Classification and

Identification of
Microorganism and Parasites
Core Values

SOCIETAL RESPONSIBILITY EXCELLENCE

Your first encounter with MOs
Acellular and
Prokaryotic Microbes
 Microbes can be divided into those that are
truly cellular (bacteria, archaea, algae,
protozoa, and fungi) and those that are
acellular (viruses, viroids, and prions).

Cellular microbes (microorganisms) can be

Categories of divided into those that are prokaryotic
Microbes (bacteria and archaea) and those that are
eukaryotic (algae, protozoa, and fungi).

Viruses, viroids, and prions are often

referred to as acellular microbes or
infectious particles.
Acellular Microbes: Viruses
◦ Complete virus particles are called virions.
◦ Very small and simples in structure (10 – 300 nm)
◦ No type of organism is safe from viral infection
◦ Some viruses, called oncogenic viruses or oncoviruses.
◦ A typical virion consists of a genome of either DNA or
RNA, surrounded by a capsid (protein coat), which is
composed of protein units called capsomeres.
◦ Some viruses (enveloped viruses) have an outer
envelope composed of lipids and polysaccharides.
Acellular Microbes: Viruses
Viruses have five properties that distinguish them from living cells:
1. They possess either DNA or RNA, whereas living cells possess both.
2. They are unable to replicate on their own.
3. Unlike cells, they do not divide by binary fission, mitosis, or meiosis.
4. They lack the genes and enzymes necessary for energy production.
5. They depend on the ribosomes, enzymes, and metabolites of the host cell
for protein and nucleic acid production.
Acellular Microbes: Viruses
Origin of Viruses
◦ Coevolution theory - coevolved with bacteria and archaea from the
primordial soup
◦ Retrograde evolution theory – viruses evolved from free-living prokaryotes
that invaded other living organisms, and gradually lost functions which were
provided by the host cell
◦ Escaped gene theory – viruses are a piece of host cell RNA or DNA that have
escaped from living cells and are no longer under cell control -- currently
most widely accepted
Acellular Microbes: Viruses
Bacteriophages
Viruses that infect bacteria are known as bacteriophages or simply
phages.
Categorized based on shape, nucleic acid, and events that occur after
entry into a host cell
◦ Shape: icosahedron, filamentous, complex
◦ Nucleic acid: ss DNA, ds DNA, ss RNA, ds RNA
◦ Events: virulent vs temperate
Acellular Microbes: Viruses
Virulent bacteriophages vs. temperate
bacteriophages
•Virulent bacteriophages always cause what is known
as the lytic cycle, which ends with the destruction of
the bacterial cell.
•The five steps in the lytic cycle are attachment,
penetration, biosynthesis, assembly, and release.
Acellular Microbes: Viruses
Lytic cycle of bacteriophages
Acellular Microbes:
Viruses
Temperate bacteriophages
(lysogenic phages)

◦ Do not immediately initiate the

lytic cycle
◦ Instead, integrates their DNA into
the bacterial cell chromosome
◦ Phage switches to lytic cycle as a
result of environmental clues
Acellular Microbes:
Viruses
Uses of Bacteriophages

◦ Destroy bacterial pathogens

◦ Treat bacterial infection
◦ Prevent food contamination
Acellular Microbes: Viruses
Animal Viruses ◦ Steps in the multiplication of animal
◦ Infect animals or viruses are:
humans ◦ Attachment
◦ DNA or RNA ◦ Penetration
◦ Simple or complex ◦ Uncoating
◦ Biosynthesis
◦ Assembly
◦ Release
Acellular Microbes: Viruses
Latent virus infections

◦ Viral infections in which the virus is able

to hide from a host’s immune system by
entering cells and remaining dormant.
◦ e.g Herpes viral infections.

