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Objective: To investigate and compare the performance of urinary cytology and the Xpert BC Monitor test in the detection of bladder cancer in various clinically significant patient cohorts, including patients with carcinoma in situ (CIS), in a prospective multicentre setting, aiming to identify potential applications in clinical practice. Patients and Methods: A total of 756 patients scheduled for transurethral resection of bladder tumour (TURBT) were prospectively screened between July 2018 and December 2020 at six German University Centres. Central urinary cytology and Xpert BC Monitor tests were performed prior to TURBT. The diagnostic performance of urinary cytology and the Xpert BC Monitor was evaluated according to sensitivity (SN), specificity (SC), negative predictive value (NPV) and positive predictive value (PPV). Statistical comparison of urinary cytology and the Xpert BC Monitor was conducted using the McNemar test. Results: Of 756 screened patients, 733 (568 male [78%]; median [interquartile range] age 72 [62–79] years) were included. Bladder cancer was present in 482 patients (65.8%) with 258 (53.5%) high‐grade tumours. Overall SN, SC, NPV and PPV were 39%, 93%, 44% and 92% for urinary cytology, and 75%, 69%, 59% and 82% for the Xpert BC Monitor. In patients with CIS (concomitant or solitary), SN, SC, NPV and PPV were 59%, 93%, 87% and 50% for urinary cytology, and 90%, 69%, 95% and 50% for the Xpert BC Monitor. The Xpert BC Monitor missed four tumours (NPV = 98%) in patients with solitary CIS, while potentially avoiding 63.3% of TURBTs in inconclusive or negative cystoscopy and a negative Xpert result. Conclusion: Positive urinary cytology may indicate bladder cancer and should be taken seriously. The Xpert BC Monitor may represent a useful diagnostic tool for correctly identifying patients with solitary CIS and unsuspicious or inconclusive cystoscopy. [ABSTRACT FROM AUTHOR]

Background: Distinguishing nontuberculous mycobacteria pulmonary disease (NTM-PD) from pulmonary tuberculosis (PTB) is a challenge especially in patients with positive sputum smear of acid-fast bacilli (AFB). This study aimed to compare and identify the clinical characteristics between the two diseases among patients with positive sputum AFB. Methods: From February 2017 through March 2021, patients with positive sputum AFB were reviewed in two hospitals of China. Among them, clinical data of NTM-PD and PTB patients was collected and compared. Results: 76 cases of NTM-PD and 92 cases of PTB were included in our study. When compared with PTB, NTM-PD patients were older (59.2 ± 11.4 vs 44.2 ± 19.5 years, P

Introduction: Tubercular meningitis (TBM) is a serious public health problem in developing countries as it leads to significant mortality and residual neurological sequelae. The estimated mortality due to TBM in India is 1.5 per 100,000 population. In resource-limited settings, only the Ziehl-Neelsen (ZN) stain, which has very little sensitivity, is available. The World Health Organization recommended the Loop Mediated Isothermal Amplification (TB LAMP) assay for pulmonary tuberculosis only. We evaluated this test for tubercular meningitis as well. Methodology: In a cross-sectional study of 2-year duration, we have taken 239 cerebrospinal fluid samples from suspected cases of tubercular meningitis patients. ZN staining along with Mycobacteria Growth Indicator Tube (MGIT) TB culture, Xpert MTB/RIF Ultra assay, and commercial TB LAMP assay were performed for each sample. Results: Out of 239 samples, 40 samples (16.73%) were found TB LAMP assay positive, 48 samples (20.08%) were found Xpert ultra-assay positive, 12 samples (5.02%) were MGIT TB culture positive and acid-fast bacillus smear positive in ten samples (4.18 %). Out of 12 MGITpositive samples, all samples (100%) were TB LAMP and Xpert ultra positive and one sample (8.33%) was ZN smear positive. In 199 negative samples from the TB LAMP assay, eight samples were positive by Xpert, none by MGIT TB culture and AFB smear. Sensitivity and specificity were found as 100% and 87.66%, respectively, for the TB LAMP assay. Conclusion: TB LAMP assay is a rapid, cost-effective, sensitive, and specific test for tubercular meningitis infection in resource-limited settings. [ABSTRACT FROM AUTHOR]

BACKGROUND: Xpert® MTB/RIF, a rapid, molecular TB diagnostic assay, can detect Mycobacterium tuberculosis and rifampin resistance directly from clinical sputum samples in

Abstract The Xpert MTB/RIF test (Xpert) can help in the accurate screening of tuberculosis, however, its widespread use is limited by its high cost and lack of accessibility. Pooling of sputum samples for testing is a strategy to cut expenses and enhance population coverage but may result in a decrease in detection sensitivity due to the dilution of Mycobacterium tuberculosis (Mtb) by sample mixing. We investigated how the mixing ratio affected the detection performance of Xpert. We used frozen sputum samples that had been kept after individual Xpert assays of the sputa from Mtb-confirmed TB patients and non-TB patients. Our results showed that the overall sensitivity of the Xpert pooling assay remained higher than 80% when the mixing ratio was between 1/2 and 1/8. When the mixing ratio was raised to 1/16, the positive detection rate fell to 69.0%. For patients with either a high sputum Mtb smear score ≥ 2+, a time-to-positive culture ≤ 10 days, or an Xpert test indicating a high or medium abundance of bacteria, the pooling assay positivity rates were 93.3%, 96.8%, and 100% respectively, even at a 1/16 mixing ratio. For participants with cavities and cough, the pooling assay positivity rates were 86.2% and 90.0% at a 1/8 ratio, higher than for those without these signs. Our results show that the Xpert pooled assay has a high overall sensitivity, especially for highly infectious patients. This pooling strategy with lower reagent and labor costs could support TB screening in communities with limited resources, thereby facilitating reductions in the community transmission and incidence of TB worldwide.

Background Microbiological diagnosis of pediatric tuberculosis (TB) using conventional microbiological techniques has been challenging due to paucibacillary nature of the disease. Molecular methods using cartridge-based tests like Xpert, have immensely improved diagnosis. A novel next-generation cartridge test, Xpert Ultra, incorporates two additional molecular targets and claims to have much lower detection limit. We attempted to compare the two techniques in presumptive pediatric TB patients. Objectives The aim of this study was to compare the diagnostic performance of Xpert MTB/Rif Ultra with Xpert MTB/Rif for the detection of pediatric TB. Study design This is an observational comparative analytical study. Methods Children under 15 years of age with presumptive TB were enrolled. Appropriate specimens were obtained (sputum, induced sputum or gastric aspirate for suspected pulmonary TB, cerebrospinal fluid for suspected tubercular meningitis and pleural fluid for suspected tubercular pleural effusion), subjected to smear microscopy, mycobacterial culture, Xpert and Xpert ultra tests and other appropriate diagnostic investigations. Results Out of 130 enrolled patients, 70 were diagnosed with TB using a composite reference standard (CRS). The overall sensitivity of Xpert was 64.29% [95% confidence interval (CI) 51.93–75.93%] and that of Xpert Ultra was 80% (95% CI 68.73–88.61%) with 100% overall specificity for both. The sensitivity of Xpert and Xpert Ultra in pulmonary specimens (n  = 112) was 66.67% and 79.37% and in extrapulmonary specimens (n  = 18) was 42.86% and 85.71%, respectively. Conclusion Our study found Ultra to be more sensitive than Xpert for the detection of Mycobacterium tuberculosis in children. Our findings support the use of Xpert Ultra as initial rapid molecular diagnostic test in children under evaluation for TB. [ABSTRACT FROM AUTHOR]

The Xpert MTB/RIF test (Xpert) can help in the accurate screening of tuberculosis, however, its widespread use is limited by its high cost and lack of accessibility. Pooling of sputum samples for testing is a strategy to cut expenses and enhance population coverage but may result in a decrease in detection sensitivity due to the dilution of Mycobacterium tuberculosis (Mtb) by sample mixing. We investigated how the mixing ratio affected the detection performance of Xpert. We used frozen sputum samples that had been kept after individual Xpert assays of the sputa from Mtb-confirmed TB patients and non-TB patients. Our results showed that the overall sensitivity of the Xpert pooling assay remained higher than 80% when the mixing ratio was between 1/2 and 1/8. When the mixing ratio was raised to 1/16, the positive detection rate fell to 69.0%. For patients with either a high sputum Mtb smear score ≥ 2+, a time-to-positive culture ≤ 10 days, or an Xpert test indicating a high or medium abundance of bacteria, the pooling assay positivity rates were 93.3%, 96.8%, and 100% respectively, even at a 1/16 mixing ratio. For participants with cavities and cough, the pooling assay positivity rates were 86.2% and 90.0% at a 1/8 ratio, higher than for those without these signs. Our results show that the Xpert pooled assay has a high overall sensitivity, especially for highly infectious patients. This pooling strategy with lower reagent and labor costs could support TB screening in communities with limited resources, thereby facilitating reductions in the community transmission and incidence of TB worldwide. [ABSTRACT FROM AUTHOR]

