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Pooling samples to increase testing capacity for Tuberculosis and COVID-19 diagnosis.

Iem, Vibol (2023) Pooling samples to increase testing capacity for Tuberculosis and COVID-19 diagnosis., Thesis (Doctoral), Liverpool School of Tropical Medicine.

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The COVID-19 pandemic created an overwhelming burden for National Tuberculosis (TB) Programs who struggled to maintain essential services while coping with diversion of equipment and personnel. This resulted in delays and stock-outs in procurement of laboratory equipment including due to lockdowns, leading to TB testing requirement exceeding the capacity of TB laboratories.
International development partners are increasingly requesting countries to commit to co-financing mechanisms from government-funded schemes for the procurement of recommended molecular TB tests (Xpert MTB/RIF or Xpert Ultra), but such tests can be expensive, especially for low- and middle-income countries (LMIC).
One strategy to improve cost-efficiency and access to these tests is through pooled testing. This approach consists of mixing (pooling) sputum specimens from several individuals into a single pool, which is then tested with a single test. If the pooled test is negative, all samples in the pool are considered negative. If the pooled test is positive, it means at least one of the individual samples is positive, and each individual sample is then re-tested to identify the positive sample(s).
The potential cost and time savings of the pooling method appear promising but there remains minimal evidence, especially from LMIC settings, on whether pooled testing can increase testing capacity while at the same time offering reliable performance with similar accuracy to individual testing.
In Lao People’s Democratic Republic (Lao PDR), a LMIC with moderate TB burden, we evaluated whether pooled testing was suitable to implement within routine passive and active case finding strategies, the two main approaches for TB screening in Lao PDR. More precisely, we described the level of agreement between individual and pooled testing, investigated potential discrepancies between test results, and assessed whether the pooling approach would result in assay cost savings.
First, we reviewed the literature to assess the sensitivity/specificity of GeneXpert-based pooled testing compared to individual testing and potential cartridge/time savings. We found that testing pools with 4 sputum samples with Xpert-MTB/RIF and Xpert Ultra had 91% and 98% sensitivity, with 99%–100% specificity and 27%–31% cartridge savings. However, the review found that the number of high-quality studies available in the literature was too small to develop evidence-based guidance to inform policy and decision makers.
Second, we conducted cross-sectional surveys comparing the individual vs pooled sample methods using Xpert-Ultra and Xpert-MTB/RIF in Lao PDR and Nigeria. Surveys using Xpert-Ultra showed an agreement between individual vs pooled testing of 100% and 94%, with considerable Xpert-Ultra cartridge savings, ranging from 42% to 46%. Higher savings were observed in populations where the proportion of positive tests was lower. Pooling with Xpert-MTB/RIF in Lao PDR and Nigeria showed 98% and 94% agreement between pooled and individual testing and saved 38% and 35% in cartridge costs. Pooled testing with Xpert-Ultra had similar agreement (100%) whether active or passive case finding strategies were used.
Third, to respond in real time to an urgent public health need, we temporarily pivoted to assess the feasibility of the pooled testing strategy when applied to SARS-CoV-2 testing at the height of the COVID-19 pandemic in Lao PDR, during which demand for SARS-CoV-2 testing outstripped capacity. Pooling samples for SARS-CoV-2 using the Xpert Xpress SARS-CoV-2 reduced the number of tests required by 67% and tripled the laboratory testing capacity.
Fourth, we conducted a cost-minimization analysis of individual vs pooled TB testing to establish the value for money of pooling. This showed that pooling can lead to significant savings related to cartridge expenditure, but the amount of savings varies significantly depending on the proportion of positive tests, with lower prevalence and positivity rates leading to higher savings.
There remains a need for high-volume rapid testing for both TB and COVID-19, especially in LMIC. Our results show that pooling samples increased testing capacity, reduced costs per positive test, improved maintenance of stocks, and enhanced essential services during the pandemic. Pooling could continue to provide cost and time savings post-pandemic for TB and SARS-CoV-2 screening and could also be of preparedness for future infectious pandemics or emergences.

Item Type: Thesis (Doctoral)
Subjects: WC Communicable Diseases > WC 20 Research (General)
WC Communicable Diseases > Virus Diseases > Viral Respiratory Tract Infections. Respirovirus Infections > WC 506 COVID-19
WF Respiratory System > WF 20 Research (General)
WF Respiratory System > Tuberculosis > WF 200 Tuberculosis (General)
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Item titleItem URI
Pooled testing of sputum with Xpert MTB/RIF and Xpert Ultra during tuberculosis active case finding campaigns in Lao People’s Democratic Republic
Pooling samples to increase testing capacity with Xpert Xpress SARS-CoV-2 during the Covid-19 pandemic in Lao People's Democratic Republic
Pooling sputum samples for Xpert® MTB/RIF and Xpert® Ultra testing for TB diagnosis
Pooling sputum testing to diagnose tuberculosis using xpert MTB/RIF and xpert ultra: a cost-effectiveness analysis
Systematic Review of Pooling Sputum as an Efficient Method for Xpert MTB/RIF Tuberculosis Testing during the COVID-19 Pandemic
Pooling sputum for Xpert MTB/RIF and Xpert Ultra testing during the Covid-19 pandemic in Lao People’s Democratic Republic
Faculty: Department: Clinical Sciences & International Health > Clinical Sciences Department
Depositing User: Lynn Roberts-Maloney
Date Deposited: 04 Oct 2023 12:58
Last Modified: 04 Jan 2024 04:12


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