OVERVIEW OF MICROBIOLOGY AND INTRODUCTION TO BACTERIOLOGYMICROBIOLOGY

Derived from 3 Greek words:MICROS small, minute or tiny

BIOS Life, livingLOGOS Science/ study

BASIC MICROBIOLOGY | BRANCHESBacteriology (bacteria)

Virology (virus)Parasitology (parasites)

Mycology (fungi)Protozoology (protozoan)

Phycology (algae)

APPLIED MICROBIOLOGYAgricultural Microbiology - Relationship of microbe to crops, and how to

increase crop productionFood and Dairy Microbiology - Studying the detrimental effects/ beneficial

effects of microbes in foods & drinksMicrobial Ecology - Study of microbes and its relationship to the

environmentImmunology

Molecular BiologyEARLY DEVELOPMENT - CONTRIBUTORS

Anton Van Leeuwenhoek - “animalcules”- Bacteria, Algae, Protozoans & yeast- Discovered the 3 forms of bacteria (rod,

spherical, spiral shape)

Robert Hooke - Confined Leeuwenhoek’s discovery using a compound microscope

Francisco Redi - Spontaneous theory did not apply to animals- Flies did not develop spontaneously from

putrefied meat (Putrefaction- decomposition of organic matter)

Lazaro Spallanzani - Contaminating air- 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

Franz Schultze - Boiled infusions and admitted air passed through strong sulfuric acid. No growth of microorganism seen.

Theodore Schwann - Heated flasks containing infusions and allowed 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

Shroeder and Van Dusch - Cotton plugs can filter air thus preventing growth of microbes and boiled solutions

Loius Pasteur - Constructed a swan-neck flask demonstrating 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

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Robert Koch - 1 disease, 1 agent- Relationship between disease agent and a

specific disease conditionExamples:- Whooping cough is caused only by Pertussis- Etiologic agents of anthrax and tuberculosis

through his KOCH’S POSTULATEMODERN DEVELOPMENTS

Genetic EngineeringProduction of New Vaccines

Gene TherapyStem Cell Therapy

Continuous Discoveries of New Strains of OrganismsKOCH’S POSTULATE

1. A specific microbe can ALWAYS be found associated with a given DISEASE.2. The microbe can be ISOLATED and GROWN in pure culture in the laboratory.3. The pure culture of the microbe will produce the disease when injected into a susceptible HOST.4. It is possible to RECOVER the injected microbe from the experimentally infected animal.

MICROORGANISMS EXAMPLE GIVENACELLULAR 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

Small poxVaricella

PRIONS- Proteinaceous and infectious particle, which may have

the same amino acid sequence of a normal but differs physically (due to FOLDING/ REFOLDING)

Creutzfeldt-Jacob diseaseKuru

CELLULARProkaryotes

BACTERIAARCHAEABACTERIA

Microbial EukaryotesPROTISTS

ALGAE- Organisms that

produce OXYGEN as a product of photosynthesis

- Contain chlorophyll- Unicellular/

multicellular organisms

Dinoflagellates – red tide- Gonyaulax sp.

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PROTOZOA- Unicellular non-

photosynthetic protists

Flagellates – flagella- Giardia lamblia- Trichomonas

vaginalisCiliates – cilia

- Balantidium coliAmoeba – pseudopodia

- Entamoeba histolytica

Sporozoa – immobile strictParasites

- Cryptosporidium sp.- Isospora beli

FUNGI- Non- photosynthetic

protists growing as a mass of branching interlacing filaments (hyphae) known as MYCELIUM

Major subdivision:

- Chytridiomycota- Zygomycota- Ascomycota- Basidiomycota- Deuteromycetes

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

PROKARYOTES vs. EUKARYOTESCharacteristics Prokaryotes Eukaryotes

NucleusAbsent (NUCLEOID)

EXCEPT planctomycetesPresent

DNA structure

Present(Most with a SINGLE circular naked

strand with NO PROTEIN)EXCEPT:

- Vibrio cholera (2 circular)- Borrelia burgdoferi (linear)- Streptomyces coelicolor (linear)

Present(MULTIPLE chromosomes; protein

associated with DNA)

Organelles Absent Present(lysosomes, mitochondria, golgi body, ER)

RibosomesPresent

(Smaller, free in cytoplasm)

70s

Present(Larger bound to membrane)

80sCell Wall

Generally PresentComplex chemical composition

Present in some typesAbsent in others

Reproduction Binary Fission MitosisExample Bacteria Fungi, protozoa, algae, slime molds

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BACTERIAL SHAPE AND ARRANGEMENT

