Medical Microbiology and Immunology for Nurses PDF 2015/2016

MEDICAL MICROBIOLOGY AND IMMUNOLOGY FOR NURSES DR Ayman A. Allam Professor of Microbiology and Immunology Faculty of Medicine Zagazig University I II To the soul of my father, my mother and my family First Edition...

MEDICAL MICROBIOLOGY AND IMMUNOLOGY FOR NURSES DR Ayman A. Allam Professor of Microbiology and Immunology Faculty of Medicine Zagazig University I II To the soul of my father, my mother and my family First Edition 2015/2016 III  ‫الطبعة االولي ‪2016/2015‬‬ ‫رقم االيداع بدار الكتب ‪4729/ 2016‬‬ ‫حقوف الطبع محفوظة للمؤلف‬ ‫‪2024‬‬ ‫‪IV‬‬  Contents General bacteriology ----------------------------------------------------------------------------------1 Bacterial structure--------------------------------------------------------------------------------------2 Bacterial genetics---------------------------------------------------------------------------------------6 Bacterial physiology------------------------------------------------------------------------------------8 Virulence factors & How bacteria produce disease-------------------------------------------9 Normal flora--------------------------------------------------------------------------------------------11 Specimen collection ---------------------------------------------------------------------------------13 Bacterial staining-------------------------------------------------------------------------------------15 Bacterial culture--------------------------------------------------------------------------------------16 Cocci------------------------------------------------------------------------------------------------------19 Staphylococcus aureus------------------------------------------------------------------------------20 MRSA-----------------------------------------------------------------------------------------------------21 Bacilli-----------------------------------------------------------------------------------------------------21 Enteric fever --------------------------------------------------------------------------------------------22 Mycobacterium tuberculosis.-----------------------------------------------------------------------24 General mycology------------------------------------------------------------------------------------25 General virology--------------------------------------------------------------------------------------28 Common viruses---------------------------------------------------------------------------------------32 Hepatitis viruses--------------------------------------------------------------------------------------34 Sterilization & Disinfection -------------------------------------------------------------------------39 Antibiotics-----------------------------------------------------------------------------------------------44 Immunology ------------------------------------------------------------------------------------------48 Cells of immune response---------------------------------------------------------------------------49 Innate immunity---------------------------------------------------------------------------------------52 Humeral immunity------------------------------------------------------------------------------------52 Antibodies (Immunoglobulins)---------------------------------------------------------------------53 Cell mediated immunity-----------------------------------------------------------------------------54 Passive and active immunity-----------------------------------------------------------------------55 Immunization-------------------------------------------------------------------------------------------56 Nosocomial infection---------------------------------------------------------------------------------59 Infection control---------------------------------------------------------------------------------------60 Hand hygiene-------------------------------------------------------------------------------------------61 Personal protective equipments--------------------------------------------------------------64 V INTRODUCTION:  Microbiology is the study of microorganisms, which are tiny organisms that live around us and inside our body. An organism is a living thing that ingests and breaks down food for energy and nutrients, excretes undigested food as waste, and is capable of reproduction.  Microorganisms are the subject of microbiology, which is the branch of science that studies microorganisms.  