Microbiology is another branch of Pathology. It involves the study of microorganisms and consists of four major disciplines which are Bacteriology, Virology, Mycology and Parasitology.​

The Clinical Bacteriology Laboratory is important for the detection and identification of pathogenic bacteria. It is also important in determining the sensitivity and resistance mechanisms of different bacteria. Biomedical scientists identify the pathogens from an array of different specimens such as pus, faeces, urine, sputum, blood, cerebrospinal fluid to name a few. Identification of bacteria includes direct staining and microscopic examination of these specimens as well as the isolation of the pathogenic bacteria on different culture media. Identification of these pathogenic bacteria is done on the basis of growth characteristics, metabolic and biochemical tests and reactivity with specific antibodies. Another important aspect of clinical bacteriology is the determination of sensitivity of the pathogens to different antibiotics. This is of utmost importance for patient treatment and management, even more so in recent years where antibiotic resistance is on the rise. Advances in diagnostic clinical bacteriology include the automation for biochemical identification and sensitivity testing as well as the introduction of molecular techniques for faster identification of the pathogens.

A subdivision of the Clinical Bacteriology Lab is Parasitology, where different human parasites are identified according to their ova and cysts by means of direct microscopical examination of faeces and urine.

The Clinical Mycology Laboratory specialises in the study of pathogenic fungi in humans. Diagnosis involves the microscopic examination of various specimens, culture to identify the fungi and sensitivity testing of these pathogenic fungi to aid the clinicians to administer the appropriate antifungal treatment.

The Clinical Virology Laboratory specialises in the identification of human viruses such as respiratory viruses, herpes viruses, enterovirus etc. that cause an array of diseases. It is also important in monitoring viral illnesses by monitoring the viral loads of chronic diseases such as HIV and the quantitative assessment of viral infection or reactivation in immunocompromised patients e.g. CMV and EBV. Identification of these viruses are done by various molecular methods, rapid antigen testing and serology. Advances in diagnostic clinical virology include the introduction of molecular techniques such as PCR and gene sequencing.

