1 biology of microorganisms presented by د. آصف احمد محمد جي مان فطاني...

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Biology of Microorganisms

Presented by

فطاني. مان جي محمد احمد آصف د) عبدالعزيز ) الملك جامعة والجراحة الطب بكاالوريوس

) مانشستر ) جامعة والجزيئية الطبية الدقيقة الكائنات ماجستير) بريطانيا ) – مانشستر جامعة الطبية الدقيقة الكائنات دكتوراه

Dr Asif Jiman-Fatani, MB ChB, MSc, PhD (UK)

Assistant Professor in Medical Microbiology,Faculty of Medicine, King Abdulaziz University

Consultant MicrobiologistHead, Clinical Microbiology Laboratories

King Abdulaziz University Hospital1431 H – 2010 G

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Learning objectives At the end of the lecture you should be able to:

1. Outline the main groups of microorganisms

2. Describe their important structural features

3. Know the medically significant microorganisms

4. Discuss the structural features that are important medically and for identification

5. Discuss how the metabolism and growth of microorganisms affect their infectivity and their control

6. Describe the indigenous flora of the human body, the areas colonized and the potential for infection

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Classifying Microorganisms

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Naming Microorganisms For each organism 2 names (2 parts):

Genus الجنس noun, always capitalized -إسم Species الفصيلة أو النوع adjective, lowercase - إسم

Both italicized or underlined

First letter may be used in an abbreviated version. Staphylococcus aureus (S. aureus) Bacillus anthracis (B. anthracis) Escherichia coli (E. coli)

A common name is derived from historical use, e.g. pneumococcus for Streptococcus pneumoniae.

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Major categories of microorganism

The main groups of microorganisms are:

Bacteria √ Fungi √ Helminths Protozoa Viruses √

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(1). Bacteria

Single-celled organisms )prokaryotes بدائية ، النواة أولية)النواة

Have a cell wall Contain both DNA and RNA Have no defined nucleus. May possess surface features

such as pili )fimbriae(, flagella or capsules.

Do not have mitochondria or other organelles

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Bacteria

Staining Reactions

The Gram stain Many species can be defined

as;

1. Gram-positive, e.g. streptococci, or

2. Gram-negative, e.g. Neisseria spp.

Some organisms stain poorly with Gram stain but can be stained with other stains as mycobacteria (Ziehl-Neelsen stain).

Gram NegativeGram NegativeGram PositiveGram Positive

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Bacteria

Shape & Arrangement

Three shapes are seen:

1. Spherical (coccus) مكورة2. Straight rod (bacillus) عصوية3. Curved or spiral ملتوية

There is diversity within these groups;

For example, cocci may be arranged in:

1. Clusters )staphylococci(,

2. Chains )streptococci(, or

3. Pairs )pneumococci(.

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Bacteria

Shapes (cont.) Cocci المكورات

o Gram-positive, e.g. staphylococci, streptococcio Gram-negative, e.g. Neisseria spp.

Bacilli العصوياتo Gram-positive, e.g. clostridia - Bacillus spp.,o Gram-negative, e.g. Escherichia coli -

Pseudomonas spp.o Acid-fast, e.g. mycobacteria )Mycobacterium

tuberculosis(

Spiral or curved rods e.g. vibrios, spirochaetes

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(2). Fungi الفطريات

Fungi possess DNA and RNA, a defined nucleus and a cell wall.

There are two major types: Yeasts: Small, round,

unicellular. Moulds: grow as filaments

)hyphae( that may form mass )mycelium(.

Dimorphic fungi exist in both forms, e.g. Histoplasma.

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Fungal reproduction Asexual reproduction –

spores are formed through budding or in conidia.

Sexual reproduction – spores are formed following fusion of male & female strains.

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(3). Viruses الفيروسات

They grow inside a living cell (obligate intracellular parasites).

Composed of a nucleic acid, either DNA or RNA, and a coat of protein subunits (capsomeres).

A lipid envelope is found in some species.

Viral particles have helical, icosahedral or no regular symmetry.