BACTERIAL STRUCTURE

GLYCOCALYX

- Synthesized substances surrounding cellCOMPOSITION

- Polysaccharide EXCEPT in Bacillus anthracis & Bacilus licheniformis (polymerized D- glutamic acid)

Polysaccharide layers:- CAPSULE – firmly attached, well defined layer- SLIME LAYER – loose

FUNCTION- Antiphagocytic increase invasiveness- Adherance (e.g. Streptococcus mutans – cause dental caries)

CELL MEMBRANE

- Multilayered structure external to cell membraneFUNCTION

- 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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GRAM POSITIVE GRAM NEGATIVE- Thicker peptidoglycan (40 sheets) - Thinner peptidoglycan (1-2 sheets)

TEICHOIC ACID and TECHURONIC ACIDS2 types:

1. Wall teichoic acid2. Membrane teichoic acid (or Lipoteichoic acid)

LIPOPROTEIN- Stabilize outer membrane & anchors it to

peptidoglycan

FUNCTION- Bears antigenic determinants- -Streptococcus pneumoeae (Forssman

antigen) -M. tuberculosis (tuberculin) -S. aureus (A protein) -S. pyrogenes (M protein)

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 antigen3. core polysaccharides – ketodeoxyoctanoic acid

(KDO) and heptosePERIPLASMIC SPACE

- space bet. The inner & outer membranes- contains peptidoglycan layer, binding proteins,

hydrolytic enzymes, detoxifying enzymes that neutrolyze/ inactivate certain antibiotics

ACID FAST CELL WALLS - contains mycolic acids- Mycobacterium tuberculosis

MYCOPLASMA

- Lack cell walls/ peptidoglycan- Wall less Archaea- Resistant to many drugs such as Penicillin and

Cephalosposporins- Mycoplasma pneumoniae

CELL MEMBRANE- “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 - Single polar flagellum

LOPHOTRICHOUS- Multiple polar flagella

PERITRICHOUS - Flagella distributed to the

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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 - No true nucleus- COMPOSITION: DNA- FUNCTION: directs activity of cell

RIBOSOMES - 70s- FUNCTION: protein synthesis

INCLUSIONS/ GRANULES - 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 organismsTaxonomic Ranking

Kingdom Share 1 or few general characteristics (E. coli: Procaryotae)

Phylum ProteobacteriaClass GammaproteobacteriaOrder EnterobacterialesFamily EnterobacteriaceaGenus Escherichia

Species Organisms share majority of characteristics (Escherichia coli)

BERGY’s MANUAL OF SYSTEMATIC BACTERIOLOGYPHYLUM

CLASS ORDER IMPORTANT GENERA

PROTEOBACTERIAAlpha Proteobacteria

RickettsialesEhrlichiaRickettsia

Rhizobiales BartonellaBrucella

Beta proteobacteria Burkholderiales BordatellaNeisseriales Neisseria

Gamma Proteobacteria Thiotrichales FrancicellaLegionellales LegionellaPseudomonadales MoraxellaVibrionales Vibrio

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Enterobacteriales Citrobacter SalmonellaEnterobacter SerratiaEschirichia ShigellaKlebsiella YersiniaProteus

Pasteurellales Pasteurella HaemophillusEpsilon proteobacteria Camphylobacterales Campylobacter HelicobacterFirmicutes (Low G+C G(+) bacteria Clostridialles Clostridium

Mycoplasmatales Mycoplasma UreaplasmaBacillales Bacillus

ListeriaStaphylococcus

Lactobacillales Enterococcus StreptococcusLactobacillus

Actinobacteria (highG+C G(+) bacteria

Actinomycetalles ActinomycesCornebacteriumGardnerellaMycobacteriumNocardiaPropionobacteriumStreptomyces

BACTERIAL CLASSIFICATION

Gram (+) cocciStaphylococcus sp.Streptococcus sp.Enterocoocus sp.

Gram (-) cocci Neiserria sp.Veilonella

Gram (-) Facultative Anaerobic Bacteria

Escherichia sp.Klebsiella sp.

Salmonella sp.Shigella sp.Proteus sp.Yersinia sp.

Gram (-) Non-enteric bacilliVibrio sp.

Haemophilus sp.Pasteurella sp.

