Polymerase chain reaction (PCR) testing for infectious diseases
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PCR Testing for Infectious Diseases: Sensitivity, Specificity, and Clinical Impact
Polymerase chain reaction (PCR) testing has become a cornerstone in the diagnosis of infectious diseases due to its high sensitivity and specificity. PCR can detect genetic material from bacteria, viruses, fungi, and parasites directly from clinical samples, often identifying pathogens that are difficult or slow to grow in culture Zauli2019Thompson2011Lucas2019. This molecular approach is especially valuable for detecting low-abundance pathogens and for use in patients who have already started antimicrobial therapy, which can reduce the yield of traditional cultures Putnam2025Lucas2019.
Broad-Range and Multiplex PCR: Applications and Limitations
Broad-range PCR (BR-PCR) and multiplex PCR technologies allow for the simultaneous detection of multiple pathogens or broad groups of organisms in a single test. BR-PCR is particularly useful when fastidious or rare organisms are suspected, or when standard cultures are negative despite clinical suspicion of infection Putnam2025Lucas2019. However, studies show that while BR-PCR can identify additional pathogens not found by culture, its overall sensitivity compared to culture is moderate, and the results only change clinical management in a small percentage of cases (about 6%) Putnam2025Li2021Lucas2019. This suggests that BR-PCR is best used as a complementary tool rather than a replacement for traditional methods Putnam2025Li2021Lucas2019.
Multiplex PCR systems, including recent innovations like 3′ Tth endonuclease cleavage PCR (3TEC-PCR), enable the detection of multiple pathogens and even single-nucleotide polymorphisms in a single reaction, improving diagnostic speed and accuracy for diseases such as bacterial meningitis and respiratory infections Higgins2021Hedberg2024. These systems help reduce diagnostic bias and streamline the identification of co-infections, as seen with SARS-CoV-2, influenza, and RSV .
Advances in Digital PCR and Automation
Digital PCR (dPCR), including droplet digital PCR (ddPCR), represents a significant advancement over conventional PCR. These methods allow for absolute quantification of pathogen DNA without the need for calibration curves, offering higher sensitivity and reproducibility, especially for low-abundance targets Li2018Choi2022. Automation of PCR processes, such as with the Roche COBAS systems, has reduced manual labor and increased throughput, making PCR more accessible for routine clinical use . Integration with Internet of Things (IoT) technology further enables rapid, onsite, and multiplexed detection, which is crucial for point-of-care testing and outbreak response .
PCR in Specific Clinical Contexts
PCR has proven especially valuable in certain clinical scenarios. For ocular infections, PCR outperforms culture for detecting herpes simplex virus, varicella zoster virus, Chlamydia trachomatis, and Acanthamoeba, while culture remains important for adenovirus . In pediatric and immunocompromised populations, BR-PCR can identify pathogens missed by conventional testing, but its impact on changing treatment is limited, highlighting the need for careful selection of cases where PCR adds the most value Li2021Lucas2019.
Conclusion
PCR testing has revolutionized the diagnosis of infectious diseases by providing rapid, sensitive, and specific detection of a wide range of pathogens. While broad-range and multiplex PCR technologies offer important advantages, their clinical impact is maximized when used alongside traditional methods, particularly in complex or culture-negative cases. Advances in digital PCR and automation continue to improve the accuracy, speed, and accessibility of molecular diagnostics, supporting better patient care and public health response Putnam2025Zauli2019Jungkind2001+7 MORE.
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Broad-range polymerase chain reaction and sequencing for the diagnosis of infectious diseases
BR-PCR complements standard of care for uncommonly isolated and fastidious organisms, but should not replace routine culture methods at this time.
Automation of laboratory testing for infectious diseases using the polymerase chain reaction-- our past, our present, our future.
The COBAS AmpliPrepTM automated specimen preparation system significantly reduces the time required for preparing serum or plasma samples for hepatitis C virus PCR by 76% compared to manual specimen preparation methods.
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A 13-year retrospective review of polymerase chain reaction testing for infectious agents from ocular samples.
PCR is a routine diagnostic test for detecting both common and infrequent ocular pathogens, with cell culture isolation being the definitive test for adenovirus and HSV and Acanthamoeba.
Reducing Diagnostic Bias Through Multiplex Polymerase Chain Reaction (PCR) Testing for SARS-CoV-2, Influenza A/B, and RSV.
Multiplex PCR testing for SARS-CoV-2, Influenza A/B, and RSV can reduce diagnostic bias and improve detection rates in infectious diseases cases.
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