Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study
<h3 dir="ltr">Background</h3><p dir="ltr">Neonatal sepsis remains a major cause of morbidity and mortality, with 1.3 million annual cases and over 200,000 sepsis-related neonatal deaths. Premature infants are particularly vulnerable, especially in neonatal inten...
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| مؤلفون آخرون: | , , , , , , , , , , , , , , , , , , , , , , |
| منشور في: |
2025
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إضافة وسم
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| _version_ | 1864513521622974464 |
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| author | Faisal E. Ibrahim (19962788) |
| author2 | Maha Waleed (23752992) Dina Abushanab (10696501) Jameela Roshanuddin (22789550) Layla I. Mohammed (23752995) Sonia Boughattas (508422) Bala Subramani Gattu Linga (23752902) Hind H. Adi (22789553) Aseel Al-Dewik (17039797) Ayla J. Ahmedoglu (22789556) Mohammad Abu Zainah (23752998) Farah M. Shurrab (16324961) Jihad Al Shouli (17046393) Mahmoud Abu Halwa (23753001) M. Walid Qoronfleh (14153088) Abdul Rouf Pallivalappil (17760150) Muthanna Samara (11619435) Daoud Al-Badriyeh (832403) Mai AlQubaisi (11619465) Peter Coyle (787159) Hilal Al Rifai (17039850) Fatiha M. Benslimane (6695087) Samer Taha (23753004) Nader Al-Dewik (4166527) |
| author2_role | author author author author author author author author author author author author author author author author author author author author author author author |
| author_facet | Faisal E. Ibrahim (19962788) Maha Waleed (23752992) Dina Abushanab (10696501) Jameela Roshanuddin (22789550) Layla I. Mohammed (23752995) Sonia Boughattas (508422) Bala Subramani Gattu Linga (23752902) Hind H. Adi (22789553) Aseel Al-Dewik (17039797) Ayla J. Ahmedoglu (22789556) Mohammad Abu Zainah (23752998) Farah M. Shurrab (16324961) Jihad Al Shouli (17046393) Mahmoud Abu Halwa (23753001) M. Walid Qoronfleh (14153088) Abdul Rouf Pallivalappil (17760150) Muthanna Samara (11619435) Daoud Al-Badriyeh (832403) Mai AlQubaisi (11619465) Peter Coyle (787159) Hilal Al Rifai (17039850) Fatiha M. Benslimane (6695087) Samer Taha (23753004) Nader Al-Dewik (4166527) |
| author_role | author |
| dc.creator.none.fl_str_mv | Faisal E. Ibrahim (19962788) Maha Waleed (23752992) Dina Abushanab (10696501) Jameela Roshanuddin (22789550) Layla I. Mohammed (23752995) Sonia Boughattas (508422) Bala Subramani Gattu Linga (23752902) Hind H. Adi (22789553) Aseel Al-Dewik (17039797) Ayla J. Ahmedoglu (22789556) Mohammad Abu Zainah (23752998) Farah M. Shurrab (16324961) Jihad Al Shouli (17046393) Mahmoud Abu Halwa (23753001) M. Walid Qoronfleh (14153088) Abdul Rouf Pallivalappil (17760150) Muthanna Samara (11619435) Daoud Al-Badriyeh (832403) Mai AlQubaisi (11619465) Peter Coyle (787159) Hilal Al Rifai (17039850) Fatiha M. Benslimane (6695087) Samer Taha (23753004) Nader Al-Dewik (4166527) |
| dc.date.none.fl_str_mv | 2025-11-26T00:00:00Z |
| dc.identifier.none.fl_str_mv | 10.57945/manara.32051331.v1 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/conference_contribution/Accelerating_Sepsis_Diagnosis_Through_Culture-Free_Genomics_Early_Findings_And_Cost-Effectiveness_From_A_Pilot_Study/32051331 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Microbiology Biomedical and clinical sciences Paediatrics Health sciences Public health Neonatal sepsis Oxford Nanopore Technology Microbial diversity 16S ribosomal gene Species-level detection |
| dc.title.none.fl_str_mv | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| dc.type.none.fl_str_mv | Text Conference contribution info:eu-repo/semantics/publishedVersion text conference object |
