Search Results (316)

In recent decades, the problem of resistant strains, which present resistance to different types of antimicrobials, has increased. Klebsiella pneumoniae is one of the most important species that exhibits an acquired resistance phenotype to at least one agent in three or more classes of antimicrobials and is thus characterized as a multidrug-resistant bacterium (MDR). 98 nosocomial strains of K. pneumoniae were isolated during the pre-COVID-19 period, and more specifically, from February 2015 to March 2019, were analyzed for the detection of class A, D, and B carbapenemase genes. The existence of KPC, OXA-48 like, IMP, VIM, and NDM carbapenemases has been examined. The immunochromatography showed that NDM carbapenemases are more frequently detected in the samples, reaching a percentage of 30.7%, while correspondingly the percentage for VIM carbapenemases was 7.68% among the strains with resistant phenotypes. No strain with carbapenemase IMP was found. Real-time multiplex polymerase chain reaction (PCR) showed, in contrast to immunochromatography kits, that a high percentage of bacterial isolates (94.26%) carry NDM and VIM carbapenemase genes, while no IMP carbapenemase genes were detected. Regarding the KPC enzymes, the immunochromatography kits showed that KPC positive strains are reaching 53.1%, and OXA-48 positive strains are reaching 3.1% among the strains with resistant phenotypes. Real-time multiplex polymerase chain reaction revealed a much higher percentage of 89.6% KPC positive isolates and a percentage of 14.6% OXA-48 carbapenemase producers. The aforementioned results indicate the dominance of the Multiplex Real-Time PCR as a “gold standard” method. This study could not fully support the usefulness of rapid immunochromatographic tests as a fast and useful diagnostic tool in the laboratory daily routine, as per the results of previous studies. Thus, more studies need to be conducted in this field to introduce these rapid tests safely into the daily laboratory workflow as a screening tool. Additionally, this study underlines the predominance of KPC enzymes from clinical isolates of ICUs and a significant shift over the OXA-48 like enzymes that are not limited to the ICU environment. Full article

Background/Objectives: Acute respiratory infections remain a major global public health concern affecting individuals across all ages. Accurate and rapid diagnosis of respiratory pathogens is crucial for effective patient management and infection control. Multiplex real-time polymerase chain reaction (PCR) assays have gained prominence over conventional methods for routine viral detection in clinical laboratories owing to their enhanced sensitivity and specificity; however, comparative performance data for PowerChek™ RVP remain limited. This study aimed to evaluate the diagnostic performance of the PowerChek™ Respiratory Virus Panel 1/2/3/4, which detects 16 respiratory viruses, including SARS-CoV-2, in nasopharyngeal swab (NPS) specimens. Methods: Overall, 336 NPS specimens were analyzed using the PowerChek™ RVP, BioFire^® RP 2.1plus, and Allplex™ RP assays, with nucleic acid extraction performed using the Advansure™ E3 system. The performance metrics were calculated using two-by-two contingency tables. Results: Among 336 NPS specimens (232 positive, 104 negative), PowerChek™ RVP detected 226 positives with minimal discrepancies, showing high concordance with BioFire^® RP 2.1plus (accuracy 94.6%, kappa 0.843–1.000). Fifteen discordant cases were identified in this study. Eleven could not be sequenced because of amplification failure and most had high Ct values (>30). Sequencing of four samples confirmed concordance with BioFire^® RP 2.1plus and PowerChek™ RVP, whereas Allplex™ RP showed false-negative results. Conclusions: The PowerChek™ RVP assay demonstrated a high level of relative sensitivity, specificity, accuracy, diagnostic predictive values and strong concordance with comparable reference assays in identifying its targets. This assay is a reliable and efficient diagnostic tool for clinical laboratories to facilitate the accurate identification of respiratory pathogens. Full article

Although bovine respiratory syncytial virus (BRSV) is a key contributor to bovine respiratory disease (BRD) worldwide, there are few detailed reports of BRSV-related outbreaks in Brazil. This study describes the clinical, pathological, immunohistochemical (IHC), and molecular findings from a BRD outbreak in adult dairy cows from Southern Brazil. The affected cattle had dyspnea, nasal discharge, and coughing. One cow died, and samples were collected for diagnosis. Histopathology revealed interstitial pneumonia with multinucleated giant cells. IHC identified BRSV antigens in pulmonary tissue. A multiplex real-time PCR identified BRSV, Histophilus somni, and Pasteurella multocida in nasal and oral swabs, while only BRSV and H. somni were detected in the tissues of the cow that died. All animals had co-infections involving BRSV. The average cycle threshold (Cq) values for BRSV were 27.43 (nasal) and 32.68 (oral), with significant differences (p = 0.016), indicating higher nasal shedding. This qPCR assay was effective for detecting BRD pathogens, the quantification of viral and bacterial loads in animals with BRD and can be used for the rapid detection of respiratory pathogens. The elevated BRSV detection in oral samples suggests that this route may be an alternative for the collection of samples in cattle with profuse nasal discharge. Full article