SCIENTIFIC NOMENCLATURE- All organisms have binomial names

Genus and Species- e.g. Escherichia coli E. coli

Escherichia coli E. coli

SPORULATIONSpore 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

GERMINATIONEndospore can remain dormant for thousands of years

Favorable conditions

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Breakdown layers surrounding endosporeSTAGESACTIVATION

- agent that overcome its dormancy (heat, acidity)

INITIATION- 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 LESS IMPORTANT ORGANISMS

Skin

S. epidermidis S. aureusCorynebacterium diptheriaeVarious StreptococciPseudomonas aeruginosaYeast

NoseS. aureus S. epidermis

Corynebacterium diptheriaeVarious Streptococci

MouthS. viridans Various Streptococci

Eikenella corrodensDental Plaques Streptococci mutans Provetella intermedia

Throat

Streptococci viridans Various StreptococciNeisseriaH. influenzaS. epidermidis

Colon

Bacteroides fragilisE. coli

FusobacteriumLactobacillusEnterococcus faecalisEubacteriumClostridium

Vagina

LactobacillusE. coligroup B streptococci

Various StreptococciGram (-) rodsB. fragilisC. albicans

STERILE SITESBlood

Cerebrospinal fluid (CSF)Urinary BladderPericardial fluid

Synovial fluid

TRANSMISSION OF DISEASECONTACT TRANSMISSION

Direct transmission

- contact between the source and hostExample:

- hand-to-hand- STD- Bacterial & viral respiratory tract diseases- Kissing- congenital

Indirect Contact - from reservoir to susceptible host- by means of non-living objects

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Example- Fomites – inanimate objects

Droplet Transmission - Spread through droplet nuclei that travel through short distance

VEHICLE TRANSMISSION- Waterbourne, foodborne, airborne

VECTOR- Animal/ insects carry agents from host to another- Arthropods- Mechanical transmission (e.g. HOUSEFLY)- Biological transmission (e.g. MOSQUITO BITE)

DEFINITION OF TERMSNormal Flora - “normal microbiota”

- They are mixture of microorganisms usually found in body sites and DO NOT CAUSE ANY DISEASE

Nosocomial Infection - An infection that develops during a stay in the HOSPITAL and is usually unrelated to the primary condition

Community acquired infections

- An infection contracted outside of health care setting, usually community based, and are infection present on admission

Endogenous infection - Infection caused by a PATHOGEN from an individual’s OWN bodyExogenous infection - Infection caused by a PATHOGEN acquired acquired OUTSIDE of the body

that have gained access to the bodyColonization - The presence and multiplication of microorganisms without tissue invasion

or damageCarrier - Any person or animal that HARBORS a particular infectious agent without

discernable clinical disease and serves as a potential source of infectionParasitism - 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

Host - An organism infected by a pathogenMutualism - 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

Commensalism - A symbiotic relationship in which two species live together and ONE species BENEFITS from the relationship without harming or benefiting the other

Virulence - The extent to which severe disease is produced in a population with clinically manifest disease

- Rabies= high virulentInvasiveness - The ability of microorganisms to ENTER the body and spread.Pathogenicity - The ability of microorganisms to produce clinically apparent illness in an

infected population- Measles= high pathogenicity

Toxigenicity - The ability the ability of microorganisms to produce TOXIN.Oppotunistic infection - An infection caused by normally nonpathogenic organisms in a host whose

resistance has been decreasedPathogen - A disease-causing microorganism.

MORPHOLOGIC DIFEERENCES AMONG THE BACTERIA

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Circular (Coccus) StreptococcusStaphylococcus

Neisseria

Rod (Bacillus)

CorynebacteriumListeriaBacillusClostridium

Mycobacterium (acid-fast)

ENTERICS: live in the GIT- Escherichia coli- Shigella- Salmonella- Yersinia- Klebsiella- Proteus- Enterobacter- Serratia- Vibrio- Camphylobacter- Helicobacter- Pseudomonas- Bacteroides (anaerobic)

HaemophilusBordetellaLegionellaYersiniaFrancisellaBrucellaPasteurellaGardnerella

Spiral

Spirochetes:- Treponema- Borrelia- Leptospira

Branching filamentous growth (like fungi)

Actinomycetes (anaerobic)Nocardia (partially acid-fast)

Pleomorphic ChlamydiaRickettsiae

No cell wall Mycoplasma

OXYGEN SPECTRUM

OBLIGATE AEROBES FACULTATIVE ANAEROBES

MICROAEROPHILIC OBLIGATE ANAEROBES

Gram (+)

NocardiaBacillus cereus

StaphylococcusBacillus anthracisCorynebacteriumListeriaActinomyces

Streptococcus Clostridium

Gram (-)

NeisseriaPseudomonasBordetellaLegionellaBrucella

Most other gram-negative rods

Spirochetes:- Treponema- Borrelia- Leptospira

Camphylobacter

Bacteroides

Acid-fastMycobacteriumNocardia

No cell wall Mycoplasma

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