Nucleic acid amplification in infectiology

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Nucleic acid amplification is a widely used method for the diagnosis and management of infectious diseases. The interpretation of Polymerase Chain Reaction (PCR) results varies depending on the pathogens detected, the site of infection and the clinical presentation. For some infections, PCR tests are now considered a reference method while for others they are only a diagnostic aid. With the development of antiviral treatments, quantitative PCRs have become indispensable for the evaluation of therapeutic efficacy. Contact with the laboratory performing the analysis is important in order to interpret the PCR results correctly

Nucleic acid amplification by Polymerase Chain Reaction

(PCR) techniques or RT-PCR (reverse transcription-PCR, on RNA) is the reference technique for the diagnosis and the therapeutic management of numerous viral but also bacterial infections. The direct detection of nucleic acids by PCR of these pathogens has reduced the delay leading to diagnosis, particularly with reference to culture-based techniques or the detection of specific antibodies.

Central nervous system infections (CNS)

Viral infections and toxoplasmosis,
Acute meningitis and encephalitis in immunocompetent individuals and opportunistic infections in immunosuppressed individuals. In both situations, PCR diagnosis has become a tool of choice. The most common cause of acute meningitis is enterovirus infections. Herpes simplex virus encephalitis (HSV) is sporadic .Opportunistic CNS infections associated with human immunodeficiency virus (HIV), the detection by PCR of EBV (primary CNS lymphoma), Toxoplasma gondii, JC virus responsible for progressive multifocal leukoencephalopathy, and HIV in the CSF is very useful in addition to imaging and can lead to a diagnosis of high probability without resorting to cerebral biopsy.

Bacterial infections

As with viruses, bacterial pathogen-specific PCR methods in the CNS are more sensitive than microscopy or culture. In our experiment, two PCRs, one specific to Neisseria meningitidis and the other to Streptococcus pneumoniae, For Listeria infections, PCR is only useful if initial antibiotic therapy has been started because the results of CSF and blood culture are usually sufficient to make the diagnosis.

Respiratory infections

The diagnosis of bacterial respiratory infections has benefited from PCR techniques, especially for atypical pneumonia because the cultures are long, it is no longer necessary to rely on serology alone, but it remains the definitive proof of an infection that has caused an immune response and is therefore still considered by some to be a reference test. The diagnosis of C. pneumoniae and M. pneumoniae by PCR can be made on samples that are easy to perform and that are not invasive for the patient, such as the throat swab. For Legionella pneumophila infections, PCR seems to be more sensitive than culture. Urinary antigen detection is currently the most widely used method . Tuberculosis is also a respiratory infection where the PCR plays a necessary role.

Infections of intestinal tract

PCRs generally have little interest in detecting these infections because cultures are easy for bacteria (Salmonella spp., Shigella spp., Campylobacter spp) and agglutination tests are sufficiently sensitive for viruses such as rotavirus or adenoviruses. In adults, the first cause of viral gastroenteritis is Norovirus (Norwalk-like, Calicivirus), which is only detectable by RT-PCR. This technique is therefore useful for determining the origin of an epidemic and identifying the source and the etiological agent. Microscopy remains the technique of choice to search for and identify parasites. Amplification tests may be interesting in a particular context to detect specific enterohemorrhagic E. coli toxins (EHEC or VTEC) leading to serious diseases (haemolytic and uremic syndrome).

Infections of the genital tract

Nucleic acid amplification techniques are very useful for genital infections because the germs responsible for sexually transmitted diseases are difficult to cultivate: Chlamydia trachomatis grows only on cell culture and Neisseria gonorrhoeae on specific media. Detection of human papillomavirus (HPV) can be performed in parallel with C. trachomatis and N. gonorrhoeae on endocardial smears. Infection with certain types of HPV increases the risk of cervical cancer

Systemic infections (Including blood detective hepatitis)

In the context of the diagnosis of acute hepatitis, PCR tests are only useful for hepatitis C (HCV) given the significant delay before the appearance of specific antibodies. Serological markers (IgM or antigens) are generally sufficient for the diagnosis of hepatitis B (HBV) and A (HAV). During acute HIV infection, plasma viral RNA can be detected about four days before the p24 antigen but there are few clinical situations where a 4th generation test is negative in the presence of positive viremia. PCR detection of EBV DNA is useful for the diagnosis and therapeutic follow-up of lymphoproliferative diseases after transplantation, as well as for nasopharyngeal carcinoma. The concentration of EBV in the blood is correlated with the severity of the tumor.

Interpretation of PCR results

Sensitivity is an essential factor in the diagnosis. It is important for a clinician to know the specifications of the PCR methods used by the laboratory conducting the analysis and / or to have a result with a specific comment in order to interpret the results correctly. The most important factors influencing the sensitivity of PCR(NCBI) methods are the choice of primers, the quality and the quantity of the sample.

PCR as a reference technique

In recent years, PCR techniques have become the reference techniques for diagnosis in virology first and then for many bacteria, particularly respiratory and genital tract infections. They have also established themselves as the techniques of choice in the management and therapeutic follow-up of chronic viral infections.

Tommy Ounas

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Nucleic acid amplification in infectiology

Nucleic acid amplification by Polymerase Chain Reaction

Central nervous system infections (CNS)

Bacterial infections

Respiratory infections

Infections of intestinal tract

Infections of the genital tract

Systemic infections (Including blood detective hepatitis)

Interpretation of PCR results

PCR as a reference technique

Tommy Ounas

Share your thoughts Cancel reply

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