◦ Once acquired, herpes virus infections)

never completely go away.
◦ e,g chickenpox may be followed,
years later, by shingles both the result
of the same virus.
Acellular Microbes: Viruses
Antiviral agents

◦ Antibiotics are not effective against viral

infections
◦ Antiviral agents are drugs that are used
to treat viral infections.
◦ These agents interfere with virus-
specific enzymes and virus production
by disrupting critical phases in viral
multiplication or inhibiting synthesis of
viral DNA, RNA, or proteins.
Acellular Microbes: Viruses
Oncogenic viruses or Oncoviruses
◦ These viruses cause cancer.
◦ Examples include Epstein–Barr virus, human
papillomaviruses, Hepatitis B and C, and human
herpesvirus 8

Human immunodeficiency virus (HIV)

◦ This virus causes acquired immunodeficiency
syndrome (AIDS).
◦ It is an enveloped, single-stranded RNA
retrovirus.
◦ The primary targets for HIV are CD4+
cells⎯those having CD4 receptors on their
surface.
Acellular Microbes: Viroids and Prions
Viroids and prions are smaller and less
complex infectious particles than viruses
Viroids
◦ Viroids are short, naked fragments of single-
stranded RNA, which can interfere with the
metabolism of plant cells.
◦ Viroids are transmitted between plants in the
same manner as viruses.
◦ Examples of plant diseases caused by viroids
are potato spindle tuber and citrus exocortis.
◦ Does not cause animal disease
Prions
◦ Prions are small infectious proteins that
cause fatal neurologic diseases in animals
and humans
◦ Scrapie
◦ Mad cow disease
All are fatal spongiform
◦ Kuru
encephalopathies
◦ Creutzfeldt–Jacob disease
◦ Fatal Familial insomnia
◦ Of all pathogens, prions are the most
resistant to disinfectants.
◦ The mechanism by which prions cause
disease remains a mystery.
Domain Bacteria: Characteristics
Bacteria are divided into three
major phenotypic categories:

◦ Those that are Gram-negative and

have a cell wall
◦ Those that are Gram-positive and
have a cell wall
◦ Those that lack a cell wall
(Mycoplasma spp.)
Domain Bacteria:
Cell Morphology
There are three basic categories of
bacteria based on shape:
◦ Cocci (round bacteria)
◦ Bacilli (rod-shaped bacteria)
◦ Curved and spiral-shaped bacteria
Domain Bacteria:
Cell Morphology
•Cocci may be seen singly or in pairs (diplococci),
chains (streptococci), clusters (staphylococci),
packets of 4 (tetrads), or packets of 8 (octads).
◦ Medically relevant: Enterococcus, Neisseria, Staphylococcus,
Streptococcus
Domain Bacteria: Cell Morphology
Bacilli
◦ They are often referred to as rods; they may be short or long, thick or thin, and pointed or
with curved or blunt ends.
◦ They may occur singly, in pairs (diplobacilli), in chains (streptobacilli), in long filaments, or
branched.
◦ Extremely short bacilli are called coccobacilli.
◦ Examples of medically important bacilli: Escherichia, Klebsiella, Proteus, Pseudomonas,
Haemophilus, and Bacillus spp.
Domain Bacteria: Cell Morphology
➢Curve (comma shaped)
◦ Medically relevant example: Vibrio
◦ usually occur single, but some may form pairs

➢Spiral shape – called spirochetes

◦ Vary in length, rigidity, size, number and amplitude of their coils, and tightness of coils
◦ Treponema pallidum (syphilis), Borrelia (Lyme disease)