Clinical Chemistry
Clinical chemistry involves the measurement of the concentration (or level) of various chemical components in body fluids, most commonly in blood or urine samples. The components measured in the clinical chemistry laboratory include:
·         Enzymes (e.g. cardiac enzymes),
·         Blood glucose,
·         Electrolytes (e.g. sodium and potassium),
·         Hormones (e.g. thyroid stimulating hormone TSH, thyroxine T4, and male and female fertility hormones),
·         Tumour markers (e.g. prostate specific antigen PSA),
·         Lipids (e.g. cholesterol and triglycerides),
·         Proteins (e.g. total protein and albumin), and
·         Other metabolic products (e.g. creatinine and uric acid).
These chemical components are measured with the use of specialised automated instruments or manual techniques, most of which are based on the use of photometric or immunoassay reactions.
The assays carried out in the clinical chemistry laboratory are essential for the diagnosis of metabolic diseases, monitoring of disease progression, and the efficacy of drug therapy. The clinical chemistry laboratory is also involved in screening programs, including those for colorectal cancer and newborn screening for congenital hypothyroidism, and in the assessment of male fertility as part of the work up prior to in-vitro fertilisation (IVF).
Haematology and Coagulation
Haematology is the branch of medicine concerning the study of blood, the blood-forming organs and blood diseases. Haematology tests include laboratory assessments of blood cell composition and blood formation and any disorders affecting these processes.
Some examples of these tests are:
  • Full blood count - A count of the total number of red blood cells, white blood cells and platelets present in blood.
  • Blood film - Blood is smeared over a glass slide that is stained with specific dyes and viewed under a microscope. The number, shape and size of blood cells and the presence of any abnormal cells or immature cells are noted.
  • Staining may also detect blood parasites such as Malaria, Toxoplasmosis, and Microfiliariasis.
  • The erythrocyte sedimentation rate (ESR) may be tested.  This test is often used as an inflammatory marker.
  • The bone marrow is the blood-forming organ. This may be examined in situations when there are abnormalities in the blood, such as the presence of leukaemia cells.
  • The Iron status is also assessed using specialised stains to identify the iron stores in the bone marrow.
Coagulation tests measure the blood’s ability to clot and how long it takes to clot.  This is important to ascertain a balance between activation of the Coagulation system and the prevention of thrombosis, which is unnecessary blood clot formation.  Coagulation tests ensure that when there is injury, the body can stop the bleeding and that such activation does not occur spontaneously.  In fact, they are routinely requested before surgery.  Coagulation tests are also useful in monitoring people who take medicines that affect clotting ability.  For instance, the Prothrombin Time (PT/INR) is used to monitor Warfarin therapy, whilst the Activated Partial Thromboplastin Time (APTT) is used to monitor Heparin therapy.  Other more specialised tests measure various Coagulation proteins and their function.
Flow cytometry, another Haematology speciality, measures multiple characteristics of individual cells. These include cellular size, complexity and the antigenic composition of the different blood cells.  During maturation within the bone marrow, the different blood cells acquire and loose antigens, which give the individual blood cells a unique phenotype. Flow cytometry uses fluorochrome labelled antibodies to identify these antigens, thus assigning cellular lineage and stage of maturation.
Some clinical applications of Flow cytometry include:
  1. Identification of leukaemias and lymphomas from blood, bone marrow, tissue specimens and body fluids,
  2. The measurement of proliferative activity and DNA ploidy in Haematological Malignancies
  3. The immunologic monitoring of HIV-infected individuals, and
  4. The assessment of structural and functional properties of erythrocytes, leukocytes, and platelets
The Polymerase Chain Reaction (PCR) has rapidly become an invaluable technique for the detection, molecular characterisation and clinical management of a wide variety of Haematological disorders.  PCR is an automated process that specifically amplifies selected DNA or RNA sequences that are usually chosen to reflect the presence of abnormal genes, mutations, deletions, inversion or chromosomal translocation in the sample material. Many genetic alterations result in the onset of diseases and have prognostic and therapeutic impact. Since these genetic abnormalities are easily detected using PCR, such technique can be used both as a diagnostic and prognostic tool.  The major effect of PCR in this area is that genetically abnormal cells can be detected within a normal cell population at a far lower incidence level than any other existing technology. Within the Haematology laboratory, PCR is widely used for the identification of Leukaemia and Lymphoma associated genetic abnormalities. The hallmark in the diagnosis of certain Leukaemias, such as Chronic Myeloid Leukaemia and Acute Promyelocytic Leukaemia, is the identification of specific chromosomal translocations.
The Biomedical Scientists work in close association with the Haematology Clinical Team, ensuring that analysis and diagnosis is supported by expert clinical advice.
Cellular/Histo Pathology

Cellular pathology, also known as anatomical (or anatomic) pathology is the branch of pathology that involves the study of body organs and tissues (groups of cells). Cellular pathology is considered one of the diagnostic branches of medicine, along with radiology and other pathology specialties. Its roles include determining the cause of certain diseases and the effect(s) that they are having on the body, assisting with the choice of treatment that will be given, aiding in giving a prognosis and determining what may have caused a person’s death. Cellular pathology is vital in those parts of medicine where a specimen of tissue or a sample of tissue cells are taken from the patient and sent to the laboratory. In these situations cellular pathology is the specialty that gives the definitive diagnosis and allows clinicians to give the most appropriate advice and treatment to their patients. There are two main subdivisions within cellular pathology;

The first subdivision is Cytopathology (cytology), which is the examination of single cells. Material from gynaecological and other body sites obtained without the need for surgery is examined microscopically to detect any changes, including the presence of pre-malignant or malignant cells. Cytology specimens from a patient are smeared onto a slide and stained. The prepared slides are then examined under the microscope by the biomedical scientists and surgical pathologists to look at the number of cells on the slide, what types of cells they are, how they are grouped together and what the cell details are (shape, size, nucleus etc). This information is useful in determining whether a disease is present and what is the likely diagnosis.

