases such as malaria & tuberculosis has become more common recently.  ‘New’ and newly recognized Infectious Diseases in Humans & Animals since 1976 In USA alone, many million cases of infectious diseases occur every year and cause many thousand deaths and costs tens of billion dollars in health care.  Reasons for emerging or re-emerging infectious diseases 1. Pathogens’ ability to infect new hosts e.g. HIV & COVID-19. 2. Changes in infectious agents' virulence e.g. E. coli O104:H4. 3. Changing life-styles brings opportunities for infectious agents to spread e.g. hantavirus pulmonary syndrome. 4. Resistance to antibiotics or antimicrobial medication e.g. tuberculosis and malaria. 5. Ignorance for childhood vaccination e.g. measles. 6. Increased proportion of elderly people 7. Immunocompromised individuals become susceptible to variety of infections such as tuberculosis. 8. Global travel and mobile population e.g. COVID-19.  Chronic diseases caused by bacteria/viruses Peptic ulcers & chronic indigestion have recently been shown to be caused by bacteria Helicobacter pylori. Cervical cancer caused by human papillomavirus (HPV). Infectious microbes may play important roles in other chronic diseases.  Microbial World All living microorganisms are classified into three major groups called ‘domains’ Bacteria Archaea Eucarya (Eukarya) Members of ‘Bacteria’ & ‘Archaea’ are collectively termed ‘prokaryotes’ (Prenucleus). Although, ‘Bacteria’ and ‘Archaea’ members have structural similarities, they differ in their chemical composition and are unrelated.  The bacteria are single-celled prokaryotes. lack a true nucleus & intracellular lipid bound organelles. genetic information is stored in DNA in a region called nucleoid. most commonly are spherical, cylindrical, or spiral. have rigid cell walls (provides shape), which contain peptidoglycan which is not found in other domains. multiply by binary fission. may have appendages (flagella) for motion which can also attribute pathogenicity.  The Archaea In many ways similar to bacteria: – Single-celled prokaryotes; same shape, size & appearance; have rigid cell walls, have flagella; multiply by binary fission. Do not have peptidoglycans in the cell wall. Other chemical differences also exist. Tend to grow in extreme environments inhospitable to most life (high salt, high temperatures, & extreme cold).  The Eucarya Members of ‘Eucarya’ domain are collectively termed ‘eukaryotes’ (true nucleus) and are distinctively different from prokaryotes. Eukaryotes – May be single-celled or multicellular. – Always contain a true membrane-bound nucleus. – contain internal cell organelles (mitochondria & chloroplasts) & are far more complex than prokaryotes. – Have an internal scaffolding, the cytoskeleton, which gives cells their shape. Algae, fungi, protozoa & multicellular parasites (e.g. helminths) are eukaryotes.  Scientific names The binomial system of nomenclature is used for microbes. The first name is the genus, with first letter capitalized. The second is the species name, which is not capitalized. Both words are always italicized. Example: Escherichia coli First word abbreviated with first letter capitalized: E. coli Members of the same species may vary from one another in minor ways & are given different strain designation e.g. – E. coli strain B or E. coli strain K12. Groups of microbes are often referred to informally by names resembling the genus names but are not italicized – e.g. species of Staphylococcus are called staphylococci.  Morphology of bacteria Bacteria have different shapes which are used to describe, classify and identify microorganisms. Most common bacteria exhibit in 2 major shapes – Coccus (plural cocci): spherical shape – Rod (bacillus) (plural bacilli): cylindrical shape Term bacillus should not be confused with genus Bacillus. Coccobacillus: a rod-shaped bacterium which is short enough to be mistakenly considered as coccus. Morphology of bacteria Bacteria also display a variety of other shapes – Vibrio (plural: vibrios): a short- curved rod. – Spirillum (plural: spirilla): a curved rod long enough to form spirals – Spirochete (plural: spirochetes): long spiral-shaped cell with a flexible cell wall and a unique mechanism of motility. – Pleomorphic: This is not an actual shape but the bacteria that vary in their shape.  Grouping of bacteria The colony structure is related to the means Neisseria bacteria use to divide. gonorrhoeae Members of Most prokaryotes genus (bacteria) reproduce by Streptococcus binary fission. Members They form chains, packets, of genus or clusters of cells Sarcina depending upon the plane in which they divide. Staphylococcus sps. form Typical cell groupings is grapelike mainly observed in cocci clusters as they can divide in ≥ one plane. Some prokaryotes/bacteria live This helps in identification as multicellular associations of some bacteria. e.g. myxobacteria.  Acellular infectious agents Viruses, viroids and prions are acellular infectious agents meaning that they are not composed of cells. Are they alive??? (big question). Viruses, viroids, & prions can not reproduce independently. Thus, they are considered non-living and are not considered microorganisms. Viruses consist of a protein coat, surrounding nuclear material and have variety of shapes. are incapable of proliferation outside a host cell and can only multiply inside living host cells. considered obligate intracellular parasites/agents.  Viroids and Prions Viroids: simpler than viruses & consist of a single short piece of nucleic acid (mostly RNA) without a protective coat. Viroids are much smaller than viruses and like viruses, they can reproduce only inside cells. Viroids cause number of plant diseases. Prions are consisted of protein only without any nucleic acid. Prions cause neurodegenerative diseases called Transmissible Spongiform Encephalopathies (TSEs). Acellular Infectious agents Learn key terms from the chapter 1 front page: Domain, prokaryote, prokaryote cell, eukaryote, eukaryotic cell, virus, viroid & prion.  Sizes of molecules, non-living agents and organisms Nucleus Small Proteins Viruses Mitochondria molecules Prion fibril Atoms Lipids Ribosomes Smallest Most Most eukaryotic cells Adult roundworm bacteria bacteria Human height Electron microscope Light microscope Unaided human eye 0.1 nm 1 nm 10 nm 100 nm 1 µm 10 µm 100 µm 1 mm 1 cm 0.1 m 1m 10 m The basic unit of length is the meter (m), and all These units of measurement correspond to units other units are fractions of a meter. in an older but still widely used convention. nanometer (nm) = 10–9 meter =.000000001 meter 1 angstrom (Å) = 10–10 meter micrometer (µm) = 10–6 meter =.000001 meter 1 micron (µ) = 10–6 meter millimeter (mm) = 10–3 meter =.001 meter 1 meter = 39.4 inches  Next lecture Cells and methods to observe them (Chapter 3, selected topics).