Search Results (197)

Background/Objectives: The rapid identification of carbapenemase genes directly from positive blood culture (BC) samples shortens the time needed to initiate optimal antimicrobial therapy for Carbapenemase-Producing Enterobacterales (CPE) infections. Several commercial automated PCR systems are available for detecting CPE resistance genes but are expensive. The Xpert^® Carba-R assay (Cepheid GeneXpert System) has high sensitivity and specificity for the detection of carbapenamase genes from bacterial colonies or rectal swabs, with an affordable price. This assay was not used for positive BC testing of CPE resistance genes. Whole-Genome Sequencing (WGS) for resistance genes can be used as the gold standard at a research level. In this study, we evaluated the performance of the Xpert^® Carba-R assay for the early detection of carbapenamase genes directly from positive BCs, using WGS as the gold standard. Methods: A prospective observational study was conducted at Children’s Cancer Hospital-Egypt (CCHE-57357). All positive BCs underwent direct gram staining and conventional cultures. A total of 590 positive BCs containing Gram-negative rods (GNRs) were identified. The Xpert^® Carba-R assay was used to detect carbapenemase genes directly from the positive BC bottle compared with WGS results. Results: Among the 590 GNR specimens, 178 were found to carry carbapenemase genes using the Xpert^® Carba-R assay, with results obtained in approximately one hour. The main genotypes detected were bla_NDM, bla_OXA-48-like, and dual bla_NDM/bla_OXA-48-like at 27%, 29%, and 33%, respectively. The agreement between Xpert^® Carba-R assay and WGS results was almost perfect for the genotype resistance pattern of isolates and individual gene detection. Conclusions: The use of the Xpert^® Carba-R assay directly from BC bottles was an easy-to-use, time-saving, affordable tool with high accuracy in identifying carbapenemase genes and, thus, shortens the time needed to initiate optimal antimicrobial therapy for CPE infections. Full article

Background: Tuberculous meningitis (TBM) is the most severe form of tuberculosis and is associated with high morbidity and mortality, especially in resource-limited settings. In Mozambique, where both tuberculosis and HIV are highly prevalent, TBM poses significant diagnostic and therapeutic challenges. This study aimed to describe the clinical characteristics and to identify predictors of TBM mortality among persons living with HIV (PLWH) in a rural hospital in Mozambique. Methods: We conducted a retrospective cohort study at Carmelo Hospital of Chokwe (CHC) between 2015 and 2020. We included 372 PLWH diagnosed with TBM (PTBM); data on demographics, clinical presentation, and laboratory findings were extracted from patient records. TBM diagnosis was considered for confirmed cases based on a hospital-adapted algorithm incorporating clinical features, cerebrospinal fluid (CSF) analysis, TB-LAM, and Xpert MTB/RIF testing. Cox proportional hazard models were used to identify independent predictors of mortality, and Kaplan–Meier survival curves with log-rank tests were used to assess survival differences across clinical subgroups. Significance was considered at a p value ≤ 0.05 with an adjusted hazard ratio (AHR) 95% CI in the multivariate analysis. Results: Overall, 372 PTBM contributed to a total of 3720 person-months (PM) of treatment follow-up, corresponding to a mortality incidence of 3.76 deaths per 100 person-months. Factors independently associated with increased mortality included male sex (adjusted hazard ratio [aHR]: 1.80; 95% CI: 1.21–2.68; p = 0.004), BMI < 18.5 kg/m² (aHR: 2.84; 95% CI: 1.46–5.55; p = 0.002), Immunovirological failure to ART (aHR: 2.86; 95% CI: 1.56–5.23; p = 0.001), CSF opening pressure >40 cmH₂O (aHR: 2.67; 95% CI: 1.46–4.86; p = 0.001), and TBM severity grading III (aHR: 4.59; 95% CI: 1.79–11.76; p = 0.001). TBM involving other organs also significantly worsened survival (aHR: 2.03; 95% CI: 1.27–3.25; p = 0.003). Conclusions: TBM mortality in PLWH was driven by ART failure, high CSF pressure, and malnutrition. Male sex and severe neurology also increased risk. Urgent interventions are proposed: optimize ART, manage intracranial pressure, provide nutritional support, and use corticosteroids. An integrated care approach is essential to improving survival in resource-limited settings. Full article

