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MICROBIOLOGY Derived from 3 Greek words: MICROS BIOS LOGOS BASIC MICROBIOLOGY | BRANCHES Bacteriology (bacteria) Virology (virus) Parasitology (parasites) Mycology (fungi) Protozoology (protozoan) Phycology (algae) APPLIED MICROBIOLOGY Relationship of microbe to crops, and how to increase crop production Food and Dairy Microbiology Studying the detrimental effects/ beneficial effects of microbes in foods & drinks Microbial Ecology Study of microbes and its relationship to the environment Immunology Molecular Biology EARLY DEVELOPMENT - CONTRIBUTORS animalcules Anton Van Leeuwenhoek Bacteria, Algae, Protozoans & yeast Discovered the 3 forms of bacteria (rod, spherical, spiral shape) Confined Leeuwenhoeks discovery using a Robert Hooke compound microscope Spontaneous theory did not apply to animals Francisco Redi Flies did not develop spontaneously from putrefied meat (Putrefaction- decomposition of organic matter) Contaminating air Lazaro Spallanzani Microorganisms in heated infusions in sealed flasks showed no evidence of growth of microorganisms once the seal was broken, microbial growth was evident. Microorganisms did not spontaneously but came from CONTAMINATING AIR Boiled infusions and admitted air passed Franz Schultze through strong sulfuric acid. No growth of microorganism seen. Heated flasks containing infusions and allowed Theodore Schwann reheated air to enter the flasks. Unsealed flask showed no evidence of growth in the infusion no matter how long the allowed heated air to enter the flask. Microorganisms in the air were killed by heating and therefore no growth of microbes observed Cotton plugs can filter air thus preventing Shroeder and Van Dusch growth of microbes and boiled solutions Constructed a swan-neck flask demonstrating Loius Pasteur that air free of microbes could not create life in organic infusions. - Conclusion: Microorganisms and not spontaneous generation were responsible for the growth in the flask. - Pasteurization technique killing of microorganisms by heat Agricultural Microbiology small, minute or tiny Life, living Science/ study

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1. 2. 3. 4.

1 disease, 1 agent Relationship between disease agent and a specific disease condition Examples: - Whooping cough is caused only by Pertussis - Etiologic agents of anthrax and tuberculosis through his KOCHS POSTULATE MODERN DEVELOPMENTS Genetic Engineering Production of New Vaccines Gene Therapy Stem Cell Therapy Continuous Discoveries of New Strains of Organisms KOCHS POSTULATE A specific microbe can ALWAYS be found associated with a given DISEASE. The microbe can be ISOLATED and GROWN in pure culture in the laboratory. The pure culture of the microbe will produce the disease when injected into a susceptible HOST. It is possible to RECOVER the injected microbe from the experimentally infected animal.

Robert Koch



MICROORGANISMS VIRUSES Small infectious particles Lack many attributes of cells Replicates ONLY when it infects cells Consists of NUCLEIC ACID molecule, either DNA/ RNA, enclosed in a protein coat or capsid PRIONS Proteinaceous and infectious particle, which may have the same amino acid sequence of a normal but differs physically (due to FOLDING/ REFOLDING) BACTERIA Prokaryotes ARCHAEABACTERIA ALGAE Organisms that produce OXYGEN as a Microbial Eukaryotes product of PROTISTS photosynthesis Contain chlorophyll Unicellular/ multicellular organisms


Small pox Varicella

Creutzfeldt-Jacob disease Kuru

Dinoflagellates red tide Gonyaulax sp.

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PROTOZOA Unicellular nonphotosynthetic protists

FUNGI Non- photosynthetic protists growing as a mass of branching interlacing filaments (hyphae) known as MYCELIUM SLIME MOLDS Organisms that contains PLASMODIUM (amoeboid multinucleate mass) as a stage in their life cycle Their growth depends on the nutrients provided by bacteria or plant cells

Flagellates flagella Giardia lamblia Trichomonas vaginalis Ciliates cilia Balantidium coli Amoeba pseudopodia Entamoeba histolytica Sporozoa immobile strict Parasites Cryptosporidium sp. Isospora beli Major subdivision: Chytridiomycota Zygomycota Ascomycota Basidiomycota Deuteromycetes