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Viruses (cont.) Single-stranded DNA viruses, e.g.

parvovirues

Double-stranded DNA viruses, e.g. adenoviruses, herpesviruses, papovaviruses, poxviruses

Single-stranded RNA viruses, e.g. bunyaviruses, coronaviruses, orthomyxoviruses, paramyxoviruses, picornaviruses, retroviruses, rhabdoviruses

Double-stranded RNA viruses, e.g. neoviruses

Segmented RNA viruses, e.g. arenaviruses

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Size smaller Larger

Nucleus - +

Organelles - +

Chromosomes 1 circular Multiple, linear

Ribosomes smaller 70s Larger 80sr

Eukaryotic cellProkaryotic cell

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Morphology and Physiology of

Microorganisms

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The bacterial cell is composed of the following structure

Essential structure: Cell wall. Cytoplasmic membrane. Intracytoplasmic structures :

Nuclear apparatus. Ribosomes

Non-essential structures: Structures outside the cell

wall Capsules Flagella Fimbriae )pili(. Inclusion granulesOther non-essentials: Plasmids

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Essential structure1. Bacterial cell wall

Functions of the bacterial cell wall

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. Important in determining the cell's reaction to Gram

stain. Contains antigens that stimulate the patient’s antibody

response. Plays an essential role in cell division. With the exception of mycoplasmas, all bacteria possess a cell wall

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GRAM POSITIVEGRAM POSITIVE

GRAM NEGATIVEGRAM NEGATIVE

CytoplasmCytoplasm

CytoplasmCytoplasm

Lipoteichoic acid Peptidoglycan-teichoic acid

Cytoplasmic membrane

Inner )cytoplasmic( membrane

Outer Membrane

Lipopolysaccharide

Porin

Braun lipoprotein

Peri

plas

mic

spa

ce

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Cell Wall The Gram-positive cell wall

contains:

1. Thick layer of peptidoglycan.

2. Teichoic acids.

The Gram-negative cell wall contains:

1. Peptidoglycan is much thinner

2. Lipoproteins.

3. Outer membrane protein

4. Lipopolysaccharides.

5. Periplasmic space.

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2. Cell Membrane

The cell membrane is enclosed by the cell wall Mycoplasmas lack a cell wall and have an exposed cell

membrane.

Functions of the cytoplasmic membrane It plays a role in DNA replication. It is the site of respiration.

It is a permeability barrier and contains proteins involved in selective and active transport of solutes.

Active transport of ions )H+, Na+, K+, etc …( and nutrients into the cell.

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3. Bacterial Chromosomal DNA Single, supercoiled chromosome.

There is no nuclear membrane, no nucleolus, no mitotic apparatus, and no histones

The chromosome carries the genetic information to daughter cells and it is duplicated before cell division.

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4. Ribosomes Made of 60% ribosomal RNA

& 40% protein

Consist of 2 subunits: large & small

Site of protein synthesis

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1. Capsule External to the cell wall.

Confers resistance to phagocytosis.

2. Pili (Fimbriae) Hair-like structures that protrude

from the outer surface of some bacterial species

Assist in adhesion to external surfaces.

Non-essential structures

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3. Flagella Flagella are long thin structures that

protrude from the surface of some bacteria

Organs of locomotion responsible for movement.

4. Inclusions granules Intracellular storage bodies. Examples: glycogen,, gas vesicles for

floating, sulfur and polyphosphate granules

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5. Plasmids5. Plasmids Extra-chromosomal

DNA Coding

pathogenesis and antibiotic resistance factors

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Spores األبواغ Resting, dormant cells. Withstand extremes in heat, drying,

freezing, radiation & chemicals not a means of reproduction

Produced by some G+ genera.

Have a 2-phase life cycle :1. Sporulation -formation of

endospores. It contains contains calcium calcium dipicolinatedipicolinate

2. Germination- return to vegetative growth

Pressurized steam at 120oC for 20-30 minutes will destroy.

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Bacterial Metabolism

Factors that affect the rate of growth are:1. Temperature: Most bacterial species

will grow at 37oC.2. Hydrogen ion concentration (pH):

Most pathogenic species can grow at pH 7.2 – 7.6.

3. Gaseous atmosphere: The gaseous environments used include: Aerobic: oxygen Anaerobic: lacks oxygen Microaerophilic: low oxygen Capnophilic: carbon dioxide.

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Bacterial growth Bacterial growth follows

recognisable stages.