Background: Tuberculosis (TB) remains a leading cause of death among people living with HIV (PLWH), yet diagnostic methods vary in accuracy, accessibility, and implementation. Understanding how diagnostic modality influences TB detection is essential to optimizing co-infection management. Methods: We conducted a retrospective analysis of institutional data from Bamrasnaradura Infectious Diseases Institute (BIDI), Thailand, covering 2016–2023. TB detection rates were assessed across five diagnostic methods—chest radiography (CXR), smear microscopy, acid-fast bacilli (AFB) staining, culture, and GeneXpert MTB/RIF—relative to annual HIV-related visit volumes. Results: Among 56,599 HIV-related visits, TB detection rates varied substantially by diagnostic method. CXR was the most commonly used tool, detecting TB in up to 99 cases out of 6964 visits (1.42%) in 2016, though declining to 23 cases out of 6947 visits (0.33%) in 2023. GeneXpert was employed more consistently, yielding between 7 cases out of 7577 visits (0.09%) and 13 cases out of 6593 visits (0.20%) annually. Smear microscopy and AFB staining declined markedly, falling below 0.22% after 2020. These patterns reflect a gradual transition toward molecular diagnostics, which offer improved accuracy but remain underutilized in lower-tier settings. To address these gaps, we incorporated trend analyses confirming significant temporal shifts and propose a tiered TB screening framework tailored to resource availability across healthcare levels. Conclusions: TB detection among PLWH is strongly influenced by the diagnostic method used. Unlike HIV diagnosis—which is definitive and standardized—TB diagnosis remains fragmented and resource-dependent. Context-sensitive screening protocols are urgently needed to improve TB case detection and management, particularly in lower-level HIV care facilities. Full article

Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder caused by the BCR::ABL1 fusion gene, resulting from a reciprocal translocation between chromosomes 22 and 9. Quantification of BCR::ABL1 transcript levels in peripheral blood by RT-qPCR represents the gold standard for molecular response (MR) monitoring, providing essential clinical information on treatment efficacy. Xpert^® BCR-ABL Ultra is a fully automated in vitro diagnostic test that quantitatively detects e13a2 and e14a2 BCR::ABL1 transcripts using a single-use cartridge that integrates RNA extraction, cDNA synthesis, nested real-time PCR, and signal detection within a rapid, closed, and user-friendly system. In this study, we evaluated Xpert^® BCR-ABL Ultra as an alternative to validated systems currently used by four highly specialized Italian laboratories affiliated with the Italian national laboratory network for CML. A total of 129 peripheral blood samples from CML patients at various disease stages, along with two external quality control materials, were analyzed. We assessed the test’s repeatability, specificity, and stability. Concordance of BCR::ABL1%IS values generated by the different methods was evaluated using EUTOS criteria and Bland–Altman analysis. Finally, MR value concordance was analyzed based on European LeukemiaNet recommendations or calculated using the formula 2 − log₁₀(BCR::ABL1%IS). Xpert^® BCR-ABL Ultra demonstrated high repeatability and stability. The BCR::ABL1%IS values obtained with this assay showed strong concordance with those generated by local reference methods, and MR classifications were consistent across platforms. These findings confirm the robustness, accuracy, and efficiency of the Xpert^® BCR-ABL Ultra assay, supporting its use as a reliable alternative to currently validated systems for the routine clinical monitoring of CML patients. Full article

