CLASSIFICATION,IDENTIFICATION
OF MICRO-ORGANISMS
Micro-organisms may be classified in;-
(1)-algae.
(2)-protozoa.
(3)-slime moulds.
(4)-fungi.
(5)-bacteria.
(6)-archaea.
(7)-viruses.
The
algae,protozoa,slime moulds,and fungi
,include the larger and highly
micro-organisms,their cells have the same general type of structure and
organization describes as eukaryotic.
The
bacteria (including,the mycoplasma and Chlamydia)with blue green
algae
, include the smaller micro-organisms with a simple form the cellular
organization described as prokaryotic.
The
archaea
are a phylogenetic group of prokaryotes that bear only
ancestral relationship to other organisms.
The
viruses
are the smallest of the infective agents,they have a simple
structure that is not comparable with that of the cell,and their mode of
reproduction is different from that of cellular organisms.
Taxonomy
Taxonomy consist of three components;-
(1)-Classification: allows the orderly grouping of microorganisms
(2)-Nomenclature: concerns the naming of those organisms
(3)-Identification: the correct naming of isolate microorganisms according to
agreed system of classification, as in clinical practice. Identification is
preformed based:
1-
On growth or activity in the biochemical test system.Some tests are
definitive genus or species(e.g. production of catalase enzyme and
cytochrome C in Staphylococcus spp. and Pseudomonas aeruginosa).
2-
Other characters may be unique to spp. and serve to differentiate them from
organisms with similar biochemical activity profiles.
3-
Some B. do not grow in the laboratory (leprosy bacillus,treponemes) so
identify by genetic methods.
Eukaryote
prokaryote
The taxonomic ranks used in the classification of bacteria are ;-
The first letter of the genus name is always capitalized and the species name
being with a lower case letter, both names are printed in italics.
At present no standard classification of baceria is universally accepted and
applied,although Bergeyś Manual of Determinative Bacteriology is widely
used as an authoritative source.
Bacterial nomenclature is governed by International Committee on System
Bacteriology and published as approved lists of bacterial names in the
International Journal of Systematic and Evolutionary Microbiology ,most
new spp. are also first described in this journal and considered to be validly
published.
The taxonomic hierarchy for classification of bacteria (figure 1)that
resembles a family tree.Those graphs provide summary of the major
characteristics of the particular microorganisms.(e.g. Staphylococcus reveal that
they have rigid cell well + simple unicellular+ free living organisms + G
+
cocci).
Kingdom
Prokaryotae
Division
Gracilicutes
Class
Scotobacteria
Order
Eubacteriales
Family
Enterobacteriaceae
Genus
Escherichia
Species
coli
Classification in clinical practice
The table (1) outlines a simple , but practical classification scheme in
which organisms are grouped according to a few shared characteristics. Within
those groups, organisms may be farther identified,to species level by a few
supplementary tests. Protozoa and Fungi can often be identified on
morphological criteria alone.
Protozoa
Are unicellular non photosynthetic,eukaryotic organisms that come in
various shapes and sizes ,their surface membranes vary in complexity and
rigidity from: a thin flexible membrane in amoebae with changes in the cell
shape(production pseudopodia) to a stiff pellicle in ciliate sprozoa,preserving a
characteristic cell shape.
Most free living but others clinically important parasites of human can be ;-
(1)-intracellular parasites.
(2)-extracellular parasitic.
Transmission by ingestion of a infection stage of the parasite or by insect
bite.
Some parasitic spp. digest food material or feed on bacteria,so Itś regarded as
lowest forms animals life , flagellate protozoa are closely related to
photosynthetic flagellate algae in plant kingdom.
The most important groups of medical protozoa are the sporozoa (malaria)
amoebae and flagellate (table 1).
