Diagnostic microbiology
Diagnostic microbiology is the study of microbial identification. Since the discovery of the germ theory of disease, scientists have been finding ways to harvest specific organisms. Using methods such as differential media or genome sequencing, physicians and scientists can observe novel functions in organisms for more effective and accurate diagnosis of organisms. Methods used in diagnostic microbiology are often used to take advantage of a particular difference in organisms and attain information about what species it can be identified as, which is often through a reference of previous studies. New studies provide information that others can reference so that scientists can attain a basic understanding of the organism they are examining.
Aerobic vs anaerobic
s require an oxygen-free environment. When culturing anaerobic microbes, broths are often flushed with nitrogen gas to extinguish oxygen present, and growth can also occur on media in a chamber without oxygen present. Sodium resazurin can be added to indicate redox potential. Cultures are to be incubated in an oxygen-free environment for 48 hours at 35 °C before growth is examined.Anaerobic bacteria collection can come from a variety of sources in patient samples, including blood, bile, bone marrow, cerebrospinal fluid, direct lung aspirate, tissue biopsies from a normally sterile site, fluid from a normally sterile site, dental, abscess, abdominal or pelvic abscess, knife, gunshot, or surgical wound, or severe burn.
Incubation length
Incubation times vary based upon the microbe that requires culturing. Traditional culturing techniques, for example, require less than 24 hours culture time for Escherichia coli but 6–8 weeks for successful culturing of Mycobacterium tuberculosis before definitive results are expressed. A benefit of non-culture tests is that physicians and microbiologists are not handicapped by waiting periods.Incubation follows a growth curve variable for every microorganism. Cultures follow a lag, log, stationary, and finally death phase. The lag phase is not well known in microbiology, but it is speculated that this phase consists of the microorganism adjusting to its environment by synthesizing proteins specific for the surrounding habitat. The log phase is the period where a culture experiences logarithmic growth until nutrients become scarce. The stationary phase is when culture concentration is the highest and cells stop reproducing. When nutrients in the environment are depleting, organisms enter the death phase where toxic metabolites become abundant and nutrients are depleted to the point where cell death exceeds reproduction.
Rapid identification after culture
Automated culturing systems
s are becoming popular because of their ability to maintain a sterile growth environment and remove strain on the laboratory staff involving repetitive experimentation. Laboratories can also set incubation times to adjust for the lag period involved in bacterial growth.Blood cultures
s can allow for diagnostic results after culture. Recent development of DNA based PCR diagnostics have provided faster diagnostic results as opposed to overnight biochemical tests. DNA diagnostic test can diagnose with near the same specificity as biochemical test, resulting in the same diagnostic result in 90% of cases.Breath tests
for microbial diagnosis on patients has been used in a clinical setting for bacteria, including Helicobacter pylori. Diagnostic test using the breath of patients look for metabolites excreted that were manufactured by the infectious microorganism. H. pylori is tested by testing patients for CO2 concentration, increased because of the organism's ability to convert urea into other derivatives.Conventional tests
Antibody detection
A benefit of antibody detection is that protein identification on a microorganism becomes faster than a western blot. Antibody detection works by attaching an indicator to an antibody with a known specificity and observing whether the antibody attaches. ELISA can also indicate viral presence and is highly specific, having a detection specificity of 10−9-10−12 moles per litre detection. By knowing the epitope sequence of the antibody, ELISA can also be used for antigen detection in a sample.Histological detection and culture
methods used for microbiology are useful because of their ability to quickly identify a disease present in a tissue biopsy.Microscopy
Staining
used in microbiology identification include: Gram stain, Acid-fast stain, Giemsa stain, India ink stain, Ziehl–Neelsen stain.Wet Prep
Analytical methods
Mass spectrometry
MALDI-TOF is a specific type of mass spectrometry that is able to identify microorganisms. A pure culture is isolated and spread directly on a stainless steel or disposable target. The cells are lysed and overlaid with a matrix, which forms protein complexes with the bacterial proteins. The MALDI fires a laser and ionizes the protein complexes, which break off and travel up the vacuum where they are detected based on mass and charge. The resulting protein spectra is compared to a known database of previously catalogued organisms, resulting in rapid diagnosis of microorganisms. Recent studies have suggested that these tests can become specific enough to diagnose down to the sub-species level by observing novel biomarkers.The MALDI-TOF identification method requires pure cultures that are less than 72 hours old. This places the organism in log phase with an abundance of ribosomal proteins, which are the most common proteins detected in the spectra. Identifications with this technology can also be impacted if the culture is exposed to cold temperatures, as this would change the typical protein distribution.