The Impact of Xpert MTB/RIF Ultra and Stool-Based TB Diagnosis in Sierra Leone: A Retrospective Analysis of Routine GeneXpert Data, 2022–2023

The Impact of Xpert MTB/RIF Ultra and Stool-Based TB Diagnosis in Sierra Leone: A Retrospective Analysis of Routine GeneXpert Data, 2022–2023 | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article The Impact of Xpert MTB/RIF Ultra and Stool-Based TB Diagnosis in Sierra Leone: A Retrospective Analysis of Routine GeneXpert Data, 2022–2023 Zein Souma, Sulaiman Mansaray This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7828053/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract This study evaluates the implementation of the Xpert MTB/RIF Ultra diagnostic cartridge and the Simple One-Step (SOS) stool method across tuberculosis diagnostic sites in Sierra Leone between 2022 and 2023. The Ultra cartridge, designed to enhance sensitivity for Mycobacterium tuberculosis (MTB) and rifampicin resistance (RR-TB), was deployed nationally to improve case detection, especially among children and individuals unable to produce sputum. Analysis of routine GeneXpert data reveals increased diagnostic throughput, improved detection of drug-sensitive TB, and a modest decline in RR-TB prevalence. The integration of stool-based testing further expanded access to vulnerable populations. These findings underscore the transformative role of Ultra in strengthening TB control efforts in resource-limited settings. Laboratory Diagnostics MTB Rif Ultra in Sierra Leone TB Testing Introduction Tuberculosis remains a major public health challenge in Sierra Leone, with rifampicin-resistant TB posing significant threats to treatment success and disease containment. Molecular diagnostics have become central to TB control strategies, particularly with the introduction of the Xpert MTB/RIF Ultra cartridge—a next-generation tool offering improved sensitivity over its predecessor. This study assesses the impact of Ultra on national TB diagnostics, explores trends in RR-TB detection, and highlights the role of stool-based testing in expanding access to underserved populations. Methods Routine diagnostic data were collected from 16 sites in 2022 and 21 sites in 2023. Monthly and quarterly aggregates were analyzed for four test outcomes: MTB not detected, MTB detected with rifampicin sensitivity (DS-TB), MTB detected with rifampicin resistance (RR-TB), and Error/Invalid/Indeterminate results. The study also evaluated the performance of the SOS stool method, introduced in 2023 to facilitate TB diagnosis in children and non-sputum-producing patients. Comparative analysis was conducted using descriptive statistics and site-level performance metrics. Results Diagnostic Coverage and Throughput Diagnostic sites increased from 16 in 2022 to 21 in 2023. Total tests rose from 14,158 in 2022 to over 18,000 in 2023. MTB detection rates remained stable: 28.6% in 2022 and approximately 26% in 2023. Rifampicin Resistance Trends Year RR-TB Cases % of MTB-Positive 2022 206 5.1% 2023 140 4.2% A modest decline in RR-TB detection was observed, suggesting earlier diagnosis and improved treatment adherence. Error and Invalid Results Year Invalid/Error Cases % of Total Tests 2022 1,271 9.0% 2023 ~ 1,000 ~ 5.5% Error rates improved significantly, reflecting better cartridge handling and equipment maintenance. Site-Level Performance (2023) Site Total Tests DS-TB Cases RR-TB Cases Makeni 1,403 312 13 Connaught Chest Clinic 784 272 13 Koidu-Govt. Hospital 502 165 2 PCMH / ODCH 502 160 3 Bo 317 99 2 Makeni and Connaught Chest Clinic consistently led in throughput and RR-TB detection. Scientific Relevance Diagnostic Innovation: Ultra vs. Previous Methods The Ultra cartridge enhances sensitivity by targeting multicopy DNA sequences (IS6110 and IS1081), enabling detection of as few as 16 CFU/mL compared to 113 CFU/mL for the original Xpert. This improvement is critical for detecting TB in smear-negative, pediatric, and HIV-positive populations. Global studies have demonstrated: Sensitivity: 88–94% for smear-negative TB Specificity: 97–100% Faster turnaround: ~80 minutes These advantages have translated into earlier diagnosis, reduced transmission, and improved treatment outcomes. Expanding Access: The SOS Stool Method The SOS stool method allows TB diagnosis using stool samples, particularly beneficial for children and patients unable to produce sputum. It requires minimal equipment and training, making it ideal for decentralized settings. Evidence from other countries: Bangladesh: Stool Ultra sensitivity 72% vs. 24% for sputum Xpert in children Ethiopia: Strong agreement between stool and sputum Ultra results (kappa = 0.83) Nigeria: Pediatric TB notifications increased by 40% after stool testing rollout In Sierra Leone, stool testing was introduced in 2023, contributing to increased pediatric case detection and reducing diagnostic delays. Discussion The deployment of Xpert MTB/RIF Ultra and the SOS stool method has significantly strengthened TB diagnostics in Sierra Leone. The modest decline in RR-TB detection suggests earlier case identification and improved treatment linkage. The reduction in error rates reflects operational improvements, while the expansion to new districts has broadened diagnostic reach. However, challenges remain: Limited uptake in newly added districts Need for pediatric-specific data and treatment follow-up Continued investment in training, supply chain, and