microbiology medical microbiology pharmaceutical...

Medical Microbiology lecture1

Microbiology: Microbiology can be defined as the biology of microscopic organisms, or life too small to be seen with the naked eye. Medical microbiology is both a branch of medicine and microbiology which deals with the study of microorganisms including bacteria, viruses, fungi and parasites which are of medical importance and are capable of causing infectious diseases in human beings. Pharmaceutical microbiology: The study of microorganisms that are related to the production of antibiotics, enzymes,vitamins, vaccines, and other pharmaceutical products and that cause pharmaceutical contamination and spoil. Microbial biotechnology: The manipulation of microorganisms at the genetic and molecular level to generate useful products. Microbes or Microorganisms

Microbes are subcellular entities (prions, viruses), prokaryotic bacteria, eukaryotic fungi and protozoa, metazoan animals, such as parasitic worms (helminthes), and some arthropods. There are two components in bacteriology “ Basic Bacteriology and Clinical Bacteriology” Basic Bacteriology The science that is mainly concerned with studying the architecture of the Bacteria with its growth media, biochemical reactions, internal organelles, genetic information…etc.


Clinical Bacteriology Deals with signs and symptoms associated when these bacteria infect a human being and how the immune system responds against those pathogenic bacteria. Basically life is divided into two forms Prokaryotic and Eukaryotic cells. Prokaryotic cells: are a group of organisms whose cells lack a cell nucleus (karyon), or any other membrane-bound organelles. While Eukaryotic cell: is an organism whose cells contain complex structures & a nucleus enclosed within membranes. Prokaryotic cells are divided in to two groups Bacteria and Archaea. Archaea: This domain includes forms that live under extreme environmental conditions, including thermophilic, hyperthermophilic, halophilic, and methanogenic microorganisms. The earlier term for the archaea was archaebacteria(ancient bacteria), and they are indeed a kind of living fossil.Thermophilic archaea thrive mainly in warm, moist biotopes such as the hot springs at the top of geothermal vents.The hyperthermophilic archaea, a more recent discovery, live neardeep- sea volcanic plumes

Bacteria are classified into three types: - Classic bacteria: These organisms reproduce asexually by binary transverse fission. They do not possess the nucleus typical of eukarya. The cell walls of these organisms are rigid (with some exceptions, e.g., the mycoplasma). - Chlamydiae: These organisms are obligate intracellular parasites that are able to reproduce in certain


human cells only and are found in two stages: the infectious, non-reproductive particles called elementary bodies (0.3 lm) and the noninfectious, intracytoplasmic, reproductive forms known as initial (or reticulate) bodies (1 lm). - Rickettsiae: These organisms are obligate intracellular parasites, rod shaped to coccoid, that reproduce by binary transverse fission. The diameter of the individual cell is from 0.3–1 lm. - Mycoplasmas: Are bacteria without rigid cell walls. They are found in a wide variety of forms, the most common being the coccoid cell (0.3–0.8 lm). Threadlike forms also occur in various lengths. Importance of Bacteria in our life The bacteria that are involved in photosynthesis are responsible for more than 50% of earth’s oxygen. Also bacteria are involved in decomposition and nutrient recycling. They are necessary for the production of bread, cheese, beer, antibiotics, vaccines, vitamins, enzymes, and many other important products. Indeed, modern biotechnology rests upon a microbiological foundation. Microorganisms are indispensable components of our ecosystem.They make possible the cycles of carbon, oxygen, nitrogen, and sulfur that take place in terrestrial and aquatic systems. They also are a source of nutrients at the base of all ecological food chains and webs.Extraction of copper from ore is being done by the help of bacteria Bioremediation is the use of microbes to degrade organic matter in sewage and detoxify pollutants such as oil spills.


History of Medical Microbiology Infectious diseases have been known for thousands of years, although accurate information on their etiology has only been available for about a century. In the medical teachings of Hippocrates, the cause of infections occurring frequently in a certain locality or during a certain period (epidemics)was sought in “changes” in the air according to the theory of miasmas. ("pollution") Microbes were first observed by Antonie van Leeuwenhoek using a simple microscope by which he saw the first bacteria. At that time the theory of “spontaneous generation”—creation of life from dead organic material—stood in the way of implicating the bacteria found in the corpses of infection victims as the cause of the deadly diseases.Then came Pasteur disproved the doctrine of spontaneous generation in the second half of the 19th century that a new way of thinking became possible. By the end of that century, microorganisms had been identified as the causal agents in many familiar diseases by applying the Henle-Koch postulates formulated by R. Koch in 1890. This postulate stated that: 1-The microbe must always be present in every case of the disease. 2-It must be isolated in pure culture on artificial media. 3-When inoculated into healthy animal host it should produce the same disease. 4-It must be isolated from the diseased animal again. Louis Pasteur: a French chemist and microbiologist who was one of the most important founders of medical microbiology. Showed microbes caused


fermentation in 1848, studied spoilage and introduced “Pasteurization” to prevent it and used cotton plugs in his cultures to prevent air bornecontamination, he also devised Aseptic Technique. Ignaz Semmelweis, a Hungarian physician introduced hand washing as a means of preventing transfer of puerperal sepsis in obstetrical patients and is regarded as the pioneer in the antiseptic procedures. Nomenclature Linnaeus introduced the binomial system of scientific nomenclature Each organism has two names: the genus and species epithet Italicized or underline .Genus name is capitalized and species in lower case. Staphylococcus aurous or Staphylococcus aurous describes clustered arrangement of cells and golden yellow color of colonies Escherichia coli Honors the discoverer, Theodor Escherich and describes its habitat, the colon. After the first use, scientific names may be abbreviated with the first letter of the genus and full species epithet. (Ex: E. coli)