Background: The Xpert MTB/RIF (Xpert) assay has been widely used to diagnose suspected active tuberculosis (TB) and rifampicin-resistant TB cases. Despite its excellent performance record, false-positive Xpert rifampicin (RIF) resistance results are obtained for specimens with extremely low bacterial loads. Objective: We aimed to study the feasibility of repeat Xpert testing as a strategy for reducing the odds of obtaining false-positive results when testing paucibacillary TB patients. Methods: We enrolled previously tested TB patients with very low initial bacterial loads from May 2016 to February 2022 for Xpert retesting. A total of 251 TB patients were retested using the Xpert assay. Results: RIF resistance was noted in 65 (25.9 %) patients when tested by Xpert at initial diagnosis. Only 107 (42.6 %) of 251 patients tested positive for MTB when retested via Xpert. The majority (98.6 %) of RIF-susceptible cases were still susceptible to RIF when retested. Initial Xpert testing yielded 35 positive results for MTB in the RIF-resistant group, of whom 25 (71.4 %) still exhibited RIF resistance when retested. All culture-positive MTB isolates in the RIF-susceptible group were also RIF-susceptible by phenotypic DST. In the RIF-resistant group, 10 of 14 culture-positive MTB isolates exhibited RIF resistance, of which 4 isolates were deemed RIF-susceptible by phenotypic DST. The proportion of double mutations within the MTB rpoB RRDR sequence, as detected by hybridization of Xpert D and E probes, was significantly higher in the RIF-susceptible group than in the RIF-susceptible group. Conclusions: Our results demonstrated that initial RIF-susceptible results were more accurate than RIF-resistant results. Additionally, patients with double mutations that delayed probe D/E hybridization were more likely to have false-positive Xpert results. Our findings emphasize that repeat Xpert MTB/RIF testing is necessary for TB patients with extremely low bacterial loads who are at high risk for RIF-resistant TB.

Background: Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis (MTB) is essential for proper patient management. We investigated discordance between genotypic (Xpert MTB/RIF and MTBDRplus) and phenotypic (MGIT 960) methods for the detection of rifampicin (RIF) and isoniazid (INH) resistant MTB and its correlation with patient treatment outcomes in Jimma, Southwest Oromia, Ethiopia. Methods: A retrospective study was conducted on 57 stored MTB isolates with known Xpert RIF resistance status (45 RIF resistant and 12 RIF susceptible) at Jimma University Mycobacteriology Research Center from November 2, 2021, to December 28, 2022. We did MTBDRplus and phenotypic DST (using the Mycobacterial Growth Indicator Tube (MGIT) system). The Xpert and MTBDRplus results were compared using phenotypic DST as a reference standard method. The treatment outcome was determined as per national guideline. The discordance between the genotypic and phenotypic DST was calculated using GraphPad software. Results: Among the 57 MTB isolates, six (10.5 %) had discordant results between the two DST methods. Xpert yielded five discordant results for RIF when compared with phenotypic DST (kappa coefficient (κ) = 0.76, 95 % confidence interval 0.56–0.96). The MTBDRplus compared with phenotypic DST gave three discordant results for RIF (κ = 0.86, 95 % confidence interval 0.71–1.00) and three for INH (κ = 0.86, 95 % confidence interval 0.70–1.00). Compared with Xpert, MTBDRplus yielded lower discordance with phenotypic DST for RIF. Out of six patients with discordant results, three had unfavorable outcomes while the other three were cured. Of the three patients with unfavorable outcomes, only one patient has received an inappropriate treatment regimen. There was no correlation between unfavorable outcomes and incorrect treatment regimens due to discordant results (Χ2 = 0.404; P = 0.525). Conclusions: Discordance between genotypic and phenotypic DST for RIF or INH occurred in 10.5 % of isolates. Only one patient with discordant results has received an inappropriate treatment regimen, resulting in an unfavorable outcome. The impact of parallel use of rapid molecular assay with phenotypic DST on patient treatment outcomes requires further study.

Background/Purpose: Tuberculosis (TB) is an infectious bacterial disease caused by Mycobacterium tuberculosis (MTB). It is a matter of serious public health concern in lower-income and lower-middle-income countries. Methods: In this study, a comparative analysis of stool samples from 101 adult (91 pre-confirmed pulmonary TB patients, 10 sputum negative patients) and 99 children (presumptive TB patients). Their stool samples were collected, processed and analyzed using Xpert MTB/RIF Ultra technique and AFB microscopy. Results: While using Xpert MTB/RIF Ultra assay as our "reference standard", a sensitivity of 96 %, Specificity of 83%, Positive Predictive Value (PPV) of 87 %, and Negative Predictive Value (NNP) of 87 % was observed with stool Xpert MTB/RIF Ultra technique. Also, Ziehl Neelsen's Stain Microscopy has a Sensitivity of 64%, Specificity of 12%, PPV of 80% and NNP of 20% while Fluorescence Stain Microscopy reveal a Sensitivity of 94 %, Specificity of 20 %, PPV of 80 %, and NNP of 20 % in stool sample. Conclusion: This study has elucidated Xpert MTB/RIF Ultra assay in stool samples provide an alternative option to sputum in the diagnosis of pulmonary tuberculosis with high level of diagnostic accuracy and precision. Furthermore, Fluorescence Stain Microscopy has shown to be more sensitive and specific than Ziehl Neelsen's stain Microscopy. [ABSTRACT FROM AUTHOR]

Abstract Background Low- and middle-income countries (LMICs) account for nearly 85% of the global cervical cancer burden, yet have the least access to high-performance screening. International guidelines recommend human papillomavirus testing (HPV) as primary screening, yet implementation is inhibited by the cost of HPV testing. Atila AmpFire® HPV Assay (AmpFire) is both affordable and easy to use, and offers individual genotyping. The objective of this study was to compare the performance of the AmpFire HPV assay to the Xpert® HPV assay in detection of both HPV and clinically significant cervical disease. Methods We utilized stored cervical specimens from a prospective cohort study of women living with human immunodeficiency virus (HIV) in Botswana conducted from May to July 2018. Positive and negative percent agreement was calculated for the AmpFire and Xpert assays, as was detection of high-grade cervical dysplasia. Results 63 stored cervical specimens had detectable DNA after thawing and were included in the analysis. The positive percent agreement was 91.2% (95%CI 76.3–98.1) and negative percent agreement was 79.3% (95% CI 60.3–92.0). Six cases positive by AmpFire but negative by Xpert were HPV genotypes 35, 52 (n = 2), 58, 68, and co-infection with HPV 45 and 68. Both Xpert and AmpFire assays detected HPV in all 10 samples of women who had high-grade cervical dysplasia. Conclusions The AmpFire HPV assay demonstrated excellent analytic performance in both detection of HPV and clinically significant cervical disease. AmpFire HPV is a promising option to increase access to affordable, type-specific HPV screening for cervical cancer in LMICs.

The Xpert MTB/RIF (Xpert) assay has been widely used to diagnose suspected active tuberculosis (TB) and rifampicin-resistant TB cases. Despite its excellent performance record, false-positive Xpert rifampicin (RIF) resistance results are obtained for specimens with extremely low bacterial loads. We aimed to study the feasibility of repeat Xpert testing as a strategy for reducing the odds of obtaining false-positive results when testing paucibacillary TB patients. We enrolled previously tested TB patients with very low initial bacterial loads from May 2016 to February 2022 for Xpert retesting. A total of 251 TB patients were retested using the Xpert assay. RIF resistance was noted in 65 (25.9 %) patients when tested by Xpert at initial diagnosis. Only 107 (42.6 %) of 251 patients tested positive for MTB when retested via Xpert. The majority (98.6 %) of RIF-susceptible cases were still susceptible to RIF when retested. Initial Xpert testing yielded 35 positive results for MTB in the RIF-resistant group, of whom 25 (71.4 %) still exhibited RIF resistance when retested. All culture-positive MTB isolates in the RIF-susceptible group were also RIF-susceptible by phenotypic DST. In the RIF-resistant group, 10 of 14 culture-positive MTB isolates exhibited RIF resistance, of which 4 isolates were deemed RIF-susceptible by phenotypic DST. The proportion of double mutations within the MTB rpoB RRDR sequence, as detected by hybridization of Xpert D and E probes, was significantly higher in the RIF-susceptible group than in the RIF-susceptible group. Our results demonstrated that initial RIF-susceptible results were more accurate than RIF-resistant results. Additionally, patients with double mutations that delayed probe D/E hybridization were more likely to have false-positive Xpert results. Our findings emphasize that repeat Xpert MTB/RIF testing is necessary for TB patients with extremely low bacterial loads who are at high risk for RIF-resistant TB. [ABSTRACT FROM AUTHOR]

The delayed diagnosis of tuberculous meningitis (TBM) leads to poor outcomes, yet the current diagnostic methods for identifying Mycobacterium tuberculosis in cerebrospinal fluid (CSF) are inadequate. The first comparative study of the new GeneXpert MTB/RIF Ultra (Xpert Ultra) for TBM diagnosis suggested increased sensitivity of Xpert Ultra. Two subsequent studies have shown Xpert Ultra has improved sensitivity, but has insufficient negative predictive value to exclude TBM. Collecting and processing large volumes of CSF for mycobacterial testing are important for optimal diagnostic test performance. But clinical, radiological, and laboratory parameters remain essential for TBM diagnosis and empiric therapy is often needed. We therefore caution against the use of Xpert Ultra as a single diagnostic test for TBM; it cannot be used to "rule out" TBM.

