Classification of bacteria

1. BABCOCK UNIVERSITY
COURSE CODE: MLSC 417
LECTURE TOPIC: TAXANOMY AND
CLASSIFICATION OF BACTERIA

2. • TAXANOMY
• It is likened to a skilful blend in which it is
not easy to discern the ingredients (Cowan
& Steele).
• Ingredients: Classification,
Nomenclature and Identification.

3. Classification: Orderly arrangement of units
into groups based on acceptable set of
criteria.
Nomenclature: Naming or labeling of the
groups or units and individuals within the
group.
Identification: Entails the assignation of an
unknown organism to a group within a
scheme of classification.

4. Classification of Bacteria
There is no official classification of bacteria.
Taxanomy remains a matter of scientific
judgment and a generally accepted standard.
The commonly accepted classification is as
listed in 2nd edition of Bergey’s Manual of
Systematic Bacteriology.

5. Types of classification
1. Phylogenic classification
Based on evolutionary (ancestry) origins. The
ancestors of present day bacteria existed for 3
billion years. This system was used to
recognise two domains of Bacteria and
Archaea.
It is the basis of naming (nomenclature) of
bacteria.

6. 2. Classification by phenotypic
characteristics
• Morphological characteristics
• Biotyping
• Serotyping
• Antibiogram patterns
• Pyocin typing
• Phage typing

7. Morphology: Microscopic and macroscopic
morphologies of bacteria were the first
characteristics used to identify bacteria.
• Still the cornerstone for most identification
algorithms used today, e.g.
i) The Gram’s stain is used to classify bacteria
based on their shape and staining reaction.
ii) Macroscopic appearance of colonies on
culture plates such as haemolysis on blood
agar plates, pigmentation on culture media.

8. • Biochemical typing is the most used
method for definitive identification.
Biotyping is also used for dividing group
of organisms beyond species level.
• Serological typing is useful to identify
organisms that are inert in biochemical
testing e.g. Treponema pallidum, for rapid
identification of some species e.g. Strep.
pyogenes etc.

9. • Antimicrobial pattern: pattern of
susceptibility to antibiotics.
• Pyocin typing: Pyocins are a group of low
molecular weight bactericidal proteins. Their
bactericidal activity pattern can be used to
classify bacteria.
• Phage typing: Susceptibility to phages (or
bacterial viruses) is used to identify bacteria.

10. 3. Classification by analytical
characteristics.
• Cell wall analysis
• Whole cell lipid analysis
• Whole cell protein analysis
• Enzyme typing

11. • Cell wall content of mycolic acid has been
used to identify species of mycobacteria
(ZN stain).
• Analysis of lipid content of the whole cell
is used to characterise some bacteria.
• Commercial systems are available for
performing this analysis.

12. • Whole cell protein typing are handy tools
in characterising bacteria especially at
species level for epidemiological
purposes.
• This is done in reference laboratories.
• Cellular enzyme typing is a handy tool in
characterising bacteria especially at
species level for epidemiological
purposes.

13. 4.Numerical classification:
This a mathematical approach whereby all
features are assigned equal values. This is
the original Adansonian concept.
• The advent of computers has made this
approach to taxanomy easier to apply.
• Used mainly for research

14. 5. Genetic classification aka Molecular
genetics:
This is most precise and accurate.
Includes systems such as:
a) Guanine:Cytosine ratio:
This is now obsolete and the method has been
discarded.

15. • b) DNA hybridization: Involves comparison
of base sequence compatibility between two
strains: to determine if two isolates were in
the same genus or species.
• DNA probe: A probe from a marker strain is
annealed with DNA from test strain. If the
marker is bound to the DNA of test strain, the
identity is confirmed.

16. • Put in another way, DNA from the organism to
be identified is extracted and exposed to the
species specific probes. If the probes bind to
the DNA, then the organism’s identity is
confirmed.
• Can be applied directly to clinical specimens.
• It is definitive but tedious and requires
expertise to handle.

17. c) Nuleic acid sequencing aka DNA
amplification
Extension of the hybridization method is
Nucleic Acid sequencing or DNA amplification.
Most recent and modern, probes are used to
localise sequences that are unique to genus,
species, sub-species.

18. Various methods are used but the
commonest are PCR and LCR.
This method is changing the face of
laboratory diagnosis of infections.
It requires expertise and it is pretty
expensive.
Very wide application.

19. • d) Other genetic typing include
• i)Ribotyping and
• Ii) Plasmid analysis and
• Iii) Chromosomal DNA fragments.
• These are highly sophisticated systems
and are not in routine use.
• .