A microorganism can be one cell or a cluster of cells that can be seen only by using a microscope.  Microorganisms are organized into six fields of study: bacteriology, virology, mycology, phycology, protozoology, and parasitology. General Bacteriology Eukaryotes & Prokaryotes  Cells have evolved into two different types:  Eukaryotic: Human cells, Fungi, protozoa and helminthes are eukaryotic,  Prokaryotic: Bacteria are prokaryotic. Viruses are not cells and do not have a nucleus. Bacterial Size: Bacteria range in size from about 0.2 to 5 µm. 1 Shape of Bacteria: Bacteria are classified by shape into three basic groups:  Cocci: round  Bacilli: rods z  Spirochetes: spiral-shaped Arrangement: Bacteria are arranged single  Diplococcic in pairs (diplococcic)  Streptococci in chains  Staphylococci in grapelike clusters The Bacerial Structure: The bacteria is formed of essential components and non essential components. The essential components: A. The cell wall B. The cytoplasmic membrane C. The cytoplasm D.The nucleus The non -essential components: A. The plasmid 2 The bacterial cell  B. The flagella C. The pili (fimbria) D.The capsule E. The spore 1-Bacterial Cell Wall: -It is the outer most basic structure of the bacterial cell. 1. Cell Wall of Gram Positive Bacteria Consists of:  thick layer of peptidoglycan 50:60% of the cell wall. It is the site of action of penicillins, cephalosporins and lysozyme enzyme.  Techoic acid. 2. Cell Wall of Gram Negative Bacteria Consists of:  Inner layer ofpeptidoglycan : thin layer (5-10% of the cell wall)  Outer membrane (OM): composed of lipopolysaccharide (LPS) containing and lipid A layer (endotoxin).  It is the endotoxin causes the fever and hypotension and induce septic shock. 3 2-Cytoplasmic Membrane: is composed of a phospholipid bilayer. It is generally do not contain sterol (Except the genus Mycoplasma). The membrane has four important functions: (1) active transport of molecules into the cell (2) energy generation by oxidative phosphorylation, (3) secretion of enzymes and toxins. 3- Cytoplasm An amorphous matrix that contains : 1. Ribosomes: are the site of protein synthesis. 2. Granules: serve as storage areas for nutrients. 3. The Nucleus. 4. The Plasmids The Nucleus: 3. It is formed of DNA. 4. It is single, circular molecule 5. It contains genes. 6. It contains no nuclear membrane, no nucleolus, and no histones whereas eukaryotic DNA does. Plasmid: It is extrachromosomal, double-stranded, circular DNA molecules It can replicates independently of the bacterial chromosome It can be transmitted from cell to cell by conjugation. 4 Plasmids carry the genes for the following functions: 1.Resistance to antibiotics (R plasmid). 2.Sex Pili (F Factor) responsible for congugation. 3. Exotoxins, 4. Several antibiotics produced by Streptomyces. 5-Capsule  The capsule is a gelatinous layer covering the entire bacterium.  It is a determinant of virulence of many bacteria since it limits the ability of phagocytes to engulf the bacteria as in pneumococci.  Are used as in certain vaccines. 6-Flagella: Flagella are long, whiplikeappendages that move the bacteria (Organ of motility). Responsible for H antigen 7-Pili (Fimbriae) Two types:  Ordinarypili mediate the attachment of bacteria to the human cell surface.  The sexpilus, forms the attachment between the (donor) and the (recipient) bacteria during conjugation. 7-Spores: 5 1. These highly resistant structures are formed in response to adverse conditions. 2. Formed by the genus Bacillus, and the genus Clostridium, which. 3. It is resistant to heat, dehydration, radiation, and chemicals. 4. It can be killed by autoclaving. Bacterial Genetics Bacteria are haploid as they have a single chromosome and therefore a single copy of each gene. Eukaryotic cells (such as human cells) are diploid, which means they have a pair of each chromosome and therefore have two copies of each gene. -The Gene: is the basic unit of inheritance formed of a segment of DNA molecule that carries the genetic information for specific biochemical or physiological function. The Nucleic acids are either DNA or RNA. DNA is double stranded molecule formed of complementary double stranded molecule (Adenine-Thymine or Guanine-Cytosine base pairing). It carries the genes. RNA is single stranded molecule. Uracil substitutes thymine of DNA and ribose instead of Deoxy-ribose. It is found in three forms: 1. mRNA( messenger RNA) carries the genetic information from DNA to ribosome. 