Search Results (52)

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/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

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

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/Objectives: High rates of sexually transmitted infections (STIs) increase HIV transmission risk among adolescent girls and young women (AGYW) in South Africa. AGYW prefer discreet self-testing options for HIV and pregnancy; however, other STI self-testing options are currently unavailable in this region. Methods: Seven Chlamydia trachomatis (CT), Neisseria gonorrhea (NG) and Trichomonas vaginalis (TV) assays were validated for AGYW self-test use (using self-collected vaginal samples) in a cross-sectional study (PROVE). Paired GeneXpert^® NG/CT (Cepheid_®, Sunnyvale, CA, USA) and OSOM^® Trichomonas test (Sekisui Diagnostics, Burlington, MA, USA) results from nurse-collected samples served as reference results to calculate sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV). One test, the polymerase chain reaction (PCR)-based Visby Medical™ Sexual Health Test device (Visby Medical™, San Jose, CA, USA), was validated for accuracy of positive test results using self-collected samples and home-based testing in a longitudinal follow-up study enrolling AGYW aged 16–18 years. Paired GeneXpert^® NG/CT and TV results from nurse-collected vaginal samples served as reference tests. Results: In PROVE, 146 AGYW contributed 558 paired samples. The Visby Medical™ Sexual Health Test exhibited moderate to high sensitivity (66.7–100%), specificity (80–100%), NPV (66.7–100%), and PPV (66.7–100%) for NG, CT, and TV. The remaining tests’ performances were markedly lower. In the longitudinal study, 28 AGYW contributed 84 paired samples, and the Visby Medical™ Sexual Health Test demonstrated 100% accuracy of positive results for CT, NG, and TV. Conclusions: The Visby Medical™ Sexual Health Test demonstrated high reliability as a potential option for AGYW to discreetly self-test for multiple STIs concurrently. Testing of its acceptability, utility, and feasibility in a larger sample of AGYW is in progress. Full article

Determining the physical parameters of pulsating variable stars such as RR Lyrae is essential for understanding their internal structure, pulsation mechanisms, and evolutionary state. In this study, we present a machine learning framework that uses feedforward artificial neural networks (ANNs) to infer stellar parameters—mass (M), luminosity (log($L/L_{\odot }$)), effective temperature (log($T_{\mathrm{eff}}$)), and metallicity (Z)—directly from Transiting Exoplanet Survey Satellite (TESS) light curves. The network is trained on a synthetic grid of RRab light curves generated from hydrodynamical pulsation models spanning a broad range of physical parameters. We validate the model using synthetic self-inversion tests and demonstrate that the ANN accurately recovers the input parameters with minimal bias. We then apply the trained model to RRab stars observed by the TESS. The observed light curves are phase-folded, corrected for extinction, and passed through the ANN to derive physical parameters. Based on these results, we construct an empirical period–luminosity–metallicity (PLZ) relation: log($L/L_{\odot }$) = (1.458 ± 0.028) log(P/days) + (–0.068 ± 0.007) [Fe/H] + (2.040 ± 0.007). This work shows that ANN-based light-curve inversion offers an alternative method for extracting stellar parameters from single-band photometry. The approach can be extended to other classes of pulsators such as Cepheids and Miras. Full article

de Grijs and Bono (ApJS 2020, 246, 3) compiled a list of distances to M87 from the literature published in the last 100 years. They reported the arithmetic mean of the three most stable tracers (Cepheids, tip of the red giant branch, and surface brightness fluctuations). The arithmetic mean is one of the measures of central tendency of a distribution; others are the median and mode. The three do not align for asymmetric distributions, which is the case for the distance moduli ${\mu }_0$ to M87. I construct a kernel density distribution of the set of ${\mu }_0$ and estimate the recommended distance to M87 as its mode, obtaining ${\mu }_0=\left(31.06\pm 0.001{\left(\mathrm{statistical}\right)}_{-0.06}^{+0.04}\left(\mathrm{systematic}\right)\right)$ mag, corresponding to $D={16.29}_{-0.45}^{+0.30}$ Mpc, which yields uncertainties smaller than those associated with the mean and median. Full article

This paper presents a new model-independent constraint on the Hubble constant ($H_0$) by anchoring relative distances from Type Ia supernovae (SNe Ia) observations to absolute distance measurements from time-delay strong Gravitational Lensing (SGL) systems. The approach only uses the validity of the cosmic distance duality relation (CDDR) to derive constraints on $H_0$. By using Gaussian Process (GP) regression to reconstruct the unanchored luminosity distance from the Pantheon+ compilation to match the time-delay angular diameter distance at the redshift of the lenses, one yields a value of $H_0=75.57\pm 4.415$ km/s/Mpc at a 68% confidence level. The result aligns well with the local estimate from Cepheid variables within the $1\sigma$ confidence region, indicating consistency with late-universe probes. Full article