Cytology is most often used as a screening tool; to look for disease and to decide whether or not more histological tests need to be performed. An example of screening would be the investigation of a breast lump. In combination with examination by the clinician and imaging tests, a needle aspirate of the lump submitted for cytology will show whether the breast cells are suspicious for cancer/ diagnostic of breast cancer. If they look suspicious or are malignant, a core biopsy with a larger needle (trucut biopsy) may be performed which takes more tissue, allowing for a definitive diagnosis to be made before deciding what type of surgery is required (local removal of the lump or removal of the whole breast). Cervical smears, fine needle aspirates from various organs, lung specimens and  serous fluids are examples of Cytological specimens.

The second is Histopathology, which involves the examination of sampled tissues under the microscope. Patients` tissues removed during surgery include;


-      Larger specimens including whole organs or parts thereof, which are removed during surgical operations. Examples include a uterus after a hysterectomy, the large bowel after a colectomy or tonsils after a tonsillectomy.

-      Pieces of tissue rather than whole organs are removed as biopsies, which often require smaller surgical procedures that can be performed whilst the patient is still awake but sedated. Biopsies include excision biopsies, in which tissue is removed with a scalpel (e.g. a skin excision for a suspicious mole) or a core biopsy, in which a needle is inserted into a suspicious mass to remove a slither or core of tissue that can be examined under the microscope (e.g. to investigate a breast lump).


After gross examination, tissue processing, embedding and cutting, tissues are stained using dyes and other chemicals to show changes in the cell structure of the tissues.  These changes are characterized to identify abnormalities like inflammation, infection, foreign body or cancer.   Histochemistry and Immunohistochemistry are specialised branches of histology.  These techniques aid more specific  tumour grading / staging, possible indication of therapy regimen and follow-up to identify whether treatment was effective or otherwise.


Immunology is the study of the immune system. The immune system uses various mechanisms to protect our body from infections. One of these mechanisms is the production of antibodies in response to the presence of a foreign organism or substance. Low levels of antibodies result in low immunity which increases the possibility of infections, however an uncontrolled production of antibodies may lead to autoimmune disease. Clinical laboratory immunology is the study of these autoimmune diseases and through the use of various specialized tests is able to diagnose conditions such as rheumatoid arthritis, SLE (lupus), Chron’s and coeliac disease. The Biomedical Scientists working in this field use techniques like fluorescence microscopy to identify the presence of these autoantibodies.

Transfusion Medicine

Transfusion medicine is the process of collecting, processing, testing, storing, and transfusing blood and blood products. This is a vital process in any hospital since many patients are dependent on the availability of blood components either after an operation or else to maintain adequate blood parameters (such as haemoglobin and platelets) which can be affected from treatment such as chemotherapy and radiotherapy. Biomedical scientists working in this field will process the blood to produce various components such as red cell concentrate, plasma and platelets. Biomedical scientists will then perform rigorous testing to check the quality of these blood products before being transfused to the patient.  These tests include screening for unexpected red cell antibodies, transmissible infectious diseases such as hepatitis and HIV, and bacterial contamination of platelets.  Other tests are also performed before the product is transfused to the patient to ensure that the product is compatible with the patient. The aim of these tests is to ensure that the patient is provided with a blood product which is safe.

Public Health

The function of the public health laboratory is to perform tests on the quality of food and also environmental samples to ensure their safety to the general public. Biomedical Scientists perform both microbiological and chemical tests on samples like sea water and also food which is to be consumed by the general public. These tests will identify the presence of any bacterial contamination which could lead to food poisoning if ingested or the presence of high levels of toxic chemicals in food or water.

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