Background: In 2023, tuberculosis (TB) caused 1.25 million deaths globally, remaining a leading infectious killer. Central Asia and Southern Caucasus face high TB burdens, particularly Mongolia. This review synthesizes TB prevalence data and diagnostic capabilities in these regions to support public health strategies. Methods: This systematic review aimed to synthesize current data on TB prevalence in Central Asia, Southern Caucasus, and Mongolia to support public health strategies and research priorities. A comprehensive search of PubMed and Google Scholar was conducted for English-language articles published up to 2023. Studies were assessed using a modified Newcastle–Ottawa Scale. Nine studies met the inclusion criteria, covering Kazakhstan, Kyrgyzstan, Uzbekistan, Tajikistan, Turkmenistan, Mongolia, Georgia, Armenia, and Azerbaijan. Results: TB incidence ranged from 67 per 100,000 in Kazakhstan to 190 per 100,000 in Kyrgyzstan, with the highest prevalence of 68.5% in Mongolia. TB affected men more frequently (65.3%), and the key risk factors included HIV (30.5%), comorbidities, and undernutrition. Diagnostic performance varied significantly (microscopy sensitivity, 45–65%; GeneXpert MTB/RIF, 89–96% sensitivity and 98% specificity for rifampicin resistance). Diagnostic turnaround times ranged from hours (molecular) to weeks (conventional). Only 58% of TB facilities had GeneXpert technology, with urban–rural disparities in diagnostic access. Drug-resistant TB imposed a significant economic burden, with treatment costs ranging from USD 106 to USD 3125. Conclusions: Strengthening surveillance, improving data collection, and conducting longitudinal studies are essential for designing effective TB control strategies in these regions. Significant diagnostic gaps persist across these regions, especially with regard to drug-resistant strains. Point-of-care molecular diagnostics, improved algorithms, and expanded laboratory training show promise. Future research should focus on rapid biomarker-based diagnostics, field-deployable technologies for settings with limited resources, and AI integration to enhance diagnostic accuracy and efficiency. Full article

Background/Objectives: The concurrent circulation of SARS-CoV-2 with influenza A and B viruses and respiratory syncytial virus (RSV) represents a new diagnostic challenge in the post-COVID-19 area, especially considering that these infections have overlapping clinical presentations but different approaches to treatment and management. Multiplexed molecular testing on point-of-care platforms that focus on the simultaneous detection of multiple respiratory viruses in a single tube constitutes a useful approach for diagnosis of respiratory infections in decentralized clinical settings. This study evaluated the analytical performances of the VitaSIRO solo™ SARS-CoV-2/Flu/RSV Assay performed on the VitaSIRO solo™ Instrument (Credo Diagnostics Biomedical Pte. Ltd., Singapore, Republic of Singapore). Methods: With a view to accreditation, the criteria of the 2022-revised EN ISO 15189:2022 norma were applied for the retrospective on-site verification of method using anonymized respiratory specimens collected during the last 2024–2025 autumn–winter season in France. Results: Usability and satisfaction were comparable to current reference point-of-care platforms, such as the Cepheid GeneXpert^® Xpress System (Cepheid Diagnostics, Sunnyvale, CA, USA). Repeatability and reproducibility (2.34–4.49% and 2.78–5.71%, respectively) demonstrated a high level of precision. The platform exhibited a low invalid rate (2.9%), with most resolving on retesting. Analytical performance on 301 clinical samples showed high overall sensitivities: 94.8% for SARS-CoV-2 (Ct ≤ 33), 95.8% for influenza A and B viruses, 95.2% for RSV, and 95.4% for all viruses. Specificities were consistently high (99.2–100.0%). False negatives (2.6%) were predominantly associated with high Ct values. Agreement with the comparator reference NeuMoDx™ Flu A-B/RSV/SARS-CoV-2 Vantage Assay (Qiagen GmbH, Hilden, Germany) was almost perfect (Cohen’s κ 0.939–0.974), and a total of 91.1%, 94.8%, and 100.0% of Ct values were within the 95% limits of agreement for the detection of SARS-CoV-2, influenza A and B viruses, and RSV, respectively, by Bland–Altman analyses. Passing–Bablok regression analyses demonstrated good Ct values correlation between VitaSIRO solo™ and NeuMoDx™ assays, with a slight, non-significant, positive bias for the VitaSIRO solo™ assay (mean absolute bias +0.509 to +0.898). Conclusions: These findings support VitaSIRO solo™ Instrument as a user-friendly and reliable point-of-care platform for the rapid detection and differentiation of SARS-CoV-2, influenza A and B viruses, and RSV responding to the EN ISO 15189:2022 criteria for accreditation to be implemented in hospital or decentralized settings. Full article

