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UNLABELLED: Candida auris is a multidrug-resistant fungal pathogen with a propensity to colonize humans and persist on environmental surfaces. C. auris invasive fungal disease is being increasingly identified in acute and long-term care settings. We have developed a prototype cartridge-based C. auris surveillance assay (CaurisSurV cartridge; research use only) that includes integrated sample processing and nucleic acid amplification to detect C. auris from surveillance skin swabs in the GeneXpert instrument and is designed for point-of-care use. The assay limit of detection (LoD) in the skin swab matrix was 10.5 and 14.8 CFU/mL for non-aggregative (AR0388) and aggregative (AR0382) strains of C. auris, respectively. All five known clades of C. auris were detected at 2-3-5× (31.5-52.5 CFU/mL) the LoD. The assay was validated using a total of 85 clinical swab samples banked at two different institutions (University of California Los Angeles, CA and Wadsworth Center, NY). Compared to culture, sensitivity was 96.8% (30/31) and 100% (10/10) in the UCLA and Wadsworth cohorts, respectively, providing a combined sensitivity of 97.5% (40/41), and compared to PCR, the combined sensitivity was 92% (46/50). Specificity was 100% with both clinical (C. auris negative matrix, N = 31) and analytical (non-C. auris strains, N = 32) samples. An additional blinded study with N = 60 samples from Wadsworth Center, NY yielded 97% (29/30) sensitivity and 100% (28/28) specificity. We have developed a completely integrated, sensitive, specific, and 58-min prototype test, which can be used for routine surveillance of C. auris and might help prevent colonization and outbreaks in acute and chronic healthcare settings. IMPORTANCE: This study has the potential to offer a better solution to healthcare providers at hospitals and long-term care facilities in their ongoing efforts for effective and timely control of Candida auris infection and hence quicker response for any potential future outbreaks.

BackgroundHousehold contact investigations are effective for finding tuberculosis (TB) cases but are hindered by low referral uptake for clinic-based evaluation and testing. We assessed the acceptability and feasibility of in-home testing of household contacts (HHC) using the GeneXpert Edge platform.MethodsWe conducted a 2-arm, randomized study in Eastern Cape, South Africa. HHCs were verbally assessed using the World Health Organization-recommended 4-symptom screen. Households with ≥1 eligible symptomatic contact were randomized. Intervention households received in-home GeneXpert MTB/RIF molecular testing. GeneXpert-positive HHCs were referred for clinic-based treatment. Standard-of-care households were referred for clinic-based sputum collection and testing. We defined acceptability as agreeing to in-home testing and feasibility as generation of valid Xpert MTB/RIF results. The proportion and timeliness of test results received was compared between groups.ResultsEighty-four households were randomized (n = 42 per arm). Of 100 eligible HHCs identified, 98/100 (98%) provided consent. Of 51 HHCs allocated to the intervention arm, all accepted in-home testing; of those, 24/51 (47%) were sputum productive and 23/24 (96%) received their test results. Of 47 HCCs allocated to standard-of-care, 7 (15%) presented for clinic-based TB evaluation, 6/47 (13%) were tested, and 4/6 (67%) returned for their results. The median (interquartile range) number of days from screening to receiving test results was 0 (0) and 16.5 (11-15) in the intervention and standard-of-care arms, respectively.ConclusionsIn-home testing for TB was acceptable, feasible, and increased HHCs with a molecular test result. In-home testing mitigates a major limitation of household contact investigations (dependency on clinic-based referral), revealing new strategies for enhancing early case detection.

The GeneXpert HBV Viral Load test is a simplified tool to scale up screening and HBV monitoring in resource-limited settings, where HBV is endemic and where molecular techniques to quantify HBV DNA are expensive and scarce. However, the accuracy of field diagnostics compared to gold standard assays in HBV-endemic African countries has not been well understood. We aim to validate the diagnostic performance of the GeneXpert HBV Viral Load test in freshly collected and stored plasma and dried blood spot (DBS) samples to assess turn-around-time (TAT) for sample processing and treatment initiation, to map GeneXpert machines and to determine limitations to its use in The Gambia. Freshly collected paired plasma and DBS samples (n = 56) were analyzed by the GeneXpert test. Similarly, stored plasma and DBS samples (n = 306, n = 91) were analyzed using the GeneXpert HBV test, in-house qPCR and COBAS TaqMan Roche. The correlation between freshly collected plasma and DBS is r = 0.88 with a mean bias of −1.4. The GeneXpert HBV test had the highest quantifiable HBV DNA viremia of 81.4% (n = 249/306), and the lowest was detected by in-house qPCR at 37.9% (n = 116/306) for stored plasma samples. Bland–Altman plots show strong correlation between GeneXpert and COBAS TaqMan and between GeneXpert and in-house qPCR with a mean bias of +0.316 and −1.173 log10 IU/mL, respectively. However, paired stored plasma and DBS samples had a lower mean bias of 1.831 log10 IU/mL, which is almost significant (95% limits of agreement: 0.66–3.001). Patients (n = 3) were enrolled in the study within a TAT of 6 days. The GeneXpert HBV test displayed excellent diagnostic accuracy by detecting HBV viremia in less than 10 IU/mL. [ABSTRACT FROM AUTHOR]

Background and objective: Our objective was to assess whether GeneXpert BC can be used as a triage test to exclude urinary bladder cancer (UBC) for patients with macroscopic hematuria. Methods: We conducted a prospective study that include consecutive patients being evaluated for macroscopic hematuria between September 2020 and December 2022. Before cystoscopy, study participants provided a voided urine sample for GeneXpert BC analysis according to a case-control design with an emphasis on UBC detection. Descriptive statistics are reported for patient and tumor characteristics. To assess the diagnostic accuracy of the GeneXpert BC test, the sensitivity, specificity, and negative predictive value (NPV) were calculated, using the histopathologically proven UBC as the ground truth. Key findings and limitations: In total, 1505 subjects presenting with macroscopic hematuria were enrolled in the study. After randomization and exclusions, GeneXpert BC testing was carried out for 312 participants. Of these, 151 patients from the case arm had UBC, 122 patients from the control arm (random 10%) were negative for UBC, and 39 patients from the case arm did not have malignancy. Using a predefined linear discriminant analysis (LDA) threshold of ≥0.22, the test had sensitivity of 0.94 (95% confidence interval [CI] 0.90–0.97), specificity of 0.52 (95% CI 0.42–0.59), and NPV of 0.99 (95% CI 0.98–0.99). All false-negative tumors were of low grade (Ta grade 1–2). Cystoscopy and computed tomography urography could have been omitted in 44% of the patients with macroscopic hematuria. At a secondary LDA threshold of ≥0.45, the test had sensitivity of 0.79 (95% CI 0.73–0.86), specificity of 0.83 (95% CI 0.76–0.89), and NPV of 0.97 (95% CI 0.96–0.98). Conclusions and clinical implications: GeneXpert BC is a reliable triage test for deciding on whether further investigations are necessary in patients with macroscopic hematuria. Patient summary: We assessed a test called GeneXpert BC for the detection of bladder cancer in patients with blood in their urine. GeneXpert BC performed well in ruling out bladder cancer for patients who did not have cancer according to further tests. Use of GeneXpert BC could help in avoiding scans and invasive tests for patients with a negative result.

Objective: To identify the clinical, laboratory, and radiological markers that could predict a positive GeneXpert result in patients suspected of tuberculous meningitis. Methods: In this prospective, observational study, patients with tuberculous meningitis were systematically evaluated. Various clinical, laboratory [including cerebrospinal fluid (CSF) microscopy, culture, and GeneXpert], and neuroimaging factors were examined. All participants were administered anti-tuberculous treatment and corticosteroids. A six-month follow-up was done to evaluate the outcome. Results: Of the 116 patients studied, 54 (46.6%) tested positive for GeneXpert, while 62 (53.4%) were negative. Third cranial nerve involvement (OR 3.71, 95% CI 1.052-13.09, P=0.04) and the presence of basal exudates on neuroimaging (OR 5.22, 95% CI 2.03-13.42, P=0.001) emerged as independent predictive factors for a positive GeneXpert result. A positive CSF GeneXpert result (P=0.002) and drug resistance (P=0.004) were significantly linked to adverse outcomes. Additionally, a high score on the Medical Research Council stage III (OR 5.64, 95% CI 1.18-26.87, P=0.03) and elevated CSF cell counts (OR 1.002, 95% CI 1.00-1.001, P=0.03) were identified as independent predictors of poor prognosis. Conclusions: Third cranial nerve involvement and the presence of basal exudates were significant indicators of a positive GeneXpert result. MRC stage III disability and elevated CSF cell counts predicted poor outcomes.

