- Heather Maughan Ph. D.heathermaughan at gmail dot comUniversity of Toronto, Canada
Disclaimer: this article is not medical advice, any person suspecting/having contracted a venereal/sexually trasnmitted disease should consult with licensed medical professionals. This article is for an individual with interest in understanding the clinical diagnosis of venereal diseases
Pathogenic microorganisms that are transmitted by human sexual behaviors infect over 400 million new people each year according to World Health Organization (WHO). Treatments that are meant to kill these pathogens must be tailored to specific intruders, making identification of particular pathogens crucial for disease diagnoses and the administration of appropriate therapies. Because multiple pathogens can cause similar symptoms, identification of the causative pathogen typically requires more than consultation with a physician. Rigorous microscopic and molecular methods have been developed for use by clinical microbiologists to accurately and routinely identify pathogens in human blood, serum, urine, and saliva. This article describes the most commonly used clinical microbiology testing methods, focusing on the most pervasive pathogens. This document serves only as a guide; readers should be aware of national and local standards for testing before initiating a testing regime.
Optimization of treatments requires identification of infecting pathogens. However, this is not the only reason clinical microbiologists are diligent in their methods of identification. Tracking the movement of pathogens is crucial for keeping the population healthy, and epidemiologists rely on reports from clinical laboratories and hospitals to identify potential epidemics. Moreover, identifying the presence of pathogens in human samples is important for managing supplies of donated blood and sera.
Clinical microbiology testing methods must balance sensitivity, specificity, cost, and time required.
Sensivity: There are inherent difficulties in identifying pathogens present in low numbers, making the sensitivity of clinical tests an issue to be considered. Many testing methods require viable microorganisms, which leads to requirements for the utmost care during collection in the clinic and subsequent transport to the laboratory. Therefore, pathogen abundance and viability must be taken into account when considering the sensitivity of diagnostic tests.
Specificity: Methods used for identification are usually designed to provide the utmost specificity, so that pathogens are not mistakenly identified as present or absent. Tests must be able to distinguish pathogenic from the normal microbiota present; thus, test specificity is required for effective diagnostics.
Cost and time: Other considerations include budgetary constraints, as well as completing the tests in a timely manner so as to inform the treating physician.
Sexually transmitted pathogens are microbes that comprise several viruses, bacteria, and single-celled eukaryotic parasites. Bacteria and parasites typically need not replicate within the human host cells, but viruses must, as their genomes do not encode complete machinery for nucleic acid replication and gene transcription. Although these groups of microorganisms are distinct in the types of diseases they cause, and are subject to different treatments, many of the methods used to identify them overlap. Bacteria and parasites always have DNA genomes, whereas viruses may have RNA or DNA genomes. Table 1 summerizes the common sexually transmitted pathogens.
|Name||Type of organism||Disease caused||Common method of diagnosis|
|Chlamydia trachomatis||Bacteria||Chlamydia||Aptima combo assay (NA-based)|
|Neisseria gonorrhoeae||Bacteria||Gonorrhoea||Aptima combo assay (NA-based)|
|Treponema pallidum||Bacteria||Syphilis||Dieterle stain (microscopy based)|
multiple serological tests
|Trichomonas vaginalis||Protozoan||Trichomoniasis||InPouchTV (microscopy and culture based)|
|Hepatitis B||Virus||Hepatitis||ELISA or PCR (NA-based)|
|Herpes simplex virus||Virus||Herpes||DFA or PCR|
|Human immunodeficiency virus||Virus||AIDS||Ag/Ab ELISA|
|Human papillomavirus||Virus||Cervical cancer|
|Cervical smear (microscopy based) or visual inspection|
Chlamydia trachomatis is a Gram-negative bacterium that must replicate within eukaryotic cells, thus it has an obligate intracellular lifestyle. C. trachomatis causes Chlamydia, the most common sexually transmitted bacterial infection in the United States. C. trachomatis has typically been classified into serovars, based on its Major Outer Membrane Protein (MOMP). C. trachomatis may be identified by enzyme immunoassays (EIAs) that target the MOMP, nucleic acid (NA) recognition methods, or selective culturing. The NA recognition methods are most sensitive, and recent findings from comparative genomics have called into question the use of the MOMP for reliable diagnosis .