Worldwide, polymicrobial infections (PMIs) account for an estimated 20–50% of severe clinical infection cases, with biofilm-associated and device-related infections reaching 60–80% in hospitalized patients. This review discusses the clinical burden of major infections in which PMIs are almost inevitable, such as diabetic foot infections, intra-abdominal infections, pneumonia, and biofilm-associated device infections. Globally, the PMI landscape is diverse; however, the Indian subcontinent is a PMI hotspot where high comorbidities, endemic antimicrobial resistance, and underdeveloped diagnostic capacity elevate the risks of poor outcomes. Existing diagnostic like culture-based methods, PCR panels, sequencing, and biomarker-based assays are constrained by sensitivity, turnaround times (TATs), and high costs. Vulnerable populations, particularly neonates, the elderly, immunocompromised patients, and socioeconomically marginalized groups, show case-fatality rates 2-fold higher than monomicrobial infections in similar settings. Emerging diagnostic solutions include CRISPR-based multiplex assays, artificial intelligence-based metagenomic platforms, and sensitive biosensors with point-of-care applicability. These technologies show potential in reducing the TAT (<2 h) with high accuracy (>95%). However, their translation to real-world settings depends critically on affordability, integration into healthcare pathways, and supportive policy. This will provide equitable diagnostic access, particularly in low- and middle-income countries (LMICs). Full article

Background/Objectives: Late diagnosis and inefficient treatment regimens lead to poor prognosis, with a low 5-year survival rate for both non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC). New targeted therapeutic agents can be developed and introduced only by first discovering new driver oncogenes and with a thorough investigation of the known driver genes. The aim of the current study is to investigate the prevalence of alterations in the eight most frequently altered genes in lung cancer—BRAF, EGFR, KRAS, ALK, ROS1, HER2, PD-L1 and PIK3CA. Methods: Real-time polymerase chain reaction (RT-PCR) was used to detect KRAS and EGFR mutations, multiplex PCR and microarray hybridization for KRAS/BRAF/PIK3CA mutations. Immunohistochemical analysis was performed for the detection of ALK, HER2/NEU, ROS-1 and PD-L1 alterations. Results: Overall, 221/603 patients (36.65%) had at least one genetic alteration, of which 22 patients (3.65%) had two genetic alterations and two patients had more than two genetic alterations. Additionally, 50 patients were identified with one or more KRAS mutations (8.29%), 45 patients with EGFR mutations (7.46%), and 1.82% with PIK3CA mutations and 0.66% with BRAF mutations. Furthermore, 50% of the co-occurring alterations were either on KRAS and PIK3CA genes (3/6), on KRAS and BRAF genes (2/6, 33.33%) or on EGFR and PIK3CA genes (1/6, 16.67%), and 10.45% of the patients exhibited PD-L1 overexpression, 5.31% ALK rearrangements, and 2.36% HER2/NEU expression, with no ROS-1 rearrangements detected. Conclusions: Comprehensive testing for somatic alterations in EGFR, BRAF, KRAS, and PIK3CA is significant in guiding therapeutic decisions in lung cancer management. Such testing should be routinely conducted to establish a thorough genetic profile of lung cancers in a manner that is both time-efficient and cost-effective. Full article

Objective: This study aimed to validate the clinical utility of a salivary molecular platform (Oral Predict^®) for periodontal pathogen detection across preventive, therapeutic, and maintenance settings. Methods: A longitudinal randomized study was conducted involving 78 adults who provided saliva samples at baseline, one month, and three months after professional dental hygiene. Participants were randomized into two groups: control group (n = 39) and probiotic group with Oral Predict^® probiotic supplementation (n = 39). Crude saliva was processed directly without nucleic acid extraction and analyzed by multiplex real-time PCR using either the compact Real-time PCR system or standard thermocyclers. Results: At baseline, Fusobacterium nucleatum was the most prevalent pathogen (84.6%), followed by Tannerella forsythia (53.8%) and Porphyromonas gingivalis (46.2%). The Total Pathogen Burden Score (TPBS) showed progressive increases with age, smoking, and poor oral hygiene, and was significantly higher in participants with gingival bleeding. Among individual pathogens, no significant associations were observed with periodontitis staging or grading. Professional hygiene induced mean reductions of 1–2 logs across all pathogens, with TPBS decreasing from 8.7 ± 3.2 to 4.1 ± 2.8 (p < 0.001). At three months, 69.2% of the control group experienced bacterial rebound, whereas 85% of probiotic users sustained or improved bacterial reductions. Conclusions: Salivary molecular testing provides a robust, non-invasive approach for periodontal pathogen detection, treatment monitoring, and long-term maintenance assessment. The flexibility of the Oral Predict^® platform across point-of-care and laboratory settings, combined with automated interpretation, supports integration into preventive protocols and personalized periodontal care. These findings demonstrate the potential of saliva-based molecular diagnostics to shift periodontal management from reactive to predictive and precision-based strategies. Full article