Abstract Background Tuberculous meningitis (TBM) is a severe central nervous system (CNS) infection with a challenging diagnosis due to inadequate detection methods. This study evaluated current clinical detection methods and their applicability. Methods A cohort of 514 CNS infection patients from 2018 to 2020 was studied. Data on general demographics, Cerebrospinal Fluid (CSF) analysis, epidemiology, and clinical outcomes were collected. TBM patients were identified, and the sensitivities of mmetagenomic next-generation sequencing (NGS), GeneXpert, and microbial culture were compared. Kappa statistic assessed the consistency between methods. Results Among the patients involved, TBM (29%) and neurosyphilis (25%) were the two most prevalent CNS infections. CSF analysis indicated that 76% of patients had leukocytosis, suggesting a potential CNS inflammation. In TBM cases, 92.5% had elevated CSF protein and leukocyte counts. Moreover, the percentage of positive mNGS results was 55.6%. GeneXpert and MTB cultures alone had lower sensitivity, but combined use resulted in a 53.4% positive rate. Conclusions This study highlights the high sensitivity of mNGS, comparable to GeneXpert and MTB culture. The combined methods are cost-effective and straightforward, and can partially substitute for mNGS, offering valuable alternatives for TBM diagnosis and providing insights into multiple diagnostic strategies in clinical practice.

Abstract Background In 2022, fewer than half of persons with tuberculosis (TB) had access to molecular diagnostic tests for TB due to their high costs. Studies have found that the use of artificial intelligence (AI) software for chest X-ray (CXR) interpretation and sputum specimen pooling can each reduce the cost of testing. We modeled the combination of both strategies to estimate potential savings in consumables that could be used to expand access to molecular diagnostics. Methods We obtained Xpert testing and positivity data segmented into deciles by AI probability scores for TB from the community- and healthcare facility-based active case finding conducted in Bangladesh, Nigeria, Viet Nam, and Zambia. AI scores in the model were based on CAD4TB version 7 (Zambia) and qXR (all other countries). We modeled four ordinal screening and testing approaches involving AI-aided CXR interpretation to indicate individual and pooled testing. Setting a false negative rate of 5%, for each approach we calculated additional and cumulative savings over the baseline of universal Xpert testing, as well as the theoretical expansion in diagnostic coverage. Results In each country, the optimal screening and testing approach was to use AI to rule out testing in deciles with low AI scores and to guide pooled vs individual testing in persons with moderate and high AI scores, respectively. This approach yielded cumulative savings in Xpert tests over baseline ranging from 50.8% in Zambia to 57.5% in Nigeria and 61.5% in Bangladesh and Viet Nam. Using these savings, diagnostic coverage theoretically could be expanded by 34% to 160% across the different approaches and countries. Conclusions Using AI software data generated during CXR interpretation to inform a differentiated pooled testing strategy may optimize TB diagnostic test use, and could extend molecular tests to more people who need them. The optimal AI thresholds and pooled testing strategy varied across countries, which suggests that bespoke screening and testing approaches may be needed for differing populations and settings.

Background: Tuberculosis (TB) remains a significant public health challenge in developing countries, including India, where children under 15 years account for 12% of all TB cases. The National Tuberculosis Elimination Programme (NTEP) recommends the use of GeneXpert/Cartridge-Based Nucleic Acid Amplification Test (CBNAAT) for TB diagnosis, followed by Line Probe Assay (LPA) for detecting drug resistance. This study aimed to determine the prevalence of TB and rifampicin resistance in pediatric patients and to evaluate the utility of CBNAAT in comparison with LPA and Ziehl-Neelsen staining. Methods: This retrospective study was conducted over one year, from 1st January 2022 to 31st December 2022, at a tertiary care hospital in western Maharashtra. A total of 528 samples from pediatric patients (aged

Background: Tuberculous meningitis (TBM) is a severe central nervous system (CNS) infection with a challenging diagnosis due to inadequate detection methods. This study evaluated current clinical detection methods and their applicability. Methods: A cohort of 514 CNS infection patients from 2018 to 2020 was studied. Data on general demographics, Cerebrospinal Fluid (CSF) analysis, epidemiology, and clinical outcomes were collected. TBM patients were identified, and the sensitivities of mmetagenomic next-generation sequencing (NGS), GeneXpert, and microbial culture were compared. Kappa statistic assessed the consistency between methods. Results: Among the patients involved, TBM (29%) and neurosyphilis (25%) were the two most prevalent CNS infections. CSF analysis indicated that 76% of patients had leukocytosis, suggesting a potential CNS inflammation. In TBM cases, 92.5% had elevated CSF protein and leukocyte counts. Moreover, the percentage of positive mNGS results was 55.6%. GeneXpert and MTB cultures alone had lower sensitivity, but combined use resulted in a 53.4% positive rate. Conclusions: This study highlights the high sensitivity of mNGS, comparable to GeneXpert and MTB culture. The combined methods are cost-effective and straightforward, and can partially substitute for mNGS, offering valuable alternatives for TBM diagnosis and providing insights into multiple diagnostic strategies in clinical practice. [ABSTRACT FROM AUTHOR]

Objective: To identify the clinical, laboratory, and radiological markers that could predict a positive GeneXpert result in patients suspected of tuberculous meningitis. Methods: In this prospective, observational study, patients with tuberculous meningitis were systematically evaluated. Various clinical, laboratory [including cerebrospinal fluid (CSF) microscopy, culture, and GeneXpert], and neuroimaging factors were examined. All participants were administered anti-tuberculous treatment and corticosteroids. A six-month follow-up was done to evaluate the outcome. Results: Of the 116 patients studied, 54 (46.6%) tested positive for GeneXpert, while 62 (53.4%) were negative. Third cranial nerve involvement (OR 3.71, 95% CI 1.052-13.09, P =0.04) and the presence of basal exudates on neuroimaging (OR 5.22, 95% CI 2.03-13.42, P =0.001) emerged as independent predictive factors for a positive GeneXpert result. A positive CSF GeneXpert result (P =0.002) and drug resistance (P =0.004) were significantly linked to adverse outcomes. Additionally, a high score on the Medical Research Council stage III (OR 5.64, 95% CI 1.18-26.87, P =0.03) and elevated CSF cell counts (OR 1.002, 95% CI 1.00-1.001, P =0.03) were identified as independent predictors of poor prognosis. Conclusions: Third cranial nerve involvement and the presence of basal exudates were significant indicators of a positive GeneXpert result. MRC stage III disability and elevated CSF cell counts predicted poor outcomes. [ABSTRACT FROM AUTHOR]

Background Tuberculosis (TB) remains a significant global health challenge, particularly with the rise of drug-resistant strains. Heteroresistance, where subpopulations of bacteria show varying levels of resistance within the same patient, complicates diagnosis and treatment. This study aims to assess the prevalence of heteroresistance to rifampicin and isoniazid in clinical samples from patients with presumptive drug-resistant tuberculosis. Materials and Methods A cross-sectional study was conducted from January to June 2024 at a tertiary care hospital. Clinical samples, including sputum and bronchial lavage, were collected from 200 patients suspected of having drug-resistant TB. Samples were processed using the GeneXpert MTB/RIF assay and Löwenstein-Jensen culture for drug susceptibility testing. Isolates were tested for heteroresistance to rifampicin and isoniazid using the BACTEC MGIT 960 system and molecular techniques like whole-genome sequencing. Results Out of 200 samples, 150 (75%) were confirmed to have Mycobacterium tuberculosis complex. Among these, 60 samples (40%) exhibited heteroresistance to rifampicin, while 45 samples (30%) showed heteroresistance to isoniazid. Dual heteroresistance to both drugs was observed in 20 samples (13.3%). Whole-genome sequencing revealed mutations in the rpoB and katG genes associated with resistance. The presence of heteroresistant populations was associated with prior TB treatment history and poor treatment outcomes. Conclusion The study highlights a substantial prevalence of heteroresistance to rifampicin and isoniazid in patients with presumptive drug-resistant TB. This underscores the need for advanced diagnostic techniques to detect heteroresistant strains and guide effective treatment regimens. Tailored therapeutic strategies are crucial to managing and controlling the spread of drugresistant TB. [ABSTRACT FROM AUTHOR]

Objectives: Fiji could be the first country to eliminate tuberculosis. To inform this strategy, we aimed to identify how many GeneXpert® machines are required to enable over 90% of Fijians to be within one‐hour easy access. Methods: We used Geographic Information System (Quantum GIS; QGIS), OpenStreetMap and population data (Kontur) to map possible facilities in relation to QGIS generated 60‐min drive‐time isochrones, with correction for missing road data. For outer islands, we calculated a distance to nearest hub operation. Results: The solution comprised 24 GeneXpert® machines, allocating 7 GeneXpert® to Viti Levu, 6 GeneXpert® to Vanua Levu and 11 to other islands. This resulted in 827,810 people, 93.6% of Fiji's population, being within 1 h of a machine. Twenty‐one thousand four hundred seventy‐nine people on outer islands were an average of 43 km by water from the nearest facility. Conclusions: We conclude that over 90% of Fijians could be within an hour of a GeneXpert® machine with placement of 24 machines. [ABSTRACT FROM AUTHOR]