Neisseria gonorrhoeae is a Gram-negative bacterium that causes Gonorrhea, otherwise known as "The Clap". N. gonorrhoeae can be selectively cultured by growing on Thayer-Martin agar, which contains various antibiotics that inhibit other microbes. A widely used assay based on NA amplification method detects both C. trachomatis and N. gonorrhoeae (discussed in Figure 4).
Treponema pallidum is a Gram-negative spirochaete bacterium responsible for Syphilis. Trep. pallidum can be identified using the Dieterle microscopy stain, or any one of multiple serological tests , in addition to NA amplification methods.
Trichomonas vaginalis is a motile protozoan parasite that causes Trichomoniasis. The most common method of diagnosis is microscopical examination and culture, both performed using the InPouch TV.
Hepatitis B is a DNA virus that can spread through bodily fluids, and causes liver inflammation. Hepatitis B is often detected by testing for its antigen, or antibodies produced in response to the viral antigen . As with the non-viral pathogens described above, NA amplification methods are becoming more common for detection of hepatitis B virus .
Herpes simplex virus (HSV) is a DNA virus that causes skin lesions in the genital or oral areas. This virus can be detected using microscopy with a Tzanck smear , a direct fluorescent antibody, or by amplifying NA using PCR with specific primers . Testing for antibodies against HSV has typically been hampered by the inability to distinguish between antibodies produced against HSV-1 (mainly oral) or HSV-2 (mainly genital); however, an immunoassay based on antibodies against glycoprotein G is promising .
Human papillomavirus (HPV) is a DNA virus that can lead to cervical cancer in women, and genital warts in both sexes. Testing for HPV relies mostly on the symptoms themselves: abnormal cells near the cervix or wart structures near the genitals. Although several NA-based tests have been developed , they are not yet widely used.
Human immunodeficiency virus (HIV) has received a lot of attention throughout the years, and this is well deserved, as HIV can cause destruction of the immune system, resulting in the inability of individuals to fight off other infections and cancerous growth. HIV is an RNA virus that attaches to and infects immune cells, ultimately resulting in death of these cells. Tests for HIV typically rely on enzyme linked immunosorbant assays (ELISAs), and although NA amplification tests have been developed, they are not as widely available.
Diagnostic methods examine organismal morphology (via microscopy), metabolism (via selective culturing), cellular macromolecules (via immunoassays), and NA sequence specificities (via amplification and/or hybridization). These tests can also be combined, for example, using a fluorescent NA probe with microscopy (Figure 1). Often times the tests are most important for distinguishing the invaders from the microbiota that normally inhabit the urogenital tract. Because viable organisms are required for several methods, the transport of clinical samples should be carefully planned. Table 2 summerizes the common diagnostic methods.
|Microscopy||Proper staining or visualization tools.||Fast, and inexpensive if equipment is available.||Difficult to find pathogen if density is low.|
|Culture||Proper selective medium and incubation environment.||Organism in hand for additional tests (e.g., MIC).||Sample transport must ensure organisms remain viable.|
|Immunoassay||Specific antigen or antibody.||Fast, relatively inexpensive, and little equipment required.||Time between infection and antibody production may result in false negatives.|
|Nucleic acid||Specific sequence probe for hybridization or amplification priming.||High specificity and versatility. Epidemiological information can also be obtained.||Relatively expensive and time consuming, but costs and duration are decreasing quickly.|
Microscopy is one of the oldest methods used for identification. Persons with a trained eye are able to distinguish pathogen from normal microbiota, but this is dependent on whether the density of pathogen is high enough to be seen in the examined fields of view. Examination under the microscope can be especially useful for those pathogens with characteristic morphologies, such as the spirochaete cell morphology of Trep. pallidum or the motility and relatively larger size of Trich. vaginalis.
Different microscopy methods can be used for optimal recognition. Gram stains and phase contrast microscopy can provide additional information on microbial identification.
Clinical microbiologists use tests that rely on probing a molecule that is unique to the suspected pathogen. For example, fluorescently labeled specific antibodies or NA probes may be washed over the microscope slide, tagging the pathogen with fluorescence for easy identification. The stained pathogens can be readily observed under a microscope. There are many variations of stains with antibodies or other moeties. The following is a typical process.