6 2. rRNA (Ribosomal RNA) is a constituent of ribosome. It reads the genetic code on mRNA and form protein according to it. 3. tRNA (Transfer RNA): carries the amino acids from cytoplasm to ribosome. The Bactriophage or Phage Is the virus which attack and infect bacteria. It is composed of DNA or RNA genetic material coated by a protein capsid with a tail and attachment fibrils. Types: The lytic or virulent phage: It directly replicates in the host bacterial cell causing its lysis. Lysogenic or temperate phage: This phage incorporates its genome into the bacterial host genetic material. So it gives the bacterial host a new property eg Toxin production. Medical importance of phage: 1. Phage typing of bacteria for epidemiological trace the source of infection. 7  Bacterial physiology Bacterial Reproduction: Bacteria reproduce by binary fission, a process by which one parent cell divides to form two progeny cells. The doubling (generation) time of most bacteria is as little as 20 minutes as Escherichia coli. Oxygen Requirement of Bacteria: 1. Obligate aerobes: require oxygen to grow. 2. Obligate anaerobes: cannot grow in the presence of oxygen as Clostridium tetani. 3. Facultative anaerobes: as E. coli, are they can grow in the presence or absence of oxygen. 4. Microaerophilic Bacteria: require oxygen in concentration less than its athospheric pressure. Nutritional requirement: 1. Heterotrophs:require preformed organic compounds (Sugars, amino acids). Most pathologic bacteria are heterotrophs 2. Autotrophs: Can synthesize organic compounds from inorganic compounds (chemolithotrophs) or from CO2 and water by the light (photolithotrophs). Virulence: A quantitative measure of pathogenicity and is measured by the number of organisms required to cause disease, it is the degree of pathogenicity. Virulence Factors: Certain structures or products that help microorganisms to overcome body defence mechanisms and cause disease. 8  HOW BACTERIA PRODUCE DISEASE? Bacteria produce disease through invasion or toxin production. Invasion is facilitated through capsule and degradative enzymes. Invasive bacteria, on the other hand, grow to large numbers locally and induce an inflammatory response consisting of erythema, edema, warmth, and pain. 1. Capsule: capsulated bacteria as Streptococcus pneumoniae, and Neisseria meningitidis resist phagocytosis. 2. Pili: pili help bacteria to adhere to the surface of host cells as in gonococci. 3. Enzymes :  Collagenase and hyaluronidase, which degrade collagen and hyaluronic acid, respectively, thereby allowing the bacteria to spread through subcutaneous tissues; they are especially important in cellulitis caused by Streptococcus pyogenes.  Coagulase produced by Staphylococcus aureus produce fibrin from its precursor fibrinogen (this clot may protect the bacteria from phagocytosis by walling off the infected area and by coating the organisms with a layer of fibrin).  Immunoglobulin A (lgA) protease, which degradeslgA,.  Leukocidins, which can destroy leukocytes. 4- Bacterial toxins: There are two types of toxins. 9 exotoxin is a polypeptides secreted by an organism. Exotoxins are very toxic. A very small amount can be fatal to a host organism and even though the immune system can often identify and attack the toxin, the toxin spreads so quickly that the host does not have an opportunity to mount a defense. Endotoxins are lipopolysaccharides (LPS), which form an integral part of the cell wall. Endotoxins occur only in gram-negative rods and cocci cause fever, hypotension, and other generalized symptoms even septic shock. Difference between Exotoxins and Endotoxins Property Exotoxin Endotoxin Source Certain species of gram-positive Cell wall of gram-negative and gram-negative bacteria bacteria Secreted from Yes No cell Chemistry Polypeptide Lipopolysaccharide Location of Plasmid or bacteriophage Bacterial chromosome genes Toxicity High Low (fatal dose on the order of hundreds of micrograms) Clinical Various effects Fever, shock effects Mode of Various modes Includes TNF and interleukin-1 action Antigenicity Induces high-titer antibodies Poorly antigenic called antitoxins Vaccines Toxoids used as vaccines No toxoids formed and no vaccine available Heat stability Destroyed rapidly at 60°C (except Stable at 100°C for 1 hour staphylococcal enterotoxin) Typical Tetanus, botulism, diphtheria Meningococcemia, sepsis by diseases