This study investigates the effectiveness of combining helical piles (HPs) with geogrid reinforcement compared to conventional piles in improving pullout performance in dense sand, addressing a key challenge in reinforced foundation design. A comprehensive experimental program was conducted to evaluate the pullout behavior of HPs embedded in Shahriyar sand reinforced with geogrid layers. The research focused on quantifying the effects of critical parameters—pile configuration, helix pitch, and geogrid placement depth—on ultimate pullout capacity and displacement response to better understand hybrid reinforcement mechanisms. Pullout tests were performed using a Zwick/Roell Z150 universal testing machine with automated data acquisition via TestXpert11 V3.2 software. The experimental program assessed the following influences: (1) pile configurations—plain, single-helix, and double-helix; (2) helix pitch ratios of 1.00, 1.54, and 1.92 (pitch-to-shaft diameter); and (3) geogrid placement depths of 7.69, 11.54, and 15.38 (depth-to-shaft diameter) on pullout behavior. Results demonstrate that geogrid reinforcement substantially enhances pullout resistance, with single-helix HPs achieving up to a 518% increase over plain piles. Pullout resistance is highly sensitive to geogrid spacing, with optimal performance at a non-dimensional distance of 0.47 from the pile–soil interface. Additionally, double-blade HPs with geogrid placed at 0.35 exhibit a 62% reduction in displacement ratio, underscoring the role of geogrid in improving pile stiffness and load-bearing capacity. These findings provide new insights into the synergistic effects of helical pile geometry and geogrid placement for designing efficient reinforced granular foundations. Full article

Background/Objectives. Women living with human immunodeficiency virus (WLWH) have a six-fold higher risk of developing cervical cancer associated with high-risk human Papillomavirus (HR-HPV) than HIV-negative women. We herein assessed HR-HPV genotype distribution and plasma levels of the cancer antigen 125 (CA-125) in WLWH in a rural town in Gabon, in Central Africa. Methods. Adult WLWH attending the local HIV outpatient center were prospectively enrolled and underwent cervical visual inspection and cervicovaginal and blood sampling. HIV RNA load and CA-125 levels were measured from plasma using the Cepheid^® Xpert^® HIV-1 Viral Load kit and BioMérieux VIDAS^® CA-125 II assay, respectively. HPV detection and genotyping were performed via a nested polymerase chain reaction (MY09/11 and GP5+/6+), followed by sequencing. Results. Fifty-eight WLWH (median age: 52 years) were enrolled. Median CD4 count was 547 cells/µL (IQR: 412.5–737.5) and HIV RNA load 4.88 Log₁₀ copies/mL (IQR: 3.79–5.49). HPV prevalence was 68.96%, with HR-HPV detected in 41.37% of women. Among HR-HPV-positive samples, 87.5% (21/24) were genotypes targeted by the Gardasil vaccine, while 12.5% (3/24) were non-vaccine types. Predominant HR-HPV types included HPV-16 (13.8%), HPV-33 (10.34%), HPV-35 (5.17%), HPV-31, and HPV-58 (3.45%). Most participants had normal cervical cytology (62.07%), and a minority (14.29%) had elevated CA-125 levels, with no correlation to cytological abnormalities. Conclusions. In the hinterland of Gabon, WLWH are facing an unsuspected yet substantial burden of cervical HR-HPV infection and a neglected risk for cervical cancer. Strengthening cervical cancer prevention through targeted HPV vaccination, sexual education, and accessible screening strategies will help in mitigating associated risk. Full article

