In microbiology a specimen came from a patient with an unknown infection what test might you perform to help physician to effectively treat the patient?

Answer 1

Conventionally, the first "test" performed on many specimens arriving in the clinical microbiology laboratory is a direct microscopic examination. This typically involves staining a smear of the specimen on a microscope slide by the Gram's staining method, an Acid-Fast staining method, or, if a fungal infection is suspected, a technique that allows for visualization of fungal elements within the specimen (e.g., Calcofluor white stain). Additionally, more specific stains can be performed depending upon the etiologic agent suspected. For example, fluorescent antibody "stains" that are specific for certain respiratory viruses can be used to directly probe the specimen for said virus(es).

The next step of the process is usually growing the microorganism(s), which allows for identification and, subsequently, antimicrobial drug sensitivity testing. Traditionally, cultures of bacteria and fungi are grown in either Petri dishes and/or in glass tubes containing growth medium that supports the growth of either a wide variety of microbes (supportive or non-selective media) or only a few specific types of microbes (selective media). After inoculation and incubation of the media, microbial growth can be identified by many different means, including more advanced molecular methods. Finally, antimicrobial drug sensitivity testing will be performed on the growth, if such testing is appropriate. From this information, the physician will be able to decide upon one or more antimicrobial drugs that are useful for treating the infection.


Viruses, however, require different types of testing. Specimens for virus identification are typically inoculated onto a growing monolayer of mammalian cells (e.g., human newborn foreskin cells, monkey kidney cells, etc.). Since viruses require a living cell in which to replicate, specimens for virus culture cannot be inoculated onto an artificial medium such as blood agar, for example. Subsequently, the cell monolayers are incubated and periodically examined for evidence of replication of viruses. In some instances, viruses will destroy or alter the cells in which they've replicated; this is evidenced by sometimes virus-specific cytopathic effect (e.g., rounding of cells, complete obliteration of some areas of the cell monolayer, syncytia formation, etc.). In other instances, there's very little evidence that the virus has infected and replicated within the cells of the monolayer. Regardless, samples of the cells are transferred to microscope slides and probed with virus-specific antibodies conjugated to fluorescent molecules. When viewed under a fluorescent microscope, cells will fluoresce if infected with a particular virus after staining with the virus-specific antiserum. Also, viruses can be detected from the cell cultures, and even the original patient specimen, using molecular techniques, such as polymerase chain reaction (a.k.a. PCR). After identification of the virus or viruses infecting the patient, a physician can choose an appropriate anti-viral drug that combats the infection, if one is available.


For eukaryotic parasites (e.g., tapeworms, malaria, Giardia), sometimes the only means for identification will be direct microscopic exam of the specimen, as culturing these critters is very time consuming, requires very specialized media, or is sometimes impossible. Also, serologic techniques are useful for identification of some parasites.


I'm hopeful that this information is helpful to you. Good luck!


- Microbioman