Medical Microbiology and Parasitology Lecture Notes PDF

Medical Microbiology and Parasitology Presented by Prof. Asif Jiman-Fatani, MB ChB, MSc, PhD (UK) Professor in Medical Microbiology, Faculty of Medicine, King Abdulaziz University Consultant Microbiologist Head, Clinical Microbiology Laboratories King Abdulaziz University Hospital WELCOME to Me...

Medical Microbiology and Parasitology Presented by Prof. Asif Jiman-Fatani, MB ChB, MSc, PhD (UK) Professor in Medical Microbiology, Faculty of Medicine, King Abdulaziz University Consultant Microbiologist Head, Clinical Microbiology Laboratories King Abdulaziz University Hospital WELCOME to Medical Microbiology and Parasitology Push yourself, because no one else is going to do it for you ! What is Microbiology ? Microbiology is the science that deals with tiny organisms or microbes that can t be seen by naked eye. These organisms are widely distributed in nature. Some of them are beneficial to man and others are harmful and cause diseases. Medical Microbiology and Parasitology Course objectives: At the end of the course the student will be able to : Identify the basic structure of different types of microorganisms with medical relevance, their characters, mode of transmission and pathogenesis of different diseases. Describe various methods of sterilization and disinfection. Describe the mechanism of action of antimicrobial agents and how micro-organisms develop resistance to them. Perform the basic laboratory tests and interpret their results . Discuss the treatment and prevention for each infectious disease studied. Textbooks College library Shugry Medical Book Center Mars Khazindar Jarir Title Author Publisher ISBN Medical Microbiology Murray ASM Press 9781555813710 Microbiology Harvey Lippincott 0781782155 Medical Microbiology Jawetz McGraw Hill 0071412077 Medical Microbiology Mims Mosby 0323035752 General Bacteriology Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of microorganisms Scientific naming Bacterial morphology and arrangements Bacterial structure Essential structures Non-essential structures Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of microorganisms Scientific naming Bacterial morphology and arrangement Bacterial structure Essential structures Non-essential structures What is microorganism (microbe)? Microorganisms: are tiny organisms that are usually cannot be seen by naked eye. Bacteria Viruses Fungi Parasites As physicians: We MUST be familiar with: Names of microbes Names of infectious diseases Mode of transmission Clinical features Laboratory diagnosis Treatment Control & Prevention Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of organisms Scientific naming Bacterial morphology and arrangement Bacterial structure Essential structures Non-essential structures Basic classification of organisms : Eukaryotic: Large, complicated Contains a true nucleus, organelles No cell wall Divides by meiosis or mitosis. Prokaryotic: Small, simple, single (unicellular) No true nucleus nor organelles Has a cell wall Division by binary fission. Properties Prokaryotic Eukaryotic Size Small (< 5 Large (> 10 Nuclear membrane No Yes Cell organelles No Yes Chromosome One circular Multiple linear Division Binary fission Mitosis and meiosis Ribosome 70S 80S Histones or introns No Yes Comparison of Infectious Agents Characteristic Viruses Bacteria Fungi Protozoa and Helminths Cells No Yes Yes Yes Approximate diameter ( m)1 0.02-0.2 1-5 3-10 (yeasts) 15-25 (trophozoites) Nucleic acid Either DNA or RNA Both DNA and RNA Both DNA and RNA Both DNA and RNA Type of nucleus None Prokaryotic Eukaryotic Eukaryotic Ribosomes Absent 70S 80S 80S Mitochondria Absent Absent Present Present Nature of outer surface Protein capsid and lipoprotein envelope Rigid wall containing peptidoglycan Rigid wall containing chitin Flexible membrane Motility None Some None Most Method of replication Not binary fission Binary fission Budding or mitosis2 Mitosis3 1For comparison, a human red blood cells has a diameter of 7 m. 2Yeasts divided by budding, whereas molds divide by mitosis. 3Helminth cells divide by mitosis, but the organism reproduces itself by complex, sexual life cycles. Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of microorganisms Scientific naming Bacterial morphology and arrangement Bacterial structure Essential structures Non-essential structures Scientific naming of bacteria For each organism; 2 names (2 parts): Genus Species - noun, always capitalized - adjective, lowercase Both italicized or underlined Examples : Staphylococcus aureus Escherichia coli Streptococcus pneumoniae A common name is derived from historical use, e.g. pneumococcus for Streptococcus pneumoniae. Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of microorganisms Scientific naming Bacterial morphology and arrangement Bacterial structure Essential structures Non-essential structures Bacterial morphology Morphology Appearance Example Spherical (cocci) Staphylococcus aureus Straight rod (bacilli) Escherichia coli Curved Vibrio cholerae Spiral Treponema pallidum Bacterial arrangement Arrangement Appearance Example Clusters Staphylococcus aureus Chains Streptococcus pyogenes Pairs Neisseria gonorroheae Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of microorganisms Scientific naming Bacterial morphology and arrangement Bacterial structure Essential structures Non-essential structures Bacterial structure The bacterial cell is composed of the following structures Essential structure: Cell wall. Cytoplasmic membrane. Intracytoplasmic structures: Nuclear apparatus. Ribosomes Non-essential structures: Outside the cell wall Capsules Flagella Fimbriae (pili) Spore Other non-essentials: Inclusion granules Plasmids BACTERIAL CELL STRUCTURES Bacterial structure Essential structures: 1. Cell wall: composed of peptidoglycan (also called murein) (peptide=amino acids, glycan=carbohydrates). Maintains cell shape and rigidity. Barrier against external damage. Contains surface antigens. Important for cell division. Gram stain (Gram-positive or Gram negative) Responsible for gram staining a nity (gram-positive or gramnegative) Bacterial structure Essential structures: 1. Cell wall: Cell wall classification: Gram-positive bacteria (e.g. S. aureus) Thick peptidoglycan 50% Of cell wall Teichoic acids Gram-negative bacteria (e.g. E. coli) Thin peptidoglycan 5-10% Of cell wall Outer membrane Lipoproteins (LP) Lipopolysaccharides (LPS) Periplasmic space Functions of the cell wall 1. It is a rigid structure shape 2. Protects the cytoplasmic membrane from bursting in hypotonic solution 3. Its composition plays an important role in determining the cell s reaction to Gram stain 4. It plays a role in cell division Cell wall classification: Cell wall (cont.) The peptidoglycan is composed of two alternating amino sugars: N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). The alternating sugars are connected by a -(1,4)-glycosidic bond. Each NAM is attached to a short amino acid chain, L-alanine, Dglutamine, L-lysine, D-alanine. Cell wall (cont.) The peptidoglycan is a target for many antibacterial agents, such as: Penicillin (inhibits cross-linking of peptidoglycan, binds to penicillin-binding protein; PBP). Lysozyme (muramidase) hydrolyse the 1,4 glycosidic bonds between NAG and NAM. Cell wall of Gram-negative bacteria GNB have two membranes; an outer and inner membranes. The peptidoglycan layer is located between the two membranes in what is called the periplasmic space. The periplasmic space is filled with gell. The outer membrane is a bilayer structure : inner layer resemble in composition to cytoplasmic membrane and outer layer which is distinguished by the presence of various embedded lipopolysaccharides. The polysaccharide portion is antigenic and can be used to identify different strains and species Outer membrane has special channels consisting of protein molecules called porins that permit the passive diffusion of small molecular weight compounds Lipopolysaccharides ( LPS) LPS of Gram-negative cell wall is composed of three units: 1. Complex lipid (phospholipid ) called Lipid A. 2. Core polysaccharide: 5 sugars linked to Lipid A. 3. Outer polysaccharide: is the somatic or O antigen of several Gram-negative bacteria that used to identify it in clinical lab. The lipid portion (Lipid A) is extremely toxic to humans and is called endotoxin . It is only released when the bacterial cells are lysed Responsible for fever and shock caused by Gram-negative bacteria (endotoxic shock) Comparison of cell walls of Gram-positive and Gram-negative bacteria Component Gram-Positive Cells Gram-Negative Cells Peptidoglycan Thicker; multilayer Thinner; single layer Teichoic acids Yes No Lipopolysaccharide (endotoxin) No Yes Essential structure 1. Bacterial cell wall Functions of the bacterial cell wall 1. 2. 3. 4. 5. 6. 7. Maintains the shape of bacteria. Protects the cell from bursting in hypotonic solutions. Protects the cell from mechanical disruption. Provides a barrier against toxic chemical and biological agents. Plays an essential role in cell division. Contains antigens that stimulate the patient s antibody response. Important in determining the cell's reaction to Gram stain. With the exception of mycoplasmas, all bacteria possess a cell wall Spheroplasts , Protoplasts and L-forms Bacterial cell wall may be lost under the effect of certain environmental conditions e.g. treatment with penicillin and lysozyme . Two types: Spheroplast (from Gram-negative) Protoplast (from Gram-positive) If such cells are able to grow and divide they are called L-forms L- forms may be formed during active infection under the effect of antibiotics since they