Pooling samples to increase testing capacity with Xpert Xpress SARS-CoV-2 during the Covid-19 pandemic in Lao People's Democratic Republic.

The COVID-19 pandemic created the need for large-scale testing of populations. However, most laboratories do not have sufficient testing capacity for mass screening. We evaluated pooled testing of samples, as a strategy to increase testing capacity in Lao PDR. Samples of consecutive patients were tested in pools of four using the Xpert Xpress SARS CoV-2 assay. Positive pools were confirmed by individual testing, and we describe the performance of the test and savings achieved. We also diluted selected positive samples to describe its effect on the assays CT values. 1,568 patients were tested in 392 pools of four. 361 (92.1%) pools were negative and 31 (7.9%) positive. 29/31 (93.5% (95%CI 77-99%) positive pools were confirmed by individual testing of the samples but, in 2/31 (6.5%) the four individual samples were negative, suggesting contamination. Pools with only one positive sample had higher CT values (lower RNA concentrations) than the respective individual samples, indicating a dilution effect, which suggested an increased risk of false negative results with dilutions >1:10. However, this risk may be low if the prevalence of infection is high, when pools are more likely to contain more than one positive sample. Pooling saved 67% of cartridges and substantially increased testing capacity. Pooling samples increased SARS-CoV-2 testing capacity and resulted in considerable cartridge savings. Given the need for high-volume testing, countries may consider implementation of pooling for SARS-CoV-2 screening.

Pooled testing of sputum with Xpert MTB/RIF and Xpert Ultra during tuberculosis active case finding campaigns in Lao People's Democratic Republic.

INTRODUCTION: Active case finding (ACF) of individuals with tuberculosis (TB) is a key intervention to find the 30% of people missed every year. However, ACF requires screening large numbers of individuals who have a low probability of positive results, typically <5%, which makes using the recommended molecular tests expensive. METHODS: We conducted two ACF surveys (in 2020 and 2021) in high TB burden areas of Lao PDR. Participants were screened for TB symptoms and received a chest X-ray. Sputum samples of four consecutive individuals were pooled and tested with Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF) (Xpert-MTB/RIF) (2020) or Xpert-Ultra (2021). The agreement of the individual and pooled samples was compared and the reasons for discrepant results and potential cartridge savings were assessed. RESULTS: Each survey included 436 participants, which were tested in 109 pools. In the Xpert-MTB/RIF survey, 25 (sensitivity 89%, 95% CI 72.8% to 96.3%) of 28 pools containing MTB-positive samples tested positive and 81 pools containing only MTB-negative samples tested negative (specificity 100%, 95% CI 95.5% to 100%). In the Xpert-Ultra survey, all 32 (sensitivity 100%, 95% CI 89.3% to 100%) pools containing MTB-positive samples tested positive and all 77 (specificity 100%, 95% CI 95.3% to 100%) containing only MTB-negative samples tested negative. Pooling with Xpert-MTB/RIF and Xpert-Ultra saved 52% and 46% (227/436 and 199/436, respectively) of cartridge costs alone. CONCLUSION: Testing single and pooled specimens had a high level of agreement, with complete concordance when using Xpert-Ultra. Pooling samples could generate significant cartridge savings during ACF campaigns.

Pooling sputum for Xpert MTB/RIF and Xpert Ultra testing during the Covid-19 pandemic in Lao People's Democratic Republic.

The global Covid-19 pandemic has limited access to molecular TB diagnostics and National Programmes are struggling to maintain essential services. The pooling method (testing several samples together) could reduce the number of cartridges and staff time needed for TB diagnosis but has not been tested within the pandemic. We conducted two independent cross-sectional surveys. Pools composed of four sputum samples were tested using either Xpert-MTB/RIF or Xpert-Ultra. Pooled and individual results were compared to determine the level of agreement. Each survey included 840 participants and 210 pools. In the Xpert MTB/RIF survey, 77/81 (sensitivity 95.1%, 95%CI 87.8%-98.6%) pools containing ≥1 positive sample tested MTB-positive and 4/81 (4.9%, 95%CI 1.4%-12.2%) tested MTB-negative. All 129/129 pools containing MTB-negative samples tested MTB-negative (specificity 100%, 95%CI 97.2%-100%), with 98.1% agreement (Kappa: 0.959). In the Xpert-Ultra survey, 70/70 (sensitivity 100%, 95%CI 94.9%-100%) pools containing ≥ 1 MTB-positive sample tested MTB-positive and 140/140 (specificity 100%, 95%CI 97.4%-100%) pools containing only MTB-negative samples tested MTB-negative, with 100% agreement (Kappa: 1). Pooled testing with Xpert-MTB/RIF and Xpert-Ultra saved 38.3% and 41.7% (322/840 and 350/840, respectively) in cartridge costs alone. The pooling method with Xpert-MTB/RIF and Xpert-Ultra has similar performance to individual testing and can reduce the number of cartridges needed. These efficiencies can facilitate maintenance of stocks and sustain essential services as countries face difficulties for laboratory procurement during the pandemic and will provide cost and time savings post-pandemic.

