What is microbiology?

Microbiology is the study of microorganisms - bacteria, protozoal parasites, viruses and fungi. These organisms can only be seen under the microscope but despite their size these microorganisms, or microbes for short, have a massive impact on our lives. It has been estimated that there are 5X1030 or 5 million trillion, trillion, microbial cells on Earth. The total amount of carbon in these cells is equivalent to that of all of the plants on the planet! They collectively constitute the largest mass of living material on earth and play a critical role in shaping the environment that we live in. Humans, plants and animals are intimately tied to the activities of microbes which recycle key nutrients and degrade organic matter. Some microbes, however, are pathogenic.
Storage Requirements (Will depend on the assay) Special Handling Notes - all samples should be treated as infectious biohazards.

Sample

Description

Blood: Whole Blood Thick, viscous liquid. Dark red in absence of oxygen, bright red in presence of oxygen. Never freeze as this lyses the red blood cells. Usually 4-8C. Blood is normally sterile but may contain infectious agents such as HIV, hepatitis B, hepatitis C and syphilis.

Plasma Watery part of blood left Usually frozen or 4when red blood cells (RBCs) 8C. are spun out. Light straw yellow in colour, usually clear but may be turbid or milky after a fatty meal. Will clot, as it contains fibrin. Serum What is left after the fibrin in plasma clots. Looks like plasma. Urine Mid-stream samples are usually clear, watery, nonviscous liquid. Colour can vary but is usually pale to dark yellow in colour. Total urine samples can be cloudy and turbid indicating Usually frozen or 48C. For drug analyses or legal blood alcohol, strict handling and legislative protocols may need to be followed. A mid-stream urine sample would usually be relatively free of microbes. For drug analyses, strict handling and legislative protocols may need to be followed.

Usually 4-8C.

the presence of cells. Faeces Highly variable in appearance, but generally the stool should be firm unless diarrhoea is present. Colour is dependent on diet and disease processes but ranges from black to brown to yellow to white. Smell is usually bad! Usually 4-8C. Faeces may contain up to 10 bacteria/g and are significant sources of contamination in the laboratory. Be very careful when weighing or homogenising faeces.
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Cerebrospinal Usually a clear liquid. May Fluid (CSF) contain blood as a result of the collection process or be cloudy if bacteria are present in the CSF. Mucus or Sputum Viscous fluid or suspension, usually clear to milky. Infection is often denoted by a yellow or green colour.

Usually 4-8C.

CSF is normally sterile.

Usually 4-8C.

Treat mucus or sputum from a tubercular patient with special care to avoid aerosols. Handle to avoid spills.

Aspirates

Pleural aspirates (lung) are Usually 4-8C. usually clear to milky. Gastric secretions (stomach) are yellow to greenishbrown with the possibility of suspended material. Peritoneal aspirates (abdominal cavity) come in various colours. Synovial (joint) and amniotic (foetal) fluids are clear and watery. Clear to milky liquid but usually absorbed on paper or a swab. Usually 4-8C.

Sweat

Sample may be very small - treat carefully.

Semen

Clear to milky viscous liquid. May be kept warm Samples stored at -196C are a prior to immediate potential cold burn hazard. analysis. Long-term storage will require special diluents and storage at 196C(liquid nitrogen). Usually 4-8C or frozen. Samples are small, easy to contaminate and usually sent for testing in sterile saline to prevent drying out. Slides are fragile and should not be dropped.

Tissue Slices, Variable appearance and Biopsies, usually small. Removed Whole during surgery. Organs Cell Smears, Cell Scrapings, Blood Films Often presented on a glass microscope slide. Blood smears appear red whilst other smears are usually white.

Often dry at room temperature but may need to be stored at lower temperatures.

Hair

Often presented in specimen bags or jars. Often presented in specimen bags or jars.

Room temperature.

Small amounts are easily lost - treat carefully. Small amounts are easily lost - treat carefully.

Nail Fragments or Clippings

Room temperature.

Biomedical samples

Bacterial Culture
Bacterial Growth Media Liquid and powder growth media specifically formulated to culture bacteria for use in applications including cloning and protein expression

Bacterial Selection Antibiotics

Fast and potent selection antibiotics for use in bacterial culture

IPTG Induction

Most efficient inducing reagents for gene expression in bacteria

-galactosidase Substrates

Commonly used substrates for measuring enzymatic activity of betagalactosidase in bacteria

Yeast Culture
Yeast Growth Media Liquid and powder growth media specifically formulated to culture yeast for use in maintaining and propagating yeast strains

Algae Culture
Algae Growth Media Gibco TAP Growth Media optimized for Chlamydomonas reinhardtii and Gibco BG-11 Growth Media optimized for Cyanobacteria

Laboratory diagnosis of diseases begins with the collection of a clinical specimen for examination or processing in the laboratory.
KEY POINTS
Specimen collection requires withdrawing blood, cerebrospinal fluid, collecting urine, or

swabs from mucosal surfaces.

 Specimen collection is performed using aseptic techniques to ensure sterility of the sample The types of biological samples accepted in most clinical laboratories are: serum samples,

and avoid contamination from bacteria or other bodily fluids.

virology swab samples, biopsy and necropsy tissue, cerebrospinal fluid, whole blood for PCR, and urine samples. These are collected in specific containers for successful processing in the laboratory.
necropsy

The pathological dissection of a corpse; particularly to determine cause of death. Applicable to the examination of any life form.
biopsy

The removal and examination of a sample of tissue from a living body for diagnostic purposes. polymerase chain reaction Laboratory diagnosis of an infectious disease begins with the collection of a clinical specimen for examination or processing in the laboratory. The laboratory, with the help of well-chosen techniques and methods for rapid isolation and identification, confirms the diagnosis. It has been observed that the most important and frequent factor affecting laboratory analysis, even in a well-functioning laboratory, is not the laboratory investigation itself but specimen preparation and errors in identification or labeling. Proper collection of an appropriate clinical specimen is, hence, the first step in obtaining an accurate laboratory diagnosis of an infectious disease. Applying ones knowledge of microbiology and immunology for the collection, transportation and storage of specimens is as important as it is in the laboratory. For starters, the interpretation of the observation may be misleading if the specimen is inadequate. There are several types of specimens recommended for diagnosis of immunological diseases including: serum samples, virology swab samples, biopsy and necropsy tissue, cerebrospinal fluid, whole blood for PCR, and urine samples. Serum is the preferred specimen source for serologic testing. Blood specimens are obtained aseptically using approved venipuncture techniques by qualified personnel . Specimens are allowed to clot at room temperature and then are centrifuged. Serum is transferred to tightly-closing plastic tubes and stored at 2 8C before shipment--which should always be prompt. Acute serum should be collected at the onset of symptoms. Convalescent specimens should follow two to four weeks later. Paired sera are tested together. Plasma is also collected for a very limited number of tests. Lipemic, hemolyzed, or contaminated sera may cause erroneous results and should be avoided as should repeated freeze-thaw c