Direct fluorescent antibody technique (Figure 1)
- obtain human samples and antibody conjugated with a fluorophore
- fix the samples to a microscope slide. Prior to fixation, it may be necessary to homogenize the sample so that it can be pipetted easily.
- fix the sample to the slide surface through air-drying, formaldehyde, or another method. Microscope slides with small wells are ideal, since a small aliquot of human sample can be placed inside the well.
- add antibody solution to the sample and incubate at a specified temperature and humidity.
- wash the slide thoroughly to remove any excess antibody, as this "loose" antibody will increase background fluorescence.
- observe under regular fluorescent or confocal microscopy.
Culturing pathogens is another old method, and is still considered as the gold testing standard for a handful of pathogens. Culturing for identification relies on there being a way to discriminate between pathogen and the background of the normal flora. If one were to simply spread sample onto a plate with rich medium, a diversity of microbes would be able to grow. The importance of selecting only those microbes of interest has led to the development of selective culture methods, where microbiologists take advantage of microbes’ unique metabolic properties or resistances. For example, the gold standard test for Trich. vaginalis is the InPouch TV, a dual anaerobic chamber that allows microscopic examination and culturing of Trich. vaginalis in (proprietary) medium with suitable nutrients and antibiotics.
Considerations for selective culturing are the nutrients needed, antibiotics for selection, and sample isolation and streaking tools (swabs, inoculation loops, etc.).
Selective culturing for bacterial pathogen of interest (Figure 2)
- Identify proper selective medium. Often these media provide nutrients that the bacteria are unable to synthesize themselves, provide substrate for a unique metabolic process, and/or antibiotics to which the bacteria are resistant. The addition of these antibiotics is important for inhibiting the growth of the normal microbiota.
- Streak clinical sample on non-selective and selective media following a well-established protocol. Be cautious that the number of cells in the human sample may be high, and that there may be a "lawn"of growth. Sometimes it is prudent to dilute the human sample in a series of 10-fold dilutions before streaking on the agar medium.
- Incubate the streaked Petri plates. This step is critical for success, as incubation temperature, humidity, oxygen concentration, and duration all have important effects on microbial growth.
- Observe growth after appropriate incubation period. If there is growth, sometimes a follow-up experiment for verification is required. For example, colonies may be streaked again on the same selective medium to confirm growth. Additional tests using NA hybridization or amplification would also be advised.
Culturing of viruses is possible but more complicated, as human cell cultures are required for virus reproduction .
Immunoassays have been widely used for the identification of many sexually transmitted pathogens, and is still the gold standard for HIV testing. In these tests, clinical microbiologists are looking for molecules that indicate pathogen presence, by measuring their specific antigen; and/or looking for signs of immune system recognition of the pathogen by measuring antibody specific to pathogen antigen. Typically these immunoassays proceed by baiting the possibly present antigen in the human sample with an antibody specific to that antigen. Binding of the antibody to the antigen is detected either using fluorescence or an enzymatic reaction.
For detection of HIV infection, clinical microbiologists used an ELISA where purified HIV virus antigen was used as "bait" to test for antibodies to HIV in human blood . Improvements on this test, including the use of recombinant HIV antigen, resulted in great accuracy and safety. However, because the time between HIV infection and production of antibodies can be several weeks, identification tests were further improved to include testing for HIV antigen and antibody using a combined sandwich ELISA method.
Enzyme-linked immunosorbent assay (ELISA) for detection of HIV antigen and antibody (Figure 3)
Commercial kits are available to perform these tests in an efficient and high throughput manner, and are sensitive enough to detect antibody or antigen in urine or saliva samples, in addition to blood. The high throughput nature of the kits helps reduce cost in screening blood donations, and the increased sensitivity helps promote testing in developing countries, thereby improving human health globally.
- Obtain sample for testing and commercially available kit; several kits are listed in Figure 3. Follow kit instructions exactly. Figure 3 gives an overview of the ELISA process, and although each kit listed detects both antigen and antibody, they may differ in the exact method or reagents used for HIV detection.