gram-negative rods 10  NORMAL FLORA (1)Normal flora is the term used to describe the various bacteria and fungi that are permanent residents of certain body sites, especially the skin, oropharynx, colon, and vagina. The normal flora organisms are often referred to as commensals. (2)Commensals are organisms that derive benefit from another host but do not damage that host. Resident flora: normally present in the site and reestablish itself after their removal by antiseptics. Transient flora: potentially pathogenic organisms acquired from the environment and don't reestablish itself after its removal by hand washing or antiseptic use. (3)CSF, Blood, urine, serous cavities is sterile sites with no normal flora. Importance of the normal flora: 1. They can cause disease, especially in immunocompromised and debilitated individuals. 2. They constitute a protective host defense mechanism. The nonpathogenic resident bacteria occupy attachment sites on the skin and mucosa that can interfere with colonization by pathogenic bacteria. If the normal flora is suppressed, pathogens may grow and cause disease. 3. They may serve a nutritional function. The intestinal bacteria produce several B vitamins and vitamin K. 11  General lines of Diagnosis of bacterial infection: 1. Specimens: according to the type of lesion; wound swab, pus aspiration, CSF, sputum, stools…etc 2. Direct smear: to show the motility of the organism 3. Stained smear: to show the staining affinity, shape and arrangement of bacteria 1)Gram stain: differentiate bacteria into gram negative or positive organisms. 2)Ziehl-Neelsen stain: show Acid Fast Bacilli. 4. Culture: on the suitable medium usually for 24 h at 37°C aerobically for aerobic organisms and anaerobically for anaerobic organisms. The colonies identified by: 1) microscopic examination 2) macroscopic shape of the colony 3) Biochemical reactions as catalase, oxidase..etc 4) serologically 5. Antibiotic sensitivity testing: to know the antibiotics effective for the causative organisms. 6. Serology: to detect specific anti-organism IgM or rising titer of specific anti organism IgG. 7. Genetic diagnosis: as Polymerase chain reaction (PCR) to amplify a DNA sequence unique to the organism to be easily detected. 12  Specimen collection in Bacteriology: There are three types of specimens:  Specimen from normally Sterile site: as CSF, Blood , Pleural effusion.  Specimen from flora containing site as stools, sputum, oral cavity, Vagina.  Valuable specimen: specimen taken during surgery or taken by painful procedure as surgical biopsy or CSF. Universal precautions for collecting and handling all specimens. 1. Whenever possible, collect all culture specimens prior to administration of any antimicrobial agents. 2. Avoid contamination with indigenous flora. 3. All specimens must be appropriately labeled. The requisition will include the patient name, hospital number, hospital service, date and time of collection, specimen type and tests requested. A requisition needs to accompany each different specimen type. 4. Deliver all specimens to the laboratory as soon as possible after collection. Specimens for bacterial culture should be transported at room temperature. If transport is delayed the following specimens should be refrigerated: urines (within 30 min), stool (within 1 h), respiratory specimens. 5. Specimens should be in tightly sealed, leak proof containers and transported in sealable, leak-proof plastic bags. Specimens for TB should be double bagged. 6. Specimens should not be externally contaminated. Specimens grossly contaminated or compromised may be rejected. 13 7. You should deal seriously with all specimens as if it is infectious and dangerous. Wound swab Some Important Bacterial Specimens: 1. Abscess – Tissue or aspirates are always superior to swab specimens. Septic wounds is sampled by wound swab. 2. Blood: Venous blood a. Amount: infants: 0.5 – 2 ml children: 2 – 5 ml adults: 5 – 10 ml b. Cleanse skin with a povidone iodine. applied in concentric circles (start at center). Allow to dry at least 1 min before venipuncture. c. Do not touch site after prep. d. Remove overcaps from blood culture bottles and cleanse each rubber septum with separate 70% alcohol swabs. Allow septum to dry for 1 min before inoculating. e. Draw the amount of blood and inoculate each bottle with this blood. Do not vent or overfill bottles. Transport time 3 mL) to the Microbiology Laboratory. Transport time