Objective: The GeneXpert MTB/RIF assay (Xpert) is a diagnostic tool that has been shown to significantly improve the accuracy of tuberculosis (TB) detection in clinical settings, with advanced sensitivity and specificity. Early detection of TB can be challenging, but Xpert has improved the efficacy of the diagnostic process. Nevertheless, the accuracy of Xpert varies according to different diagnostic specimens and TB infection sites. Therefore, the selection of adequate specimens is critical when using Xpert to identify suspected TB. As such, we have conducted a meta-analysis to evaluate the effectiveness of Xpert for diagnosis of different TB types using several specimens. Methods: We conducted a comprehensive search of several electronic databases, including PubMed, Embase, the Cochrane Central Register of Controlled Trials, and the World Health Organization clinical trials registry center, covering studies published from Jan 2008 to July 2022. Data were extracted using an adapted version of the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modeling Studies. Where appropriate, meta-analysis was performed using random-effects models. The risk of bias and level of evidence was assessed using the Quality in Prognosis Studies tool and a modified version of the Grading of Recommendations Assessment, Development, and Evaluation. RStudio was utilized to analyze the results, employing the meta4diag, robvis, and metafor packages. Results: After excluding duplicates, a total of 2163 studies were identified, and ultimately, 144 studies from 107 articles were included in the meta-analysis based on predetermined inclusion and exclusion criteria. Sensitivity, specificity and diagnostic accuracy were estimated for various specimens and TB types. In the case of pulmonary TB, Xpert using sputum (0.95 95%CI 0.91-0.98) and gastric juice (0.94 95%CI 0.84-0.99) demonstrated similarly high sensitivity, surpassing other specimen types. Additionally, Xpert exhibited high specificity for detecting TB across all specimen types. For bone and joint TB, Xpert, based on both biopsy and joint fluid specimens, demonstrated high accuracy in TB detection. Furthermore, Xpert effectively detected unclassified extrapulmonary TB and tuberculosis lymphadenitis. However, the Xpert accuracy was not satisfactory to distinguish TB meningitis, tuberculous pleuritis and unclassified TB. Conclusions: Xpert has exhibited satisfactory diagnostic accuracy for most TB infections, but the efficacy of detection may vary depending on the specimens analyzed. Therefore, selecting appropriate specimens for Xpert analysis is essential, as using inadequate specimens can reduce the ability to distinguish TB. [ABSTRACT FROM AUTHOR]

Background: Low- and middle-income countries (LMICs) account for nearly 85% of the global cervical cancer burden, yet have the least access to high-performance screening. International guidelines recommend human papillomavirus testing (HPV) as primary screening, yet implementation is inhibited by the cost of HPV testing. Atila AmpFire® HPV Assay (AmpFire) is both affordable and easy to use, and offers individual genotyping. The objective of this study was to compare the performance of the AmpFire HPV assay to the Xpert® HPV assay in detection of both HPV and clinically significant cervical disease. Methods: We utilized stored cervical specimens from a prospective cohort study of women living with human immunodeficiency virus (HIV) in Botswana conducted from May to July 2018. Positive and negative percent agreement was calculated for the AmpFire and Xpert assays, as was detection of high-grade cervical dysplasia. Results: 63 stored cervical specimens had detectable DNA after thawing and were included in the analysis. The positive percent agreement was 91.2% (95%CI 76.3–98.1) and negative percent agreement was 79.3% (95% CI 60.3–92.0). Six cases positive by AmpFire but negative by Xpert were HPV genotypes 35, 52 (n = 2), 58, 68, and co-infection with HPV 45 and 68. Both Xpert and AmpFire assays detected HPV in all 10 samples of women who had high-grade cervical dysplasia. Conclusions: The AmpFire HPV assay demonstrated excellent analytic performance in both detection of HPV and clinically significant cervical disease. AmpFire HPV is a promising option to increase access to affordable, type-specific HPV screening for cervical cancer in LMICs. [ABSTRACT FROM AUTHOR]

Background We report the yield of targeted universal tuberculosis (TB) testing of clinic attendees in high-risk groups. Methods Clinic attendees in primary healthcare facilities in South Africa with one of the following risk factors underwent sputum testing for TB: human immunodeficiency virus (HIV), contact with a TB patient in the past year, and having had TB in the past 2 years. A single sample was collected for Xpert-Ultra (Xpert) and culture. We report the proportion positive for Mycobacterium tuberculosis. Data were analyzed descriptively. The unadjusted clinical and demographic factors' relative risk of TB detected by culture or Xpert were calculated and concordance between Xpert and culture is described. Results A total of 30 513 participants had a TB test result. Median age was 39 years, and 11 553 (38%) were men. The majority (n = 21734, 71%) had HIV, 12 492 (41%) reported close contact with a TB patient, and 1573 (5%) reported prior TB. Overall, 8.3% were positive for M. tuberculosis by culture and/or Xpert compared with 6.0% with trace-positive results excluded. In asymptomatic participants, the yield was 6.7% and 10.1% in symptomatic participants (with trace-positives excluded). Only 10% of trace-positive results were culture-positive. We found that 55% of clinic attendees with a sputum result positive for M. tuberculosis did not have a positive TB symptom screen. Conclusions A high proportion of clinic attendees with specific risk factors (HIV, close TB contact, history of TB) test positive for M. tuberculosis when universal testing is implemented. [ABSTRACT FROM AUTHOR]

Introduction: Streptococcus agalactiae, also known as group B streptococci (GBS), is associated with invasive infections in neonates. Identification of GBS vaginal colonization in pregnant women before delivery is essential for treatment with antibiotics to prevent intrapartum vertical transmission to the newborn. This study was designed to evaluate applicability of two rapid real‐time PCRs in comparison to standard culture identification. Material and methods: We compared the Xpert GBS assay, hereafter referred to as Xpert, and GenomEra GBS PCR, hereafter referred to as GenomEra. The standard culture identification consisted of two different agar plates as well as an enrichment broth. Results: We analyzed vaginal samples of 260 pregnant women; 42 samples were tested GBS‐positive by using standard culture as a gold standard, 30 by Xpert, and 37 by GenomEra. Xpert and GenomEra assays performed with sensitivities of 71.4% and 88.1% as well as specificities of 98.6% and 99.1%, respectively. Twelve vaginal samples were false‐negative by Xpert and five samples by GenomEra. Interestingly, three negative Xpert results of standard culture‐positive samples exhibited high Ct‐values indicating the presence of GBS. If higher Ct‐values are taken into consideration, the sensitivity of Xpert increases up to 78.6%. Moreover, only three Xpert PCRs had to be repeated, whereas two Genomera were invalid even after repetition and further 15 GenomEra PCRs were repeated because of borderline results or inhibition of the PCR test. Conclusions: In this study, GenomEra assay performed with a higher sensitivity than the Xpert PCR. On the other hand, the Xpert assay needs less hands‐on‐time for a sample preparation and requires approximately four‐fold less repetitions as compared to the GenomEra assay. This robust performance of the Xpert assay make it applicable as a rapid intrapartum point‐of‐care test, although a higher sensitivity would be desirable. Therefore, culture in the 35–37 week of gestation remains the gold standard to detect vaginal colonization. [ABSTRACT FROM AUTHOR]