Background: In 2022, fewer than half of persons with tuberculosis (TB) had access to molecular diagnostic tests for TB due to their high costs. Studies have found that the use of artificial intelligence (AI) software for chest X-ray (CXR) interpretation and sputum specimen pooling can each reduce the cost of testing. We modeled the combination of both strategies to estimate potential savings in consumables that could be used to expand access to molecular diagnostics. Methods: We obtained Xpert testing and positivity data segmented into deciles by AI probability scores for TB from the community- and healthcare facility-based active case finding conducted in Bangladesh, Nigeria, Viet Nam, and Zambia. AI scores in the model were based on CAD4TB version 7 (Zambia) and qXR (all other countries). We modeled four ordinal screening and testing approaches involving AI-aided CXR interpretation to indicate individual and pooled testing. Setting a false negative rate of 5%, for each approach we calculated additional and cumulative savings over the baseline of universal Xpert testing, as well as the theoretical expansion in diagnostic coverage. Results: In each country, the optimal screening and testing approach was to use AI to rule out testing in deciles with low AI scores and to guide pooled vs individual testing in persons with moderate and high AI scores, respectively. This approach yielded cumulative savings in Xpert tests over baseline ranging from 50.8% in Zambia to 57.5% in Nigeria and 61.5% in Bangladesh and Viet Nam. Using these savings, diagnostic coverage theoretically could be expanded by 34% to 160% across the different approaches and countries. Conclusions: Using AI software data generated during CXR interpretation to inform a differentiated pooled testing strategy may optimize TB diagnostic test use, and could extend molecular tests to more people who need them. The optimal AI thresholds and pooled testing strategy varied across countries, which suggests that bespoke screening and testing approaches may be needed for differing populations and settings. [ABSTRACT FROM AUTHOR]

Background Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), primarily affecting lung tissue but also capable of infecting pleura, lymph nodes, bones, and other extrapulmonary sites. Lipoarabinomannan (LAM) is a critical lipopolysaccharide in the outer wall of mycobacterial cells and can be detected in the urine of TB patients as an antigen. Objective This study aimed to assess the sensitivity and specificity of the LAM test compared to GeneXpert in urine samples from suspected TB patients. Methods A quasi-experimental design was employed, where urine samples were collected from patients diagnosed with TB at Sidawangi Lung Hospital, West Java Province. The LAM test was performed on 40 samples by applying 60 µL of urine onto LAM test strips, while MTB presence in urine was examined using GeneXpert. Results LAM test results showed 32.5% positivity, while 67.5% were negative. GeneXpert results indicated 20% positivity and 80% negativity. The LAM test demonstrated a sensitivity of 100% and specificity of 79.4% compared to GeneXpert, with an area under the curve (AUC) value of 0.897. Conclusion The LAM test showed high sensitivity and moderate specificity compared to GeneXpert in urine samples of suspected TB patients.

Aspergilloma is often misdiagnosed as tuberculosis (TB) in developing countries where the prevalence of TB is high, hemoptysis is often equated with TB, and most patients are diagnosed clinically. This study aims to determine the Occurrence and Distribution of Aspergillus species among presumptive tuberculosis patients in Otukpo Local Government Area of Benue State, Nigeria. A total of 461 clients gave their consent and were involved in this research work from four (4) different healthcare facilities in the Otukpo Local government area. The samples were packaged in triple nylon, stored in a cold chain box, and were taken to the general hospital Otukpo laboratory and/or St Charles Hospital Adoka laboratory for analysis. Each Sputum sample was divided into two parts. One part was analyzed for Tuberculosis using PCR (GeneXpert Machine) and the second part was inoculated on Sabouraud Dextrose Agar Medium for identification of Aspergillus species. The Aspergillus species isolated were identified using cultural and comparative pictorial characteristics. Exactly 216 patients had an Aspergillus species prevalence rate of 46.9 %, and 245 patients with 53.1% showed no growths of fungal. The males had a prevalence rate of 113(44.8 %), with the highest rate of 27(10.7 %) in the age group 31 – 40, and females had a prevalence rate of 103(49.3 %), with the highest rate of 18(8.6 %) in the age groups 21 – 30 and 31 – 40 with a significant p-value of 0.015. Co-infections of Aspergillus species/tuberculosis in relation to age range distribution and gender had a total prevalence of 22(4.77 %). The males had a co-infection prevalence rate of 14(3.03%) compared to the females having a co-infection prevalence rate of (1.74%). The age range of 31- 40 had the highest co-infection prevalence rate, followed by the age range of 41-50. There is a significant co-infection of Aspergillus/tuberculosis with a p-value of 0.007. Four species of Aspergillus were identified; Aspergillus niger (38 %) ranked highest, followed by Aspergillus fumigatus (25 %), Aspergillus flavus (24 %), Aspergillus oryzae (6 %), and other fungi isolated were 7%. This research shows a significant positive result of patients with aspergillosis, which is a significant co-morbidity in pulmonary tuberculosis patients in Otukpo Local Government Area of Benue State; this could be misdiagnosed as relapse or treatment failures in the absence of reliable diagnostic and clinical management. The progress of the disease and prolonged treatment with antibiotics or immunosuppressive agents make TB patients susceptible to fungal infection. Patients with persistent clinical symptoms despite TB treatment should be subjected to fungal investigations before re-treatment. Aspergillosis is also one of the nosocomial infections, so patients and healthcare givers should be encouraged to always go for routine fungal infection investigation if few of the symptoms are experienced.

BackgroundClinically diagnosed pulmonary tuberculosis (TB) (CDPTB) patients account for a huge proportion of TB. However, little is known about the genetic diversity and drug resistance profile of Mycobacterium tuberculosis Complex (MTBC) strains in this group of patients.MethodUnmatched case–control study was conducted among 313 PTB patients to compare the genetic diversity of MTBC and their drug resistance profiles among CDPTB (n = 173) and bacteriologically confirmed pulmonary TB (BCPTB) (n = 140) patients. Lowenstein-Jensen (LJ) culture, geneXpert and acid fast staining were performed on sputum specimen collected from both CDPTB and BCPTB patients. Spoligotyping, whole genome sequencing (WGS) and phenotypic drug resistance testing (DST) were done for a subset of LJ grown MTBC isolates. Data was analyzed by STATA version 17 software and a p-value 0.05). A single lineage 3 strain resistant to all the primary anti-TB drugs was detected in one CDPTB by both DST methods.ConclusionThe observed differences in the genotypes of MTBC isolates between CDPTB and BCPTB patients may be attributed to challenges in the identification of CDPTB that requires further investigation on sequenced genome of the MTBC strains for better understanding and recommendation based on the current finding. There was also primary drug resistant TB among culture positive CDPTB patients which would be otherwise missed by current national protocols.

Abstract Introduction Tuberculous lymphadenitis (TBLN) is an infection of the lymph node caused by Mycobacterium tuberculosis. Histological diagnoses of presumptive patients are often accompanied by cytomorphological features. However, the sensitivities of these features are often precluded by the variable degrees of narrative similarities compared to other diagnostic modalities. Objective The aim of this study was to investigate and compare the cytomorphological and clinical features of presumptive TBLN patients with bacteriological detection methods. Methods A similar cohort of TBLN patients from our previous study who were enrolled prospectively from the ALERT Specialized Hospital, Addis Ababa, Ethiopia, was considered for this analysis. SPSS version 26 was used for data analysis. Descriptive analysis was conducted to characterize the study population using the independent variable and presented with frequency tables. The chi-square test was used to measure the association. A P-value of