➢Shape can be lost due to adverse growing conditions

➢Some bacteria can exist in a variety of shapes (pleomorphic)
Domain Bacteria: Staining Procedures
Most bacteria are colorless, transparent,
and difficult to see
Three major categories of staining
procedures
◦ Simple staining procedure
◦ Structural staining procedures
◦ Capsule staining
◦ Spore staining
◦ Flagella staining
◦ Differential staining procedures
◦ Gram and acid-fast staining procedures
Domain Bacteria: Staining Procedures
•Bacterial smears must be fixed prior to staining.
•The fixation process serves to kill organisms, preserve their
morphology, and anchor the smear to the slide.
•The two most common techniques of fixation:
◦ Heat fixation- not a standardized technique; excess heat will
distort bacterial morphology
◦ Methanol fixation- a standardized technique; the preferred
method
Simple Bacterial Staining Technique
Domain Bacteria: Staining Procedures
Gram Stain
Divides bacteria into two major groups:
◦ Gram-positive (bacteria end up being blue to purple)
◦ Gram-negative (bacteria end up being pink to red)

The final Gram reaction (positive or negative) depends on the organism’s cell wall structure.
◦ The cell walls of Gram-positive bacteria have a thick layer of peptidoglycan, making it difficult to
remove the crystal violet–iodine complex.
◦ Gram-negative organisms have a thin layer of peptidoglycan, making it easier to remove the crystal
violet; the cells are subsequently stained with safranin.
Gram stain
Technique
Domain Bacteria: Staining Procedures
•Some bacteria are neither consistently purple nor pink after
Gram staining; they are known as Gram-variable bacteria, for
example, Mycobacterium spp.
•Mycobacterium spp. are often identified using the acid-fast
stain.
•THE ACID-FAST STAIN
◦ Carbol fuchsin is the red dye that is driven through the bacterial
cell wall using heat.
◦ Heat is used to soften the waxes in the cell wall.
◦ Because mycobacteria are not decolorized by the acid–alcohol
mixture, they are said to be acid-fast.
Domain Bacteria: Motility
If a bacterium is able to “swim,” it is said to be motile.
Bacterial motility is most often associated with flagella and
less often with axial filaments.
Most spiral-shaped bacteria and about 50% of bacilli are
motile;cocci are generally nonmotile.
Motility can be demonstrated by stabbing the bacteria into a
tube of semisolid medium
Domain Bacteria: Colony
Morphology
A bacterial colony contains millions of organisms.
Colony morphology (appearance of the colony) varies from one
species to another.
Colony morphology includes size, color, overall shape, elevation,
and the appearance of the edge or margin of the colony.
Colony morphology can also include the results of enzymatic
activity on various types of media.
As is true for cell morphology and staining characteristics, colony
morphology is an important “clue” to the identification
(speciation) of bacteria.
Domain Bacteria: Atmospheric
Requirements
Bacteria can be classified on the basis of their atmospheric requirements, including their
relationship to O2 and CO2.
With respect to O2, bacterial isolates can be classified as
◦ Obligate aerobes
◦ Microaerophilic aerobes
◦ Facultative anaerobes
◦ Aerotolerant anaerobes
◦ Obligate anaerobes

Capnophilic organisms grow best in the presence of increased concentrations of CO2 (usually
5%–10%)
Domain Bacteria: Atmospheric Requirements
Domain Bacteria:
Nutritional Requirements
All bacteria require some form of the elements such as
carbon, hydrogen, oxygen, sulfur, phosphorus, and nitrogen
for growth.
Some bacteria require special elements (e.g., calcium, iron, or
zinc) or vitamins
Organisms with especially demanding nutritional
requirements are said to be fastidious (“fussy”).
The nutritional needs of a particular organism are usually
characteristic for that species and are sometimes important
clues to its identity.
Domain Bacteria: Biochemical
and Metabolic Activities
As bacteria grow, they produce many waste products and
secretions
Pathogenic strains of many bacteria, such as staphylococci and
streptococci, can be tentatively identified by the enzymes they
secrete.
In particular environments, some bacteria produce gases such
as carbon dioxide or hydrogen sulfide.
To identify bacteria in the laboratory, they are inoculated into
various substrates (i.e., carbohydrates and amino acids) to
determine whether they possess the enzymes necessary to
break down those substrates.
Domain Bacteria:
Pathogenicity
Many pathogens are able to cause disease because they
possess capsules, pili, or endotoxins, or because they secrete
exotoxins and exoenzymes that damage cells and tissues.
Frequently, pathogenicity is tested by injecting the organism
into mice or cell cultures.
Examples of some common pathogenic bacteria:
◦ Neisseria meningitidis, Salmonella typhi, Shigella spp., Vibrio
cholerae, Yersina pestis, and Treponema pallidum
Domain Bacteria: Genetic
Composition
Laboratory identification of bacteria is moving toward
analyzing the organism’s DNA or RNA

The composition of the genetic material (DNA) of an organism

is unique to each species.

