Pocket Guide to Clinical Microbiology, Fourth Edition

The quality of any laboratory diagnostic test is directly dependent on the quality of the specimen that is submitted for analysis. This is particularly true for the diagnosis of infectious diseases, where specimen integrity is of paramount importance. Not only is it critical to collect an appropriate specimen that would contain the pathogen of interest, but it is also important that the specimen be transported to the laboratory in a timely manner and under conditions that preserve organism viability and ensure the reliability of the diagnostic procedure (e.g., culture, microscopy, and antigen or antibody tests). The following guidelines can be used for the most commonly submitted specimens. For further information, please consult the ASM Manual of Clinical Microbiology, 11th ed. As a general guideline for all specimens, the following considerations should be kept in mind.

Historically, viral infections have been diagnosed by culture in primary or continuous cell lines and by detection of antibody responses to infection. However, these methods are insensitive and slow, such that results are rarely available in a clinically relevant time frame. Molecular methods or nucleic acid amplification testing (NAAT) have replaced culture due to their superior sensitivity and more rapid turnaround time. In addition, antigen capture immunoassays, which allow for the direct detection of viruses in clinical specimens, have also been widely adopted. Despite these technological advances, serology remains an important diagnostic tool for many viral infections. Initially, many serological tests were conducted with the labor-intensive complement fixation and neutralization tests. However, those methods have largely been replaced by commercially prepared enzyme immunoassays. This technical change allows many smaller laboratories to perform tests that were previously available only in reference laboratories. This section summarizes the tests currently available for the laboratory diagnosis of the most common viral infections. For additional information, the reader is referred to the ASM Manual of Clinical Microbiology and Clinical Virology Manual by Specter et al. (see the Bibliography).

Diagnosis of most parasitic infections has traditionally been made by the microscopic examination of clinical material, necessitating that highly trained technologists spend a significant amount of time examining individual specimens. In most developed countries, the prevalence of parasitic infection is very low, and as a result, many laboratories send their parasitic testing to large referral laboratories where expertise is centralized and competency can more easily be maintained. For the detection of more common parasites, immunoassays have been developed (e.g., Entamoeba histolytica, Giardia duodenalis, and Cryptosporidium parvum). However, these tests are adjuncts to the microscopic examination of specimens for ova and parasites and can rarely replace microscopy. Likewise, a number of tests have been developed to detect parasite-specific nucleic acids, and recently, these assays have been FDA cleared for direct detection from stool.