Clinical Bacteriology Prelim Reviewer - LS1 PDF

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LESSON 1: INTRODUCTION TO MICROBIOLOGYHistory Anton van Leeunwenhoek - first observations of bacteria at the microscopic level  Huygens: free living protozoa  Robert Hooke (1667): filamentous microscopic fungi  Pietro Antonio Micheli: described 900 species of molds  Cicero and Fracastorius- fev...

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CLINICAL BACTERIOLOGY PRELIM REVIEWER LESSON 1: INTRODUCTION TO MICROBIOLOGY

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History  Anton van Leeunwenhoek - first observations of bacteria at the microscopic level  Huygens: free living protozoa  Robert Hooke (1667): filamentous microscopic fungi  Pietro Antonio Micheli: described 900 species of molds  Cicero and Fracastorius- fevers might be caused by minute animals (contagium vivum)

History 

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History

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Spontaneous Generation

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Louis Pasteur - when air is filtered through cotton wool, large numbers of microorganisms are held back. John Tyndall - existence of heat-stable forms of certain bacteria - removal of which involved the process of repeated heating and rest

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Spontaneous Generation     

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the curve of the flask prevents outside air from entering the flask. No contamination occurs.

When the neck of the flask is broken off, bacteria reach the sterile broth and organism growth occurs. Boiling the broth kills microorganism

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To progress - Improvement in microscopes - Development of methods for culturing microorganisms Robert Hooke (end of 16th century) - Microscope with 3-500x - Recognized cellular structures Ferdinand Cohn (1849) - staining of histological specimens Robert Koch (1877) - Methylene blue to stain - Important paper on the investigation, prevention, and photograohing of bacteria. Robert Koch (1882) - staining the tubercle bacillus with - Employing for the stain to penetrate the waxy envelope Hans Christian Gram (1884) - Gram’s stain Frederick Loeffler (1890) - demonstrate the presence of bacterial flagella ultraviolet microscope (1919) electron microscope (1934) - Belgian physicist Marton scanning electron microscope (1965) Pasteur (1860) - Semisynthetic medium Ferdinand Cohn (1872) - basal medium, to which various additions could be made Solid medium - Introduction of gelatine and then agar in 1882 Silica gel media Julius Richard Petri (1887): - petri dish Beijerinck (1898): - enrichment culture media

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McIntosh and Fildes: - anaerobic jar Chamberland (1884): - Autoclave Edward Jenner (1796) - Cowpox virus used to immunized a boy against smallpox Ignaz Semmelweiss (1844) - Childbed fever Louis Pasteur (1865) - disease must be airborne Joseph Lister • Metchnikoff (1882): cellular immunity, phagocytes • Ehrlich (1891) - active and passive immunity Charles Calmette - BCG vaccine

Taxonomy 

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3 discipline - Classification - Nomenclature - identification Importance: - Use a common label for every organisms - Minimizes confusions about names Classification - Organization of microorganisms that share similar morphology, physiology and genetic components into specific group/ “taxa”  Specie - Collection of bacterial strains that share common physiologic & genetic features Subspecie; biotype; serotype; genotype.  Genus - Comprises of different species with common and sufficiently different features  Family  Order  Class  Division  Kingdom

Nomenclature 

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Naming of microorganisms according to established rules & guidelines - BINOMIAL: Every organism is assigned a genus and species name in Latin or Greek derivation  Components:  Genus: Always capitalized  specie: never capitalized Genus + specie In print: italics In script: underlined Example: Streptococcus pyogenes or Streptococcus pyogenes May be abbreviated: S. pyogenes Informal designations: streptococcus

Identification  

Describe key features of microorganism Methods: - Genotypic characterization  Genetic makeup  Genes and nucleic acids - Phenotypic characterization  Readily observable characteristics

Genotypic criteria DNA base composition ratio Nucleic acid base sequence analysis Phenotypic criteria Macroscopic morphology

Principles G, C, A, T (nitrogenous bases) Used as indicator of relatedness Order of bases along RNA or DNA strands - Measure of degree of relatedness

Microbial growth pattern in culture media - colonial size, texture and pigmentation Size, shape, intracellular inclusions Microscopic or appendages, arrangement of morphology bacterial cells Ability of the organism to be stained Staining characteristic with a particular stain Environmental Temperatures, presence or absence of oxygen, pH levels presence of requirements ions and salts

CLINICAL BACTERIOLOGY PRELIM REVIEWER Host-Microorganism Interaction Stage:

Physical encounter between host and microorganim

Physical encounter between host and microorganim

Exposure is dependent on human activities Reservoir - Place of origin of infecting agent

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RESERVOIR Human

Microorganism colonization of host surfaces

Microorganism entry, invasion and dissemination

Animal

OUTCOME

Physical encounter between host and microorganim Intervening agent  

Vector Vehicle

Environme nt

Examples Direct Indirect  Conatal  Nosocomia  Blood l infections transfusio  Ingestion n of  Sexual contamina ted food transmiss or water ion Direct Indirect  Bite  Bite of insect vector  Water food supply  Animal for human food  Inhalation of soil and dust particles or inoculatio n