Through the use of 16S rRNA sequencing, the degree of

relatedness between two different bacteria can be
determined.
Domain Bacteria:
Unique Bacteria
Rickettsias, chlamydias, and mycoplasmas are
bacteria, but they do not possess all the attributes of
typical bacterial cells.
Rickettsias and Chlamydias have a Gram-negative type
of cell wall and are obligate intracellular pathogens
Rickettsias
◦ Disease transmitted by arthropods
◦ Cause typhus and spotted fever rickettsiosis
◦ have “leaky membranes.”
Domain Bacteria: Unique
Bacteria
Chlamydias

◦ are “energy parasites,” meaning they prefer to use ATP

molecules produced by their host cell.
◦ Transferred by aerosols or direct contact
◦ Cause trachoma, inclusion conjunctivitis, nongonococcal
urethritis, pneumonia, and respiratory disease
Domain Bacteria: Unique
Bacteria
Mycoplasmas
◦ smallest of the cellular microbes.
◦ lack a cell wall and therefore assume many shapes (i.e.,
pleomorphic)
◦ May be free living or parasitic
◦ Pathogenic to many animals and some plants
◦ In humans, pathogenic mycoplasmas cause primary atypical
pneumonia and genitourinary infections.
◦ Because they have no cell wall, they are resistant to drugs like
penicillin that attack cell walls.
Domain Bacteria:
Photosynthetic bacteria
Photosynthetic bacteria include purple bacteria, green bacteria, and
cyanobacteria
they all use light as an energy source (photosynthesis), but not in the
same way.
◦ Purple and green bacteria do not produce oxygen (anoxygenic
photosynthesis), whereas cyanobacteria do (oxygenic photosynthesis)
Cyanobacteria
◦ Believed to be the first organisms capable of carrying out oxygenic
photosynthesis
◦ When appropriate conditions exist in a pond or lake, a water bloom
will occur
◦ Perform nitrogen fixation
◦ Produce toxins
Eukaryotic Microbes
Domain: Eukaryota
Three major groups are of interest medical microbiologists as
directly causing disease:
•Protozoans
• Algae
• Slime & Water Molds

•Fungi
•Helminth
• Some arachnids and insects
 Protozoans
➢Protozoans are generally defined by four characteristics:

- Eukaryotic
- Single-celled (unicellular)
- No cell wall
- Motility (nearly all are able to move
due to cilia, flagella or pseudopodia)

➢Require moist environments.

➢Most are free-living and harmless. Very few are pathogens.

➢Motile feeding stage called trophozoite.

➢Many have hardy resting stage called cyst.