are resistant to cell wall inhibiting antibiotics as penicillin 2. Cell membrane 2. Cell membrane Mainly made of proteins and phospholipids. Selective barrier for ions and nutrients. Site of DNA replication, phosphorylation and respiration. Maintains a constant environment. Essential structures 3. Chromosomal DNA Single, long molecule composed of a double stranded DNA. Carries genetic information to daughter cells. There is no nuclear membrane or nucleolus. Essential structures: 4. Ribosome Responsible for protein synthesis. Composed of sedimentation co-efficient of 70S (Eukaryotes have 80S). Points to be covered in this lecture: Definitions of microbes and microbiology Basic classification of microorganisms Scientific naming Bacterial morphology and arrangement Bacterial structure Essential structures Non-essential structures Non-essential structures 1. Flagella Long helical filaments made of protein flagellin Responsible for cell motility Important virulence factor 2. Pili (fimbriae) Straight, short filamentous attached to the outer surface of some bacteria Help in adhesion to external surfaces Considered as virulence factors. Lab.: Helps in typing certain bacterial Non-essential structures 3. Capsule: Helps to resist phagocytosis (virulence factor). Mostly composed of polysaccharide outside cell wall .. except Bacillus anthracis in which the capsule is made of D-glutamic acid (protein). 4. Glycocalyx ( Slime layer ) : It is a loose polysaccharide meshwork of fibrils extending outward from the cell of some bacteria. It allows the bacteria to adhere firmly to various structures as prosthetic heart valves and catheter . Non-essential structures 3. Others: Plasmid: A small double-stranded extra-chromosomal DNA. Responsible for coding for pathogenesis and antibiotic-resistance . Transposones: Small pieces of DNA that move readily from one site to another, either within or between the DNAs of bacteria, plasmids, and bacteriophages. Called jumping genes Non-essential structures 3. Others: Spores Highly resistant resting (dormant) state. Only in some Gram-positive. Formed when surrounding environment is not safe. Resist extreme environments (heating, drying, lack of nutrients) for many years. Sterilization of spores is by Autoclaving Moist Heat Autoclaving Because bacterial spores are resistant to boiling (100 C at sea level), they must be exposed to a higher temperature; this cannot be achieved unless the pressure is increased. Autoclaves work on the same principle as the domestic pressure cooker: saturated steam is produced under pressure, resulting in temperatures >100 C; this ensures total destruction of all microorganisms, including spores. A typical cycle would be 15 pounds/square inch at 121 C for 15 minutes. Autoclaves in the Clinical Microbiology Laboratory, King Abdulaziz University Hospital Microbial growth Increase in the number of cells .. by cell division binary fission . NOT cell size..!!! One cell can produce a colony of billion cells. Bacterial growth Curve Many antibiotics are effective during this phase 1/17/2021 Dr.Rasha Ahmed Abou Kamer Factors affecting bacterial growth Nutrients. Temperature. Oxygen. pH. Generation time. Nutrients requirements: Number 1: WATER . Most medically important bacteria require: Carbon Water Organic carbon Organic carbon Nitrogen Salts required NOT required AUTOTROPHS HETEROTROPHS Temperature requirements: Oxygen requirements: O2 requirement Specification Example Obligate aerobic Requires atmospheric O2 Mycobacterium tuberculosis Obligate anaerobic Require NO O2 to grow Clostridium tetanii Facultative anaerobic Microaerophilic Can grow in presence or absence of O2 Staphylococcus aureus Capnophilic Require CO2 only Require O2 (5-10%) Campylobacter jejuni Thermus acquaticus ** Most medically important bacteria are Facultative anaerobic ** Some are obligate anaerobes ** Few are obligate aerobes Gaseous requirement of bacteria : a. Oxygen: Bacteria are classified into 5 groups pH requirements: Most pathogenic bacteria grow best in slightly alkaline pH (7.2 7.4) V. cholera grows best in pH( 8.0 8.4) Lactobacillus grows best in pH (3.0 4.0) Helicobacter pylori can survive gastric acidity to infect mucous layer Generation time: Time required for the cell to divide into two daughter cells. Average for bacteria is 1-3 hours Escherichia coli generation time = 17 min 20 generations (7 hours), 1 cell 1 million cells! Examples of generation times: Bacterium Medium Generation Time (minutes) Escherichia coli Glucose-salts 17 Bacillus megaterium Sucrose-salts 25 Streptococcus lactis Milk 26 Streptococcus lactis Lactose broth 48 Staphylococcus aureus Heart infusion broth 27-30 Lactobacillus acidophilus Milk 66-87 Rhizobium japonicum Mannitol-salts-yeast extract 344-461 Mycobacterium tuberculosis Synthetic 792-932 Treponema pallidum Rabbit testes 1980