The Use of the Laboratory in the Investigation, Management, and Prevention of Infection

Abstract

The pre-analytical stage is broadly classified into four elements: 1. Appropriate selection and use of diagnostic tests; 2. Proper filling in of request forms (paper or electronic); 3. Collection and transport of specimens; and 4. Checks made when the specimen and request form reach the laboratory to ensure the correct patient, sample, and request have been made. A large part of the laboratory role is to advise on the collection of appropriate samples in order to ensure the best chance of diagnosing a suspected infection syndrome or specific pathogen. This requires having a working knowledge of the range and processes of tests available in the laboratory for each clinical syndrome, and the ability to appreciate their strengths and weaknesses, sensitivities and specificities. In addition, advice on the sampling technique may need to be provided regarding the timing of the sample, the type of sample, number or volume of samples, and optimal storage and transport conditions that are required for the specific test. Failure to take sufficient amount of the correct sample, at the correct time, and using the correct container, or storing it in a suboptimal manner, may lead to falsely negative or positive results. Most laboratories have manuals for guidance on sampling details and the tests performed. It is vital that this information is available to clinical staff. Microbiologists and virologists contribute to this guide and assist in ensuring it is communicated to the clinicians taking the samples. This is particularly important for precious samples that cannot easily be repeated, e.g surgical biopsies, CSF from lumbar punctures. Ensuring the correct completion of the request form is vital. Important clinical details should be included on the request to help guide the most appropriate tests. Examples of important information to be documented on the request include travel history, antibiotic history, immune status, underlying diseases, and site of suspected infection. The analytical stage consists of the actual testing of the sample. Examples of common tests performed in this stage include microscopy, culture, sensitivity testing, serology, and molecular detection, as well as more novel techniques such as mass spectrometry, bioinformatics, and sequencing.