| description | <h3 dir="ltr">Background</h3><p dir="ltr">Neonatal sepsis remains a major cause of morbidity and mortality, with 1.3 million annual cases and over 200,000 sepsis-related neonatal deaths. Premature infants are particularly vulnerable, especially in neonatal intensive care units (NICUs). Timely and accurate pathogen identification is essential to improve outcomes. We hypothesized that a culture-free, genomic guided diagnostic strategy for late-onset sepsis is feasible and could accelerate pathogen identification in clinical settings. This pilot study evaluated the feasibility and utility of Oxford Nanopore Technology (ONT) 16S rRNA sequencing, coupled with the EPI2ME 16S QULSS2025 workflow, for real-time pathogen detection directly from blood samples, alongside a cost-effectiveness assessment. </p><h3 dir="ltr">Methods</h3><p dir="ltr">Blood samples from 19 NICU neonates with suspected late-onset sepsis were analyzed using ONT’s 16S rRNA Barcoding Kit. Sequencing was performed on an ONT flow cell, with real-time analysis using the EPI2ME platform, Minimap2 aligner, and NCBI RefSeq database. Cost-effectiveness was evaluated from a public healthcare perspective using the incremental cost-effectiveness ratio (ICER) and Monte Carlo simulations. </p><h3 dir="ltr">Results</h3><p dir="ltr">ONT sequencing identified pathogens in 10/19 (52.6%) samples, including <i>Burkholderia cepacia</i> (n=6), <i>Staphylococcus epidermidis</i> (n=2), <i>Staphylococcus haemolyticus</i> (n=1), and <i>Campylobacter ureolyticus</i> (n=1). Blood cultures were positive in only 4/19 (21%) samples, while both methods were negative in 7 cases. Turnaround time was significantly shorter with ONT (17 hours vs. 72–96 hours). Genomic testing was also more cost-effective, saving 3,335 QAR (≈ $ 914 USD) per case. </p><h3 dir="ltr">Conclusion</h3><p dir="ltr">ONT-based 16S rRNA sequencing offers a rapid, sensitive, and cost-effective alternative to traditional blood cultures for diagnosing neonatal sepsis, with the potential to significantly improve clinical outcomes in NICU settings.</p><h2 dir="ltr">Other Information</h2><p dir="ltr">Conference information: 18th Edition of the Qatar University Life Sciences Symposium Bio-Environment: Advances and Innovations. (26 - 27 Nov 2025, Qatar University, Doha - Qatar)<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" rel="noreferrer noopener" target="_blank">https://creativecommons.org/licenses/by/4.0/</a></p><p dir="ltr">See the conference information on the organizer's website: <a href="https://www.qu.edu.qa/en-us/conference/QULSS2025/Pages/default.aspx" rel="noreferrer noopener" target="_blank">https://www.qu.edu.qa/en-us/conference/QULSS2025/Pages/default.aspx</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_8ccd8a2974c3012673d813a54d4bb48f |
| identifier_str_mv | 10.57945/manara.32051331.v1 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/32051331 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot StudyFaisal E. Ibrahim (19962788)Maha Waleed (23752992)Dina Abushanab (10696501)Jameela Roshanuddin (22789550)Layla I. Mohammed (23752995)Sonia Boughattas (508422)Bala Subramani Gattu Linga (23752902)Hind H. Adi (22789553)Aseel Al-Dewik (17039797)Ayla J. Ahmedoglu (22789556)Mohammad Abu Zainah (23752998)Farah M. Shurrab (16324961)Jihad Al Shouli (17046393)Mahmoud Abu Halwa (23753001)M. Walid Qoronfleh (14153088)Abdul Rouf Pallivalappil (17760150)Muthanna Samara (11619435)Daoud Al-Badriyeh (832403)Mai AlQubaisi (11619465)Peter Coyle (787159)Hilal Al Rifai (17039850)Fatiha M. Benslimane (6695087)Samer Taha (23753004)Nader Al-Dewik (4166527)Biological sciencesGeneticsMicrobiologyBiomedical and clinical sciencesPaediatricsHealth sciencesPublic healthNeonatal sepsisOxford Nanopore TechnologyMicrobial diversity16S ribosomal geneSpecies-level detection<h3 dir="ltr">Background</h3><p dir="ltr">Neonatal sepsis remains a major cause of morbidity and mortality, with 1.3 million annual cases and over 200,000 sepsis-related neonatal deaths. Premature infants are particularly vulnerable, especially in neonatal intensive care units (NICUs). Timely