Protozoans
•Protozoans are generally defined by four characteristics:
•Eukaryotic
• Single-celled (unicellular)
• No cell wall
• Motility (nearly all are able to move due to cilia, flagella
or pseudopodia)
•Require moist environments.
•Most are free-living and harmless. Very few are pathogens.
•Motile feeding stage called trophozoite.
•Many have hardy resting stage called cyst.
Dysentery
Inflammatory disorder of the intestine, especially
the colon, that results in severe diarrhea
containing mucus and/or blood in the feces.
Untreated, dysentery can be fatal due to massive
dehydration.
Can be caused by bacteria, protozoans or
parasitic worms.
Protozoan Species: Giardia
lamblia (aka G. intestinalis)
Pathogenic species that feed off the intestinal lining.
Infection results from eating food / drinking water
contaminated by the organism - usually from feces.
A large number generates inflammation, which causes
nausea, stomachache, and diarrhea.
Chronic infection may result in malnourishment, blocking
absorption of food across their intestinal wall.
Protozoan Species:
Entamoeba histolytica
• A type of amoebae.
• Eat and move by extending parts of their bodies to
form pseudopods.
• Exists asymptomatically in 10% of world’s population.
• When disease develops, can be fatal (kills 100,000
annually).
• Feeds on the lining of the gut. Irritation created can
lead to condition known as amoebic dysentery.
• Contracted by eating or drinking fecally contaminated
food or water.
Toxoplasmosis
Caused by parasite: Toxoplasma gondii.
Can get from contaminated water, eating undercooked
infected meat (especially pork, lamb & venison), or contact
with cat feces that contain Toxoplasma.
Mild symptoms are flu-like.
Pregnant women and people with compromised immune
systems could develop serious health problems.
Severe toxoplasmosis can damage the brain, eyes and other
organs. Severe cases are more likely in individuals who have
weak immune systems.
Malaria
Life-threatening disease caused by Plasmodium
protozoan parasites transmitted through the
bites of infected mosquitoes.

Symptoms include fever, chills, and flu-like

illness. Left untreated can cause coma and death
if progresses to cerebral malaria.
 Fungi
▪Heterotrophic (consumers) digest their food externally, secrete digestive
enzymes and then absorb nutrient molecules into their cells. Examples:
yeasts, molds, and mushrooms.
▪Often have important symbiotic relationships with other organisms, mainly
plants. (Plants photosynthesize and provide carbon to the fungi in return for
nutrients that fungi take up from the soil).
▪Fungi are also used extensively by humans:
• yeasts responsible for fermentation of beer & bread
• mushroom farming is big industry
• produce some antibiotics

• ~30% can cause disease in plants, animals & humans. Pathogenic

fungi very resistant to antimicrobial drugs.
• Fungi and bacteria are the primary decomposers of organic matter.
Fungal Infections
Also called mycoses (singular mycosis)
If you have ever had athlete's foot or a yeast
infection, you can blame a fungus.
Reproduce through tiny spores in the air. You
can inhale the spores or they can land on you.
As a result, fungal infections often start in the
lungs or on the skin.
You are more likely to get a fungal infection if
you have a weakened immune system or take
antibiotics.
Fungal Infections: Types
of Mycoses
•Happen when fungi pass the resistance barriers of
the body and establish infection.
•Characterize mycoses by how widely / deeply
infection has penetrated:
• Superficial
• Cutaneous
• Subcutaneous
• Systemic
True Fungal Pathogens vs. Opportunistic Fungi

True pathogenic fungi have the ability to actively

attack and invade tissues of healthy individuals.
Have specific enzymes and proteins that help
them survive and reproduce within the body. Opportunist:
Aspergillus

Opportunistic fungi do not cause disease in

healthy individuals but can cause disease in those
with weakened immune system.

Pathogen:
Blastomyces
True Fungal Pathogen
Species: Blastomyces dermatitidis
•Cause: fungus in soil
•Mode of transmission: inhalation of spores
•Incubation: 30 to 100 days
•Types:
• Pulmonary Blastomycosis
• Disseminated Blastomycosis
Opportunistic Fungal Pathogen:
Aspergillus fumigatus
Can cause the disease Aspergillosis.
Has become leading infectious cause of
death in leukemia and bone marrow
transplant patients.
Can result in:
◦ allergic reaction
◦ pulmonary mass
◦ systemic infection
◦ can also exacerbate asthma
Helminths
•Helminths are parasitic worms that live inside
their host.
•Examples: hook, whip, pin, heart and round
worms
•Belong to the Kingdom Animalia.
•Live in and feed off living hosts.
Hookworms
Tapeworms
Thank you!