Skip to Main Content

We have a new app!

Take the Access library with you wherever you go—easy access to books, videos, images, podcasts, personalized features, and more.

Download the Access App here: iOS and Android


Clinical microbiology laboratories play a fundamental and indispensable role in providing reliable and timely information regarding the identification of infectious disease agents. Clinicians use this information not only to make or confirm a diagnosis but also to guide clinical decisions and treatment options, so this information needs to be definitive, significant, and relevant to the case under consideration. Obtaining accurate results that can be interpreted with high confidence is dependent on the laboratory receiving high-quality patient specimens.

Since specimen selection and collection are typically the responsibility of the medical staff, clinicians should (1) understand the pathogenesis of the infection and ensure proper collection of an adequate quantity of specimen from the body site that is most likely to yield growth of the infecting organism, while avoiding contamination from the normal flora; (2) ensure that the integrity of the specimen is not compromised during transport and that the specimen is handled in such a way to preserve the viability of any anaerobes or fastidious organisms; and (3) provide ancillary information to guide the laboratory personnel who will process and analyze the specimen.

As diagnostic microbiology testing becomes more complex, clear communication and strong partnerships between microbiology lab professionals and clinicians will remain a top priority. Clinicians communicate crucial clinical information about a patient to microbiology lab staff that will then allow lab personnel to direct clinicians toward context-appropriate tests and optimized sample collection methods that have the most diagnostic value, which will ultimately lead to better outcomes for patients.

Traditionally, diagnosis has relied on culture, microscopic and phenotypic characterization of an organism (Table 9–1), and serologic testing, in which the organism is identified by the detection of organism-specific antibodies in the patient’s serum. More recently, advances in the fields of molecular biology and genomics have resulted in more accurate and rapid identification of causative organisms. There are now several US Food and Drug Administration (FDA)-approved nucleic acid and proteomic-based assays for identifying infectious agents (discussed below), and their routine implementation in the clinical laboratory setting has resulted in improved patient care, better antibiotic stewardship resulting in decreased antimicrobial resistance rates, and increased efficiency of the laboratory and healthcare facility in the processing and analysis of clinical samples.

TABLE 9–1General Approach to the Diagnosis of a Bacterial Infection

Pop-up div Successfully Displayed

This div only appears when the trigger link is hovered over. Otherwise it is hidden from view.