and accurate pathogen identification is essential to improve outcomes. We hypothesized that a culture-free, genomic guided diagnostic strategy for late-onset sepsis is feasible and could accelerate pathogen identification in clinical settings. This pilot study evaluated the feasibility and utility of Oxford Nanopore Technology (ONT) 16S rRNA sequencing, coupled with the EPI2ME 16S QULSS2025 workflow, for real-time pathogen detection directly from blood samples, alongside a cost-effectiveness assessment. </p><h3 dir="ltr">Methods</h3><p dir="ltr">Blood samples from 19 NICU neonates with suspected late-onset sepsis were analyzed using ONT’s 16S rRNA Barcoding Kit. Sequencing was performed on an ONT flow cell, with real-time analysis using the EPI2ME platform, Minimap2 aligner, and NCBI RefSeq database. Cost-effectiveness was evaluated from a public healthcare perspective using the incremental cost-effectiveness ratio (ICER) and Monte Carlo simulations. </p><h3 dir="ltr">Results</h3><p dir="ltr">ONT sequencing identified pathogens in 10/19 (52.6%) samples, including <i>Burkholderia cepacia</i> (n=6), <i>Staphylococcus epidermidis</i> (n=2), <i>Staphylococcus haemolyticus</i> (n=1), and <i>Campylobacter ureolyticus</i> (n=1). Blood cultures were positive in only 4/19 (21%) samples, while both methods were negative in 7 cases. Turnaround time was significantly shorter with ONT (17 hours vs. 72–96 hours). Genomic testing was also more cost-effective, saving 3,335 QAR (≈ $ 914 USD) per case. </p><h3 dir="ltr">Conclusion</h3><p dir="ltr">ONT-based 16S rRNA sequencing offers a rapid, sensitive, and cost-effective alternative to traditional blood cultures for diagnosing neonatal sepsis, with the potential to significantly improve clinical outcomes in NICU settings.</p><h2 dir="ltr">Other Information</h2><p dir="ltr">Conference information: 18th Edition of the Qatar University Life Sciences Symposium Bio-Environment: Advances and Innovations. (26 - 27 Nov 2025, Qatar University, Doha - Qatar)<br>License: <a href="https://creativecommons.org/licenses/by/4.0/" rel="noreferrer noopener" target="_blank">https://creativecommons.org/licenses/by/4.0/</a></p><p dir="ltr">See the conference information on the organizer's website: <a href="https://www.qu.edu.qa/en-us/conference/QULSS2025/Pages/default.aspx" rel="noreferrer noopener" target="_blank">https://www.qu.edu.qa/en-us/conference/QULSS2025/Pages/default.aspx</a></p>2025-11-26T00:00:00ZTextConference contributioninfo:eu-repo/semantics/publishedVersiontextconference object10.57945/manara.32051331.v1https://figshare.com/articles/conference_contribution/Accelerating_Sepsis_Diagnosis_Through_Culture-Free_Genomics_Early_Findings_And_Cost-Effectiveness_From_A_Pilot_Study/32051331CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/320513312025-11-26T00:00:00Z |
| spellingShingle | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study Faisal E. Ibrahim (19962788) Biological sciences Genetics Microbiology Biomedical and clinical sciences Paediatrics Health sciences Public health Neonatal sepsis Oxford Nanopore Technology Microbial diversity 16S ribosomal gene Species-level detection |
| status_str | publishedVersion |
| title | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| title_full | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| title_fullStr | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| title_full_unstemmed | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| title_short | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| title_sort | Accelerating Sepsis Diagnosis Through Culture-Free Genomics: Early Findings And Cost-Effectiveness From A Pilot Study |
| topic | Biological sciences Genetics Microbiology Biomedical and clinical sciences Paediatrics Health sciences Public health Neonatal sepsis Oxford Nanopore Technology Microbial diversity 16S ribosomal gene Species-level detection |