Classification of Bacteria Classification Systems The classification of bacteria serves a variety of different functions. Because of this variety, bacteria may be grouped using many different typing schemes. The critical feature for all these classification systems is an organism identified by one individual (scientist, clinician, epidemiologist), is recognized as the same organism by another individual. At present the typing schemes used by clinicians and clinical microbiologists rely on phenotypic typing schemes. These schemes utilize the bacterial morphology and staining properties of the organism, as well as growth requirements of the species combined with a variety of biochemical tests. For clinicians, the environmental reservoir of the organism, the vectors and means of transmission of the pathogen are also of great importance. taxonomic techniques that allow for the comparison of highly conserved genes among different species. As a result of these comparisons a phylogenetic tree can be developed that displays the degree of relatedness of different organisms. A relatively new application of this technology has been the recognition and characterization of noncultivatable pathogens and the diseases that they cause. Phenotypic classification systems: Gram stain and bacterial morphology: Of all the different classification systems, the Gram stain has withstood the test of time. Discovered by H.C. Gram in 1884 it remains an important and useful technique to this day. It allows a large proportion of clinically


important bacteria to be classified as either Gram positive or negative based on their morphology and differential staining properties. Slides are sequentially stained with crystal violet, iodine, then destained with alcohol and counter-stained with safranin. Gram positive bacteria stain blue-purple and Gram negative bacteria stain red. The difference between the two groups is believed to be due to a much larger peptidoglycan (cell wall) in Gram positives. As a result the iodine and crystal violet precipitate in the thickened cell wall and are not eluted by alcohol in contrast with the Gram negatives where the crystal violet is readily eluted from the bacteria. As a result bacteria can be distinguished based on their morphology and staining properties. Some bacteria such as mycobacteria (the cause of tuberculosis) are not reliably stained due to the large lipid content of the peptidoglycan. Alternative staining techniques ( acid fast stain) are therefore used that take advantage of the resistance to destaining after lengthier initial staining. Growth Requirements: Microorganisms can be grouped on the basis of their need for oxygen to grow. Facultatively anaerobic bacteria can grow in high oxygen or low oxygen content and are among the more versatile bacteria. In contrast, strictly anaerobic bacteria grow only in conditions where there is minimal or no oxygen present in the environment. Bacteria such as bacteroides found in the large bowel are examples of anaerobes. Strict aerobes only grow in the presence of significant quantities of oxygen.


Pseudomonas aeruginosa, an opportunistic pathogen, is an example of a strict aerobe. Microaerophilic bacteria grow under conditions of reduced oxygen and sometimes also require increased levels of carbon dioxide. Neisseria species (e.g., the cause of gonorrhea) are examples of micraerophilic bacteria. Aerobic

Biochemical reactions: Clinical microbiology laboratories typically will identify a pathogen in a clinical sample, purify the microorganism by plating a single colony of the microorganism on a separate plate, and then perform a series of biochemical studies that will identify the bacterial species. Serologic systems: Selected antisera can be used to classify different bacterial species. This may be based on either carbohydrate or protein antigens from the bacterial cell wall or the capsular polysaccharide. (Group A streptococcal M proteins or O and H polysaccharide antigens of salmonella). Intracellular Bacteria Environmental Reservoirs: When considering likely pathogens it is also important to know which of the different species are found in different locations. Environmental reservoirs are generally divided into those that are endogenous (i.e., on or within the human body) and exogenous (somewhere in the environment). When considering the likely cause of an infection the likely source of the infection is important in your differential diagnosis. For example, an anaerobic organism resident in the large bowel is the likely cause of an abdominal abscess that develops after large bowel surgery. A skin rash developing in a hiker with a history of multiple tick bites is more likely to be borrelia,


the agent of Lyme disease. An outbreak of food poisoning traced to imported unpasteurized cheese might be due to listeria. Endogenous reservoirs account for a large proportion of human infections. Many parts of the body have their own normal flora. S. epidermidis is found on the skin. Viridans streptococci are a part of the normal oropharyngeal flora and S. aureus is a commensal of the anterior nares. Genotypic systems: Universal Phylogenetic Tree: Woese has developed a “universal phylogenetic tree” for all living organisms that establishes a tripartite division of all living organisms– bacteria, archaea and eucarya. His work is based on a comparison of 16s ribosomal RNA sequences. These sequences are highly conserved and undergo change at a slow, gradual and consistent rate. They are therefore useful for making comparisons among the different living organisms. Ribosomal RNA (rRNA) sequence analysis: This has emerged as a major method for classification. It has been used to establish a phylogenetic tree. Inaddition, it is now also used to rapidly diagnose the pathogen responsible for an infection, to help select appropriate therapy and to identify noncultivatable microorganisms. Molecular subtyping: Sometimes it is necessary to determine whether strains from the same species are the same or different. For example, if there is an outbreak of


infections that appear due to the same bacterial species, the hospital epidemiologist will want to know if all of the infections are due to the same strain. Clues can be obtained by examining the biochemical studies or the antibiotic susceptibility profile, but a more reliable method is by molecular analysis. Pulsed Field Gel Electrophoresis (PFGE) is the most frequently used molecular technique. Chromosomal DNA is digested with arestriction enzyme that makes relatively infrequent cuts in the DNA and as a result creates large DNA fragments. The DNA fragments from the different strains are then run on a gel and compared.

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