Objective: To compare the diagnostic performance of laboratory assays on the ultrasound-guided core needle biopsy samples for diagnosis of extra-pulmonary tuberculosis (EPTB) in HIV-positive and HIV-negative patients. Methods: A total of 217 patients suspected to have EPTB underwent lesion biopsy from 2017 to 2020. Results of laboratory tests on the biopsy and non-biopsy samples were collected with clinical data for retrospective analysis of test utility. The calculated diagnostic accuracy of the tests was stratified according to the specimen types and HIV status. Results: The cohort contained 118 patients with a final positive diagnosis of extrapulmonary tuberculosis (EPTB group, 54.4%) and 99 finally diagnosed as without TB (non-EPTB group, 45.6%). The risk factor for EPTB was HIV co-infection (OR 2.22, 95% CI 1.17-4.28, p = 0.014). In biopsy samples, GeneXpert (Xpert) showed higher sensitivity (96.6% [91.6-98.7], p < 0.0001) than culture (56.1% [47.0-64.9]). Regardless of HIV status, Xpert had the highest sensitivity (>95%) and specificity (nearly 100%) of any methods. In non-biopsy samples, only T-SPOT.TB (T-SPOT) showed higher sensitivity than culture (90.9% [62.3-99.5] vs 35.3% [17.3-58.7], p = 0.0037). Furthermore, the sensitivities of Xpert were lower in non-biopsy samples (60.0% [23.1-92.9], p = 0.022) than in biopsy samples (100% [86.7-100]). Even in smear-negative biopsy samples, Xpert still had higher sensitivity than culture and retained high specificity (100% [95.7-100]). Conclusion: Superior performance of Xpert in diagnosing EPTB was observed regardless of HIV status and specimen types. Nevertheless, the biopsy samples still substantially facilitated the accurate diagnosis of extrapulmonary tuberculosis. [ABSTRACT FROM AUTHOR]

Abdominal tuberculosis is an ancient problem with modern nuances in diagnosis and management. The two major forms are tuberculous peritonitis and gastrointestinal tuberculosis (GITB), while the less frequent forms are esophageal, gastroduodenal, pancreatic, hepatic, gallbladder and biliary tuberculosis. The clinicians need to discriminate the disease from the close mimics: peritoneal carcinomatosis closely mimics peritoneal tuberculosis, while Crohn's disease closely mimics intestinal tuberculosis. Imaging modalities (ultrasound, computed tomography, magnetic resonance imaging and occasionally positron emission tomography) guide the line of evaluation. Research in diagnostics (imaging and endoscopy) has helped in the better acquisition of tissue for histological and microbiological tests. Although point-of-care polymerase chain reaction–based tests (e.g. Xpert Mtb/Rif) may provide a quick diagnosis, these have low sensitivity. In such situations, ancillary investigations such as ascitic adenosine deaminase and histological clues (granulomas, caseating necrosis, ulcers lined by histiocytes) may provide some specificity to the diagnosis. A diagnostic trial of antitubercular therapy (ATT) may be considered if all diagnostic armamentaria fail to clinch the diagnosis, especially in TB-endemic regions. Objective evaluation with clear endpoints of response is mandatory in such situations. Early mucosal response (healing of ulcers at two months) and resolution of ascites are objective criteria for early response assessment and should be sought at two months. Biomarkers, especially fecal calprotectin for intestinal tuberculosis, have also shown promise. For most forms of abdominal tuberculosis, six months of ATT is sufficient. Sequelae of GITB may require endoscopic balloon dilatation for intestinal strictures or surgical intervention for recurrent intestinal obstruction, perforation or massive bleeding. [ABSTRACT FROM AUTHOR]

Abstract Background Xpert MTB/Rif, a molecular test to detect tuberculosis (TB), has been proven to have high sensitivity and specificity when compared with liquid culture in clinical settings. However, little is known about its performance in community TB screening. Methods In Vietnam, a national TB prevalence survey was conducted in 2017. Survey participants who screened positive by chest X-ray, cough symptoms and/or recent history of tuberculosis were requested to provide at least two sputum samples that were tested for Mycobacterium tuberculosis by Xpert MTB/Rif G4 (Xpert) and BACTEC MGIT960 culture (MGIT). Results There were 4,649 eligible participants provided both samples for testing. Among them, 236 (5.1%) participants tested positive for TB by Xpert, 244 (5.3%) tested positive by MGIT and 317 tested positive by at least one test; 163 (51.4%) had discordant test results. Of the positive Xpert, 162 (68.6%) showed a low or very low bacterial load. In multivariate logistic regression comparing discordant with Xpert-MGIT concordant positive results, discordant Xpert-positive results occurred more often among participants who had low sputum bacterial load, male sex, a history of TB treatment, or night sweats. The associated factors were male sex, abnormal chest X-ray and having night sweats when the logistic model was against those with both Xpert and MGIT negative. Conclusions We found high rates of discordance in the performance of Xpert and MGIT for community-based TB case finding. In situations where the majority of TB cases are expected to have a low bacterial load, multiple diagnostic tests and/or multiple samples are required to reach sufficient sensitivity.

Liwei Yao,1 Xudong Xu,2 Gang Chen,2 Yanqin Shen,2,* Weixian Jiang1,* 1Department of Nursing, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China; 2Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yanqin Shen, Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 East Huancheng Road, Hangzhou, Zhejiang, People’s Republic of China, Email yanqinshen@yeah.net Weixian Jiang, Department of Nursing, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 East Huancheng Road, Hangzhou, Zhejiang, People’s Republic of China, Email jwxmed@163.comPurpose: To evaluate the diagnostic accuracy of the CapitalBio Mycobacterium real-time polymerase chain reaction assay (CapitalBio test) testing of core needle biopsy (CNB) specimens for tuberculous lymphadenitis (TBL) and to compare it with Xpert MTB/RIF.Methods: We retrospectively analyzed the medical data on patients with suspected peripheral TBL. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of the CapitalBio test, Xpert MTB/RIF, and parallel test (positive result for either of these two tests) were calculated to evaluate their diagnostic efficacy compared with the final clinical diagnosis.Results: The study included 114 patients. For diagnosing TBL using CNB samples, the sensitivity, specificity, PPV, NPV, and AUC were 65.0%, 100.0%, 100.0%, 28.6%, and 0.83, respectively, for the CapitalBio test; 72.0%, 100.0%, 100.0%, 33.3%, and 0.86, respectively, for Xpert MTB/RIF; and 82.0%, 100.0%, 100.0%, 43.8%, and 0.91, respectively, for the parallel test.Conclusion: The accuracy of the CapitalBio test and Xpert MTB/RIF for diagnosing TBL using CNB specimens was moderate, while the sensitivity and NPV of these two tests were relatively low. The diagnostic accuracy of the CapitalBio test was slightly lower than that of Xpert MTB/RIF, but the difference between the two was not statistically significant. Parallel test might improve the diagnostic accuracy but not substantially over a single test.Keywords: CapitalBio test, Xpert, tuberculous lymphadenitis, core needle biopsy, diagnostic accuracy

Yanqin Shen, Likui Fang, Bo Ye, Xudong Xu, Guocan Yu,&ast; Lihong Zhou&ast; Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Zhejiang Chinese Medicine and Western Medicine Integrated Hospital, Hangzhou, Zhejiang, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Guocan Yu; Lihong Zhou, Email dabaitwo@163.com; zhoulh198508@163.comBackground: Early lymph node tuberculosis (LNTB) diagnosis is still difficult. The majority of LN specimens require the undertaking of invasive and unpleasant procedures.Purpose: To evaluate the diagnostic efficacy of pathology when combined with molecular tests for the diagnosis of LNTB in core needle biopsy (CNB) specimens and to compare that diagnostic efficacy with that deriving from tissue specimens’ examination alone.Methods: We retrospectively analyzed the medical records of LNTB patients who met the inclusion criteria. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of pathology, molecular tests, and parallel test (positive result for either of these two assays) were calculated to evaluate their diagnostic efficacy compared with a composite reference standard.Results: A total of 289 patients were included in the study. The overall sensitivity, specificity, PPV, NPV, and AUC of pathology, molecular tests, and parallel test were 94.5%, 97.2%, 99.6%, 71.4%, 0.96; 73.1%, 100.0%, 100.0%, 34.6%, 0.87; and 98.4%, 97.2%, 99.6%, 89.7%, 0.98, respectively. For CNB specimens, these values for pathology, molecular tests, and parallel test were 93.3%, 96.2%, 99.4%, 69.4%, 0.95; 76.4%, 100.0%, 100.0%, 40.0%, 0.88; and 99.4%, 96.2%, 99.4%,96.2%,0.98, while those same values for the tissue were 96.6%, 100.0%, 100.0%, 76.9%, 0.98; 67.1%, 100.0%, 100.0%, 25.6%, 0.84; and 96.6%, 100.0%, 100.0%, 76.9%,0.98, respectively.Conclusion: The validity of pathology and molecular testing when using CNB specimens was similar to that of tissue specimens for relevant assessment approaches. For the LNTB diagnosis, CNB specimens were preferred for the simultaneous undertaking of pathological examination and molecular testing.Keywords: pathology, molecular tests, CapitalBio assay, Xpert, lymph node tuberculosis, CNB, tissue, accuracy