Characteristics Nucleus

DNA structure

Organelles Ribosomes Cell Wall Reproduction Example

PROKARYOTES vs. EUKARYOTES Prokaryotes Eukaryotes Absent (NUCLEOID) Present EXCEPT planctomycetes Present Present (Most with a SINGLE circular naked (MULTIPLE chromosomes; protein strand with NO PROTEIN) associated with DNA) EXCEPT: Vibrio cholera (2 circular) Borrelia burgdoferi (linear) Streptomyces coelicolor (linear) Absent Present (lysosomes, mitochondria, golgi body, ER) Present Present (Smaller, free in cytoplasm) (Larger bound to membrane)

Generally Present Complex chemical composition Binary Fission Bacteria

Present in some types Absent in others Mitosis Fungi, protozoa, algae, slime molds

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Synthesized substances surrounding cell COMPOSITION Polysaccharide EXCEPT in Bacillus anthracis & Bacilus licheniformis (polymerized Dglutamic acid) Polysaccharide layers: CAPSULE firmly attached, well defined layer SLIME LAYER loose FUNCTION Antiphagocytic increase invasiveness Adherance (e.g. Streptococcus mutans cause dental caries) Multilayered structure external to cell membrane FUNCTION Provide structure, support, maintains shape Osmotic protection Anchors flagella Serves as primer in cell division Contributes to pathogenicity Site of action of some antibiotics

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COMPOSITION PEPTIDOGLYCAN (MUREIN, MUCOPEPTIDE) 3 parts: Has alternating N-ACETYLGLUCOSAMINE and N-ACETYLMURAMIC ACID (backbone) - same in all species Set of identical TETRAPEPTIDES side chains consisting of D- and L- amino acids attached to NAM vary in different species Set of identical PEPTIDE CROSS BRIDGES vary in different species PENICILLIN: inhibit synthesis LYSOZYME: can hydrolyze it Tetrapeptide side chains: L- alanine position 1 (attached to N-acetylmuramic acid) D- glutamate position 2 D- alanine position 4 Position 3: most variable - Gram (-): diaminopimelic acid - Gram (+): L- lysine

BACTERIA - GRAM STAINING Classified as Gram (+)= PURPLE/BLUE or Gram (-)= RED/PINK Gram staining procedure developed by HANS CHRISTIAN GRAM Depends on ability of bacteria to retain the CRYSTAL VIOLET-IODINE COMPLEX

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Thicker peptidoglycan (40 sheets) TEICHOIC ACID and TECHURONIC ACIDS 2 types: 1. Wall teichoic acid 2. Membrane teichoic acid (or Lipoteichoic acid) FUNCTION Bears antigenic determinants -Streptococcus pneumoeae (Forssman antigen) -M. tuberculosis (tuberculin) -S. aureus (A protein) -S. pyrogenes (M protein)

Thinner peptidoglycan (1-2 sheets) LIPOPROTEIN Stabilize outer membrane & anchors it to peptidoglycan OUTER MEMBRANE Bilayered structure Excludes hydrophilic & hydrophobic molecules thereby protecting the cell from harmful substances Contains special channels: PORINS passive diffusion of LMW hydrophilic compounds like sugar, ions LIPOPOLYSACCHARIDE (LPS) Endotoxin Consists: 1. Lipid A toxic; 2. O polysaccharide (O Antigen) highly immunogenic; function as antigen 3. core polysaccharides ketodeoxyoctanoic acid (KDO) and heptose PERIPLASMIC SPACE space bet. The inner & outer membranes contains peptidoglycan layer, binding proteins, hydrolytic enzymes, detoxifying enzymes that neutrolyze/ inactivate certain antibiotics




contains mycolic acids Mycobacterium tuberculosis Lack cell walls/ peptidoglycan Wall less Archaea Resistant to many drugs such as Penicillin and Cephalosposporins Mycoplasma pneumoniae

CYTOPLASMIC MEMBRANE COMPOSITION Phospholipid bilayer and proteins No sterols (EXCEPT for Mycoplasma) FUNCTIONS Selective barrier and active transport of solutes Electron transport and oxidative phosphorylation in aerobic species Excretion of hydrolytic co-enzymes Bears enzymes and carrier molecules for biosynthesis of DNA, cell wall polymers & membrane lipids Bears receptors and carrier molecules & other proteins of the chemotactic & other sensory transduction system FLAGELLA Long filamentous thread- like appendages (12-30nm) composed of entirely protein Made up several thousand molecules of a protein subunit called FLAGELLIN FUNCTION Motility Bears H-antigen THREE TYPES OF ARRANGEMENT MONOTRICHOUS LOPHOTRICHOUS Single polar flagellum Multiple polar flagella