Physical encounter between host and microorganim Reservoir

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Direct Indirect

Reservoir

Modes of transmission  Direct  Indirect - Vectors - Vehicle *insects - Vector rather than reservoir - Arthropods ** useful in determining ideal specimens for isolation precautionary measures

CLINICAL BACTERIOLOGY PRELIM REVIEWER Microorganism colonization of host surfaces HOST  Microbial colonization - Persistent survival of microorganism in surface of human body - Dependent in human defenses that protects internal tissues an organs  Skin  Physical and chemical barrier  Mucous membrane Microorganism colonization of host surfaces a. skin structure Protective activity Dermal layer  physical barrier  capability to slough off  provide dry, acidic and cool conditions Hair follicles, glands  produce acids, alcohols and toxic lipids Conjunctival  tears (flushing epithelium(eyes) action) SALT  specific and nonspecific immunity Microorganism colonization of host surfaces b. mucus membrane structure Protective activity Mucosal cell  capability to slough off  tight intercellular junction Goblet cell  mucus production: - protective lubrication - bacterial trapping - contains AB - provide antibacterial substances: (lysozyme, lactoferrin, lactoperoxidase) MALT  specific ad nonspecific immunity

Microorganism colonization of host surfaces MICROORGANISM  colonizers / normal flora - microorganisms that inhabits human body resident o survive, thrive and multiply o presence is more permanent transient o survive but not multiply on the surface - vary with anatomic location *** useful in determining clinical significance of microorganism isolated from patient specimens Microorganism colonization of host surfaces MICROORGANISM  microbial colonization - last step in establishment of long-lasting, commensal relationship between colonizer and human host - first step in developing infection and disease Microorganism colonization of host surfaces MICROORGANISM Factors contributing to successful colonization Survival against  localization in environmental moist area conditions  protection within ingested debris  expression of specific metabolic characteristics Attachment and  pili adherence to host cell  adherence surface proteins Motility, production of subs, that may compete with host for acquisition of nutrients, ability to coexist w/ other microorganism

CLINICAL BACTERIOLOGY PRELIM REVIEWER Microorganism entry, invasion and dissemination HOST Factors contributing to disruption of physical barrier trauma  wounds  abrasions  burns inhaltion  smoking  toxic gases Implantation of medical devices Other diseases  DM, alcoholism Childbirth and overuse of antibiotics Microorganism entry, invasion and dissemination HOST  Responses to microbial invasion - Nonspecific response Biochemical or cellular o Phagocytes o inflammation Microorganism entry, invasion and dissemination HOST  responses to microbial invasion - nonspecific response phagocytes o cells that ingest and destroy foreign particle PMN macrophage First cell on the scene --Bone marrow-circulation Bone marrow-circulationtissues Days or less in survival Several day to weeks --Mediates immune system defenses Microorganism entry, invasion and dissemination

Microorganism entry, invasion and dissemination Cell name Tissue distribution Monocyte Blood Liver Kupffer cell Lung Alveolar macrophage Connective tissue Histiocyte Peritoneum Peritoneal macrophage Microglial cell Central nervous system Kidney Mesangial cell macrophage Spleeh, lymph nodes Microorganism entry, invasion and dissemination HOST  responses to microbial invasion - nonspecific response - inflammation swelling redness heat pain Microorganism entry, invasion and dissemination HOST  responses to microbial invasion - nonspecific response - inflammation

CLINICAL BACTERIOLOGY PRELIM REVIEWER Microorganism entry, invasion and dissemination HOST  Responses to microbial invasion - Specific response (immune system) - Antibody – mediated immunity - Cell – mediated immunity

Microorganism entry, invasion and dissemination HOST  Responses to microbial invasion - Specific response (immune system) cellular B cells T cells NK cells Circulation residence Lymphoid tissues & lymphoid tissues Produce AB Similar to function *Helper T cytotoxic Subtypes * B cells but not * Plasma cells require of cells *Cytotoxic * BT cells Ag to memory *Suppressor function Cells cells Microorganism entry, invasion and dissemination MICROORGANISM  Infection -

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Growth and multiplication of microorganisms that result in damage to host

Disease -

Infection produce notable changes in human physiology

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Pathogens

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Virulence factors

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Microorganism entry, invasion and dissemination MICROORGANISM Microbial virulence factor  Attachment - Microbial attachment to surface through different MOT - Pathogens vs colonizers  Invasion - Traumatic factors - Direct action of virulence factors - Examples:  Capsule: Klebsiella pneumonia  Enzymes: Staphylococcus aureus Microorganism entry, invasion and dissemination MICROORGANISM Microbial virulence factor  Surviving inflammation - Phagocytes  Production of capsule and toxins  Inhibit fusion of phagosomelysosome  Active and rapid replication - Complement system  Capsule to hide surface molecules  Produce substances that:  Inhibit complement activation  Destroy specific complement proteins Microorganism entry, invasion and dissemination Microorganisms Type of Mechanism (or interference responsible factor) Pseudomonas Resist “surface slime” phagocytosis (polysaccharide) aeruginosa (unless Ab present)

Microorganism causing infection/ disease Characteristics that enable them to cause disease