Background/Objectives: The emergence and spread of carbapenemase-producing Enterobacterales (CPE) represents a significant challenge prompting the need to optimize diagnostic tools to detect CPE carriers. The Xpert^® Carba-R assay (Cepheid, Sunnyvale, CA, USA), a Real-Time PCR-based test, can detect the bla_KPC, bla_VIM, bla_OXA-48, bla_NDM and bla_IMP carbapenemase genes directly from rectal swabs. This study assessed the performance of the Xpert^® Carba-R assay using FecalSwab™ (Copan, Brescia, Italy), a liquid-based collection device. Methods: The first part of the study aimed to establish the FecalSwab^TM volume which gave the most similar Ct values to those obtained by the Transystem™ double swab (Copan). The best volume was then used to assess the limit of detection (LoD) for each target and compare the accuracy of different FecalSwab^TM storage conditions (room temperature or 4 °C after 16 h compared to T₀). Results: The results indicated that using 200 µL of the FecalSwab™ medium provided reliable Ct values, with the lowest number of invalid samples compared to traditional methods. The average LoDs for different carbapenemases ranged from 4.7 × 10³ to 6.8 × 10³ CFU/mL. FecalSwab™ showed a better performance after 16 h at room temperature compared to storage at 4 °C. Conclusions: This study supports single sampling with the FecalSwab™ medium for both molecular and cultural methods, for the potential optimization of CPE screening. Full article

We analyzed the whole genome sequences (WGS) and antibiograms of 35 Enterobacter isolates, including E. hormaechei and E. asburiae, and the recently described E. bugandensis, E. kobei, E. ludwigii, and E. roggenkampii species. Isolates were obtained from human blood and urinary tract infections in patients in the United States. Our goal was to understand the genetic diversity of antimicrobial resistance genes and virulence factors among the various species. Thirty-four of 35 isolates contained an AmpC class bla_ACT allele; however, the E. roggenkampii isolate contained bla_MIR-5. Of the six Enterobacter isolates resistant to ertapenem, imipenem, and meropenem, four harbored a carbapenemase gene, including bla_KPC or bla_NDM. All four isolates were mCIM-positive. The remaining two isolates had alterations in ompC genes that may have contributed to the resistance phenotype. Interpretations of cefepime test results were variable when disk diffusion and automated broth microdilution results were compared due to the Clinical Laboratory and Standards Institute use of the “susceptible dose-dependent” classification. The diversity of the bla_ACT alleles paralleled species identifications, as did the presence of various virulence genes. The classification of recently described Enterobacter species is consistent with their resistance gene and virulence gene profiles. Full article

The diagnosis of Clostridioides difficile infection (CDI) in the pediatric population is complicated by the high prevalence of asymptomatic colonization, particularly in infants. Many laboratory diagnostic methods are available, but there continues to be controversy over the optimal laboratory testing approach to diagnose CDI in children. We evaluated commonly used C. difficile diagnostic commercial tests in our pediatric hospital population at Sidra Medicine in Doha, Qatar. Between June and December 2023, 374 consecutive stool samples from pediatric patients aged 0–18 years old were tested using: Techlab C. diff Quik Chek Complete, Cepheid GeneXpert C. difficile, QIAstat-Dx Gastrointestinal Panel, and culture using CHROMagar C. difficile. The results of these tests as standalone methods or in four different testing algorithms were compared to a composite reference method on the basis of turnaround time, ease of use, cost, and performance characteristics including specificity, sensitivity, negative predictive value, and positive predictive value. Our study showed variability in test performance of the different available assays in diagnosing CDI. In our population, a testing algorithm starting with Cepheid GeneXpert C. difficile PCR assay or QIAstat-Dx Gastrointestinal panel as a screening test followed by toxin immunoassay for positive samples using the Techlab C. diff Quik Chek Complete kit showed the best performance (100% specificity and 100% positive predictive value) when combined with clinical review of the patient to assess risk factors for CDI, clinical presentation, and alternative causes of diarrhea. Full article

Quantitative assessment of nucleophosmin 1 (NPM1) mutation status is integral to evaluating measurable residual disease (MRD) in NPM1-mutated acute myeloid leukemia (AML) patients. In a retrospective study, leftover peripheral blood (PB) specimens (n = 40) which were collected for routine clinical diagnostic evaluations of AML disease burden were tested by both a novel automated RT-qPCR quantitative NPM1 assay (Xpert NPM1 mutation assay) and the NPM1 mutA, mutB&D MutaQuant kit. Based on a Deming regression analysis, there was a high correlation (slope = 0.92; intercept = 0.12; Pearson’s r = 0.982) between the quantitative results of the Xpert NPM1 mutation assay and the NPM1 mutA, mutB&D MutaQuant kit. The Xpert test quantitative results are thus highly correlated with the comparator method and the former has potential as a useful alternative for the monitoring of AML patients with a known NPM1 mutation. Full article

