Biology of Microorganisms

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Biology of Microorganisms

• Presented by
• ?. ??? ???? ???? ?? ??? ?????
• ?????????? ???? ???????? (????? ????? ?????????)
• ??????? ???????? ??????? ?????? ????????? (?????
  ???????)
• ??????? ???????? ??????? ?????? (????? ???????
  ????????)
• Dr Asif Jiman-Fatani, MB ChB, MSc, PhD (UK)
• Assistant Professor in Medical Microbiology,
• Faculty of Medicine, King Abdulaziz University
• Consultant Microbiologist
• Head, Clinical Microbiology Laboratories
• King Abdulaziz University Hospital
• 1431 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 ??? ?????- noun, always capitalized
• Species ??? ????? ?? ??????? - adjective,
  lowercase
• 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 v
• Fungi v
• Helminths
• Protozoa
• Viruses v

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(1). Bacteria

• Single-celled organisms (prokaryotes ????? ??????
  ? ?????? ??????)
• 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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BacteriaStaining Reactions

• The Gram stain
• Many species can be defined as
• Gram-positive, e.g. streptococci, or
• 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 Stain

Gram Negative
Gram Positive
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BacteriaShape Arrangement

• Three shapes are seen
• Spherical (coccus) ?????
• Straight rod (bacillus) ?????
• Curved or spiral ??????
• There is diversity within these groups
• For example, cocci may be arranged in
• Clusters (staphylococci),
• Chains (streptococci), or
• Pairs (pneumococci).

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BacteriaShapes (cont.)

• Cocci ????????
• Gram-positive, e.g. staphylococci, streptococci
• Gram-negative, e.g. Neisseria spp.
• Bacilli ????????
• Gram-positive, e.g. clostridia - Bacillus spp.,
• Gram-negative, e.g. Escherichia coli -
  Pseudomonas spp.
• Acid-fast, e.g. mycobacteria (Mycobacterium
  tuberculosis)
• Spiral or curved rods e.g. vibrios, spirochaetes

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(2). Fungi ????????

• 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 ?????????

• 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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Eukaryotic cell
Prokaryotic 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 granules
• Other 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 patients
  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 POSITIVE
Lipoteichoic acid
Peptidoglycan-teichoic acid
Cytoplasmic membrane
Cytoplasm
GRAM NEGATIVE
Lipopolysaccharide
Porin
Outer Membrane
Braun lipoprotein
Periplasmic space
Inner (cytoplasmic) membrane
Cytoplasm
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Cell Wall

• The Gram-positive cell wall contains
• Thick layer of peptidoglycan.
• Teichoic acids.
• The Gram-negative cell wall contains
• Peptidoglycan is much thinner
• Lipoproteins.
• Outer membrane protein
• Lipopolysaccharides.
• 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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Non-essential structures

• 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.

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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. Plasmids

• Extra-chromosomal DNA
• Coding pathogenesis and antibiotic resistance
  factors

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Spores ???????

• 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
• Sporulation -formation of endospores. It contains
  calcium dipicolinate
• 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
• 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.
• Lag phase no increase in cell number
• Log phase maximum increase in cell number
• Stationary phase no net increase in cell number
  as a result of substrate limitation or inhibition
  by metabolite accumulation
• 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 tract

• 1. Mouth
• Both a-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 ß-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 babys 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