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Definition, Types, Methods used for identification of microbes, Types of specimen collection - Micro organism | 11th Nursing : Chapter 6 : Nursing - Infection Control

Chapter: 11th Nursing : Chapter 6 : Nursing - Infection Control

Micro organism

Microorganism or microbe is a living thing that is too small which is invisible to the naked eye but it can be visible under microscope.

Micro organism



Microorganism or microbe is a living thing that is too small which is invisible to the naked eye but it can be visible under microscope. The study of microbes is called as microbiology.

Microorganisms are divided into seven types.

·           Bacteria

·           Archea

·           Protozoa

·           Algae

·           Fungi

·           Viruses

·           Multi cellular animal parasites (helminthes)

Each type has a characteristic cellular composition morphology, motility or locomotion, reproduction.

Bacteria are prokaryotic organism. (single celled microbes). The cell structure is simple than that of other organism. Bacteria are classified into many groups according to the Morphology of Bacteria:

Type of Bacteria based on morphology:-

Bacteria can be divided into two,

1.        Beneficial bacteria

2.        Harmful bacteria (pathogenic bacteria)

Beneficial bacteria in the body is plays an important role in human survival. Bacteria in the digestive system break down the food substance and produce Vitamin K (E.coli.) Beneficial bacteria are also called probiotics. The normal flora are bacteria which are found in or on bodies. The presence may be temporary or permanent basis without causing any disease.


Harmful bacterial infection

Harmful bacteria are called pathogenic bacteria because they cause disease and illness in human and animals.

Classification of bacteria into gram positive and gram negative based on the cell wall composition.

Gram positive cocci in chains – Streptococcus pyogenes

Gram positive cocci in Clusters – Staphylococcus aureus

Gram negative Cocci in pairs– Neisseria meningitis

Gram positive Bacilli in chains other bacteria – Bacillus anthracis

Acid fast bacilli – Mycobacterium tuberculosis

Endospore forming – Clostridium tetani

Pleomorphic – Corynebacterium diphtheria

Gram Negative Bacilli – Escherichia coli When bacteria is present in our

When bacteria is present in our body in the absence of disease is called as colonizer. However people can get infection from Pathogenic bacteria through contaminated water, food and air

Skin infection:-

The organism most commonly found in the skin and mucous membrane. It cause superficial and systemic infections.

e.g. Staphylococcus aureus

Superficial: Boils, impetigo, foliculitis, Pneumonia, Food poisoning, bacteremia.

Respiratory tract infection: - The organism which is more found in the mouth as a normal flora. The infection may be in the upper tract or lower respiratory tract.

Ex. Streptococcus pyogenes

Upper Respiratory tract – Sore throat Laryngitis Pharyngitis

Lower Respiratory tract – Pneumonia and Tuberculosis

Gastro intestinal infection: -

Many different species of gram negative bacilli normally found in the intestinal tract. It cause inflammation of the gastrointestinal tract involving both stomach and the small intestine. Symptoms include diarrhoea, vomiting, and abdominal pain.

Genitourinary tract infection: -

A urinary tract infection (UTI) is an infection in any part of urinary system kidney, uterus, bladder, urethra. However, serious consequences can occur if a UTI spreads to your kidney.

Lower urinary tract – Cystitis

Upper urinary tract – Pyelonephritis

The most commonly UTI causing organism is Escherichia coli

Bacterial Infection



Viruses are obligatory intracellular parasites. They multiply by using the host cells. Synthesizing machinery to cause the synthesis of specialized elements that can transfer the viral nucleic acid to other cells. They are ultra-microscopic structure and are not visible in ordinary microscope. They are visible only under electron microscope.

Viral Infection


Methods used for identification of microbes:-

Bacteria are single celled microorganism and are invisible to naked eye. Bacterial identification is a necessary part of disease diagnosis and treatment without the identification of causative bacteria is very tough to provide effective treatment with available antibiotics.

Identification by morphology:-

Microscope is used to magnify the object and structure. In compound light microscopy which uses two sets of lenses, ocular, and objective lens. We calculate the total magnification of an object by multiplying the magnification of the objective lens and magnification of the ocular lens.