1. Lag phase: no increase in cell number

2. Log phase: maximum increase in cell number

3. Stationary phase: no net increase in cell number as a result of substrate limitation or inhibition by metabolite accumulation

4. Death phase: decrease in cell number owing to toxic metabolites or substrate deprivation.

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Binary Fission

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The Microbial Environment

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Air Outdoor air contains bacteria, moulds and spores. Depend on the

soil type, climate and population. Indoor air contains organisms that are found in dust, droplets and

droplet.

Water Water acts as a vehicle for microorganisms that cause diseases,

such as diarrhea, dysentery, enteric fever, cholera, hepatitis, etc

Soil Soil exposure is important cases of tetanus, gas gangrene Bacteria are found in highest numbers in the layer penetrated by

plant roots.

Animals Some organisms are animal pathogens but can cause diseases

in humans )Zoonotic disease) e.g. Brucella abortus )brucellosis in humans, septic abortion in domestic animals(

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The indigenous human flora

These organisms are normally found in harmless, close association with human body surfaces.

The tissues, blood and internal body fluids of humans are normally sterile.

Under certain circumstances, they can cause infection, e.g.

Lowered host mechanisms e.g. immunosuppressed, diabetics, leukaemic patients.

Alteration of the host tissues, e.g. Viridans streptococci may cause endocarditis after tooth extraction if the host has a predisposing heart lesion.

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Skin Exposed areas are suitable for the growth of Staphylococcus

epidermidis, coryneform bacilli, micrococci and low numbers of S. aureus.

Numbers of bacteria are higher around hair shafts.

Anaerobic bacteria (e.g. Propionibacterium acnes) are only found in anaerobic conditions of the sebaceous glands.

An alteration in skin conditions that increases hydration or damages the surface (e.g. occlusion, high humidity, or chronic inflammatory conditions such as eczema and psoriasis) increases colonisation by organisms like Staphylococcus aureus.

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Respiratory tract

In the anterior nares, the species found are similar to those on the skin of the face.

Staphylococcus aureus is present in up to 25-30% of adults.

The nasopharynx contains streptococci, Non-pathogenic Neisseria spp., Streptococcus pneumoniae and Haemophilus influenzae

Few microorganisms can be found below the larynx.

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Gastrointestinal tract1. Mouth Both α-haemolytic streptococci and non-pathogenic Neisseria are

found on many surfaces. Streptococcus sanguis (important in the formation of dental caries)

is present shortly after teeth eruption. Gingival crevice support the growth of Bacteroides spp., fusiform

bacteria and actinomycetes.

2. Stomach: Low pH and pepsin prevent the growth of most bacteria.

3. Small intestine: Motility keeps low numbers of organisms.

4. Large intestine: Anaerobic bacteria: Bacteroides fragilis Facultative bacteria: Escherichia coli and Enterococcus faecalis Other species present: staphylococci, clostridia, pseudomonads

and yeasts.

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Vagina

In childhood, the organisms are aerobic bacteria such as Enterobacteriaceae, staphylococci and yeasts.

At puberty (oestrogen) encourages the growth of lactobacilli; they create a low-pH Group B β-haemolytic streptococci may be found colonising

the adult vagina.

At the menopause: Flora similar to that found before puberty, with an increase in Enterobacteriaceae.

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Acquisition of the indigenous flora

The baby’s colon is usually colonised within about 6-12 hours of birth.

If the baby is breast-fed, this is mainly with bifidobacteria, and if bottle-fed, mainly with Enterobacteriaceae.

Once an indigenous flora has been established, it is more difficult for new species to become established in the mouth or lower gastrointestinal tract.

This has been called ‘colonisation resistance’.

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Medical importance of the indigenous flora

By definition, members of the indigenous human flora are not harmful in their normal habitat.

However, under certain circumstances, they can cause infection, e.g.

Colonic flora: urinary tract infection

Skin flora: surgical wound infection

Oral flora: dental caries, infective endocarditis

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Medical importance of the indigenous flora (cont.)

The alterations in indigenous flora seen when antibiotics are used can cause adverse effects in the patient such as:

diarrhoea, colitis

selection of antibiotic resistance

secondary infection, e.g. candidiasis