Principles of investigation

Specimen types

For the exam you are expected to have a basic understanding of the specimen types used to identify common infections. Key examples are shown below

Specimens may be cultured on liquid medium and solid medium environments. These allow for the amplification of organism quantity to allow reliable detection.

Microscopy and staining

Microbial samples are often examined using a microscope and specific stains may be used to aid identification of suspected pathogens. The table below summarises common stains and their uses:


Serology

Serology refers to the process of identifying infectious pathogens based on the immune response they elicit in the host, primarily through the detection of antibodies in blood or other body fluids. This is particularly useful when:

• The pathogen is difficult to isolate or culture
• The patient is partially treated
• Infection has occurred in the past and evidence of exposure is needed.

Diagnosis commonly depends on identifying rising or falling antibody titres in serial specimens. A fourfold rise in titre is typically considered diagnostic of recent infection.

An alternative serological approach involves detecting specific microbial antigens directly from patient samples, offering more immediate diagnostic information.

The syllabus suggests candidates be aware of bacterial capsular antigen testing in cerebrospinal fluid (CSF) for meningitis as an example. However, according to the current NICE guidelines (NG240: Bacterial meningitis and meningococcal septicaemia, 2024):

“Do not routinely use CSF bacterial antigen testing to diagnose bacterial meningitis.”

This recommendation reflects concerns over limited sensitivity and specificity, particularly when culture and PCR-based methods offer more reliable results. Antigen testing may still be considered in specific situations where other methods are not available or are inconclusive.

Molecular Techniques

Molecular diagnostics, especially nucleic acid amplification techniques (such as PCR), are widely used in infection diagnosis today.

These techniques detect the DNA or RNA of pathogens directly from clinical specimens, making them ideal when:

• The microorganism is slow-growing or difficult to culture, such as Mycobacterium tuberculosis or Chlamydia trachomatis
• Rapid or highly sensitive diagnosis is needed
• Prior antimicrobial use may have affected culture yield.

PCR testing is now central to the diagnosis of many viral, bacterial, and some parasitic infections, and is also used in CSF analysis for meningitis, providing quick and accurate identification of causative organisms.