Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar.
During outbreaks, the lack of diagnostic "gold standard" can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-08-01
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| Series: | PLoS Biology |
| Online Access: | https://doi.org/10.1371/journal.pbio.3001736 |
| _version_ | 1817986046563975168 |
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| author | Quirine Ten Bosch Voahangy Andrianaivoarimanana Beza Ramasindrazana Guillain Mikaty Rado J L Rakotonanahary Birgit Nikolay Soloandry Rahajandraibe Maxence Feher Quentin Grassin Juliette Paireau Soanandrasana Rahelinirina Rindra Randremanana Feno Rakotoarimanana Marie Melocco Voahangy Rasolofo Javier Pizarro-Cerdá Anne-Sophie Le Guern Eric Bertherat Maherisoa Ratsitorahina André Spiegel Laurence Baril Minoarisoa Rajerison Simon Cauchemez |
| author_facet | Quirine Ten Bosch Voahangy Andrianaivoarimanana Beza Ramasindrazana Guillain Mikaty Rado J L Rakotonanahary Birgit Nikolay Soloandry Rahajandraibe Maxence Feher Quentin Grassin Juliette Paireau Soanandrasana Rahelinirina Rindra Randremanana Feno Rakotoarimanana Marie Melocco Voahangy Rasolofo Javier Pizarro-Cerdá Anne-Sophie Le Guern Eric Bertherat Maherisoa Ratsitorahina André Spiegel Laurence Baril Minoarisoa Rajerison Simon Cauchemez |
| author_sort | Quirine Ten Bosch |
| collection | DOAJ |
| description | During outbreaks, the lack of diagnostic "gold standard" can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect diagnostic tests are available. We apply it to laboratory results of 2,136 samples, analyzed with 3 diagnostic tests (based on up to 7 diagnostic outcomes), collected during the 2017 pneumonic (PP) and bubonic plague (BP) outbreak in Madagascar, which was unprecedented both in the number of notified cases, clinical presentation, and spatial distribution. The extent of these outbreaks has however remained unclear due to nonoptimal assays. Using latent class methods, we estimate that 7% to 15% of notified cases were Yersinia pestis-infected. Overreporting was highest during the peak of the outbreak and lowest in the rural settings endemic to Y. pestis. Molecular biology methods offered the best compromise between sensitivity and specificity. The specificity of the rapid diagnostic test was relatively low (PP: 82%, BP: 85%), particularly for use in contexts with large quantities of misclassified cases. Comparison with data from a subsequent seasonal Y. pestis outbreak in 2018 reveal better test performance (BP: specificity 99%, sensitivity: 91%), indicating that factors related to the response to a large, explosive outbreak may well have affected test performance. We used our framework to optimize the case classification and derive consolidated epidemic trends. Our approach may help reduce uncertainties in other outbreaks where diagnostics are imperfect. |
| first_indexed | 2024-04-14T00:05:24Z |
| format | Article |
| id | doaj.art-fc086b2ba539487b963289508d0090d0 |
| institution | Directory Open Access Journal |
| issn | 1544-9173 1545-7885 |
| language | English |
| last_indexed | 2024-04-14T00:05:24Z |
| publishDate | 2022-08-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj.art-fc086b2ba539487b963289508d0090d02022-12-22T02:23:34ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852022-08-01208e300173610.1371/journal.pbio.3001736Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar.Quirine Ten BoschVoahangy AndrianaivoarimananaBeza RamasindrazanaGuillain MikatyRado J L RakotonanaharyBirgit NikolaySoloandry RahajandraibeMaxence FeherQuentin GrassinJuliette PaireauSoanandrasana RahelinirinaRindra RandremananaFeno RakotoarimananaMarie MeloccoVoahangy RasolofoJavier Pizarro-CerdáAnne-Sophie Le GuernEric BertheratMaherisoa RatsitorahinaAndré SpiegelLaurence BarilMinoarisoa RajerisonSimon CauchemezDuring outbreaks, the lack of diagnostic "gold standard" can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect diagnostic tests are available. We apply it to laboratory results of 2,136 samples, analyzed with 3 diagnostic tests (based on up to 7 diagnostic outcomes), collected during the 2017 pneumonic (PP) and bubonic plague (BP) outbreak in Madagascar, which was unprecedented both in the number of notified cases, clinical presentation, and spatial distribution. The extent of these outbreaks has however remained unclear due to nonoptimal assays. Using latent class methods, we estimate that 7% to 15% of notified cases were Yersinia pestis-infected. Overreporting was highest during the peak of the outbreak and lowest in the rural settings endemic to Y. pestis. Molecular biology methods offered the best compromise between sensitivity and specificity. The specificity of the rapid diagnostic test was relatively low (PP: 82%, BP: 85%), particularly for use in contexts with large quantities of misclassified cases. Comparison with data from a subsequent seasonal Y. pestis outbreak in 2018 reveal better test performance (BP: specificity 99%, sensitivity: 91%), indicating that factors related to the response to a large, explosive outbreak may well have affected test performance. We used our framework to optimize the case classification and derive consolidated epidemic trends. Our approach may help reduce uncertainties in other outbreaks where diagnostics are imperfect.https://doi.org/10.1371/journal.pbio.3001736 |
| spellingShingle | Quirine Ten Bosch Voahangy Andrianaivoarimanana Beza Ramasindrazana Guillain Mikaty Rado J L Rakotonanahary Birgit Nikolay Soloandry Rahajandraibe Maxence Feher Quentin Grassin Juliette Paireau Soanandrasana Rahelinirina Rindra Randremanana Feno Rakotoarimanana Marie Melocco Voahangy Rasolofo Javier Pizarro-Cerdá Anne-Sophie Le Guern Eric Bertherat Maherisoa Ratsitorahina André Spiegel Laurence Baril Minoarisoa Rajerison Simon Cauchemez Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. PLoS Biology |
| title | Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. |
| title_full | Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. |
| title_fullStr | Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. |
| title_full_unstemmed | Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. |
| title_short | Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response: Application to the 2017 plague epidemic in Madagascar. |
| title_sort | analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response application to the 2017 plague epidemic in madagascar |
| url | https://doi.org/10.1371/journal.pbio.3001736 |
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