Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals
Background: <i>Pneumocystis jirovecii</i> pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation. Methods: Retrospective...
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MDPI AG
2024-01-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/14/1/114 |
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| author | Anna Louise Watson John Woodford Sumudu Britton Rita Gupta David Whiley Kate McCarthy |
| author_facet | Anna Louise Watson John Woodford Sumudu Britton Rita Gupta David Whiley Kate McCarthy |
| author_sort | Anna Louise Watson |
| collection | DOAJ |
| description | Background: <i>Pneumocystis jirovecii</i> pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation. Methods: Retrospective audit of all positive <i>P. jirovecii</i> qPCRs on induced sputum or BAL fluid at a single centre from 2012 to 2023. Medical and laboratory records were analysed and people with HIV were excluded. Cases were categorised as colonisation, high-probability PCP or uncertain PCP infection against a clinical gold standard incorporating clinico-radiological data. Quantitative PCR assay targeting the 5s gene was utilised throughout the time period. Results: Of the 82 positive qPCRs, 28 were categorised as high-probability PCP infection, 30 as uncertain PCP and 24 as colonisation. There was a significant difference in qPCR values stratified by clinical category but not respiratory sample type. Current assay performance with a cutoff of 2.5 × 10<sup>5</sup> copies/mL had a sensitivity of 50% (95% CI, 30.65–69.35%) and specificity of 83.33% (95% CI, 62.62–95.26%). Youden Index calculated at 6.5 × 10<sup>4</sup> copies/mL had a sensitivity of 75% (56.64–87.32%, 95% CI) and specificity of 66.67% (46.71–82.03%, 95% CI). High and low cutoffs were explored. Significant variables associated with infection were age > 70 years old, the presence of fever, hypoxia or ground glass changes. Conclusions: A single qPCR cutoff cannot reliably determine <i>P. jirovecii</i> infection from colonisation. Low and high cutoffs are useful, however, a large “possible infection” cohort will remain where interpretation of clinic-radiological factors remains essential. Standardisation of assays with prospective validation in specific immunocompromised groups will allow greater generalisability and allow large-scale prospective assay validation to be performed. |
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| language | English |
| last_indexed | 2024-03-08T15:09:32Z |
| publishDate | 2024-01-01 |
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| series | Diagnostics |
| spelling | doaj.art-950c87809f0d48f1bfe94549154ff08c2024-01-10T14:54:01ZengMDPI AGDiagnostics2075-44182024-01-0114111410.3390/diagnostics14010114Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative IndividualsAnna Louise Watson0John Woodford1Sumudu Britton2Rita Gupta3David Whiley4Kate McCarthy5Infectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, AustraliaInfectious Diseases, Ipswich Hospital, Ipswich, QLD 4305, AustraliaInfectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, AustraliaPathology Queensland, Herston, QLD 4006, AustraliaPathology Queensland, Herston, QLD 4006, AustraliaInfectious Diseases, Royal Brisbane & Women’s Hospital, Metro North Health, Herston, QLD 4006, AustraliaBackground: <i>Pneumocystis jirovecii</i> pneumonia is increasingly diagnosed with highly sensitive PCR diagnostics in immunocompromised, HIV-negative individuals. We assessed the performance of our in-house quantitative PCR with the aim to optimise interpretation. Methods: Retrospective audit of all positive <i>P. jirovecii</i> qPCRs on induced sputum or BAL fluid at a single centre from 2012 to 2023. Medical and laboratory records were analysed and people with HIV were excluded. Cases were categorised as colonisation, high-probability PCP or uncertain PCP infection against a clinical gold standard incorporating clinico-radiological data. Quantitative PCR assay targeting the 5s gene was utilised throughout the time period. Results: Of the 82 positive qPCRs, 28 were categorised as high-probability PCP infection, 30 as uncertain PCP and 24 as colonisation. There was a significant difference in qPCR values stratified by clinical category but not respiratory sample type. Current assay performance with a cutoff of 2.5 × 10<sup>5</sup> copies/mL had a sensitivity of 50% (95% CI, 30.65–69.35%) and specificity of 83.33% (95% CI, 62.62–95.26%). Youden Index calculated at 6.5 × 10<sup>4</sup> copies/mL had a sensitivity of 75% (56.64–87.32%, 95% CI) and specificity of 66.67% (46.71–82.03%, 95% CI). High and low cutoffs were explored. Significant variables associated with infection were age > 70 years old, the presence of fever, hypoxia or ground glass changes. Conclusions: A single qPCR cutoff cannot reliably determine <i>P. jirovecii</i> infection from colonisation. Low and high cutoffs are useful, however, a large “possible infection” cohort will remain where interpretation of clinic-radiological factors remains essential. Standardisation of assays with prospective validation in specific immunocompromised groups will allow greater generalisability and allow large-scale prospective assay validation to be performed.https://www.mdpi.com/2075-4418/14/1/114quantitative PCRcolonisationdiagnosticsimmunocompromised hosts<i>Pneumocystis jirovecii</i>pneumonia |
| spellingShingle | Anna Louise Watson John Woodford Sumudu Britton Rita Gupta David Whiley Kate McCarthy Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals Diagnostics quantitative PCR colonisation diagnostics immunocompromised hosts <i>Pneumocystis jirovecii</i> pneumonia |
| title | Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals |
| title_full | Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals |
| title_fullStr | Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals |
| title_full_unstemmed | Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals |
| title_short | Determining <i>Pneumocystis jirovecii</i> Colonisation from Infection Using PCR-Based Diagnostics in HIV-Negative Individuals |
| title_sort | determining i pneumocystis jirovecii i colonisation from infection using pcr based diagnostics in hiv negative individuals |
| topic | quantitative PCR colonisation diagnostics immunocompromised hosts <i>Pneumocystis jirovecii</i> pneumonia |
| url | https://www.mdpi.com/2075-4418/14/1/114 |
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