Extrapulmonary tuberculosis (EPTB) remains diagnostically challenging due to its paucibacillary nature and variable presentation. Xpert and culture are limited in EPTB diagnosis due to sampling challenges, low sensitivity, and long turnaround times. This study evaluated the performance of the MPT64 antigen detection test for diagnosing EPTB, particularly tuberculous lymphadenitis (TBLN) and tuberculous pleuritis (TBP), in a high-TB, low-HIV setting. Conducted at Gulab-Devi Hospital, Lahore, Pakistan, this study evaluated the MPT64 test’s performance against conventional diagnostic methods, including culture, histopathology, and the Xpert MTB/RIF assay. Lymph node biopsies were collected, and cell blocks were made from aspirated pleural fluid from patients clinically presumed to have EPTB. Of 338 patients, 318 (94%) were diagnosed with EPTB. For TBLN, MPT64 demonstrated higher sensitivity (84%) than Xpert (48%); for TBP, the sensitivity was 51% versus 7%, respectively. Among histopathology-confirmed TBLN cases, MPT64 outperformed both culture and Xpert (85% vs. 58% and 47%). Due to the low number of non-TB cases, specificity could not be reliably assessed. The MPT64 test shows promise as a rapid, sensitive diagnostic tool for EPTB, particularly TBLN, in routine settings. While sensitivity is notably superior to Xpert, further studies are needed to evaluate its specificity and broader diagnostic utility. Full article

Extra-pulmonary tuberculosis (EPTB) can affect any organ of the body, producing a wide variety of clinical manifestations that make the diagnosis and treatment of EPTB challenging. The optimum treatment varies depending on the site of EPTB, its severity, and response to treatment. There is often uncertainty about the best management practices, with a significant departure from national guidelines. This study aims to identify gaps and barriers in adhering to the national guidelines for the diagnosis and treatment of EPTB. We included 433 patients having EPTB and followed up at predefined intervals of 2 months, 6 months, 9 months, and 12 months. Questionnaire-based interviews of the treating physician and the patients in different departments were conducted. For confirmatory diagnosis, heavy dependence on clinical-radiological diagnosis without microbiological support was observed, which is a deviation from National Tuberculosis Elimination Programme (NTEP) guidelines and raises concerns about the potential for misdiagnosis and overtreatment. Apart from patient delays, long health system delays in EPTB were observed. The median patient delay, health system delay, and total treatment delay times were 4.2, 4, and 10.1 weeks, respectively. To enhance EPTB diagnosis and management, there is a pressing need for improved access to microbiological testing, enhanced physician training on adherence to NTEP guidelines, and greater utilisation of imaging and histopathological techniques. Full article

Tuberculosis (TB) is a global public health issue requiring early and accurate diagnosis. The loop-mediated isothermal amplification (LAMP) assay is a promising alternative recommended by the WHO for the initial diagnosis of pulmonary TB, particularly in resource-limited settings. This study evaluated the sensitivity and specificity of a commercial LAMP assay for TB detection using 198 samples from different countries including Mexico. The LAMP assay results were compared to the results of standard tests: AFB smear microscopy, cell culture, and Xpert PCR. Across all samples, LAMP showed a sensitivity of 96.20% and a specificity of 84.61%. When compared specifically to “true positives” and “true negatives” (defined by the consistency across the standard tests), LAMP demonstrated 100% sensitivity and 92.30% specificity. For context, the sensitivity of AFB smear microscopy against the culture and Xpert tests was 79.04%. A significant finding was that the LAMP test detected a high percentage (92.5%) of samples found positive by the culture and Xpert tests but negative by the AFB smear, highlighting its ability to identify cases missed by traditional microscopy. This study concluded that the LAMP assay is a sensitive and specific tool for TB diagnosis with potential for rapid and accurate diagnosis, especially in resource-limited areas. Full article

