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CLASSIFICATION,IDENTIFICATION of MICRO-ORGANISMS Micro CLASSIFICATION,IDENTIFICATION OF MICRO-ORGANISMS Micro-organisms may be classified in;- (1)-algae. (2)-protozoa. Eukaryote (3)-slime moulds. (4)-fungi. (5)-bacteria. (6)-archaea. prokaryote (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. The taxonomic ranks used in the classification of bacteria are ;- Kingdom Prokaryotae Division Gracilicutes Class Scotobacteria Order Eubacteriales Family Enterobacteriaceae Genus Escherichia Species coli 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). 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 a single-celled (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. In the blood,urogenital region, intestine 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. 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). They are G+ but become G- in ageing cultures.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
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