- Monoclonal antibodies to p24, the capsid protein of HIV, are immobilized on a solid surface. Also immobilized is an antigen cocktail, with recombinant antigens representing both HIV-1 and HIV-2 strains. Also contained within the testing device are unbound labeled polyclonal anti-p24 antibodies, and unbound labeled antigen.
- An aliquot of the blood sample (often diluted) is added to the testing device. If HIV antigen is present, it will bind the anti-p24 antibodies. Similarly, if HIV antibodies are present, they will bind the labeled antigen. Wash excess label antibody and antigen from the testing device and then quantify antigen/antibody complexes by their respective labels.
Methods based on NA sequence can be some of the most sensitive, able to detect a few molecules of DNA or RNA, and are able to detect pathogens using only urine samples instead of samples from more invasive procedures (e.g., cervical or urethral swab). NA methods can have very high specificity, being able to distinguish between pathogen and normal microbiota, and even between different serovars, providing important epidemiological data along with diagnostic data. Because the presence of pathogen DNA does not necessarily indicate presence of the viable pathogen, many NA based diagnostic tests rely on ribosomal RNA, which is also in much higher copy number than DNA, thereby increasing sensitivity. NA tests are becoming routine, and as their costs are driven down by improved technology, they are apt to become the gold standard for all diagnostic tests. NA tests where whole genomes are sequenced are even likely to become more useful in the coming years, as technology becomes less expensive .
NA methods rely on hybridization and/or amplification. Hybridization methods use a fluorescently labeled NA probe of known sequence to hybridize to any complementary NA present in the sample, typically using fluorescent microscopy for detection. Amplification methods use small NA primers and PCR to selectively amplify a taxonomically informative marker gene. Amplification itself can be a positive result, or subsequent sequencing of amplicons can provide additional information. They key to the specificity of hybridization and amplification methods is the fluorescently labeled probes, or primer; these are DNA fragments whose sequences should only match, and therefore bind to, the organism of interest.
Nucleic acid probe for C. trachomatis and N. gonorrhoeae (Figure 4)
Detection of nucleic acid from these two pathogens is possible using commercially available kits such as the APTIMA COMBO 2 Assay. Although the exact method and reagents used are proprietary, the steps shown in Figure 4 provide an overview of the process performed by this kit.
- Obtain human sample for testing. From this sample, lyse any cells present so that the ribosomal RNA is accessible.
- The freed rRNA can now bind to beads coated with a specific sequence for either Chlamydia or Neisseria, such that only rRNA from these two species will bind to the beads. The beads are then removed from the mixture of cell lysate, taking the bound rRNA with them.
- The rRNA is now used as template in a reverse-transcription reaction, where complementary DNA is synthesized from the RNA. This DNA is then used as a template in Transcription Mediated Amplification. TMA is able to make thousands of copies of the sequence tag, thereby increasing the sensitivity of the test.
- Once the TMA is finished, labeled DNA complementary to the rRNA is added. The DNA and rRNA hybrids are now labeled, and can be detected and quantified by the label bound to the DNA.
Polymerase Chain Reaction with primers specific to the organism of interest is also commonly used for the detection of pathogens. Although the cost and time required of performing PCR reaction has typically hampered the widespread adoption of PCR in clinical microbiology laboratories, technology is advancing and soon enough PCR will be cheaper and faster.
Treatment of patients suffering from bacterial infections with antibiotics requires knowledge of the resistance profile of any particular bacterial pathogen. To obtain this information, clinical microbiologists typically culture the pathogen in the presence of varying concentrations of antibiotic to determine the minimal inhibitory concentration (MIC) of that antibiotic. Because resistance to antibiotics evolves quickly in bacteria and can vary considerably between strains of the same species, it is important to conduct MIC tests on each isolate, even if the same species has already been tested.
MIC using the broth dilution method (Figure 5)
For thorough guidance through the broth dilution method, readers are advised to consult references such as .
- Identify a rich culture medium that supports the growth of the bacteria of interest. Inoculate 4 or 5 fresh bacterial colonies from a Petri dish into a few milliliters of medium and culture overnight in the appropriate incubation environment (e.g., temperature, aeration). Multiple colonies are used to minimize the effects spontaneous mutation may have on antibiotic resistance.