BackgroundCervical tuberculous lymphadenitis (CTBL) is a disease often ignored in clinical work, and pathology and Xpert MTB/RIF (Xpert) are the commonly used methods for tuberculosis diagnosis. This study aimed to compare ultrasound-guided puncture biopsy combined with histopathology and Xpert in the diagnosis of lymph node tuberculosis.MethodsA total of 217 patients highly suspected for CTBL were retrospectively enrolled. All patients underwent ultrasound-guided puncture sampling. All samples were subjected to pathological examination and Xpert test. The sensitivity and specificity of the two methods were compared for all samples. The kappa value was calculated to assess the consistency of the pathological examination and Xpert test using comprehensive diagnosis as the gold standard. Receiver operating characteristic curves of the pathological examination, Xpert test, and their combination were generated, and the areas under the curve (AUCs) were calculated to compare the diagnostic value of the three methods.ResultsThe sensitivity and specificity of the pathological diagnosis of CTBL were 70.1 and 100%, respectively. The sensitivity and specificity of Xpert for CTBL diagnosis were 82.5 and 97.5%, respectively. The results of the pathological examination and Xpert test showed poor consistency in the diagnosis of CTBL, with a kappa value of 0.388. The AUC of the pathological diagnosis of CTBL was 0.850 (95% CI: 0.796–0.895), whereas that of Xpert was 0.900 (95% CI: 0.852–0.936), and the difference was statistically significant (P = 0.0483). The AUC of pathological examination combined with Xpert for the diagnosis of CTBL was 0.956 (95% CI: 0.920–0.979), and the difference between pathological examination combined with Xpert for the diagnosis of CTBL was statistically significant compared with pathological examination and Xpert alone, respectively (both P < 0.001).ConclusionThe diagnostic efficiency of Xpert test is higher than that of pathological examination, but its sensitivity is still not ideal for clinical diagnosis. According to this study, the consistency of Xpert test and pathological diagnosis is poor, and the combination of Xpert test and pathological diagnosis can significantly increase the diagnostic efficiency.

• HIV patients with TB had more advanced disease with mean CD4 of 108 • A high Bandim TBscore II was more predictive of TB diagnosis than WHO symptoms • Adding Gene Xpert testing on urine samples increased diagnostic yield of TB by 58% • 36% of HIV patients with a positive TB test were only found on urine Xpert • No specific group of HIV patients was identified to primarily offer Xpert on urine We investigated if Xpert MTB/RIF (Xpert) testing on urine samples among newly diagnosed HIV-patients as an adjunctive test to Xpert testing on sputum increases diagnosis. We sought to define subgroups of patients, for whom testing with either test is especially advantageous. We included patients >15 years, newly diagnosed with HIV, that delivered a urine sample on the day of HIV-diagnosis at the biggest HIV-clinic in Guinea-Bissau between September 5, 2016 and October 13, 2017 into a cross-sectional study. Patients were asked for a sputum sample, which was Xpert tested if returned within 30 days. A questionnaire and physical examination were completed on day of inclusion. We included 390 patients. TB prevalence was 12.6%. Adding Xpert urine test to all newly diagnosed HIV-patients increased diagnostic yield of TB by 58% compared with testing on sputum alone. Patients who tested positive by Xpert on urine samples were clinically similar to those tested with sputum, except that the sputum positives reported more cough (p=0.03). Indiscriminate Xpert urine testing in newly diagnosed HIV-patients with advanced disease increased diagnostic yield. Xpert testing for TB on urine and sputum should be offered as screening in Guinea-Bissau and possibly in similar settings. [ABSTRACT FROM AUTHOR]

Objectives: Sputum acid-fast bacilli (AFB) and Xpert examinations are the most commonly used methods in early diagnosis for pulmonary tuberculosis. It becomes difficult for the clinician to initiate treatment in patients with negative sputum smear and Xpert examinations at the stage of diagnosis. Waiting for culture results for diagnosis causes delay in treatment and increases the risk of disease transmission. We aimed to investigate the contribution of bronchoscopic lavage (BL) obtained with flexible fiberoptic bronchoscopy (FOB) to the diagnosis of tuberculosis. Methods: The BL results of 36 patients hospitalized in the tuberculosis clinic who were clinically suspected of tuberculosis, but whose sputum AFB and Xpert results were negative, and whose bronchoscopic lavages were taken by FOB, were retrospectively evaluated. Results: BL Xpert examination was the method that made the most contribution to the diagnosis with a rate of 27.7%. BL smear AFB results did not contribute to the diagnosis statistically. Sputum and BL tuberculosis culture results were found to be close to each other. In total, the diagnosis of 50% of the patients was confirmed. Conclusions: Performing Xpert examinations on bronchoscopic materials of patients with negative sputum examinations significantly increase the rate of early diagnosis. [ABSTRACT FROM AUTHOR]

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis, which infects more than 23% of the world's population. With the emergence of drug-resistant TB (DR-TB) and latent TB infection (LTBI), rapid diagnosis of DR-TB and LTBI has become a challenge for the prevention and control of TB. Herein, we highlight these challenges and discuss emerging clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics in TB detection. Currently, the clinical diagnosis of M. tuberculosis infection mainly depends on pathogenic and molecular biological methods, including sputum smear, sputum culture, and Xpert. Although CRISPR-based diagnostics have not been applied to the clinical diagnosis of TB, they have shown exciting preponderances in TB diagnosis compared with traditional methods, including higher sensitivity, less sample input, and shorter turnaround time. CRISPR-based diagnostics represent a potential tool to address the challenges and natural weaknesses associated with traditional TB diagnosis methods. Based on the currently available data, we suggest that future CRISPR-based TB diagnostics should be developed in the direction of automation, modularization, diversification, and intelligence. By combining the CRISPR platform with various systems, such as microfluidic chips, droplet microfluidics, electrochemical techniques, and optical systems, the specificity and sensitivity of TB diagnosis may be revolutionized. [ABSTRACT FROM AUTHOR]

The rapid identification of patients infected with COVID-19 during the SARS-CoV-2 pandemic is critical to operating emergency rooms effectively. Xpert Xpress SARS-CoV-2 (Xpert) assays are increasingly being used in the rapid screening of COVID-19. We evaluated the clinical performance of Xpert by comparing findings with those of qRT-PCR evaluations and included the clinical features of patients visiting the emergency department. Positive results with Xpert testing (n = 370) were compared with qRT-PCR findings, demonstrating a 91.9% intertest agreement. We reviewed the subsequent COVID-19 test results and SARS-CoV-2 infection histories for individuals showing discrepancies in Xpert and qRT-PCR testing and determined whether the findings were true-positive or false-positive. The true-positive rate for Xpert testing was 95.4% (353/370); the remaining 17 samples (4.6%) were false-positive. All false-positive data for Xpert testing showed N2 signals amplified to Ct values of ≥40 with no E gene signals. Rapid Xpert testing is highly sensitive and shows a good performance overall in challenging situations, such as an emergency room. However, we considered the possibility of false-positive Xpert results given an N2 gene signal only, especially given high Ct values. We recommend interpreting test data with caution and considering retesting over time. [ABSTRACT FROM AUTHOR]