Richard Kasadha,1,2 Raymond Atwine,3 Kennedy Kassaza,4 Saphurah Nabaasa,1 Lawrence Amadile,1 Lauben Tibenderana,1 Lydia Jolly Ninsiima,1 Hassan Wasswa,1 Fridah Gakii Mwangi,1 Frank Ssedyabane1 1Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda; 2UPDF Military Health Services, Ministry of Defence and Veteran Affairs, Bombo, Uganda; 3Department of Pathology, Mbarara University of Science and Technology, Mbarara, Uganda; 4Genomics and Translational Laboratory, Department of Microbiology, Mbarara University of Science and Technology, Mbarara, UgandaCorrespondence: Richard Kasadha, Email kasadhar3@gmail.comPurpose: Formalin-fixed tissue biopsies submitted to the Histopathology Laboratory were explored for possible use in the GeneXpert MTB/Rifampicin assay for EPTB diagnosis, therefore this study aimed to determine the diagnostic utility of the GeneXpert MTB/RIF assay in EPTB detection in formalin-fixed paraffin-embedded tissue biopsies using Ziehl-Neelsen (ZN) and Haematoxylin and Eosin (H&E) staining as a composite reference standard.Methods: A total of 89 selected archived formalin-fixed paraffin-embedded tissues with histological features of tuberculosis were included in the study. ZN and H&E staining were performed as a composite reference standard, followed by GeneXpert MTB/RIF assay as diagnostic test. Data were analysed using STATA software version 17.0.Results: Of the 89 specimens enrolled, 55% were male. The Lymph node was the commonest site (64%). 15/89 (16.9%) cases were positive for ZN, 45/89 (50.6%) were positive for H&E and 27/89 (30.3%) were positive for GeneXpert. The overall sensitivity and specificity of GeneXpert were 48.94% (95% CI: 38.55%– 59.32%) and 90.48% (95% CI: 84.38%– 96.57%), respectively, in lymph node tissues, were 52.94% (95% CI: 39.98%– 65.90%) and 82.61% (95% CI: 72.77%– 92.45%), respectively, and in Non-Lymph node tissues, were 38.46% (95% CI: 21.61%– 55.32%) and 100% (95% CI: 100%– 100%), respectively.Conclusion: The GeneXpert MTB/RIF assay is a potential tool for diagnosing EPTB in FFPE tissues and may be used in the development of an algorithm in the histopathology laboratory.Keywords: sensitivity, specificity, genexpert, ZN, H&E, EPTB

Beatrice Mahler,1– 3 Dragoș Băiceanu,3,4 Alexandru Stoichiță,1– 3 Dragoș Dendrino,3 Mihaela Mihai,3,5 Gina Ciolan,2 Elmira Ibraim,3,4 Ioana Munteanu,2,3,6 Cristina Popa,2,3 Mădălina Burecu,2,3 Paula Rusu,3 Andreea Cioacată,2 Ioana Mădălina Moșteanu,2,7 Antonela Dragomir1– 3 1Pneumology II Department, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania; 2Pneumology Clinic, “Marius Nasta” Institute of Pneumology, Bucharest, Romania; 3Tuberculosis Screening Program, “Marius Nasta” Institute of Pneumology, Bucharest, Romania; 4Research Department, “Marius Nasta” Institute of Pneumology, Bucharest, Romania; 5Faculty of Economic Cybernetics, Statistics and Informatics, The Bucharest University of Economic Studies, Bucharest, Romania; 6Faculty of Medicine, “Titu Maiorescu” University, Bucharest, Romania; 7Faculty of Medicine, University of Medicine and Pharmacy Craiova, Craiova, RomaniaCorrespondence: Dragoș Băiceanu; Alexandru Stoichiță, “Marius Nasta” Institute of Pneumology, 90 Viilor Street, Bucharest, 050159, Romania, Tel +4 0749 574 412, Email dragos.baiceanu@marius-nasta.ro; alexandru.stoichita@drd.umfcd.roIntroduction: Tuberculosis (TB) remains a global health challenge, requiring enhanced active case finding (ACF) through screening strategies. This study assesses the effectiveness of such an approach in locating TB cases among vulnerable groups, such as homeless persons, injecting drug users, those detained in prison, and people living in rural areas.Methods: The study focuses on socio-economic characteristics and TB detection rates across Romanian counties using modern techniques including computer-aided detection of lesions on chest X-ray and GeneXpert tests.Results: The results highlight the disproportionate burden of TB in vulnerable groups, by revealing significant differences in TB detection rates between regions. Notably, the TB detection rates among these vulnerable groups (250.85 per 100,000 population) are five times higher than the national incidence rate (46.1).Discussion: These findings underscore the imperative integration of ACF into National TB Program to provide customized and efficient solutions for diverse vulnerable groups, thereby informing crucial public health initiatives and interventions.Keywords: active screening, vulnerable populations, socio-demographic analysis, GeneXpert, intervention health strategies, tuberculosis

Introduction: Tuberculous lymphadenitis (TBLN) is an infection of the lymph node caused by Mycobacterium tuberculosis. Histological diagnoses of presumptive patients are often accompanied by cytomorphological features. However, the sensitivities of these features are often precluded by the variable degrees of narrative similarities compared to other diagnostic modalities. Objective: The aim of this study was to investigate and compare the cytomorphological and clinical features of presumptive TBLN patients with bacteriological detection methods. Methods: A similar cohort of TBLN patients from our previous study who were enrolled prospectively from the ALERT Specialized Hospital, Addis Ababa, Ethiopia, was considered for this analysis. SPSS version 26 was used for data analysis. Descriptive analysis was conducted to characterize the study population using the independent variable and presented with frequency tables. The chi-square test was used to measure the association. A P-value of < 0.05 was considered statistically significant. Results: Using FNAC, 60/126 (47.6%) of the participants were reported to have features consistent with TB. Of the total FNAC-positive cases, many (30/60 and 27/60) showed pattern B (caseous necrosis only) and pattern C (epithelioid granuloma with caseous necrosis), respectively. Strong concordance was observed in Pattern A (abundant caseous necrosis with few epithelioid macrophages) followed by patterns B and C with GeneXpert and MGIT culture (P value < 0.001). Night sweats and alcohol intake were shown to correlate with positive cases as reported by FNAC (P value = 0.008 respectively), GeneXpert (P value = 0.02 & 0.001), and culture methods (P-value = < 0.001 & 0.002). Conclusion: Cytomorphological features, particularly patterns A, B, and C, could be considered in the diagnosis of TBLN given their comparable outcomes with bacteriological detection methods. On another note, we recommend that due care and attention be given when treating TBLN patients based solely on clinical presentation, as these diagnostics may be prone to false results, leading to inappropriate administration of anti-TB drugs and other consequences. [ABSTRACT FROM AUTHOR]

BackgroundNewer molecular testing platforms are now available for deployment at lower-level community health centers. There are limited data on facility- and health worker-level factors that would promote successful adoption of such platforms for rapid tuberculosis (TB) testing and treatment initiation. Our study aimed to assess readiness to implement onsite molecular testing at community health centers in Uganda, a high TB burden country in sub-Saharan Africa.MethodsTo understand implementation readiness, we conducted a qualitative assessment guided by the Consolidated Framework for Implementation Research (CFIR) at 6 community health centers in central and eastern Uganda between February and April 2018. We conducted 23 in-depth, semi-structured interviews with health workers involved in TB care at each health center to assess TB-related work practices and readiness to adopt onsite molecular testing using the GeneXpert Edge platform. Interviews were transcribed verbatim and coded for thematic analysis.ResultsParticipants (N=23) included 6 nurses/nursing assistants, 6 clinicians, 6 laboratory directors/technicians, 1 medical officer, 2 health center directors, and 2 other health workers involved in TB care. Health workers described general enthusiasm that on-site molecular testing could lead to greater efficiencies in TB diagnosis and treatment, including faster turn- around time for TB test results, lack of need for trained laboratory technicians to interpret results, and reduced need to transport sputum specimens to higher level facilities. However, health workers also expressed concerns about implementation feasibility. These included uncertainty about TB infection risk, safety risks from disposal of hazardous waste, a lack of local capacity to provide timely troubleshooting and maintenance services, and concerns about the security of GeneXpert devices and accessories. Health workers also expressed the need for backup batteries to support testing or charging when wall power is unstable.ConclusionOur study generated a nuanced understanding of modifiable contextual barriers and led to direct revisions of implementation strategies for onsite molecular testing. The findings highlight that novel diagnostics should be implemented along with health system co-interventions that address contextual barriers to their effective uptake. Pre-implementation assessment of stakeholder perspectives, collaborative work processes, and institutional contexts is essential when introducing innovative technology in complex health care settings.