equipment maintenance Conclusion The Xpert MTB/RIF Ultra cartridge and stool-based testing have transformed TB diagnostics in Sierra Leone. These innovations have improved sensitivity, expanded access to vulnerable populations, and contributed to a decline in rifampicin resistance. Sustained support for infrastructure, training, and data integration will be essential to consolidate gains and accelerate progress toward TB elimination. Declarations ETHICS: The ethics review panel of Lakka Government Hospital waived the need for full review and patient consent on this retrospective study. References Kendall EA et al Estimated clinical impact of the Xpert MTB/RIF Ultra cartridge. PLOS Medicine WHO Policy Statement on Xpert MTB/RIF Ultra Wang MQ et al Diagnostic accuracy of Xpert MTB/RIF Ultra. European Journal of Clinical Microbiology & Infectious Diseases KNCV Tuberculosis Foundation SOS Stool Method Implementation Guide Pulmonology Journal Clinical impact of Xpert MTB/RIF Ultra in Brazil Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7828053","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":527740555,"identity":"b43e540d-caaa-4bc4-b4d8-091c28ce3b9e","order_by":0,"name":"Zein Souma","email":"","orcid":"https://orcid.org/0000-0001-6513-1958","institution":"National TB Reference Laboratory","correspondingAuthor":false,"prefix":"","firstName":"Zein","middleName":"","lastName":"Souma","suffix":""},{"id":527740556,"identity":"eb1726d1-5e1d-4b74-a554-159d93a5551a","order_by":1,"name":"Sulaiman Mansaray","email":"data:image/png;base64,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","orcid":"","institution":"National TB Reference Laboratory","correspondingAuthor":true,"prefix":"","firstName":"Sulaiman","middleName":"","lastName":"Mansaray","suffix":""}],"badges":[],"createdAt":"2025-10-10 14:28:41","currentVersionCode":1,"declarations":{"humanSubjects":true,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":true,"humanSubjectConsent":true,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-7828053/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7828053/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":94203278,"identity":"0de4180b-6ce5-42dd-a261-c5be0d4f92e9","added_by":"auto","created_at":"2025-10-23 14:15:08","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":31816,"visible":true,"origin":"","legend":"","description":"","filename":"Genexpert20222023.docx","url":"https://assets-eu.researchsquare.com/files/rs-7828053/v1/52f096ca3ce4e44e9a161cb3.docx"},{"id":94203280,"identity":"059850f0-16ab-476b-96cc-cfb8fc7bbae8","added_by":"auto","created_at":"2025-10-23 14:15:08","extension":"json","order_by":1,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":342,"visible":true,"origin":"","legend":"","description":"","filename":"rs7828053.json","url":"https://assets-eu.researchsquare.com/files/rs-7828053/v1/67b440b3e0a70cb468c1a105.json"},{"id":94203281,"identity":"57cf7d7d-6f53-4502-b817-737346ea77bc","added_by":"auto","created_at":"2025-10-23 14:15:08","extension":"xml","order_by":2,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":16934,"visible":true,"origin":"","legend":"","description":"","filename":"rs78280530enriched.xml","url":"https://assets-eu.researchsquare.com/files/rs-7828053/v1/bb1391e8c09f55340023f4f6.xml"},{"id":94203283,"identity":"44186972-2dbb-4ed6-9919-7b563f6772c8","added_by":"auto","created_at":"2025-10-23 14:15:08","extension":"xml","order_by":3,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":16051,"visible":true,"origin":"","legend":"","description":"","filename":"rs78280530structuring.xml","url":"https://assets-eu.researchsquare.com/files/rs-7828053/v1/bc5757d6c49a1d6a50be8fa0.xml"},{"id":94203758,"identity":"2f3c6f23-9733-4a0a-ad24-30e37b90db8f","added_by":"auto","created_at":"2025-10-23 14:23:08","extension":"html","order_by":4,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":19593,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-7828053/v1/d29d7db32369b949a894596f.html"},{"id":94203776,"identity":"5f04abdc-73fb-49a4-814c-c6594cbcaf3d","added_by":"auto","created_at":"2025-10-23 14:23:13","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":396687,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7828053/v1/bc5f8aaf-efa0-42a4-9dad-d2a9462a578d.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003e\u003cstrong\u003eThe Impact of Xpert MTB/RIF Ultra and Stool-Based TB Diagnosis in Sierra Leone: A Retrospective Analysis of Routine GeneXpert Data, 2022–2023\u003c/strong\u003e\u003c/p\u003e","fulltext":[{"header":"Introduction","content":"\u003cp\u003eTuberculosis remains a major public health challenge in Sierra Leone, with rifampicin-resistant TB posing significant threats to treatment success and disease containment. Molecular diagnostics have become central to TB control strategies, particularly with the introduction of the Xpert MTB/RIF Ultra cartridge\u0026mdash;a next-generation tool offering improved sensitivity over its predecessor. This study assesses the impact of Ultra on national TB diagnostics, explores trends in RR-TB detection, and highlights the role of stool-based testing in expanding access to underserved populations.