1.        The compound light microscope uses visible light.

2.        The maximum resolving power (ability to distinguish two points) of a compound light microscope is 0.2 μm

3.        Oil immersion lens is used to reduce the light loss and increases the resolving power.

Types of Microscope:-

·           Bright field microscope

·           Dark field microscope

·           Phase contrast microscope

·           Flourescence microscope

·           Electron microscope

Compound Light Microscope

Electron Microscope:

Electron microscope use beam of electrons and it has the magnification power of 10,000 to 1,00,000 x. It is used to view ultra-structure of viruses and other organisms

Preparation of specimens for light microscopy: -

Preparing smears and staining:

·           A smear is a thin film of material used for microscopic examination. Place a drop of saline or distilled water and mix the specimen with a sterile inoculation loop.

·           Spread the specimen uniformly on the slide.

·           Fixing uses air and heat to attach microorganisms on a slide.

Staining: -

·           Gram staining method

·           Acid-fast staining method


After smear preparation the glass slide should show for 2 to 3 times in a flame. Due to flaming the specimen get fixed perfectly on a slide and also some chemicals like formalin, Methyl alcohol, Mercuric chloride is used for fixing the specimen.

Stains: - Stains is used to make cellular shapes and arrangements visible. For e.g. The stains used in gram staining – Crystal violet, saffranin)

(decolorizer -Ethyl alcohol, Mordant agent – grams Iodine).

Hanging Drop Method: - (Glass slit method).

In hanging drop method, a drop of culture is made to hang between glass slide and slit and viewed under microscope.

The advantage of hanging drop method is we can identify mobile bacteria. Some bacteria have flagella for motility. e.g. Monotrichous, Peritrichous flagella (e.g. Proteus)

By cultural characteristics: -

Here bacteria are identified as group or culture as a whole and note individual bacteria some most bacteria grow in colonies and also divide fast. They can be easily grown into a culture in suitable nutrition media. Based on the characteristics of culture they can be identified as the size of colonies, type of elevation, margins, surface of colony, colour of culture.

Based on Antibiotic Resistance

Antibiotics (Ex-Penicillin) is added to the culture and measuring the resistance of microbe. The zone of inhibition surrounding the antiobiotic disc indicating sensitivity

No zone of inhibition surrounding the antibiotic disc indicating resistance.

By Biochemical test: -

Sugar fermentation test

·           Litmus milk test

·           Indole production test

·           Methyl Red test

·           Citrate utilization test

By differential staining: -

The identification depends on staining of bacteria. And most bacteria can be stained by specific stain like crystal violet. Gram positive bacteria are stained by gram stain while Gram negative bacteria don’t take up gram stain.

Mycobacterium tuberculosis bacteria can be stained by acid fast staining method.

Serological methods: - Here identification of bacteria is done by use of antibodies and antigens which are specific against the suspected bacteria. Antigens and antibodies are very specific and bind to single type of bacteria.

Identification of bacteria is necessary to

·           Identify the disease

·           Select suitable drug

·           Evaluation of treatment progress

·           For industrial purpose.

·           Storage


Types of specimen collection

Swabs: - It is usually collected in a sterile cotton swab, care should be taken so as to prevent contaminations of specimen. (e.g. Throat swab, Eye, Ear, Nose, Mouth, Vaginal, Abscesses swab). Materials should be taken only from the infected area.

Sputum: - It should be collected in a sterile container having wide mouth. Sputum should be collected directly after a cough and sent immediately to the laboratory.

Urine: - Urine specimen remains an important tool for clinical diagnosis. A correct urine result is influenced by the collection method, timing and handling (first morning sample, random sample). It should be collected in a sterile container.

Faeces: - Fresh stool should be collected for bacteriological examination. Specimen should be well covered and labelled.

For culture and parasite examination the specimen must be returned to the laboratory within one hour of collection.

Blood: - It is important that specimens are properly collected, prepared and preserved. When assisting the physician should adopt aseptic precautions so as to avoid contamination of specimen.

Always collect the blood specimen in hygienic area. Blood is carefully transfer from the syringe to the tube and gently invert 2-3 times to thoroughly mix the anticoagulant with the blood (heparin)


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