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Classification of Microbes E Learning Lecture Notes


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Table of Contents
A. Classification of Microbes
What is included under the general terms of 'microbiology'?
Microbiology is a broad discipline covering viruses, bacteria, fungi and protozoa. Prions are also often included in
microbiology, but it is dubious if these are true microbes. The subjects of virology, bacteriology, molecular biology,
immunology, mycology, and parasitology are all true disciplines in their own right. In addition, research in
microbiology has stimulated the emergence of the revolutionary new disciplines of molecular genetics and

How are microbes classified?
All organisms are classified using the binomial system. The fundamental units of this system are "species" (similar,
interbreeding organisms), which in turn are grouped into a "genus". Organisms are identified by two names
indicating the genus and species e.g. Escherichia coli.

Which microbes are prokaryotes and which are eukaryotes?
Microorganisms are classified as eukaryotes (fungi and protozoa), prokaryotes (bacteria) and viruses. Eukaryotic
cells contain a nucleus, which is separated from the cytoplasm by a membrane. In addition the DNA of the
eukaryotic nucleus is divided into individual units known as chromosomes. Eukaryotic cells contain other
membrane bound structures, such as mitochondria, Golgi apparatus and endoplasmic reticulum.

B. Viruses
What are viruses?
Viruses are nucleic acid fragments that are enclosed within a protein shell. Viruses are not cells and cannot
produce their own metabolic energy nor can they replicate on their own. Therefore they are obligate intracellular
parasites and are absolutely dependent on host cells. Upon entry into a host cell, they disassemble and construct
new virus particles using host- and virus-encoded enzymes. Viruses are classified according to their shape,
structure and nucleic acid content.

What is the basic structure of viruses?
The nucleic acid and enzymes of virus particles are contained within a protein shell termed the capsid. Capsids
protect the viral nucleic acid from digestion by host cell enzymes and also serve as adhesins to aid attachment and
invasion of host cells. Some viruses have a host cell-derived envelope, acquired by budding through a host
membrane, surrounding the capsid. The presence of an envelope can also be used in classification. Viruses can be
separated into three major groups on the basis of whether they have icosahedral (6 sided), helical (circular) or
complex capsids.

Do viruses contain DNA and RNA?
No. Viruses may contain DNA or RNA but never both. Thus viruses can be described as DNA viruses or RNA
viruses. In addition the nucleic acid may be double stranded or single stranded; linear or circular. Most viruses are
haploid except retroviruses, which are diploid.

C. Prions
What are prions?
Prions are proteinaceous infectious particles even more simple in their organisation than viruses. In the past
prions were considered as unconventional slow viruses, i.e. a very long incubation period that caused
spongiform encephalopathies. These encephalopathies are slow neurodegenerative diseases. Unlike viruses,
Classification of Microbes E Learning Lecture Notes

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prions do not contain any nucleic acid material and are composed of a protease-resistant (resistant to the
activity of enzymes which degrade proteins), hydrophobic glycoprotein. A protein closely related to the prion
protein occurs naturally in human cells. It remains unclear how an aberrant prion protein can cause disease.
Interaction of the prion protein with its human homologue may alter the human protein and result in the
formation of the amyloid-like plaques characteristic of the spongiform encephalopathies.

D. Bacteria
What are bacteria prokaryotes?
Bacteria are single celled organisms that do not have intracellular membrane-bound organelles. Most bacteria
are free living and relatively few species cause disease.

How bacteria are generally classified?
In the clinical laboratory, bacteria are classified primarily based on their shape/morphology and Gram-
staining characteristics on light microscopy. Bacteria can be classified as Gram-positive or Gram-negative and
can be further divided into three groups depending on their shape (cocci, rods or spiral shaped). See Bacterial
Morphology and Physiology section of notes for details. Bacteria are now increasingly classified and typed
according to genotypic characteristics. The phenotype is becoming less important with the arrival of new
technologies such as micro-arrays

What are the major methods of bacterial phenotypic classification?
These include:
Enzyme typing: Analysis of whole cell proteins and cellular enzymes (enzyme typing) are used to
characterise bacteria, usually at the subspecies level.
Whole-cell protein analysis.
Whole-cell lipid analysis.
Cell wall (mycolic acid) analysis.
a) determined by direct microscopic examination morphology and Gram-staining
b) involves subjecting the bacteria to a range of carefully selected biochemical tests biotyping
c) differentiates bacteria on the basis of the antigenic diversity of their surface antigens serotyping
d) involves analysis of patterns of susceptibility to a range of antibiotics antibiogram patterns
e) involves analysis of susceptibility to a range of bacteriophage, or bacterial viruses phage typing

What other methods are used to type bacteria using phenotypic characteristics?
These include:Enzyme typing: Analysis of whole cell proteins and cellular enzymes (enzyme typing) are used
to characterise bacteria, usually at the subspecies level.Whole-cell protein analysis.Whole-cell lipid
analysis.Cell wall (mycolic acid) analysis.