Objective: To evaluate the performance of Xpert Mycobacterium Tuberculosis/rifampicin (MTB/RIF) Ultra (Ultra) for diagnosis of childhood tuberculosis (TB) within public health systems. Methods: In this cross-sectional study, children aged

Abstract Background In 2018, the World Health Organization commenced a multi-country validation study of the Cepheid GeneXpert for a range of molecular-based point-of-care (POC) tests in primary care settings. One study arm focused on the evaluation of POC tests for screening ‘women at risk’ for chlamydia (CT), gonorrhoea (NG) and trichomonas (TV) in four countries – Australia, Guatemala, Morocco and South Africa. Methods Study participants completed a pre-test questionnaire which included demographics, clinical information and general questions on POC testing (POCT). Two vaginal swab samples (either self-collected or clinician collected) from each patient were tested on the GeneXpert at the POC and at a reference laboratory using quality-assured nucleic acid amplification tests (NAATs). Results One thousand three hundred and eighty-three women were enrolled: 58.6% from South Africa, 29.2% from Morocco, 6.2% from Guatemala, and 6.0% from Australia. 1296 samples for CT/NG and 1380 samples for TV were tested by the GeneXpert and the reference NAAT. The rate of unsuccessful tests on the GeneXpert was 1.9% for CT, 1.5% for NG and 0.96% for TV. The prevalence of CT, NG and TV was 31%, 13% and 23%, respectively. 1.5% of samples were positive for all three infections; 7.8% were positive for CT and NG; 2.4% were positive for NG and TV; and 7.3% were positive for CT and TV. Compared to reference NAATs, pooled estimates of sensitivity for the GeneXpert tests were 83.7% (95% confidence intervals 69.2-92.1) for CT, 90.5% (85.1-94.1) for NG and 64.7% (58.1-70.7) for TV (although estimates varied considerably between countries). Estimates for specificity were ≥96% for all three tests both within- and between-countries. Pooled positive and negative likelihood ratios were: 32.7 ([CI] 21.2-50.5) and 0.17 (0.08-0.33) for CT; 95.3 (36.9-245.7) and 0.10 (0.06-0.15) for NG; and 56.5 (31.6-101.1) and 0.35 (0.27-0.47) for TV. Conclusion This multi-country evaluation is the first of its kind world-wide. Positive likelihood ratios, as well as specificity estimates, indicate the GeneXpert POC test results for CT, NG and TV were clinically acceptable for ruling in the presence of disease. However, negative likelihood ratios and variable sensitivity estimates from this study were poorer than expected for ruling out these infections, particularly for TV. Trial registration Ethics approval to conduct the ProSPeRo study was granted by the WHO Ethics Review Committee, as well as local ethics committees from all participating countries.

Abstract Introduction Cervical cancer is a major public health issue in Uganda, with high incidence due to limited screening especially in rural areas. In 2019, HPV DNA testing using GeneXpert was rolled out to improve screening access. Assessing progress and challenges since its introduction is important. Aim To determine genotype distribution and explore health worker experiences with HPV screening using GeneXpert in Uganda. Methods We conducted a retrospective cohort study where HPV screening data from 66 GeneXpert labs from March 2021-May 2023 country wide was analyzed. We used descriptive statistics to provide percentages and proportions from the data. Seven focus group discussions and five interviews were done with health workers to understand experiences. Results We extracted 24,497 HPV tests that were done, and 39.1% were HPV positive. Other high-risk HPV genotypes were the most common at 65%, followed by HPV 16 (17%) and HPV 18/45 (18%). 15% of the HPV positive cases had more than one genotype. Qualitative findings showed inconsistent health worker knowledge, high workload, and complex care seeking behaviors as main challenges. It also revealed low community awareness, care seeking from traditional healers, Conclusion HPV DNA testing has been expanding since its rollout, but the yield of HPV cases is lower than expected, signaling need to address supply-side challenges. Limited information on HPV among health workers especially community health workers, demand-side barriers like myths, medical pluralism and social norms must also be tackled through trainings of health workers and awareness campaigns engaging communities. Although access to GeneXpert services has increased, health system weaknesses pose bottlenecks to screening HPV. Targeted interventions are required to strengthen HPV diagnosis, prevent cervical cancer and save lives.

Abstract Background Sexually transmitted infections caused by Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV) remain significant global health problems. The World Health Organization (WHO) has recently conducted a multi-faceted, multi-country validation study (ProSPeRo), which included an evaluation of the Xpert CT/NG and Xpert TV assays on the GeneXpert system (Cepheid, Sunnyvale, Ca., USA) in clinic-based settings across eight countries. To support the study, a training and quality management system was implemented and evaluated. Methods A comprehensive training program for the study was developed. Quality control (QC) and external quality assessment (EQA) samples were provided by an accredited quality assurance provider. QC testing was conducted at 14 point-of-care testing (POCT) clinics, while EQA samples were tested by the POCT sites and a reference laboratory supporting each clinic. Results For QC testing, concordance with the expected results for CT and NG was > 99% and rates of unsuccessful tests were 94%) for all analytes, but this cohort (which used GeneXpert systems) exhibited a high rate of unsuccessful TV tests. All but one of these unsuccessful tests was subcategorised as ‘invalid’. Conclusions The high level of concordance for QC and EQA testing confirm that the trained operators at the POC clinical sites were competent to conduct POC testing and that the training and quality systems implemented for the ProSPeRo study were effective. The quality materials used were satisfactory for CT and NG but exhibited poor performance for TV testing on the GeneXpert system. The WHO should continue to work with industry and EQA providers to provide improved materials that are reliable, stable and cost effective for quality management, as it seeks to rollout molecular-based STI POCT in non-laboratory-based settings. Trial registration Ethics approval to conduct the ProSPeRo study was granted by the WHO Ethics Review Committee.

The GeneXpert HBV Viral Load test is a simplified tool to scale up screening and HBV monitoring in resource-limited settings, where HBV is endemic and where molecular techniques to quantify HBV DNA are expensive and scarce. However, the accuracy of field diagnostics compared to gold standard assays in HBV-endemic African countries has not been well understood. We aim to validate the diagnostic performance of the GeneXpert HBV Viral Load test in freshly collected and stored plasma and dried blood spot (DBS) samples to assess turn-around-time (TAT) for sample processing and treatment initiation, to map GeneXpert machines and to determine limitations to its use in The Gambia. Freshly collected paired plasma and DBS samples (n = 56) were analyzed by the GeneXpert test. Similarly, stored plasma and DBS samples (n = 306, n = 91) were analyzed using the GeneXpert HBV test, in-house qPCR and COBAS TaqMan Roche. The correlation between freshly collected plasma and DBS is r = 0.88 with a mean bias of −1.4. The GeneXpert HBV test had the highest quantifiable HBV DNA viremia of 81.4% (n = 249/306), and the lowest was detected by in-house qPCR at 37.9% (n = 116/306) for stored plasma samples. Bland–Altman plots show strong correlation between GeneXpert and COBAS TaqMan and between GeneXpert and in-house qPCR with a mean bias of +0.316 and −1.173 log10 IU/mL, respectively. However, paired stored plasma and DBS samples had a lower mean bias of 1.831 log10 IU/mL, which is almost significant (95% limits of agreement: 0.66–3.001). Patients (n = 3) were enrolled in the study within a TAT of 6 days. The GeneXpert HBV test displayed excellent diagnostic accuracy by detecting HBV viremia in less than 10 IU/mL.

Objective The study aimed to compare the diagnostic efficacy of QuantiFERON-TB Gold （QFT-TB） detection of specific cellular immune IGRAs in tuberculosis diagnostic laboratory for pulmonary tuberculosis, extrapulmonary tuberculosis and special population samples in vitro, which may provide evidence for clinical diagnosis and treatment. Methods A total of 546 patients with tuberculosis （AFB + 146 cases, AFB-247 cases）, 117 patients with molecular biology positive tuberculosis（ Xpert 69 cases, TB-DNA 48 cases） and 36 patients with histopathological positive were collected from January to July 2023. There were 72 cases of extrapulmonary tuberculosis, 276 cases of pleural effusion and 25 cases of ascites. QFT-TB method was used for detection, chi-square test was applied for comparison between groups, and the methodological evaluation of positive rate and coincidence rate were all compared. Results The positive rates of QFT-TB in pulmonary tuberculosis, extrapulmonary tuberculosis and close contacts were 83.69 %, 69.44 %, and 32.41 %, respectively. The coincidence rates of QFT-TB in AFB +, GeneXpert, TB-DNA and pathological confirmed tuberculosis patients were 91.09%, 88.40%, 81.25%, and 72.22%, respectively. The positive rate of pleural effusion in patients with tuberculous pleurisy was 60.50 %, and the uncertainty rate was 29.71%. The positive rate of ascites was 44.00 % and the uncertainty was 36.00%. Conclusion QFT-TB test has good value in the auxiliary diagnosis of pulmonary tuberculosis, and has certain reference significance for the diagnosis of extrapulmonary tuberculosis based on the detection of pleural fluids and ascites. [ABSTRACT FROM AUTHOR]

Tuberculosis (TB) is one of the major global public health concerns particularly affecting population of lowincome countries. Early detection of disease coupled with other parameters help in treatment and reducing disease transmission. The current study was conducted to assess the sensitivity and specificity of the GeneXpert MTB/RIF (Cepheid Sunnyvale, CA, United States) in comparison to conventional techniques used for the diagnosis of TB. Our study is one of the first ones from Pakistan investigating and assessing the performance of GeneXpert. We recruited eight hundred clinically TB suspects initially and included seven hundred and sixteen clinically TB suspects in the final analysis. The results of GeneXpert were compared with Mycobacteria Growth Indicator Tube (MGIT) and Ziehl-Neelsen (ZN) staining. In comparison to MGIT and ZN staining the sensitivity of GeneXpert with 95 % confidence interval (CI) was (99.7 %, CI 0.98-0.99) and (95.1 %, CI 0.92-0.97) respectively. The positive and negative predictive values with 95 % CI were (97.1 %, CI 0.94-0.98) and (99.7 %, CI 0.98-0.99) when results of GeneXpert were compare with MGIT results. The results of this study confirm the performance of GeneXpert. With high sensitivity and rapid detection, GeneXpert is ready to be considered as preferred diagnostic tool for TB. [ABSTRACT FROM AUTHOR]