- After overnight incubation, prepare a dilution series of rich medium with varying concentrations of the test antibiotic. These dilutions can be performed in test tubes, or in a 96-well plate for higher throughput. Typically it is best to serially dilute 2-fold (Figure 5). Two tubes (or wells) should remain without antibiotic; one will serve as a "no-antibiotic" control to ensure the bacteria were able to grow well in the medium and incubation conditions while the other will serve as the "no bacteria" control to ensure the medium was not contaminated.
- Once antibiotic dilution series is ready, inoculate bacteria to a final density of 5x105 colony forming units (cfu)/mL (except for the "no bacteria" control). Bacteria can be quantified using a spectrophotometer to read the optical density (OD) of the culture. OD is associated with the cfu/ml cell count and researchers should have already determined the optimal OD for reaching the required inoculum density.
From the "no antibiotic" control, plate a small volume on agar plates for enumeration of viable colony forming units. This is important to ensure that the bacteria were not inoculated at density that was too high or low. Place agar plates and test tubes (or 96-well plate) in appropriate incubation environment.
- After overnight incubation, count colonies on agar plates and examine growth in tubes or wells to determine the minimum inhibitory concentration (MIC). The MIC is the lowest concentration of antibiotic where growth was not visible. Please refer to Figure 5 for additional details.
Similar to treatment of bacterial infections with antibiotics, viral infections are often treated with antiviral drugs. Because viruses hijack human cellular machinery to replicate, choosing antiviral drugs that do not interfere with normal human cellular processes can be difficult. In addition, because viral genomes, particularly RNA genomes, have high mutation rates, resistance to antiviral drugs can evolve very rapidly. In the case of HIV, patients are usually treated with a cocktail of antiviral drugs; these cocktails typically contain at least three drugs targeting two different stages of the HIV life cycle. Because it is less likely that viruses will evolve spontaneous resistance to multiple drugs targeting separate stages of the life cycle, antiviral therapies relying on drug cocktails have extended the lives of HIV patients considerably  .
Methods used for diagnosis of sexually transmitted pathogens are constantly changing, as new technologies are developed or optimized to deliver sensitive and specific results quickly and affordably. Methods are moving from microscopy and culture to those based on detection of proteins or NA within the pathogens.
Researchers interested in testing for these pathogens must note that governing bodies are likely to have their own set of guidelines and preferred methods, and therefore, the methods described in this article serve merely as guides for subsequent protocol development and approval. Researchers are advised to contact their local infectious disease organization for additional guidance.
- Bonino F, Chiaberge E, Maran E, Piantino P. Serological markers of HBV infectivity. Ann Ist Super Sanita. 1987;24:217-23 PMID 3331068
- Zoulim F. New nucleic acid diagnostic tests in viral hepatitis. Semin Liver Dis. 2006;26:309-17 PMID 17051445
- Folkers E, Oranje A, Duivenvoorden J, van der Veen J, Rijlaarsdam J, Emsbroek J. Tzanck smear in diagnosing genital herpes. Genitourin Med. 1988;64:249-54 PMID 3169755
- Fatahzadeh M, Schwartz R. Human herpes simplex virus infections: epidemiology, pathogenesis, symptomatology, diagnosis, and management. J Am Acad Dermatol. 2007;57:737-63; quiz 764-6 PMID 17939933
- Ashley R, Militoni J, Lee F, Nahmias A, Corey L. Comparison of Western blot (immunoblot) and glycoprotein G-specific immunodot enzyme assay for detecting antibodies to herpes simplex virus types 1 and 2 in human sera. J Clin Microbiol. 1988;26:662-7 PMID 2835389
- Busch M, Eble B, Khayam-Bashi H, Heilbron D, Murphy E, Kwok S, et al. Evaluation of screened blood donations for human immunodeficiency virus type 1 infection by culture and DNA amplification of pooled cells. N Engl J Med. 1991;325:1-5 PMID 2046708
- Jackson J, Balfour H. Practical diagnostic testing for human immunodeficiency virus. Clin Microbiol Rev. 1988;1:124-38 PMID 3060241