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Flagella distributed to the entire cell FIMBRIAE/ PILI

Hair like filament Shorter, straighter, thinner than flagella Composed of structural protein subunits termed PILINS FUNCTION Attachment (ordinary pilus) role in the adherence of symbiotic & pathogenic bacteria to host cells Reproduction (sex pilus) responsible for attachment of donor and recipient cells in bacterial conjugation

CYTOPLASM Composed of amorphous matrix NUCLEOID RIBOSOMES INCLUSIONS/ GRANULES No true nucleus COMPOSITION: DNA FUNCTION: directs activity of cell 70s FUNCTION: protein synthesis Glycogen, lipids, phosphate FUNCTION: storage for nutrients -Metachromatic granues -Polysaccharide granules -Lipid inclusions -Sulfur granules

TAXONOMY Science of classification Naming of different forms of life according to the International code of principles, rules and recommendations and the identification of unknown organisms Taxonomic Ranking Kingdom Share 1 or few general characteristics (E. coli: Procaryotae) Phylum Proteobacteria Class Gammaproteobacteria Order Enterobacteriales Family Enterobacteriacea Genus Escherichia Species Organisms share majority of characteristics (Escherichia coli) BERGYs MANUAL OF SYSTEMATIC BACTERIOLOGY PHYLUM CLASS PROTEOBACTERIA Alpha Proteobacteria ORDER Rickettsiales Ehrlichia Rickettsia Bartonella Brucella Bordatella Neisseria Francicella Legionella Moraxella Vibrio Citrobacter Enterobacter Eschirichia Klebsiella Proteus Pasteurella Campylobacter IMPORTANT GENERA

Rhizobiales Beta proteobacteria Gamma Proteobacteria Burkholderiales Neisseriales Thiotrichales Legionellales Pseudomonadales Vibrionales Enterobacteriales

Salmonella Serratia Shigella Yersinia Haemophillus Helicobacter

Epsilon proteobacteria

Pasteurellales Camphylobacterales

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Firmicutes (Low G+C G(+) bacteria

Clostridialles Mycoplasmatales Bacillales

Lactobacillales Actinobacteria (highG+C G(+) bacteria Actinomycetalles Cornebacterium Gardnerella Mycobacterium Nocardia Propionobacterium Streptomyces BACTERIAL CLASSIFICATION

Clostridium Mycoplasma Bacillus Listeria Staphylococcus Enterococcus Lactobacillus Actinomyces



Gram (+) cocci Gram (-) cocci Gram (-) Facultative Anaerobic Bacteria Gram (-) Non-enteric bacilli
SCIENTIFIC NOMENCLATURE All organisms have binomial names Genus and Species e.g. Escherichia coli E. coli Escherichia coli E. coli SPORULATION Spore formation Highly durable dehydrated resting cells Survive extreme heat, lack of water, many toxic chemicals Means of survival 1 spore from 1 vegetative cell DIPICOLINIC ACID in core Location: central, terminal, subterminal e.g. Bacillus; Clostridium GERMINATION Endospore can remain dormant for thousands of years Favorable conditions Breakdown layers surrounding endospore STAGES ACTIVATION agent that overcome its dormancy (heat, acidity) INITIATION

Staphylococcus sp. Streptococcus sp. Enterocoocus sp. Neiserria sp. Veilonella Escherichia sp. Klebsiella sp. Salmonella sp. Shigella sp. Proteus sp. Yersinia sp. Vibrio sp. Haemophilus sp. Pasteurella sp.