Background: Distinguishing nontuberculous mycobacteria pulmonary disease (NTM-PD) from pulmonary tuberculosis (PTB) is a challenge especially in patients with positive sputum smear of acid-fast bacilli (AFB). This study aimed to compare and identify the clinical characteristics between the two diseases among patients with positive sputum AFB., Methods: From February 2017 through March 2021, patients with positive sputum AFB were reviewed in two hospitals of China. Among them, clinical data of NTM-PD and PTB patients was collected and compared., Results: 76 cases of NTM-PD and 92 cases of PTB were included in our study. When compared with PTB, NTM-PD patients were older (59.2 ± 11.4 vs 44.2 ± 19.5 years, P < 0.001) and manifested more hemoptysis and dyspnea (28.9 % vs 14.1 %, P < 0.05; 48.7 % vs 17.4 %, P < 0.001 respectively). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) for Xpert were 85.9 %, 96.1 %, 96.3 %, 84.9 %, respectively, compared to 94.2 %, 81.1 %, 83.1 %, 93.5 %, respectively for T-spot in diagnosing PTB. In radiological features, NTM-PD affected more lobes (4.53 ± 0.89 vs 3.61 ± 1.41, P < 0.001) and showed more consolidation (50 % vs 32.6 %, P < 0.05), destroyed lung (22.7 % vs 9.8 %, P < 0.05), honeycomb lung (26.7 % vs 6.5 %, P < 0.001) but less nodules (80.3 % vs 95.7 %, P < 0.05), tree-in-bud sign (49.3 % vs 87 %, P < 0.001), and satellite nodules (14.5 % vs 90.2 %, P < 0.001) than PTB. Age (odds ratio [OR], 1.043; 95 % confidence interval [CI], 1.018-1.069, P < 0.05), hemoptysis (OR, 3.552; 95%CI, 1.421-8.729, P < 0.05), and dyspnea (OR, 2.631; 95%CI, 1.151-6.016, P < 0.05) were independently correlated with NTM infection., Conclusions: NTM-PD and PTB share similar clinical manifestations. Among them, advanced age, hemoptysis, and dyspnea are the independent predictors for NTM infection. Xpert is an efficiency analysis in discriminating between NTM-PD and PTB in patients with positive sputum AFB., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Objectives: We investigated if Xpert MTB/RIF (Xpert) testing on urine samples among newly diagnosed HIV-patients as an adjunctive test to Xpert testing on sputum increases diagnosis. We sought to define subgroups of patients, for whom testing with either test is especially advantageous. Methods: We included patients >15 years, newly diagnosed with HIV, that delivered a urine sample on the day of HIV-diagnosis at the biggest HIV-clinic in Guinea-Bissau between September 5, 2016 and October 13, 2017 into a cross-sectional study. Patients were asked for a sputum sample, which was Xpert tested if returned within 30 days. A questionnaire and physical examination were completed on day of inclusion. Results: We included 390 patients. TB prevalence was 12.6%. Adding Xpert urine test to all newly diagnosed HIV-patients increased diagnostic yield of TB by 58% compared with testing on sputum alone. Patients who tested positive by Xpert on urine samples were clinically similar to those tested with sputum, except that the sputum positives reported more cough (p=0.03). Conclusions: Indiscriminate Xpert urine testing in newly diagnosed HIV-patients with advanced disease increased diagnostic yield. Xpert testing for TB on urine and sputum should be offered as screening in Guinea-Bissau and possibly in similar settings.

Background: Clostridioides difficile is the number one cause of hospital-acquired diarrhoea. Accurate diagnosis of C. difficile is of utmost importance as it guides patient management and infection control practices. Studies evaluating the performance of commercially available nucleic acid amplification tests (NAATs) versus algorithms are lacking in resource-limited settings. Objective: This study assessed the performance of three commercially available tests and a two-step approach for the diagnosis of C. difficile infection using toxigenic culture (TC) as the gold standard. Methods: Two hundred and twenty-three non-duplicate loose stool samples were submitted to the National Health Laboratory Service Microbiology Laboratory at Tygerberg Hospital, Cape Town, South Africa, from October 2017 to October 2018. The samples were tested in parallel using the C. DIFF QUIK CHEK COMPLETE enzyme immunoassay (EIA) and two NAATs (Xpert C. difficile and BD MAX Cdiff), and the results were compared to TC. The performance of a two-step approach consisting of the C. DIFF QUIK CHEK COMPLETE followed by the Xpert C. difficile was also determined. Results: Of 223 faecal specimens tested, 37 (16.6%) were TC-positive. The sensitivity and specificity of the C. DIFF QUIK CHEK COMPLETE were 54.1% and 98.9%; Xpert C. difficile, 86.4% and 96.8%; BD MAX Cdiff, 89.2% and 96.8%; and two-step approach, 89.2% and 96.2%. Conclusion: The C. DIFF QUIK CHEK COMPLETE, in a two-step approach with the Xpert C. difficile, performed similarly to the NAATs on their own and offer advantages in terms of cost and workflow in low-resource settings.

A variety of commercially available urinary molecular markers have been introduced for detecting and monitoring urothelial carcinoma (UC). We prospectively evaluated the UroVysionTM Bladder Cancer Kit (FISH) and the Xpert® Bladder Cancer Detection (Xpert) test. Both tests were performed on voided urine samples after negative cystoscopy and negative abdominal ultrasound (US) and/or negative computed tomography urography (CTU). Urine specimens from 156 patients diagnosed with hematuria and suspected of having UC and 48 patients followed up after treatment of UC were analyzed using FISH and Xpert. Among 204 patients, 20 had UC, 11 located in the bladder, six in the ureter, and three in the renal pelvis. FISH had an overall sensitivity (SN) of 78%, a specificity (SP) of 93%, and a negative predictive value (NPV) of 96%. Xpert had an overall SN of 90%, an SP of 85%, and an NPV of 98%. Both tests had high SN, SP, and NPV. The SP of FISH was significantly higher. By using FISH and Xpert in addition to cystoscopy, renal and bladder US, and/or CTU in the diagnostic workup of patients with hematuria and follow-up after transurethral resection of the bladder (TURB), a substantial number of patients (10%) otherwise missed were discovered to have UC. [ABSTRACT FROM AUTHOR]

Abstract Background Molecular assays are important tools for pathogen detection but need to be periodically re-evaluated with the discovery of additional genetic diversity that may cause assays to exclude target taxa or include non-target taxa. A single well-developed assay can find broad application across research, clinical, and industrial settings. Pathogen prevalence within a population is estimated using such assays and accurate results are critical for formulating effective public health policies and guiding future research. A variety of assays for the detection of Staphylococcus aureus are currently available. The utility of commercial assays for research is limited, given proprietary signatures and lack of transparent validation. Results In silico testing of existing peer-reviewed assays show that most suffer from a lack of sensitivity and specificity. We found no assays that were specifically designed and validated for quantitative use. Here we present a qPCR assay, SaQuant, for the detection and quantification of S. aureus as might be collected on sampling swabs. Sensitivity and specificity of the assay was 95.6 and 99.9 %, respectively, with a limit of detection of between 3 and 5 genome equivalents and a limit of quantification of 8.27 genome equivalents. The presence of DNA from non-target species likely to be found in a swab sample, did not impact qualitative or quantitative abilities of the assay. Conclusions This assay has the potential to serve as a valuable tool for the accurate detection and quantification of S. aureus collected from human body sites in order to better understand the dynamics of prevalence and transmission in community settings.

A variety of commercially available urinary molecular markers have been introduced for detecting and monitoring urothelial carcinoma (UC). We prospectively evaluated the UroVysionTM Bladder Cancer Kit (FISH) and the Xpert® Bladder Cancer Detection (Xpert) test. Both tests were performed on voided urine samples after negative cystoscopy and negative abdominal ultrasound (US) and/or negative computed tomography urography (CTU). Urine specimens from 156 patients diagnosed with hematuria and suspected of having UC and 48 patients followed up after treatment of UC were analyzed using FISH and Xpert. Among 204 patients, 20 had UC, 11 located in the bladder, six in the ureter, and three in the renal pelvis. FISH had an overall sensitivity (SN) of 78%, a specificity (SP) of 93%, and a negative predictive value (NPV) of 96%. Xpert had an overall SN of 90%, an SP of 85%, and an NPV of 98%. Both tests had high SN, SP, and NPV. The SP of FISH was significantly higher. By using FISH and Xpert in addition to cystoscopy, renal and bladder US, and/or CTU in the diagnostic workup of patients with hematuria and follow-up after transurethral resection of the bladder (TURB), a substantial number of patients (10%) otherwise missed were discovered to have UC.

BackgroundSpinal tuberculosis (TB) is one of the most common forms of extrapulmonary tuberculosis, causing increased morbidity and lifelong disabilities. Here, we conducted a retrospective study to determine the impact on patient outcomes of the Xpert MTB/RIF test vs. phenotypical drug susceptibility testing for spinal TB.MethodsIn-patients with spinal TB were enrolled in 2013 and 2017 at Beijing Chest Hospital. Data were collected from an electronic patient record system that documented demographic and clinical characteristics. All the patients were routinely followed-up at 1, 3, 6, 9, and 12 months after surgery during outpatient treatment.ResultsA total of 361 patients affected by spinal TB were enrolled in our analysis, including 178 patients in 2013 and 183 patients in 2017. In 2013, the cumulative postoperative recurrence rate of patients with spinal TB was 23% (41/178), which was significantly higher than that in 2017 (8.2%, 15/183, P < 0.001). Additionally, the patients with spinal TB diagnosed in 2013 relapsed significantly sooner than those in 2017 (P < 0.001). In the multivariate analysis, rifampicin (RIF) resistance was associated with the recurrence of spinal TB. The turnaround time of Xpert ranged from 1 to 3 days, with a median of 1 day (IQR: 1–2). For the phenotypic drug susceptibility test (pDST)-based algorithm, the median turnaround time was 67 days, considerably longer than that of the Xpert-based algorithm (P < 0.001).ConclusionThe RIF resistance is an independent risk factor for postoperative recurrence in patients with spinal TB. Early detection of RIF resistance due to the application of Xpert is an effective strategy to reduce spinal TB recurrence.