What does typing mean with reference to bacteria?
Typing helps distinguish isolates of the same species that may be related or not related. For example, during
an outbreak of food poisoning caused by the same species of salmonella, e.g. Salmonella typhimurium, from a
Classification of Microbes E Learning Lecture Notes

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common source, e.g. inadequately cooked chicken at a wedding, it would be expected that the isolates from all
the patients involved in the outbreak at the wedding would be related, i.e. the same type.
Similarly, isolates of Staphylococcus aureus causing surgical site (wound) infection in five patients on a ward
would be indistinguishable or similar, if this arose due to inadequate practices of a surgeon who was a nasal
carrier of S. aureus. In contrast, isolates collected at different times and from different geographical locations,
i.e. no common source, would most likely, be unrelated.

Classification of Bacteria based on Gram-Stain and Shape.
Gram-positive Gram-negative
Cocci Bacilli Cocci Bacilli Curved Spiral
Staphylococcus Baccilus Neisseria Haemophilus* Vibrio Treponema
Streptococcus Listeria* Moraxella Escherichia Campylobacter Leptospira
Enterococcus Clostridia Proteus Helicobacter Borrelia
Corynebacterium Klebsiella
Mycobacterium Salmonella
Actinomyces Shigella
Nocardia Pseudomonas
Other bacteria: Mycoplasma, Rickettsia, Chlamydia
Frequently coccobacilli

What genotypic methods are used to type bacteria?
These include:
DNA hybridization
Plasmid analysis
Nucleic acid sequence analysis
Chromosomal DNA fragment analysis, e.g. pulsed field gel electrophoresis
The sequence of specific DNA fragments can also be used to type or distinguish between closely related
strains in epidemiological analysis. DNA sequencing of amplified ribosomal DNA (rDNA encodes ribosomes
and contains highly conserved sequences (at the family- or genus-specific) and highly variable sequences
(species- and subspecies-specific) is commonly used for this purpose and is termed ribotyping. Analysis of
plasmid patterns or chromosomal DNA restriction enzyme fragments can also be used to distinguish between
strains. Increasingly, analysis of the whole genome is being carried out and this provides a large amount of
data for analysis and interpretation

Can the genotype be used to identify bacterial isolates?
Yes. A specific DNA fragment from one bacterial species can be used as a molecular probe in DNA
hybridisation experiments to identify related bacterial species. If the probe binds to the DNA of the organism
being tested then the organism's identity is confirmed.
DNA hybridisation is a valuable tool for rapid identification of slow growing organisms or for the direct
detection of organisms in clinical specimens.
An extension of this method is to use the polymerase chain reaction (PCR) to amplify specific DNA fragments.
The ability to amplify specific DNA fragments from a clinical isolate can itself be used to identify an isolate or
alternatively the DNA sequence of the PCR product may be determined to identify the organism. For some
bacteria of importance in recent years, identification by this means rather than relying on phenotype is now
preferred, e.g.Burkholderi cepaci, Acinetobacter baumanii.

What are the mycoplasmas?
Mycoplasmas are the smallest free-living bacteria and are distinguished from other bacteria in that they lack a
cell wall but have a cytoplasmic membrane, which contains cholesterol to provide the cell with some shape.
They also contain an outer membrane, which serves as the principal antigenic interface. M. pneumoniae
causes respiratory tract infections and M. hominis, M. genitalium and Ureaplasma urealyticum cause genito-
urinary tract infections.

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E. Fungi
Are fungi prokaryotes?
No. Fungi are eukaryotes and fungal cells contain a nucleus with chromosomes, a mitochondrion, Golgi
apparatus and an endoplasmic reticulum. Thus fungi have much more in common with human cells than
bacterial cells. This has implications for the treatment of fungal infections: it is difficult to develop agents that
are selectively toxic for fungi.