20. • Other approaches to classification
• Specific features: Based on specific ,
distinguishable features shared by all in
the group. This classification is according
to Bergey’s Manual of Determinative
Bacteriology.
• The features that require difficult process
or special apparatus are not listed.

21. NOMENCLATURE
• The term species is most commonly used
in the pragmatic classifying system. It is
the basic unit in the hierarchy of microbial
world.
• The basis of this category is that members
of the same species are able to produce
others of their kind.
• The next higher category is genus.

22. • The same genus comprises several species
which may differ in some aspects.
Further up the ladder of classification,
bacteria with similar features are placed in
successive larger categories.
Thus similar genera are grouped into family;
similar families are categorised as order;
similar orders make up class and
similar classes make up the phylum
(kingdom).

23. Theoretical classification and
Identification:
• This provides the bacteriologist with a
relatively simple and pragmatic ways of
placing bacteria into categories.
• Consideration is given to:
• Colonial morphology – This requires a
measure of experience to be able to identify
an organism by colonial appearance.

24. • This is usually confirmed with a few rapid
tests.
• Most isolates are divided into commensal,
contaminants of no clinical interest,
possible pathogen or probably pathogen
based partially on this.
• Thus, it reduces the workload of a clinical
laboratory.

25. • Gram’s stain
• In 1884, a Danish scientist, Christian Gram,
introduced a staining technique that indeed
simplified and enhanced the classification of
bacteria.
• The Gram’s stain has become the foundation
on which bacterial identification is laid.
• The staining technique is cell wall dependent
and simply divides bacteria into two groups:
Gram positive and Gram negative.

26. • The “key”:
• e.g. Coagulase test divides the species of
staphylococcus into two groups: CPS and
CNS
• Note that bacterial species are polythetic
i.e. a property may vary within a species.
• Reaction pattern of an unknown isolate is
compared to the “key” and its “goodness
of fit” with each species is determined.

27. • The key is now replaced by some
identification systems such as the API
system.
• Analytical Profile Index (API)
The numerical profile of the unknown isolate
is compared with an existing numerical
pattern for a known species.

28. The highest index (best fit) as calculated for
the unknown is the identity of the unknown.
• Unusual patterns may be due to many
factors e.g. impure culture.
• Giving an isolate a species name:
• This requires careful consideration.

29. Once identified, the isolate is assumed to
possess all the implied properties including
biochemistry, pathogenicity capability etc.
• If unequivocal, state that the isolate is
unusual.
• Routine identification of bacteria
The diagnostic bacteriologist bases his
identification strategy on what is termed
Characterization tests

30. • Routine identification of bacteria
• The diagnostic bacteriologist bases
his identification strategy on what is
termed Characterization tests
• These tests include :
• Microscopic morphology:
»Cell shape e.g. coccus

31. »Size
»Arrangement .e.g. clusters, chain
»Staining e.g. Gram + or Gram -
»Capsule characteristic
»Spore morphology e.g. round, oval,
terminal
»Flagellar arrangement e.g.
monotrichous

32. • Colonial morphology
• Solid media:
• For an experienced bench bacteriologist,
data from this source is often sufficient for
identification at genus level.
• Most clinical isolates discarded as non
significant are identified usually by colonial
appearance.

33. • Further incubation may be necessary in
order to ascertain the correct colonial
morphology of a suspected pathogen.
• Action on media- Haemolysis
- Pigmentation
- Swarming

34. Biochemical tests
• Essential tool for bacterial classification
and identification.
• Examples
- Fermentation/oxidation of carbohydrates
- Waste products
- Metabolism of organic acids, lipids, proteins
and amino acids.

35. • - pH or redox range of growth
-Tolerance of chemical agents
In short, these tests collectively define
nutritional and physiological interaction of
the organism with its enviroment.
- Usually technically simple and
inexpensive

36. especially when adapted to multi point
inoculating commercial test strips or micro
titre plate formats. But they all have
hidden complexities.
- Most yield positive (+) or negative (-)
results that are easy to read.
Enzyme activity
Characterization tests also include the
action of various enyzmes or toxins
produced by organisms.

37. • Examples:
- Coagulase for Staphylococcus species
- Lecthinase for Clostridium species
- Urease for Proteus species
The above approach is pragmatic, simple
and fast enough that the bench
bacteriologist is able to play his role in the
overall management of disease.

38. »Systematic Bacteriology
The systematic approach to the
identification of an isolated bacterium is
referred to as Systematic Bacteriology.
The bench bacteriologist combines his
theoretical knowledge of bacteriology,
disease aetiology and clinical information
as contained in request form, to initiate a
systematic identification of an isolated
bacterium.

39. With this, identification as set out above
becomes easier.
MERCI