Introduction: Cervical cancer is a major public health issue in Uganda, with high incidence due to limited screening especially in rural areas. In 2019, HPV DNA testing using GeneXpert was rolled out to improve screening access. Assessing progress and challenges since its introduction is important. Aim: To determine genotype distribution and explore health worker experiences with HPV screening using GeneXpert in Uganda. Methods: We conducted a retrospective cohort study where HPV screening data from 66 GeneXpert labs from March 2021-May 2023 country wide was analyzed. We used descriptive statistics to provide percentages and proportions from the data. Seven focus group discussions and five interviews were done with health workers to understand experiences. Results: We extracted 24,497 HPV tests that were done, and 39.1% were HPV positive. Other high-risk HPV genotypes were the most common at 65%, followed by HPV 16 (17%) and HPV 18/45 (18%). 15% of the HPV positive cases had more than one genotype. Qualitative findings showed inconsistent health worker knowledge, high workload, and complex care seeking behaviors as main challenges. It also revealed low community awareness, care seeking from traditional healers, Conclusion: HPV DNA testing has been expanding since its rollout, but the yield of HPV cases is lower than expected, signaling need to address supply-side challenges. Limited information on HPV among health workers especially community health workers, demand-side barriers like myths, medical pluralism and social norms must also be tackled through trainings of health workers and awareness campaigns engaging communities. Although access to GeneXpert services has increased, health system weaknesses pose bottlenecks to screening HPV. Targeted interventions are required to strengthen HPV diagnosis, prevent cervical cancer and save lives. [ABSTRACT FROM AUTHOR]

Background: In 2018, the World Health Organization commenced a multi-country validation study of the Cepheid GeneXpert for a range of molecular-based point-of-care (POC) tests in primary care settings. One study arm focused on the evaluation of POC tests for screening 'women at risk' for chlamydia (CT), gonorrhoea (NG) and trichomonas (TV) in four countries – Australia, Guatemala, Morocco and South Africa. Methods: Study participants completed a pre-test questionnaire which included demographics, clinical information and general questions on POC testing (POCT). Two vaginal swab samples (either self-collected or clinician collected) from each patient were tested on the GeneXpert at the POC and at a reference laboratory using quality-assured nucleic acid amplification tests (NAATs). Results: One thousand three hundred and eighty-three women were enrolled: 58.6% from South Africa, 29.2% from Morocco, 6.2% from Guatemala, and 6.0% from Australia. 1296 samples for CT/NG and 1380 samples for TV were tested by the GeneXpert and the reference NAAT. The rate of unsuccessful tests on the GeneXpert was 1.9% for CT, 1.5% for NG and 0.96% for TV. The prevalence of CT, NG and TV was 31%, 13% and 23%, respectively. 1.5% of samples were positive for all three infections; 7.8% were positive for CT and NG; 2.4% were positive for NG and TV; and 7.3% were positive for CT and TV. Compared to reference NAATs, pooled estimates of sensitivity for the GeneXpert tests were 83.7% (95% confidence intervals 69.2-92.1) for CT, 90.5% (85.1-94.1) for NG and 64.7% (58.1-70.7) for TV (although estimates varied considerably between countries). Estimates for specificity were ≥96% for all three tests both within- and between-countries. Pooled positive and negative likelihood ratios were: 32.7 ([CI] 21.2-50.5) and 0.17 (0.08-0.33) for CT; 95.3 (36.9-245.7) and 0.10 (0.06-0.15) for NG; and 56.5 (31.6-101.1) and 0.35 (0.27-0.47) for TV. Conclusion: This multi-country evaluation is the first of its kind world-wide. Positive likelihood ratios, as well as specificity estimates, indicate the GeneXpert POC test results for CT, NG and TV were clinically acceptable for ruling in the presence of disease. However, negative likelihood ratios and variable sensitivity estimates from this study were poorer than expected for ruling out these infections, particularly for TV. Trial registration: Ethics approval to conduct the ProSPeRo study was granted by the WHO Ethics Review Committee, as well as local ethics committees from all participating countries. [ABSTRACT FROM AUTHOR]

Background: Sexually transmitted infections caused by Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV) remain significant global health problems. The World Health Organization (WHO) has recently conducted a multi-faceted, multi-country validation study (ProSPeRo), which included an evaluation of the Xpert CT/NG and Xpert TV assays on the GeneXpert system (Cepheid, Sunnyvale, Ca., USA) in clinic-based settings across eight countries. To support the study, a training and quality management system was implemented and evaluated. Methods: A comprehensive training program for the study was developed. Quality control (QC) and external quality assessment (EQA) samples were provided by an accredited quality assurance provider. QC testing was conducted at 14 point-of-care testing (POCT) clinics, while EQA samples were tested by the POCT sites and a reference laboratory supporting each clinic. Results: For QC testing, concordance with the expected results for CT and NG was > 99% and rates of unsuccessful tests were < 4%. For TV testing, concordance was similar (97%), but rates of unsuccessful tests were high (18%), particularly in the 'TV negative' sample. For EQA testing initially conducted in 2018, concordance was 100% for CT and NG, and 90% for TV for the reference laboratory group (which used non-GeneXpert systems). Concordance for the POCT group was also high (> 94%) for all analytes, but this cohort (which used GeneXpert systems) exhibited a high rate of unsuccessful TV tests. All but one of these unsuccessful tests was subcategorised as 'invalid'. Conclusions: The high level of concordance for QC and EQA testing confirm that the trained operators at the POC clinical sites were competent to conduct POC testing and that the training and quality systems implemented for the ProSPeRo study were effective. The quality materials used were satisfactory for CT and NG but exhibited poor performance for TV testing on the GeneXpert system. The WHO should continue to work with industry and EQA providers to provide improved materials that are reliable, stable and cost effective for quality management, as it seeks to rollout molecular-based STI POCT in non-laboratory-based settings. Trial registration: Ethics approval to conduct the ProSPeRo study was granted by the WHO Ethics Review Committee. [ABSTRACT FROM AUTHOR]

BACKGROUND: Tuberculosis (TB) is a global public health concern. The current study has been done with the objectives to assess the level of awareness about TB, GeneXpert, Nikshay, and 99-DOTS under the National Tuberculosis Elimination Program (NTEP) among the representative population of medical students. MATERIALS AND METHODS: It was a cross-sectional descriptive study conducted over a period of 2 months from October 2022 to November 2022 in a tertiary teaching medical college of Chengalpet district of Tamil Nadu among the medical students of the teaching medical college and hospital. Participants between the age of 18 and 28 years were included in the study with no serious illness. A stratified random sampling method was employed, wherein all the students were asked to fill out the online semi-structured questionnaire. Data entry was done in Microsoft Excel, and statistical analysis was done using SPSS version 16.0. RESULTS: This cross-sectional descriptive study involved 176 undergraduate medical students with a mean age of 22.5 ± 3.5 years, where there are 95 (53.9%) females and 81 (46%) males as the participants of the study. Out of 176 participants, 140 (79.5%) participants had a fairly good awareness of first-line drugs, whereas 36 (20.5%) participants lacked awareness about NTEP, GeneXpert, 99-DOTS, and Nikshay. The majority of the participants reported following most of the TB preventive measures, with hand hygiene and using a handkerchief while coughing and sneezing are the most commonly reported prevention measures. CONCLUSION: The current study reported that, despite being aware of TB as a disease, medical students had low awareness of government-led interventions such as NTEP, Nikshay, 99-DOTS, and GeneXpert. This calls for the need to intensify awareness activities among medical students to strengthen our battle against TB.

Context Pulmonary tuberculosis (TB) is still one of the most common infectious diseases in the world. It is the second leading cause of death from an infectious disease worldwide, after the human immunodeficiency virus (HIV). WHO estimated TB incidence in Egypt in 2019 at 12 000. Purpose The aim of this study was to make a re-look at the epidemiological characteristics, clinical presentations, and radiological findings of patients with smear-negative pulmonary tuberculosis (SNPT) in non-HIV infected patients. Methods Retrospective analysis was performed including non-HIV patients with smear negative TB, with studying of demographics, symptoms, radiological patterns, and radiological distribution and the used diagnostic methods. Statistical analysis The demographic, clinical, and radiological data were gathered together, tabulated, and statistically analyzed. Data analysis was performed by Statistical Package for Social Science (SPSS – version 22). Results 74 smear-negative TB, non-HIV, age mean 47.17 ± 12.8 SD, 72.2% were males, DM was present in (39.2%), fever in (83.3%), weight loss in (61.1%), cough in (59.7%), consolidation pattern in (63.8%), cavities in (36.1%), an apical segment of right upper lobe in (41.9%), bronchoscopic lavage with Ziehl–Neelsen stain (BAL ZN) diagnosed (52.7%) of sputum negative cases. Conclusion Common variables among recorded cases were male sex, middle-aged individuals, Diabetes Mellitus (DM), toxic manifestation, an involved right apical segment of the upper lobe, consolidation and cavitary patterns, and most cases were diagnosed by bronchoscopic lavage with Ziehl–Neelsen.