What are the common morphological categories of fungi?
Fungal pathogens may exist as branched filamentous forms or as yeasts or both. Filamentous forms develop a
mass of thread-like filaments (hyphae) termed a mycelium. In yeast-like forms, the characteristic form is a
single cell. Many fungal pathogens are free-living and can be contracted by inhalation or by entry through

How are fungal infections classified?
There are essentially three groups:
Superficial mycoses, infections of outermost layer of skin and hair, e.g. tinea, thrush
Subcutaneous mycoses, dermis, subcutaneous tissues, muscle and fascia infections
Systemic mycoses, infection that originate primarily in the lung but which spread to many organ systems,
e.g. pulmonary aspergillosis, candidaemia.
Superficial, cutaneous and subcutaneous fungal infections (e.g. Epidermophyton, Microsporum, Trichophyton
and Sporothrix) are usually mild whereas systemic infections (e.g. Aspergillus, Candida, Histoplasma and
Blastomyces) can be life threatening.

Aspergillus fumigatus.

What fungus may cause meningitis?
Cryptococcus neoformans

F. Parasitology
What is a parasite?
A parasite is strictly an organism that lives off another and does it harm. The term "parasite" may be applied
to all infectious agents (including bacteria, viruses and fungi). However, it is generally reserved for parasitic
protozoa, helminths (worms) and arthropods.

How do parasitic infections differ from bacterial infections?
Unlike many bacterial infections, parasitic infections are often chronic lasting months to years. Repeated
exposure to the parasite can lead to an ever-increasing parasite burden. Parasites are often not highly virulent
or are unable to replicate in the host or both. Thus the number of organisms infecting the host often dictates
the severity of parasitic infections and the immunological response of the host to the parasite also contributes
significantly to the disease manifestations.
The clinical and laboratory features of the medically important parasites are covered by International
Health and Tropical Medicine (IC2).

What are the main groups of parasites of medical importance?
Classification of Microbes E Learning Lecture Notes

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There are three major groups of human parasites:1. Protozoa2. Helminths (worms) include Nematodes,
Trematodes and Cestodes 3. Arthropods

What are protozoa?
Protozoa are single cell animals and can be divided up in terms of where in the human body they cause
infections. Thus there are intestinal and urogenital protozoa and blood and tissue protozoa. Carriage of these
organisms in humans can often be asymptomatic.

Entamoeba histolytica cysts

What are helminths and how are they classified?
Helminths are parasitic worms, which can be divided into three groups:
Nematodes, Trematodes, Cestodes

What are nematodes?
Nematodes have large unsegmented cylindrical bodies and are commonly called roundworms. Some
nematodes of medical importance include:
Ascaris lumbricoides, (commonly called the roundworm), which causes ascariasis with symptoms such as
fever, pneumonitis (similar to an asthmatic attack) and liver damage.
Enterobius vermicularis, (pinworm), which causes enterobiasis with symptoms such as pruritis, loss of sleep
and fatigue.

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What are trematodes?
Trematodes or flukes are flat leaf-shaped worms. Parasitic flukes can target the intestine, lung or bladder.
They include:
Fasciolopsis buski is the largest, most prevalent and most important intestinal fluke. Severe infections with F.
buski can cause diarrhoea, abdominal pain, intestinal obstruction and malabsorbtion syndrome similar to
Schistosoma species ultimately cause infections in the veins surrounding the bladder or small intestine.
Schistosomiasis infections result in symptoms caused by the host's allergic responses to the fluke's different
life cycle stages.

What are cestodes?
Cestodes or tapeworms have flat, segmented, ribbonlike bodies with heads that contain "suckers" for
attachment. Tapeworms target the host intestine.
Medically important tapeworms include, the pork tapeworm Taenia solium, the beef tapeworm Taenia
saginata and the fish tapeworm, Diphyllobothrium latum. Infection with these tapeworms causes symptoms
ranging from mild diarrhoea, vomiting and abdominal pain to weight loss.

What are arthopods, and are they medically important?
Arthropods are invertebrate animals, with segmented bodies, several pairs of jointed appendages and a rigid
exoskeleton. Important arthropods include Centipedes, tongue worms, arachnids (spiders, mites and ticks)
and insects (flies, mosquitoes, lice, fleas). Most arthropods do not affect human health directly but rather
serve as vectors for the transfer of infectious agents.

G. Further Reading
Medical Microbiology (Greenwood, Slack and Peutherer), chapters 2 and 3.

Problem-Orientated Clinical Microbiology and Infection (Humphreys & Irving), Cases 30, 32, 39, 50 and 55
(parasites) and 46 (prions).