Background: Xpert MTB/Rif, a molecular test to detect tuberculosis (TB), has been proven to have high sensitivity and specificity when compared with liquid culture in clinical settings. However, little is known about its performance in community TB screening.Methods: In Vietnam, a national TB prevalence survey was conducted in 2017. Survey participants who screened positive by chest X-ray, cough symptoms and/or recent history of tuberculosis were requested to provide at least two sputum samples that were tested for Mycobacterium tuberculosis by Xpert MTB/Rif G4 (Xpert) and BACTEC MGIT960 culture (MGIT).Results: There were 4,649 eligible participants provided both samples for testing. Among them, 236 (5.1%) participants tested positive for TB by Xpert, 244 (5.3%) tested positive by MGIT and 317 tested positive by at least one test; 163 (51.4%) had discordant test results. Of the positive Xpert, 162 (68.6%) showed a low or very low bacterial load. In multivariate logistic regression comparing discordant with Xpert-MGIT concordant positive results, discordant Xpert-positive results occurred more often among participants who had low sputum bacterial load, male sex, a history of TB treatment, or night sweats. The associated factors were male sex, abnormal chest X-ray and having night sweats when the logistic model was against those with both Xpert and MGIT negative.Conclusions: We found high rates of discordance in the performance of Xpert and MGIT for community-based TB case finding. In situations where the majority of TB cases are expected to have a low bacterial load, multiple diagnostic tests and/or multiple samples are required to reach sufficient sensitivity. [ABSTRACT FROM AUTHOR]

Severe lower respiratory tract infection is a common issue in Intensive Care Units that causes significant morbidity and mortality. The traditional diagnostic-therapeutic approach has been grounded on taking respiratory samples and/or blood cultures as soon as possible and starting empirical antibiotic therapy addressed to cover most likely pathogens based on the presence of the patient's risk factors for certain microorganisms, while waiting for the culture results in the following 48-72 hours to adequate the antibiotic treatment to the sensitivity profile of the isolated pathogen. Unfortunately, this strategy leads to use broad-spectrum antibiotics more times than necessary and does not prevent possible therapeutic failures. The recent development of rapid molecular diagnostic techniques, based on real time polymerase chain reaction (RT-PCR), makes it possible to determine the causative agent and its main resistance pattern between 1 and 5 hours after sampling (depending on each technique), with high precision, some of them reaching a negative predictive value greater than 98%, facilitating the very early withdrawal of unnecessary broad-spectrum antibiotics. Its high sensitivity can also detect unsuspected pathogens based on risk factors, allowing adequate treatment in the first hours of stay. This short review discusses the potential usefulness of these techniques in critically ill patients with lower respiratory tract infection and advocates their immediate implementation in clinical practice. [ABSTRACT FROM AUTHOR]

Abstract Background Xpert MTB/RIF (Xpert) has been recommended by WHO as the initial diagnostic test for TB and rifampicin-resistance detection. Existing evidence regarding its uptake is limited to public health systems and corresponding resource and infrastructure challenges. It cannot be readily extended to private providers, who treat more than half of India’s TB cases and demonstrate complex diagnostic behavior. Methods We used routine program data collected from November 2014 to April 2017 from large-scale private sector engagement pilots in Mumbai and Patna. It included diagnostic vouchers issued to approximately 150,000 patients by about 1400 providers, aggregated to 18,890 provider-month observations. We constructed three metrics to capture provider behavior with regards to adoption of Xpert and studied their longitudinal variation: (i) Uptake (ordering of test), (ii) Utilization for TB diagnosis, and (iii) Non-adherence to negative results. We estimated multivariate linear regression models to assess heterogeneity in provider behavior based on providers’ prior experience and Xpert testing volumes. Results Uptake of Xpert increased considerably in both Mumbai (from 36 to 60.4%) and Patna (from 12.2 to 45.1%). However, utilization of Xpert for TB diagnosis and non-adherence to negative Xpert results did not show systematic trends over time. In regression models, cumulative number of Xpert tests ordered was significantly associated with Xpert uptake in Patna and utilization for diagnosis in Mumbai (p-value

OBJECTIVES: Despite the acute and life-threatening repercussions that tuberculosis (TB) may have on the burgeoning older population in endemic countries like India, the spectrum of geriatric TB emergencies is not adequately understood. METHODS: We performed a prospective observational study at the emergency department of an academic hospital in north India between January 2019 and June 2020, investigating the clinical and laboratory features and outcomes of active TB in older patients aged 60 years and above. RESULTS: Out of 71 geriatric TB emergencies, central nervous system disease predominated (n = 41, 57.7%), followed by pulmonary (n = 16, 22.5%), pleural TB (n = 8, 11.3%), and multisite involvement (n = 6, 8.4%). Nearly 71.8% were male, and 77.4% belonged to low socioeconomic status (lower-middle or lower class). Usual predisposing factors were tobacco smoking (38.0%), chronic alcohol use (27.0%), and diabetes mellitus (23.9%). Atypical features were more frequent with extrapulmonary TB. Only 28.2% were microbiologically confirmed cases, and rifampicin resistance was seen in only one case. The mortality rate was considerably high (24.0%), highest with pulmonary TB (37.0%). CONCLUSION: Older patients with TB emergencies have atypical presentations, diagnostic difficulties, and high mortality.

Objectives: Subclinical tuberculosis (TB) represents a substantial proportion of individuals with TB disease, although limited evidence is available to understand the epidemiological characteristics of these cases. We aimed to explore the prevalence of subclinical patients with TB and identify the underlying association between the subclinical TB cases in the study setting and the Beijing genotype. Methods: A retrospective study was conducted among patients with incident TB at the Fifth People's Hospital of Suzhou between January and December 2018. A total of 380 patients with TB were included in our analysis. Results: Of the 380 patients, 81.8% were active TB cases, whereas the other 18.2% were subclinical TB cases. Compared with patients aged 65 years and older, the risk of having subclinical TB is higher among younger patients. The use of smear, culture, and Xpert identified 3, 16, and 13 subclinical TB cases, respectively. When using a combination of positive culture and Xpert results, the sensitivity improved to 33.3%. In addition, the neutrophil-to-lymphocyte ratio was significantly elevated in the active TB group compared with that in the subclinical TB group. We also observed that the proportion of the Beijing genotype in the subclinical TB group was significantly lower than that in the active TB group. Conclusion: To conclude, our data demonstrate that approximately one-fifth of patients with TB were subclinical in Suzhou. Mycobacterium tuberculosis could be detected by the existing microbiologic diagnostics in one-third of patients with subclinical TB. The patients with subclinical TB are more prone to having low neutrophil-to-lymphocyte ratio values than those with active TB. Additionally, non-Beijing genotype strains are associated with subclinical TB. [ABSTRACT FROM AUTHOR]

Background: Clostridioides difficile is the number one cause of hospital-acquired diarrhoea. Accurate diagnosis of C. difficile is of utmost importance as it guides patient management and infection control practices. Studies evaluating the performance of commercially available nucleic acid amplification tests (NAATs) versus algorithms are lacking in resource-limited settings. Objective: This study assessed the performance of three commercially available tests and a two-step approach for the diagnosis of C. difficile infection using toxigenic culture (TC) as the gold standard. Methods: Two hundred and twenty-three non-duplicate loose stool samples were submitted to the National Health Laboratory Service Microbiology Laboratory at Tygerberg Hospital, Cape Town, South Africa, from October 2017 to October 2018. The samples were tested in parallel using the C. DIFF QUIK CHEK COMPLETE enzyme immunoassay (EIA) and two NAATs (Xpert C. difficile and BD MAX Cdiff), and the results were compared to TC. The performance of a two-step approach consisting of the C. DIFF QUIK CHEK COMPLETE followed by the Xpert C. difficile was also determined. Results: Of 223 faecal specimens tested, 37 (16.6%) were TC-positive. The sensitivity and specificity of the C. DIFF QUIK CHEK COMPLETE were 54.1% and 98.9%; Xpert C. difficile , 86.4% and 96.8%; BD MAX Cdiff, 89.2% and 96.8%; and two-step approach, 89.2% and 96.2%. Conclusion: The C. DIFF QUIK CHEK COMPLETE , in a two-step approach with the Xpert C. difficile , performed similarly to the NAATs on their own and offer advantages in terms of cost and workflow in low-resource settings. [ABSTRACT FROM AUTHOR]