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water taken up & dipicolinic acid released OUTGROWTH emergence of new vegetative cell

NORMAL FLORA microorganisms normally residing in a particularly body site they do NOT cause infection in healthy humans LOCATION IMPORTANT ORGANISM S. epidermidis Skin

S. aureus Nose Mouth Dental Plaques Throat Bacteroides fragilis E. coli Colon S. viridans Streptococci mutans Streptococci viridans


Lactobacillus E. coli group B streptococci

LESS IMPORTANT ORGANISMS S. aureus Corynebacterium diptheriae Various Streptococci Pseudomonas aeruginosa Yeast S. epidermis Corynebacterium diptheriae Various Streptococci Various Streptococci Eikenella corrodens Provetella intermedia Various Streptococci Neisseria H. influenza S. epidermidis Fusobacterium Lactobacillus Enterococcus faecalis Eubacterium Clostridium Various Streptococci Gram (-) rods B. fragilis C. albicans

STERILE SITES Blood Cerebrospinal fluid (CSF) Urinary Bladder Pericardial fluid Synovial fluid

TRANSMISSION OF DISEASE CONTACT TRANSMISSION contact between the source and host Example: - hand-to-hand - STD - Bacterial & viral respiratory tract diseases - Kissing - congenital from reservoir to susceptible host by means of non-living objects Example - Fomites inanimate objects Spread through droplet nuclei that travel through short distance

Direct transmission

Indirect Contact Droplet Transmission

VEHICLE TRANSMISSION Waterbourne, foodborne, airborne

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VECTOR Animal/ insects carry agents from host to another Arthropods Mechanical transmission (e.g. HOUSEFLY) Biological transmission (e.g. MOSQUITO BITE) DEFINITION OF TERMS normal microbiota They are mixture of microorganisms usually found in body sites and DO NOT CAUSE ANY DISEASE An infection that develops during a stay in the HOSPITAL and is usually unrelated to the primary condition An infection contracted outside of health care setting, usually community based, and are infection present on admission Infection caused by a PATHOGEN from an individuals OWN body Infection caused by a PATHOGEN acquired acquired OUTSIDE of the body that have gained access to the body The presence and multiplication of microorganisms without tissue invasion or damage Any person or animal that HARBORS a particular infectious agent without discernable clinical disease and serves as a potential source of infection A symbiotic relationship where one organism, the parasite, lives in or on another, depending on the latter for its survival and usually at the expense of the host. Ex. Entamoeba histolytica, which derives nutrition from the human host and causes amebic dysentery An organism infected by a pathogen A symbiosis in which two organisms mutually BENEFIT from each other Ex. Termites and the flagellates, in their digestive system, which synthesize cellulose to aid in the breakdown of ingested woods A symbiotic relationship in which two species live together and ONE species BENEFITS from the relationship without harming or benefiting the other The extent to which severe disease is produced in a population with clinically manifest disease Rabies= high virulent The ability of microorganisms to ENTER the body and spread. The ability of microorganisms to produce clinically apparent illness in an infected population Measles= high pathogenicity The ability the ability of microorganisms to produce TOXIN. An infection caused by normally nonpathogenic organisms in a host whose resistance has been decreased A disease-causing microorganism.

Normal Flora

Nosocomial Infection Community acquired infections Endogenous infection Exogenous infection Colonization Carrier Parasitism

Host Mutualism -

Commensalism Virulence

Invasiveness Pathogenicity

Toxigenicity Oppotunistic infection Pathogen

Circular (Coccus)

Rod (Bacillus)

MORPHOLOGIC DIFEERENCES AMONG THE BACTERIA Streptococcus Neisseria Staphylococcus Corynebacterium ENTERICS: live in the GIT Listeria Escherichia coli Bacillus Shigella Clostridium Salmonella

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Mycobacterium (acid-fast)

Spiral Branching filamentous growth (like fungi) Pleomorphic No cell wall Actinomycetes (anaerobic) Nocardia (partially acid-fast)

Yersinia Klebsiella Proteus Enterobacter Serratia Vibrio Camphylobacter Helicobacter Pseudomonas Bacteroides (anaerobic) Haemophilus Bordetella Legionella Yersinia Francisella Brucella Pasteurella Gardnerella Spirochetes: Treponema Borrelia Leptospira

Chlamydia Rickettsiae Mycoplasma OXYGEN SPECTRUM FACULTATIVE MICROAEROPHILIC ANAEROBES Staphylococcus Streptococcus Bacillus anthracis Corynebacterium Listeria Actinomyces Most other gramSpirochetes: negative rods Treponema Borrelia Leptospira Camphylobacter

OBLIGATE AEROBES Nocardia Bacillus cereus Gram (+)


Gram (-)

Acid-fast No cell wall

Neisseria Pseudomonas Bordetella Legionella Brucella Mycobacterium Nocardia



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