Pathogenesis - First step infection and diseases development

Escherichia coli

Resist digestion Resist phagocytosis (unless Ab present)

O antigen (smooth strains) K antigen (acid polysaccharide)

Resist killing

K antigen

CLINICAL BACTERIOLOGY PRELIM REVIEWER Salmonella typhi

Cryptococcus neoformans Treponema pallidum Yersinia pestis

mycobacteria

Resist phagocytosis (unless Ab present) Resist killing Resist phagocytosis Resist phagocytosis Resist killing

Resist killing and digestion

Vi antigen

Polysaccharide capsule Cell wall Protein – carbohydrate cell wall Cell wall structure

Microorganism entry, invasion and dissemination MICROORGANISM Microbial virulence factor  Microbial toxins - Biochemically active substances released by microorganisms that have a particular effect on host cells - Can cause disease in the absence of pathogens  Intoxication  Ingestion of performed bacterial toxin  Endotoxin - Gram (-) bacteria  Exotoxin - Gram (+) bacteria - Specific and more limited effects than endotoxins Microorganism entry, invasion and dissemination MICROORGANISM Microbial virulence factor  Microbial toxins Exotoxins Endotoxins Characteristic Gram – positive Gram - negative Organism type and gram negative Part of or Part of and Part of secreted from organism secreted from organism organism Chemical Simple protein Protein – lipid polyaccharide nature

Stability to heating (100 *c) Detoxification by formaldehyde Neutralization by homologous antibody Biologic activity Toxicity compared with strychnine as 1

Labile

stable

Detoxified

Not detoxified

Complete

partial

Individual to toxin 100 to 1,000,000

Same for all toxins 0.1

OUTCOME

Encou nter & entry

Coloniz ation & entry

Invasion & dissemi nation

OUTC OME

Incuba tion stage

Prodro mal stage

Clinica l stage

Conval escent stage

*S/S *Highly commu nicable

*peak of S/S

No S/S

*full recovery *chronic infection *death

CLINICAL BACTERIOLOGY PRELIM REVIEWER Definition of Terms 

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Acute phase - Early stage of a disease preceding the adaptive phase of the immune response Anaerobe - Organism that does not require oxygen for life and reproduction. Antibody - Protein or immunoglobulin molecule characterized by specific amino acid sequence produced by the host as a result of a specific antigenic stimulation. Antigen - Substance that produces sensitivity and initiates an immune response Antisepsis - Destruction of microorganisms to prevent infection Bacteremia - Presence of viable bacteria in the blood, as evidenced by their recovery in blood cultures Bactericidal - Antimicrobial that kills a microorganism Bacteriocin - Proteins produced by some bacteria that inhibit the growth of other strains of the same organism or related specie Capnophile - Microorganism that grows best in the presence of carbon dioxide Capnophilic Disinfection - Removal of microbes that may cause disease from an environment Disinfectant - Substance designed to be used on inanimate objects to kill or destroy diseaseproducing microorganisms Etiologic agent - Microorganism causing a disease. Fastidious - Hard to grow; requires additional growth factors.

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Genotype - Genetic makeup of an organism. Gram-positive bacteria - Bacteria that retain the crystal violet–iodine complex and appear blue-black on Gramstained smears. Gram-negative bacteria - Bacteria that do not retain the crystal violet complex; stained red by the safranin counterstain. Halophilic “Salt-loving”; an organism that grows best in media with an increased concentration of NaCl. Immunocompetent - ability of an immune system to mobilize and deploy its antibodies and other responses to stimulation by an antigen. Immunocompromised - describe an individual with deficient function of the immune system Immunosuppression - describe the state of an immune system that is suppressed Latent phase - permits the infection to evolve without any obvious external symptoms. Mesophile - Organism that grows best in moderate temperature, neither hot nor cold Microaerophile - microorganism that grows in conditions of reduced oxygen and increased carbon dioxide. Microaerophilic - Microorganisms that require environments containing concentrations of oxygen lower than that present in the atmosphere Microbial load - Total number of organisms present Obligate aerobe - Microorganism that requires oxygen for growth.

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Obligate anaerobe - Microorganism that can live and reproduce only in a strict anaerobic environment (0% oxygen) Nosocomial infection - Infection acquired within 72 hours of a stay in a health care facility. Opportunistic infection - Disease caused by a microorganism with low virulence that becomes pathogenic in a host with low immunologic resistance. Pathogenicity - Ability of a microorganism to cause disease. Phenotype - Observable or measurable characteristics of an organism Sepsis - Systemic response to bacterial infection Resistant strain - not inhibited by the usual systemic concentrations of the antimicrobial agent with normal dosage schedules Susceptible - implies that an infection caused by the bacterial strain tested may be appropriately treated with the dosage of antimicrobial agent recommended for that type of infection and infecting species. Intermediate - implying that the agent might be effective for infections located at body sites where the drugs are physiologically concentrated, or when a high dosage of drug can be used. Zoonosis - Disease that humans acquire from exposure to infected animals or products made from infected animals. Zoonotic - Pertains to diseases that can be transmitted from animals to humans....