ABSTRACT Decreased susceptibility to carbapenems in Enterobacterales is an emerging concern. Conventional methods with short turnaround times are crucial for therapeutic decisions and infection control. In the current study, we used the Xpert CARBA-R (Cepheid, Sunnyvale, CA, USA) and the NG-Test CARBA 5 (NG Biotech, Guipry, France) assays for carbapenemase detection in 214 carbapenem-resistant Enterobacterales (CRE) blood isolates. We used the modified carbapenem inactivation method, conventional PCR, and sequencing to determine the production of five common carbapenemase families and their subtypes. We performed wzc-genotyping for all CR-Klebsiella pneumoniae (CRKP) and multilocus sequence typing for all carbapenemase-producing CRE isolates to reveal their genetic relatedness. The results showed a sensitivity of 99.8% and a specificity of 100% by the Xpert assay, and a sensitivity of 100% and a specificity of 99% by the NG-Test in detecting carbapenemases of 84 CRKP isolates with only one (VIM-1+IMP-8) failure in both tests. For CR-Escherichia coli, four carbapenemase-producing isolates were detected accurately for their subtypes. The two major clones of carbapenemase-producing CRKP isolates in Taiwan were ST11-K47 producing KPC-2 (n = 47) and ST11-K64 producing OXA-48-like (n = 9). Our results support the use of either test in routine laboratories for the rapid detection of common carbapenemases. Caution should be taken using the Xpert assay in areas with a high prevalence of CRE carrying blaIMP-8. IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) are emerging worldwide, causing nosocomial outbreaks and even community-acquired infections since their appearance 2 decades ago. Our previous national surveillance of CPE isolates in Taiwan identified five carbapenemase families (KPC, OXA, NDM, VIM, and IMP) with the KPC-2 and OXA-48-like types predominant. Timely detection and classification of carbapenemases in CPE may be a useful test to guide optimal therapy and infection control. Genetic detection methods using the Xpert CARBA-R assay and the immunochromatographic assay using the NG-Test CARBA 5 have been validated with the advantage of short turnaround time. Our study demonstrated that the NG and Xpert assays are convenient methods to accurately identify carbapenemases in carbapenem-resistant Klebsiella pneumoniae and carbapenem-resistant Escherichia coli blood isolates. Detecting IMP variants remains challenging, and the results of Xpert CARBA-R assay should be carefully interpreted.

Objectives: Subclinical tuberculosis (TB) represents a substantial proportion of individuals with TB disease, although limited evidence is available to understand the epidemiological characteristics of these cases. We aimed to explore the prevalence of subclinical patients with TB and identify the underlying association between the subclinical TB cases in the study setting and the Beijing genotype.Methods: A retrospective study was conducted among patients with incident TB at the Fifth People’s Hospital of Suzhou between January and December 2018. A total of 380 patients with TB were included in our analysis.Results: Of the 380 patients, 81.8% were active TB cases, whereas the other 18.2% were subclinical TB cases. Compared with patients aged 65 years and older, the risk of having subclinical TB is higher among younger patients. The use of smear, culture, and Xpert identified 3, 16, and 13 subclinical TB cases, respectively. When using a combination of positive culture and Xpert results, the sensitivity improved to 33.3%. In addition, the neutrophil-to-lymphocyte ratio was significantly elevated in the active TB group compared with that in the subclinical TB group. We also observed that the proportion of the Beijing genotype in the subclinical TB group was significantly lower than that in the active TB group.Conclusion: To conclude, our data demonstrate that approximately one-fifth of patients with TB were subclinical in Suzhou. Mycobacterium tuberculosis could be detected by the existing microbiologic diagnostics in one-third of patients with subclinical TB. The patients with subclinical TB are more prone to having low neutrophil-to-lymphocyte ratio values than those with active TB. Additionally, non-Beijing genotype strains are associated with subclinical TB.

Introduction: Early diagnosis and successful treatment of drug-resistant tuberculosis (TB) demands rapid, precise, and consistent diagnostic methods to minimise the development of resistance. Therefore, this comparative study was designed to evaluate the diagnostic performance of Xpert (MTB/RIF) and Line probe assay (LPA) for detecting drug-resistant TB., Methodology: This study comprised 389 (279 pulmonary and 110 extrapulmonary) samples from patients suspected of having TB. All samples were subjected to Xpert (MTB/RIF), LPA, solid culture, and drug-susceptibility testing. Out of 320 samples, only 180 culture (gold standard) positive were included in the final evaluation. The diagnostic characteristics for methods used were determined by calculating diagnostic sensitivity, specificity, and predictive values. The agreement between all methods was determined by calculating the kappa coefficient., Results: The sensitivity and specificity for Xpert (MTB/RIF) for detecting TB were 88.5% and 96.4%, respectively, against the solid culture. On the other hand, LPA showed sensitivity and specificity at 94.3% and 100%, respectively. Xpert (MTB/RIF) showed moderate agreement (kappa 0.65, p < 0.01) - (73.3% sensitivity; 97.6% specificity) for the detection of rifampicin resistance. However, LPA achieved better diagnostic accuracy (kappa 0.80, p < 0.01) - (84.6% sensitivity; 98.4% specificity) against drug-resistant TB., Conclusions: Xpert (MTB/RIF) and LPA have outstanding diagnostic sensitivity and specificity against RIF resistance with a shorter turnaround time, which could result in a substantial therapeutic outcome. Our findings showed LPA superiority over Xpert (MTB/RIF) for drug resistance. However, due to operational challenges, the requirement of technical expertise and infrastructure issues, LPA cannot be used as point-of-care testing in resource-limited countries., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2024 Shahida Hussain, Sikander Sultan, Saba Riaz, Hajra Hussain, Hasnain Javed, Rabia Mazhar.)

This study compared the performance of two commercial molecular assays, the STANDARD M10 Clostridioides difficile assay (M10) and the Xpert C. difficile assay (Xpert), for detecting toxigenic C. difficile in stool specimens. A total of 487 consecutive stool specimens submitted for routine C. difficile testing between June and November 2023 were included. Following routine testing using C. DIFF QUIK CHEK COMPLETE (QCC), M10 and Xpert were tested in parallel, alongside toxigenic culture (reference standard). Additionally, two-step algorithms, using QCC on the first step and either M10 or Xpert on the second step, were assessed. Both M10 and Xpert demonstrated a sensitivity and negative predictive value (NPV) of 100%. M10 exhibited significantly higher specificity and positive predictive value (PPV; 91.9% and 64.2%, respectively) than Xpert (90.3% and 59.8%, respectively). Both two-step algorithms showed a sensitivity and NPV of 98.4% and 99.8%, respectively. The specificity and PPV of the two-step algorithm using M10 (95.2% and 75.0%, respectively) were slightly higher than those of the one using Xpert (94.8% and 73.2%, respectively), without statistical significance. Receiver operating characteristic curve analysis, assessing the predictive ability of cycle threshold (Ct) values for the detection of free toxin, exhibited an area under the curve of 0.825 for M10 and 0.843 for Xpert. This indicates the utility of Ct values as predictors for the detection of free toxin in both assays. In conclusion, M10 proves to be an effective diagnostic tool with performance comparable to Xpert, whether utilized independently or as part of a two-step algorithm., Competing Interests: This study was funded by SD Biosensor, South Korea. The sponsor was not involved in the study design, data interpretation, or preparation of the manuscript.

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis, which infects more than 23% of the world’s population. With the emergence of drug-resistant TB (DR-TB) and latent TB infection (LTBI), rapid diagnosis of DR-TB and LTBI has become a challenge for the prevention and control of TB. Herein, we highlight these challenges and discuss emerging clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics in TB detection. Currently, the clinical diagnosis of M. tuberculosis infection mainly depends on pathogenic and molecular biological methods, including sputum smear, sputum culture, and Xpert. Although CRISPR-based diagnostics have not been applied to the clinical diagnosis of TB, they have shown exciting preponderances in TB diagnosis compared with traditional methods, including higher sensitivity, less sample input, and shorter turnaround time. CRISPR-based diagnostics represent a potential tool to address the challenges and natural weaknesses associated with traditional TB diagnosis methods. Based on the currently available data, we suggest that future CRISPR-based TB diagnostics should be developed in the direction of automation, modularization, diversification, and intelligence. By combining the CRISPR platform with various systems, such as microfluidic chips, droplet microfluidics, electrochemical techniques, and optical systems, the specificity and sensitivity of TB diagnosis may be revolutionized.