\u003c/p\u003e"},{"header":"Methods","content":"\u003cp\u003eRoutine diagnostic data were collected from 16 sites in 2022 and 21 sites in 2023. Monthly and quarterly aggregates were analyzed for four test outcomes: MTB not detected, MTB detected with rifampicin sensitivity (DS-TB), MTB detected with rifampicin resistance (RR-TB), and Error/Invalid/Indeterminate results. The study also evaluated the performance of the SOS stool method, introduced in 2023 to facilitate TB diagnosis in children and non-sputum-producing patients. Comparative analysis was conducted using descriptive statistics and site-level performance metrics.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e\u003ch2\u003eDiagnostic Coverage and Throughput\u003c/h2\u003e\u003cp\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003eDiagnostic sites increased from 16 in 2022 to 21 in 2023.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eTotal tests rose from 14,158 in 2022 to over 18,000 in 2023.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eMTB detection rates remained stable: 28.6% in 2022 and approximately 26% in 2023.\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eRifampicin Resistance Trends\u003c/h3\u003e\n\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Taba\" border=\"1\"\u003e\u003ccolgroup cols=\"3\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eYear\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eRR-TB Cases\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003e% of MTB-Positive\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e2022\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e206\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e5.1%\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e2023\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e140\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e4.2%\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003eA modest decline in RR-TB detection was observed, suggesting earlier diagnosis and improved treatment adherence.\u003c/p\u003e\n\u003ch3\u003eError and Invalid Results\u003c/h3\u003e\n\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Tabb\" border=\"1\"\u003e\u003ccolgroup cols=\"3\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eYear\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eInvalid/Error Cases\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003e% of Total Tests\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e2022\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e1,271\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e9.0%\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e2023\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e~\u0026thinsp;1,000\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e~\u0026thinsp;5.5%\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003eError rates improved significantly, reflecting better cartridge handling and equipment maintenance.\u003c/p\u003e\n\u003ch3\u003eSite-Level Performance (2023)\u003c/h3\u003e\n\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"No\" id=\"Tabc\" border=\"1\"\u003e\u003ccolgroup cols=\"4\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eSite\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTotal Tests\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eDS-TB Cases\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eRR-TB Cases\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eMakeni\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e1,403\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e312\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e13\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eConnaught Chest Clinic\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e784\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e272\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e13\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eKoidu-Govt. Hospital\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e502\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e165\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003ePCMH / ODCH\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e502\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e160\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eBo\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e317\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e99\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003eMakeni and Connaught Chest Clinic consistently led in throughput and RR-TB detection.\u003c/p\u003e\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e\u003ch2\u003eScientific Relevance\u003c/h2\u003e\u003cdiv id=\"Sec9\" class=\"Section3\"\u003e\u003ch2\u003eDiagnostic Innovation: Ultra vs. Previous Methods\u003c/h2\u003e\u003cp\u003eThe Ultra cartridge enhances sensitivity by targeting multicopy DNA sequences (IS6110 and IS1081), enabling detection of as few as 16 CFU/mL compared to 113 CFU/mL for the original Xpert. This improvement is critical for detecting TB in smear-negative, pediatric, and HIV-positive populations.\u003c/p\u003e\u003cp\u003eGlobal studies have demonstrated:\u003c/p\u003e\u003cp\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003eSensitivity: 88\u0026ndash;94% for smear-negative TB\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eSpecificity: 97\u0026ndash;100%\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eFaster turnaround: ~80 minutes\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003c/p\u003e\u003cp\u003eThese advantages have translated into earlier diagnosis, reduced transmission, and improved treatment outcomes.