Background and aims: India is a high-burden tuberculosis (TB) region and a drug-resistance hotspot. Despite numerous reports of pulmonary tuberculosis (PTB) cases, there needs to be more literature available on the importance of diagnostic methods in the case of extrapulmonary tuberculosis (EPTB). A prospective study was performed from July 2017 to June 2018 to compare the efficacy of conventional and molecular methods in detecting PTB and EPTB cases. Methods: Overall, 1000 presumptive PTB and 412 EPTB cases were subjected to staining (Ziehl- Neelsen [ZN] and fluorescent staining), culture, GeneXpert, and line probe assay (LPA). Results: The sensitivity, specificity, and strength of association [i.e., kappa (k) value of light-emitting diode-fluorescent microscopy, ZN, and GeneXpert] were calculated using standard formulae using solid culture as the gold standard. The sensitivity of GeneXpert in smear-positive/culture-positive PTB was comparable with the smear-negative/culture-positive PTB cases (95.7% vs. 87.5%) with an overall sensitivity and specificity of 90.5% and 90.1% in EPTB cases, respectively. However, sensitivity was lower for pleural fluid (75%) and tissues (85.7%). In pulmonary instances, 10% (6.7% Rifampicin [RIF] + isoniazid [INH] resistant and 3.3% INH monoresistant) drug resistance was observed, and no drug resistance was found in extra-pulmonary samples. Conclusion: Among conventional methods, fluorescent staining is more sensitive than ZN staining, while the sensitivity of GeneXpert varies w.r.t type of sample using culture positivity as the gold standard. In general, the present study suggests the promotion of universal drug susceptibility testing (DST) for all individuals with TB to control drug-resistant TB.

Context Pulmonary tuberculosis (TB) is still one of the most common infectious diseases in the world. It is the second leading cause of death from an infectious disease worldwide, after the human immunodeficiency virus (HIV). WHO estimated TB incidence in Egypt in 2019 at 12 000. Purpose The aim of this study was to make a re-look at the epidemiological characteristics, clinical presentations, and radiological findings of patients with smear-negative pulmonary tuberculosis (SNPT) in non-HIV infected patients. Methods Retrospective analysis was performed including non-HIV patients with smear negative TB, with studying of demographics, symptoms, radiological patterns, and radiological distribution and the used diagnostic methods. Statistical analysis The demographic, clinical, and radiological data were gathered together, tabulated, and statistically analyzed. Data analysis was performed by Statistical Package for Social Science (SPSS – version 22). Results 74 smear-negative TB, non-HIV, age mean 47.17 ± 12.8 SD, 72.2% were males, DM was present in (39.2%), fever in (83.3%), weight loss in (61.1%), cough in (59.7%), consolidation pattern in (63.8%), cavities in (36.1%), an apical segment of right upper lobe in (41.9%), bronchoscopic lavage with Ziehl–Neelsen stain (BAL ZN) diagnosed (52.7%) of sputum negative cases. Conclusion Common variables among recorded cases were male sex, middle-aged individuals, Diabetes Mellitus (DM), toxic manifestation, an involved right apical segment of the upper lobe, consolidation and cavitary patterns, and most cases were diagnosed by bronchoscopic lavage with Ziehl–Neelsen. [ABSTRACT FROM AUTHOR]

BACKGROUND: Tuberculosis (TB) is a global public health concern. The current study has been done with the objectives to assess the level of awareness about TB, GeneXpert, Nikshay, and 99-DOTS under the National Tuberculosis Elimination Program (NTEP) among the representative population of medical students. MATERIALS AND METHODS: It was a cross-sectional descriptive study conducted over a period of 2 months from October 2022 to November 2022 in a tertiary teaching medical college of Chengalpet district of Tamil Nadu among the medical students of the teaching medical college and hospital. Participants between the age of 18 and 28 years were included in the study with no serious illness. A stratified random sampling method was employed, wherein all the students were asked to fill out the online semi-structured questionnaire. Data entry was done in Microsoft Excel, and statistical analysis was done using SPSS version 16.0. RESULTS: This cross-sectional descriptive study involved 176 undergraduate medical students with a mean age of 22.5 ± 3.5 years, where there are 95 (53.9%) females and 81 (46%) males as the participants of the study. Out of 176 participants, 140 (79.5%) participants had a fairly good awareness of first-line drugs, whereas 36 (20.5%) participants lacked awareness about NTEP, GeneXpert, 99-DOTS, and Nikshay. The majority of the participants reported following most of the TB preventive measures, with hand hygiene and using a handkerchief while coughing and sneezing are the most commonly reported prevention measures. CONCLUSION: The current study reported that, despite being aware of TB as a disease, medical students had low awareness of government-led interventions such as NTEP, Nikshay, 99-DOTS, and GeneXpert. This calls for the need to intensify awareness activities among medical students to strengthen our battle against TB. [ABSTRACT FROM AUTHOR]

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The fight against tuberculosis in our country has taken a new shape with the inclusion of rapid nucleic acid amplification tests like GeneXpert MTB/RIF assay which rapidly detects Mycobacterium tuberculosis and rifampicin resistance. Rifampicin resistance detected on GeneXpert has been considered as a sine qua non for the presence of isoniazid resistance and hence classified as multidrug-resistant tuberculosis (MDR-TB). However treatment of rifampicin-resistant, isoniazid-monoresistance, and MDR-TB are different. Our study was done with the aim of identification of the prevalence of isoniazid resistance on culture, in cases which had rifampicin resistance on GeneXpert. Pulmonary samples of patients of presumptive tuberculosis were subjected to GeneXpert testing and liquid MGIT (mycobacterium growth indicator tube) culture. On detection of rifampicin resistance on MTB/RIF assay, the patients were included in our study and cultures were followed-up for sensitivity to isoniazid. A total of 76 patients were included. 76 patients of rifampicin resistance on GeneXpert MTB/RIF assay were followed-up for the sensitivity of isoniazid on culture media. Out of the 76 cases, 62 (81.57%) were found to have isoniazid resistance. Out of the 14 patients, the cultures showed no growth in 6, and in the rest, isoniazid was found to be sensitive. GeneXpert MTB/RIF assay is an excellent modality for the detection of M. tuberculosis and rifampicin resistance. The decision to exclude isoniazid from the treatment regimen in patients with rifampicin resistance should be made only after conducting further molecular/phenotypic tests. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 nucleic acid detection tests enable rapid virus detection; however, it is challenging to identify genotypes to comprehend the local epidemiology and infection routes in real-time qRT-PCR. At the end of June 2022, our hospital experienced an in-hospital cluster of COVID-19. When examined using the GeneXpert® System, the cycle threshold (Ct) value of the N2 region of the nucleocapsid gene of SARS-CoV-2 was approximately 10 cycles higher than that of the envelope gene. Sanger sequencing revealed a G29179T mutation in the primer and probe binding sites. A review of past test results revealed differences in Ct values in 21 of 345 SARS-CoV-2-positive patients, of which 17 cases were cluster-related and 4 were not. Including these 21 cases, 36 cases in total were selected for whole-genome sequencing (WGS). The viral genomes in the cluster-related cases were identified as BA.2.10, and those in the non-cluster cases were closely related and classified as being downstream of BA.2.10 and other lineages. Although WGS can provide comprehensive information, its use is limited in various laboratory settings. A measurement platform reporting and comparing Ct values of different target genes can improve test accuracy, enhance our understanding of infection spread, and be applied to the quality control of reagents.