Low prevalence of MDR-TB in Lao PDR: results from the first national anti-tuberculosis drug resistance survey.

OBJECTIVE: To present results of the first national anti-tuberculosis (TB) drug resistance survey conducted in Lao PDR between May 2016 and August 2017 to determine the prevalence of resistance to first-line anti-TB drugs among new and previously treated pulmonary TB cases in the country. METHODS: Patients with sputum smear-positive pulmonary TB were enrolled from 42 TB laboratories distributed in 40 clusters throughout the country. Survey sites were selected using probability-proportional-to-size sampling among all diagnostic centres in the country. In addition to smear microscopy, all patients underwent Xpert MTB/RIF testing and those found positive to Mycobacterium tuberculosis underwent sputum culture and drug susceptibility testing using the proportion method on solid Löwenstein-Jensen medium. RESULTS: Among 1006 eligible patients, 946 sputum smear-positive and Xpert MTB/RIF positive (Mycobacterium tuberculosis detected) patients were included in the survey, comprising 897 new and 49 previously treated TB cases. The prevalence of rifampicin-resistant TB was 1.2% (95% CI: 0.5-2.0%, n = 11/897) among new cases and 4.1% (95% CI: 0-9.6%, n = 2/49) among previously treated cases. Among the 946 TB cases confirmed by Xpert MTB/RIF, phenotypic drug sensitivity testing was available for 820 (776 new and 44 previously treated). The prevalence of multidrug-resistant TB (MDR-TB) was 0.5% (95% CI: 0-1.0%, n = 4/776) among new cases and 2.3% (95% CI: 0-6.7%, n = 1/44) among previously treated cases. No resistance to second-line injectable agents nor to fluoroquinolones was detected among MDR-TB patients. CONCLUSIONS: The first national anti-TB drug resistance survey in Lao PDR demonstrated an encouragingly low prevalence of MDR-TB. The results appear lower than previous WHO estimates, and in line with the routine surveillance based on Xpert MTB/RIF testing (conducted among 50% of presumptive TB patients in 2017). The country should continue to expand its Xpert MTB/RIF network and strive to achieve universal drug susceptibility testing.

OBJECTIF: Présenter les résultats de la première surveillance nationale de la résistance aux médicaments antituberculeux, menée en République Démocratique Populaire (RDP) Lao entre mai 2016 et août 2017 afin de déterminer la prévalence de la résistance aux médicaments antituberculeux de première intention chez les nouveaux cas et les cas déjà traités de tuberculose (TB) pulmonaire dans le pays. MÉTHODES: Les patients atteints de TB pulmonaire à frottis d'expectoration positif ont été recrutés dans 42 laboratoires TB répartis dans 40 groupes à travers tout le pays. Les sites de surveillance ont été sélectionnés sur la base d'un échantillon probabiliste proportionnel à la taille parmi tous les centres de diagnostic du pays. Outre l'examen microscopique des frottis, tous les patients ont subi un test Xpert MTB/RIF et ceux trouvés positifs pour Mycobacterium tuberculosis ont subi une culture d'expectorations et un test de sensibilité aux médicaments en utilisant la méthode des proportions sur un milieu solide de Löwenstein-Jensen. RÉSULTATS: Parmi les 1.006 patients éligibles, 946 patients à frottis positif et Xpert MTB/RIF positif (Mycobacterium tuberculosis détecté) ont été inclus dans la surveillance, comprenant 897 nouveaux cas et 49 cas de TB déjà traités. La prévalence de la TB résistante à la rifampicine était de 1,2% (IC95%: 0,5-2,0%, n = 11/897) chez les nouveaux cas et de 4,1% (IC95%: 0-9,6%, n = 2/49) chez les cas traités. Parmi les 946 cas de TB confirmés par Xpert MTB/RIF, des tests de sensibilité phénotypique aux médicaments étaient disponibles pour 820 (776 nouveaux cas et 44 cas traités antérieurement). La prévalence de la TB multirésistante (TB-MDR) était de 0,5% (IC95%: 0-1,0%, n = 4/776) chez les nouveaux cas et de 2,3% (IC95%: 0 à 6,7%, n = 1/44) parmi les cas précédemment traités. Aucune résistance aux agents injectables de deuxième intention ni aux fluoroquinolones n'a été détectée chez les patients atteints de TB-MDR. CONCLUSIONS: La première surveillance nationale de la résistance aux médicaments antituberculeux menée en RDP Lao a révélé une prévalence rassurante de la TB-MDR. Les résultats apparaissent inférieurs aux estimations précédentes de l'OMS et conformes à la surveillance de routine basée sur le test Xpert MTB/RIF (menée auprès de 50% des patients atteints de TB présumée en 2017). Le pays devrait continuer à élargir son réseau Xpert MTB/RIF et s'efforcer d'atteindre des tests universels de sensibilité aux médicaments.