Better diagnostic tools are needed to improve the diagnosis of Clostridioides difficile infections (CDI) and reduce the overtreatment of colonized children. In this study, we evaluated two polymerase chain reaction (PCR) assays (Cepheid GeneXpert C. difficile and the Gastroenteritis PCR Panel by QIAstat-Dx) as a standalone method in combination with the PCR cycle threshold (Ct) value in positive samples to predict the presence of free toxins. We also evaluated the clinical impact of reporting toxin production results and provided comments alongside the PCR results in our pediatric population. PCR-positive stool samples from pediatric patients (aged 2 to 18 years old) were included in our study and tested for the presence of toxins A and B using the C. difficile Quik Chek Complete kit. For the clinical intervention, the CDI treatment rates 6 months pre- and post-intervention were compared. The use of PCR Ct value showed excellent sensitivity (100%) at a Ct value cutoff of 26.1 and 27.2 using the Cepheid GeneXpert C. difficile and the Gastroenteritis PCR Panel by QIAstat-Dx, respectively, while the toxin test showed inferior sensitivity of 64% in the PCR-positive samples. In addition, CDI treatment rates were decreased by 23% post-intervention. The results of our study suggest that nucleic acid amplification test (NAAT) assays supplemented by the use of PCR Ct value for positive samples can be used as standalone tests to differentiate CDI from colonization. Furthermore, the reporting of toxin production along with the PCR results can help reduce the unnecessary treatment of colonized children. Full article

SARS-CoV-2, influenza A/B virus (IAV/IBV), and respiratory syncytial virus (RSV) are among the common viruses causing acute respiratory infections. Clinical diagnosis to differentiate these viruses is challenging due to similar clinical presentations; thus, laboratory-based real-time RT PCR is the gold standard for diagnosis. This retrospective study aimed to evaluate the diagnostic performance of STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor Inc., Seoul, Korea) using archived positive and negative respiratory samples for SARS-CoV-2, IAV, IBV, and RSV. A total of 322 respiratory samples were tested, comprising 215 positive samples (49 SARS-CoV-2, 48 IAV, 53 IBV, 65 RSV) and 107 negative samples. All samples were tested with both STANDARD M10 and compared to either Xpert Xpress SARS-CoV-2 or Xpert Xpress Flu/RSV (Cepheid, Sunnyvale, CA, USA). The sensitivity, specificity, positive predictive value, and negative predictive value rates of STANDARD M10 were very similar to Xpert Xpress SARS-CoV-2 or Xpert Xpress Flu/RSV ranges for each virus (98–100%). The duration of testing and workflows were similar. The overall agreement was 99.4%, including 99.1% agreement for positive samples and 100% agreement for negative samples. In conclusion, the STANDARD M10 point-of-care test is suitable for rapid simultaneous detection of SARS-CoV-2, IAV, IBV, and RSV. Full article

Infections due to antimicrobial resistant gram-negative bacteria cause significant morbidity and mortality in sub-Saharan Africa. To elucidate the molecular epidemiology of antimicrobial resistance in gram-negative bacteria, we characterized beta-lactam and fluoroquinolone resistance determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates collected from November 2017 to February 2018 (Period 1) and October 2021 to January 2022 (Period 2) in a tertiary medical center in north-eastern Nigeria. Whole genome sequencing (WGS) was used to identify sequence types and resistance determinants in 52 non-duplicate, phenotypically resistant isolates. Antimicrobial susceptibility was determined using broth microdilution and modified Kirby–Bauer disk diffusion methods. Twenty sequence types (STs) were identified among isolates from both periods using WGS, with increased strain diversity observed in Period 2. Common ESBL genes identified included bla_CTX-M, bla_SHV, and bla_TEM in both E. coli and K. pneumoniae. Notably, 50% of the E. coli in Period 2 harbored either bla_CTX-M-15 or bla_{CTX-M-1 4} and phenotypically produced ESBLs. The bla_NDM-7 and bla_VIM-5 metallo-beta-lactamase genes were dominant in E. coli and P. aeruginosa in Period 1, but in Period 2, only K. pneumoniae contained bla_NDM-7, while bla_NDM-1 was predominant in P. aeruginosa. The overall rate of fluoroquinolone resistance was 77% in Period 1 but decreased to 47.8% in Period 2. Various plasmid-mediated quinolone resistance (PMQR) genes were identified in both periods, including aac(6′)-Ib-cr, oqxA/oqxB, qnrA1, qnrB1, qnrB6, qnrB18, qnrVC1, as well as mutations in the chromosomal gyrA, parC and parE genes. One E. coli isolate in Period 2, which was phenotypically multidrug resistant, had ESBL bla_CTX-M-15, the serine carbapenemase, bla_OXA-181 and mutations in the gyrA gene. The co-existence of beta-lactam and fluoroquinolone resistance markers observed in this study is consistent with widespread use of these antimicrobial agents in Nigeria. The presence of multidrug resistant isolates is concerning and highlights the importance of continued surveillance to support antimicrobial stewardship programs and curb the spread of antimicrobial resistance. Full article