ObjectiveThe effectiveness of household contact investigations is limited by low referral uptake for clinic-based TB testing by symptomatic household contacts. We qualitatively investigated the acceptability and perceived benefits of home-based TB testing using a portable GeneXpert-I instrument (GX-I) in an urban South African township.MethodsIn-depth interviews were conducted with household contacts tested and those that observed testing. Semi-structured interviews explored household contact's understanding of TB, perceptions of the GX-I device and testing procedures, confidentiality, willingness to refer others, and views on home- vs. clinic-based testing. Focus group discussions with home-based TB testing implementing staff assessed operational considerations for scale-up. Data were analysed using a constant comparison approach to qualitatively evaluate the acceptability and feasibility of home-based TB testing.ResultsThirty in-depth interviews and two focus group discussions were conducted. Observing one's own sputum being tested resulted in an emergent trust in home-based TB testing, the GX-I device and one's test results. Home-based TB testing was considered convenient, helped to overcome apathy towards testing and mitigated barriers to clinic-based testing. Perceptions that home-based TB testing contributes to improved household and community health resulted in an emergent theme of alleviation of health insecurities. Operational concerns regarding inadvertent disclosure of one's diagnosis to household members and time spent in people's homes were identified.ConclusionsHome-based TB testing was acceptable and feasible. Individuals expressed belief in the machine by being able to witness the testing process. Though most themes mirrored qualitative studies of home-based HIV testing, the alleviation of health insecurities theme is unique to home-based TB testing. Future research must evaluate the impact of home-based TB testing on case finding yield, time-to-treatment initiation and household outcomes.

Early and accurate diagnosis of tuberculosis (TB) is necessary to initiate proper therapy for the benefit of the patients and to prevent disease transmission in the community. In this study, we developed the InnowaveDX MTB/RIF (InnowaveDX) to detect Mycobacterium tuberculosis (MTB) and rifampicin resistance simultaneously. A prospective multicentre study was conducted to evaluate the diagnostic performance of InnowaveDX for the detection MTB in sputum samples as compared with Xpert and culture. The calculated limit of detection (LOD) for InnowaveDX was 9.6 CFU/ml for TB detection and 374.9 CFU/ml for RIF susceptibility. None of the other bacteria tested produced signals that fulfilled the positive TB criteria, demonstrating a species-specificity of InnowaveDX. Then 951 individuals were enrolled at 7 hospitals, of which 607 were definite TB cases with positive culture and/or Xpert results, including 354 smear-positive and 253 smear-negative cases. InnowaveDX sensitivity was 92.7% versus bacteriologically TB standard. Further follow-up revealed that 61 (91.0%) out of 67 false-positive patients with no bacteriological evidence met the criteria of clinically diagnosed TB. Among 125 RIF-resistant TB patients diagnosed by Xpert, 108 cases were correctly identified by InnowaveDX, yielding a sensitivity of 86.4%. Additionally, the proportion of very low bacterial load in the discordant susceptibility group was significantly higher than in the concordant susceptibility group (P = 0.029). To conclude, we have developed a novel molecular diagnostic with promising detection capabilities of TB and RIF susceptibility. In addition, the discordant RIF susceptibility results between InnowaveDX and Xpert are more frequently observed in samples with very low bacterial load.

Aim The study aims to establish the diagnostic accuracy of GeneXpert MTB/RIF in CSF for early diagnosis of tubercular meningitis and to compare the efficacy of CSF GeneXpert MTB/RIF with CSF culture for mycobacterium. Methodology This was a prospective, cross-sectional study conducted in the Department of Medicine, Neurology, S.C.B Medical College, Cuttack. All patients of age >18 with clinical features suggestive of tubercular meningitis were included in the study. All routine blood tests were performed along with malaria, leptospira, chest radiograph, CT scan or MRI (selected patients) and CSF study to exclude other causes of meningitis. CSF sample subjected to biochemistry, cytology, ZN stain, MGIT culture, and Xpert MTB/RIF. The positive results for each test (ZN stain, MGIT culture, and Xpert MTB/RIF) were compared using Pearson’s chi-squared test. All statistical analyses were done using the SPSS 21.0 version. Results Out of 100 suspected TBM patients 40 were finally classified as definite TBM, 6 were probable TBM, 2 were possible TBM, and 52 were not having TBM. Tubercular meningitis occurred more commonly in the population 21-40 years and in males. The overall sensitivity of CSF GeneXpert MTB/RIF, Zn stain, and MGIT culture was 62.5%, 29.16%, and 66.5% respectively, and specificity of 100% for each in diagnosing TBM. Rifampicin resistance was detected only in two cases. Conclusion GeneXpert MTB/RIF test can rapidly confirm a diagnosis of TBM with 62.5% sensitivity and 100% specificity, along with rifampicin resistance. It can be a useful diagnostic method in patients of suspected TBM either AFB smear-negative or positive due to its rapidity and simultaneous detection of rifampicin resistance. Recommendation Positive GeneXpert results are to be read cautiously and should be well correlated with the clinical and treatment history of the patient.

BackgroundMany high burden countries are scaling-up GeneXpert® MTB/RIF (Xpert) testing for tuberculosis (TB) using a hub-and-spoke model. However, the effect of scale up on reducing TB has been limited. We sought to characterize variation in implementation of referral-based Xpert TB testing across Uganda, and to identify health system factors that may enhance or prevent high-quality implementation of Xpert testing services.MethodsWe conducted a cross-sectional study triangulating quantitative and qualitative data sources at 23 community health centers linked to one of 15 Xpert testing sites between November 2016 and May 2017 to assess health systems infrastructure for hub-and-spoke Xpert testing. Data sources included a standardized site assessment survey, routine TB notification data, and field notes from site visits.ResultsChallenges with Xpert implementation occurred at every step of the diagnostic evaluation process, leading to low overall uptake of testing. Of 2192 patients eligible for TB testing, only 574 (26%) who initiated testing were referred for Xpert testing. Of those, 54 (9.4%) were Xpert confirmed positive just under half initiated treatment within 14 days (n = 25, 46%). Gaps in required infrastructure at 23 community health centers to support the hub-and-spoke system included lack of refrigeration (n = 14, 61%) for sputum testing and lack of telephone/mobile communication (n = 21, 91%). Motorcycle riders responsible for transporting sputum to Xpert sites operated variable with trips once, twice, or three times a week at 10 (43%), nine (39%) and four (17%) health centers, respectively. Staff recorded Xpert results in the TB laboratory register at only one health center and called patients with positive results at only two health centers. Of the 15 Xpert testing sites, five (33%) had at least one non-functioning module. The median number of tests per day was 3.57 (IQR 2.06-4.54), and 10 (67%) sites had error/invalid rates > 5%.ConclusionsAlthough Xpert devices are now widely distributed throughout Uganda, health system factors across the continuum from test referral to results reporting and treatment initiation preclude effective implementation of Xpert testing for patients presenting to peripheral health centers. Support for scale up of innovative technologies should include support for communication, coordination and health systems integration.

Pulmonary tuberculosis (TB) is an infectious disease that attacks the lungs and is caused by the bacterium Mycobacterium tuberculosis. The GeneXpert RT-PCR examination (Xpert MTB / RIF) is a development of a diagnostic tool that can automatically detect the presence of Mycobacterium tuberculosis (MTB) by molecular examination and can be used to detect MTB resistance to rifampicin. Erythrocyte sedimentation rate (ESR) is a test used to determine the rate at which erythrocytes settle in the blood. The purpose of this study was to determine the relationship between GeneXpert RT-PCR results and ESR in suspected tuberculosis patients. This research uses a cross-sectional study. The sample used in this study were 56 new suspected TB patients who had never been treated for ATD and underwent GeneXpert RT-PCR examination. Sampling was carried out by purposive sampling with the TCM Rif Sen group and negative results. A total of 27 patients (96.4%) with Rif Sen's GeneXpert RT-PCR results had high ESR values. 15 patients (53.6%) with negative GeneXpert RT-PCR results had normal ESR values. The results of the Chi Square test (X2) show that p-value = 0.000 OR = 0.032. There is a significant relationship between GeneXpert and ESR values ​​in suspected tuberculosis

Background Tuberculosis (TB) commonly affects the lung (pulmonary TB). Extrapulmonary TB (EPTB) can involve many systems. Diagnosis is often difficult. EPTB may be misdiagnosed with many other inflammatory, granulomatous, and neoplastic disorders. GeneXpert mycobacterium tuberculosis /rifampicin is a valuable test in diagnosis of pulmonary TB. There is limited research about its diagnostic role in EPTB. Patients and methods The aim of this study was to assess the diagnostic value of GeneXpert in EPTB. Samples from EPTB cases were sent for standard mycobacterial culture and GeneXpert assay. The sensitivity and specificity of GeneXpert were calculated. Results A total of 100 patients were included. Overall, 61 cases were definitely diagnosed as EPTB, whereas 39 cases were negative according to culture. GeneXpert was positive in 40 cases, which represent 65.6% of EPTB cases, and negative in 21 (34.4%) cases. Sensitivity and specificity of GeneXpert was 65.6 and 97.4%, respectively. The positive predictive value and negative predictive value were 97.4 and 64.4%, respectively. Conclusion GeneXpert is a rapid, valuable tool in diagnosis of patients with EPTB. It is a highly specific test with fair sensitivity. A multicenter study with larger sample size is needed to evaluate the diagnostic role of GeneXpert in different sites of EPTB.