Fungi
Are non photosynthetic , saprophytic or parasitic eukaryotic organisms that
possess rigid cell wells. Some are (see table 1 ):
(1)-Moulds: grow as branching filaments(hyphae)which form a meshwork
(mycelium).The hyphae, a continuous multinucleate protoplasm, being either
non septate or septate with a central pore in each cross-well. Mould reproduce
sexual and asexual spores that develop from the mycelium that effects their air
bone dissemination.
(2)-Yeasts: are unicellular ovoid or spherical cells that reproduce asexually by
budding and sexual by spores. They do not form mycelium, although form a
pseudomycelium consisting of chains of elongated cells.
(3) The dimorphic fungi: produce a vegetative mycelium in artificial culture
but are yeast like in infected lesion.
In the blood,urogenital region, intestine
Table 1 : Simple classification of some cellular micro-organisms of medical
importance
Common group name Normal genus names
Eukaryotes
Protozoa
Sporozoa Plasmodium , Isospora , Toxoplasma ,
Cryptosporidium
Flagellates Giardia , Trichomonas ,Trypanosoma ,
Leishmania
Amoebae Entamoeba , Naegleria , Acanthamoeba
Other Babesia , Balantidium
Fungi
Mould-like Epidermophyton , Trichophyton , Microsporum ,
Aspergillus
Yeast-like Candida
Dimorphic Histoplasma , Blastomyces , Coccidiodes
True Yeast Cryptococcus
Prokaryotes
Bacteria
Filamentous bacteria Actinomyces , Nocardia , Streptomyces ,
Mycobacterium
True bacteria'
Gram-positive bacilli Aerobes: Corynebacterium , Listeria ,
Bacillus
Anaerobes: Clostridium , Lactobacillus ,
Eubacterium
Gram-positive cocci Staphylococcus , Sterptococcus , Enterococcus
Gram-negative cocci Aerobes:Neisseria
Anaerobes:Veillonella
Gram-negative bacilli Aerobes
Enterobacteria = Escherichia , Klebsiella ,
Proteus ,Salmonella ,Shigella , Yersinia.
Pseudomonads= Pseudomonas , Burkholderia ,
Stenotrophomonas Parvobacteria –Haemophilus ,
Bordetella , Brucella ,Pasteurella
Anaerobes : Bacteroides ,Fusobacterium
Gram-negative vibrios Vibrio , Spirillum , Campylobacter ,
And spirilla Helicobacter
Spirochaetes Borrelia , Treponema , Brachyspira,
Leptospira
Mycoplasmas Mycoplasma , Ureaplasma
Rickettsiae ,Chlamydia Rickettsia , Coxiella , Chlamydia
The higher fungi of the class Basidomycetes (mushrooms),which produce
fruiting structure of spores are not infectious for human or animals, although
some species are poisonous.
Pathogenic fungi can cause diseases ranging from skin infectious(superficial
mycoses) to serious systemic infections(deep mycoses).
Bacteria
The main groups of B. are distinguished by
microscope observation of their
morphology and staining reaction with gram stain,separates B. into:G
+
and G
-
B.
Details of structure provide a basis for a separate division into;-
(1)-Filamentous
bacteria(Actinomycetes):
most
are
capable
of
true
branching(hyphea)
and may produce a type of mycelium.
(2)-True bacteria: multiply by simple binary fission, free living, unicellular.
(3)-Spirochaetes : divide by transverse binary fission.
(4)-Mycoplasmas: lack a rigid cell well.
(5)-Rickettsiae and Chlamydiae : are strict intercellular parasites.
Filamentous bacteria
These are referred to as"higher bacteria".A few are of medical interest as
pathogens and some produce antibiotic.
Actinomyces;-
G
+
, non acid fast, tend to fragments into short coccal and
bacillus forms and not to form conidia, anaerobic (e.g Actinomyces israelii).
Nocardia;- similar to Actinomyces but aerobic and acid fast (e.g.
Nocardia asteroids).
Streptomyces;-mycelium does not fragment into short forms,conidia form in
chains from hyphae (e.g. Streptomyces griseus),produce antibiotic.