\u003c/p\u003e\u003c/div\u003e\u003c/div\u003e\n\u003ch3\u003eExpanding Access: The SOS Stool Method\u003c/h3\u003e\n\u003cp\u003eThe SOS stool method allows TB diagnosis using stool samples, particularly beneficial for children and patients unable to produce sputum. It requires minimal equipment and training, making it ideal for decentralized settings.\u003c/p\u003e\u003cp\u003eEvidence from other countries:\u003c/p\u003e\u003cp\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003eBangladesh: Stool Ultra sensitivity 72% vs. 24% for sputum Xpert in children\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eEthiopia: Strong agreement between stool and sputum Ultra results (kappa\u0026thinsp;=\u0026thinsp;0.83)\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eNigeria: Pediatric TB notifications increased by 40% after stool testing rollout\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003c/p\u003e\u003cp\u003eIn Sierra Leone, stool testing was introduced in 2023, contributing to increased pediatric case detection and reducing diagnostic delays.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eThe deployment of Xpert MTB/RIF Ultra and the SOS stool method has significantly strengthened TB diagnostics in Sierra Leone. The modest decline in RR-TB detection suggests earlier case identification and improved treatment linkage. The reduction in error rates reflects operational improvements, while the expansion to new districts has broadened diagnostic reach.\u003c/p\u003e\u003cp\u003eHowever, challenges remain:\u003c/p\u003e\u003cp\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003eLimited uptake in newly added districts\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eNeed for pediatric-specific data and treatment follow-up\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eContinued investment in training, supply chain, and equipment maintenance\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThe Xpert MTB/RIF Ultra cartridge and stool-based testing have transformed TB diagnostics in Sierra Leone. These innovations have improved sensitivity, expanded access to vulnerable populations, and contributed to a decline in rifampicin resistance. Sustained support for infrastructure, training, and data integration will be essential to consolidate gains and accelerate progress toward TB elimination.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003eETHICS:\u003c/p\u003e\n\u003cp\u003eThe ethics review panel of Lakka Government Hospital waived the need for full review and patient consent on this retrospective study.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eKendall EA et al Estimated clinical impact of the Xpert MTB/RIF Ultra cartridge. PLOS Medicine\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWHO Policy Statement on Xpert MTB/RIF Ultra\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWang MQ et al Diagnostic accuracy of Xpert MTB/RIF Ultra. European Journal of Clinical Microbiology \u0026amp; Infectious Diseases\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eKNCV Tuberculosis Foundation SOS Stool Method Implementation Guide\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePulmonology Journal Clinical impact of Xpert MTB/RIF Ultra in Brazil\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[{"identity":"bd8b2d4d-a501-449c-bb5d-bf4c916998e9","identifier":"10.13039/100004417","name":"Global Fund to Fight AIDS, Tuberculosis and Malaria","awardNumber":"1","order_by":0}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"National Leprosy and TB Control Program","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"MTB Rif Ultra in Sierra Leone, TB Testing,","lastPublishedDoi":"10.21203/rs.3.rs-7828053/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7828053/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThis study evaluates the implementation of the Xpert MTB/RIF Ultra diagnostic cartridge and the Simple One-Step (SOS) stool method across tuberculosis diagnostic sites in Sierra Leone between 2022 and 2023. The Ultra cartridge, designed to enhance sensitivity for Mycobacterium tuberculosis (MTB) and rifampicin resistance (RR-TB), was deployed nationally to improve case detection, especially among children and individuals unable to produce sputum. Analysis of routine GeneXpert data reveals increased diagnostic throughput, improved detection of drug-sensitive TB, and a modest decline in RR-TB prevalence. The integration of stool-based testing further expanded access to vulnerable populations. These findings underscore the transformative role of Ultra in strengthening TB control efforts in resource-limited settings.\u003c/p\u003e","manuscriptTitle":"The Impact of Xpert MTB/RIF Ultra and Stool-Based TB Diagnosis in Sierra Leone: A Retrospective Analysis of Routine GeneXpert Data, 2022–2023","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-10-23 14:15:03","doi":"10.21203/rs.3.rs-7828053/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"acab40ee-8a09-4880-89f2-9a6dd8dfe02b","owner":[],"postedDate":"October 23rd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":56099776,"name":"Laboratory Diagnostics"}],"tags":[],"updatedAt":"2025-11-17T07:23:44+00:00","versionOfRecord":[],"versionCreatedAt":"2025-10-23 14:15:03","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7828053","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7828053","identity":"rs-7828053","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}