Trichomonas vaginalis infection (TVI) is the most common curable sexually transmitted infection (STI). In this study, we aimed to assess the performances of different tests for TVI diagnosis in symptomatic Greek women, evaluating the TVI prevalence rate (PR) in Greece and comparing the latter with TVI-PR estimates from Europe. A laboratory-based cross-sectional analysis and a meta-analysis were conducted. Of 399 symptomatic Greek women, 17 had TVI, corresponding to a TVI-PR of 4.3%. The commercial nucleic acid amplification test (NAAT) achieved a sensitivity of 94.1%, which was 6% higher than the sensitivity of the culture method, 35% higher than that of the wet mount test, and 59% higher than that of the Giemsa stain test. The wet mount test achieved the lowest positive predictive value of 76.9%. All the tests had high specificity levels and negative predictive values. Data from 34 European TVI-PR studies in symptomatic women were pooled. The TVI-PR established in our study was similar to the TVI-PR estimates of 4.8% in Europe and 4.5% in Greece, with the second being higher than those of 2.1% in Northwestern Europe and 1.5% in Southern Europe but closer to that of 6.7% in Türkiye. In Greece, a European country with a relatively high TVI-PR among symptomatic women, the highly sensitive and specific, automated, point-of-care NAAT would facilitate rapid, accurate TVI diagnosis and the treatment of this target population to meet the WHO’s goal of ending STI epidemics by 2030. Full article

Since 2020, the Gs/Gd H5N1 influenza virus (clade 2.3.4.4b) has established itself within wild bird populations across Asia, Europe, and the Americas, causing outbreaks in wild mammals, commercial poultry, and dairy farms. The impacts on the bird populations and the agricultural industry has been significant, requiring a One Health approach to enhanced surveillance in both humans and animals. To support pandemic preparedness efforts, we evaluated the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel for their ability to detect the presence of non-seasonal, zoonotic influenza A viruses, including circulating H5N1 viruses from clade 2.3.4.4b. Both assays effectively detected the presence of influenza virus in clinically-contrived nasal swab and saliva specimens at low concentrations. The results generated using the Cepheid Xpert Xpress CoV-2/Flu/RSV plus kit and the BioFire Respiratory 2.1 Panel, in conjunction with clinical and epidemiological findings provide valuable diagnostic findings that can strengthen pandemic preparedness and surveillance initiatives. Full article

Background: Acute respiratory distress syndrome (ARDS) secondary to tuberculosis (TB) is rare and associated with high mortality. Management is further complicated by comorbidities and ICU-related complications. Methods: We report a 43-year-old woman with post-polio sequelae and uncontrolled diabetes who developed ARDS due to pulmonary TB, complicated by recurrent nosocomial infections and gastrointestinal bleeding. Early bronchoscopy and GeneXpert MTB/RIF PCR were performed on ICU Day 2, enabling anti-TB therapy initiation by ICU Day 3. The patient received lung-protective ventilation, prone positioning, tailored antibiotics, and multidisciplinary care. Results: The patient’s clinical course was complicated by two episodes of ventilator-associated pneumonia and gastrointestinal bleeding, but with individualized management, she achieved ventilator weaning and functional recovery. Conclusions: Early TB recognition in ARDS is crucial. Multidisciplinary ICU management, including prudent steroid use, improves outcomes. Full article

Pneumonia remains a critical health concern, necessitating accurate and automated diagnostic tools. This study proposes a novel approach for the binary classification of pneumonia in chest X-ray images using an adaptive contrast enhancement model and a convolutional neural network (CNN). The enhancement model, an improvement over standard contrast-limited techniques, employs adaptive tile sizing, variance-guided clipping and entropy-weighted redistribution to optimize image quality for pneumonia detection. Applied to the Chest X-Ray Images (Pneumonia) dataset (5856 images), the enhanced images enable the CNN to achieve an accuracy of 98.7%, precision of 99.3%, recall of 98.6% and F1-score of 97.9%, outperforming baseline methods. The model’s robustness is validated through five-fold cross-validation, and its feature extraction is visualized to ensure clinical relevance. Limitations, such as reliance on a single dataset, are discussed, with future evaluations planned for larger datasets like CheXpert and NIH Chest X-ray to enhance generalizability. This approach demonstrates the potential of tailored preprocessing and efficient CNNs for reliable pneumonia classification, contributing to improved diagnostic support in medical imaging. Full article