Mycobacterium;- G
+,
acid fast. Bacillus rarely branching ,aerobic (e.g.
Mycobacterium tuberculosis)
True Bacteria
Most medically important B. fall into this group.They are classified on the
basic of their shape;- (cocci,bacilli,vibrios,spirilla).
Cocci
Spherical cells are distinguished by their cell grouping and their reaction to
gram ś stain, uniform in size (1µm).Some spp. are capsulated and a very few are
motile.
Sterptococccus;- G+ cell adherent in chains (e.g. Streptococcus pyogenes)or as
diplococcal(e.g. Streptococcus pneumonia).
Staphylococcus and micrococcus;- G
+
cells,adherent in irregular clusters (e.g.
Staphylococcus aureus).
Sarcina;- G
+
cells,adherent in cubical arrays of multiples(e.g. Sarcina lutea).
Neisseria; -G
--
cells, adherent in pairs and elongated at right angles to axis of
pairs(e.g. Neisseria meningitides)
Veillonella; -G
--
cells,small cocci arranged in clusters and pairs ,anaerobic (e.g.
Veillonella parvula).
Bacilli
The primary subdivision of the rod-shaped B. is made according to their
staining reaction by the gram method and the presence or absence of
endospores.
G
+
spore-forming bacilli;- B. forms endospores as the genera Bacillus +
Paenibacillus(aerobic)and Clostridium(anaerobic).
The size,shape,and position of the spores may assist recognition of the
spp.(e.g. Clostridium tetani) has a spherical terminal spore as "drum stick" form.
G+ non spore-forming bacilli;-these include several genera.Corynebacterium
is slight curving,a club shaped or ovoid swelling of bacilli and their arrangement
in parallel or angular cluster as "chineas" letter .
Lactobacilli is distinguished by grow in chains and filaments and Listeria by
flagella that confer motility.
G
-
bacilli ;- this large grouping includes numerous genera such as
Pseudomonas , the family Enterobacteriaceae (coliform bacilli)
as well as small pleomorphic bacilli like Haemophilus,Brucella,etc….,and
anaerobes such as Bacteroides and Prevotella.
Vibrios and spirilla;-Vibrios and Campylobacter are recognized as short, non-
flexuous comma-shape bacilli(e.g. Vibrio cholerae) and spirilla as non-flexuous
spiral filaments(e.g. Anaerobiospirillum)they are G
--
,motile,having polar
flagella.
Spirochaetes
These differ from the true bacteria (spirilla) in
1- Being slender flexuous spiral filaments .
2- Motile without flagella.
These G
--
,vary in their size,shape,wave form,observed in wet preparation
by dark-ground microscope.Treponema,Leptospira and Borrelia are
medical importance.
Mycoplasmas
This differ from the true bacteria in
1- Their similar size , (0.15 to 1µm).
2- lack of a rigid cell well,which leads to extreme pleomorphism and sensitivity
to external osmotic pressure.
Rickettsiae and Chlamydiae
Rickettsiae are G
--
organism ,rod shaped , spherical or pleomorphic, smaller
than the "true bacteria". Most are strict parasites grow only in animal host
usually intracellularly(e.g. Rickettsiae prowazekii).
Chlamydiae are similar to Rickettsiae but have more complex intracellular
cycle(e.g. Chlamydia trachomatis)
Viruses
Viruses usually consist of molecules of DNA(DNA virus)or RNA(RNA
virus), but not both,enclosed in a simple protein known as capsid(or
coat).Some times the capsid may be enclosed in a lipoprotein envelope derived
largely from the host cell.Viruses are capable of growing only with in the living
cells of animal,plant,bacterial host, not in medium. The viruses infect and
parasitize B. are termed bacteriophages or phages, so the viruses are obligate
intracellular parasites that do not have a cellular structure,contain the genetic
information for their replication but require the hostś cellular structure and
enzymatic machinery to complete their replication.