Bolivian hemorrhagic fever (BHF) is a zoonotic disease caused by Mammarenavirus machupoense (MACV) featuring severe neurological and hemorrhagic symptoms and a high mortality rate. BHF is usually diagnosed by serological tests or real-time polymerase chain reaction (RT-PCR); these methods are often inaccessible in endemic regions due to a lack of laboratory infrastructure, creating a demand for sensitive and rapid equipment-free alternatives. Here, we present an isothermal method for MACV nucleic acid detection based on the Cas12a-based DETECTR system combined with recombinase polymerase amplification (RPA) in a single tube: the RT-RPA/DETECTR assay. We demonstrate the possibility of using more than one primer set for the simultaneous detection of MACV genetic variants containing multiple point mutations. The method was optimized and tested using specially developed virus-like armored particles containing the target sequence. The multiplex RT-RPA/DETECTR method achieved a limit of detection of approximately 5 × 10⁴ copies/ mL (80 aM) of armored particles. The method was validated using clinical samples spiked with virus-like particles. The assay proved to be selective and reliable in detecting certain nucleotide substitutions simultaneously. Full article

Background/Objectives: The diagnosis of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacterial (NTM) infections is accomplished by three main diagnostics methods: smear microscopy, culture, and molecular testing. Diagnostic algorithms used by laboratories can significantly impact clinical and infection control management. Current Canadian Tuberculosis Standards recommend the use of nucleic acid amplification testing (NAAT) for smear-positive patients and smear-negative patients upon request. An alternative algorithm is to utilize NAAT in the Panel approach on all samples, pulmonary and extrapulmonary, to potentially reduce time to diagnosis and treatment. This alternative approach was implemented in November 2019 at the Newfoundland and Labrador Public Health and Microbiology Laboratory (NL PHML) using a laboratory-developed multiplex real-time PCR (LDT m-qPCR) assay targeting Mycobacterium spp. (Myco spp.) and MTBC, performed in parallel with smear and culture. Methods: To investigate the impact of this alternate testing approach, we conducted an observational retrospective analysis of laboratory diagnostic and treatment data, recognizing that temporal changes in epidemiology, clinical practice, and laboratory workflow may also have influenced outcomes. To complete this, study data from three years before and four years after implementation were gathered. Results: The sensitivity/specificity of the smear, m-LDT qPCR-MTBC, m-LDT qPCR-Myco spp., and culture assays in this study were 18.1%/100%, 96.7%/99.8%, 47.6%/99.0%, and 96.8%/100%, respectively. The gold standard utilized for these calculations was clinical diagnosis for active MTBC disease and culture for NTM infections, recognizing that the use of clinical diagnosis may introduce subjectivity. The Panel approach reduced the time to diagnosis of tuberculosis MTBC by 29 days (p < 0.0001) for NL PHML, and when modelled for a laboratory with rapid culture identification, diagnosis was reduced by 14 days (p = 0.003). Among non-empirically treated tuberculosis patients, the time to treatment was decreased by 25.5 days (p < 0.001). For NTM infections, rapid diagnostics only affected one patient’s treatment. This finding agrees with clinical management guidelines, which do not routinely utilize rapid diagnostics for the diagnosis of disease or treatment decisions. The cost implications of additional NAAT testing were calculated to be an increase of CAD 23.62 per sample. Conclusions: Our findings support the adoption of a molecular assay for MTBC as an initial diagnostic tool to decrease time to diagnosis and time to treatment, depending on local epidemiology and irrespective of smear status. Utilizing a molecular assay for genus level identification of NTM had minimal impact on clinical management suggesting its limited diagnostic utility in a broad population setting. Full article

Background/Objectives: We have previously reported the engineering of a point-of-care (POC) system that fully automates the procedures for nucleic acid extraction and multiplexed real-time RT-PCR, with a major advantage of high-level multiplexing. In this study, we applied and validated the system in a respiratory tract infection setting. Methods: An automatic nested real-time RT-PCR assay was developed (POCm). It was a 40-plex assay that simultaneously detected 39 epidemiologically important respiratory pathogens in 1.5 h in the POC system. The analytical and clinical performance was evaluated. Results: The analytical sensitivities of the POCm assay were comparable to those of its single-plex counterparts performed manually on a bench-top. The minimum detectable concentrations ranged from 53 copies/mL to 5.3 × 10³ copies/mL for all pathogen targets except hCoV-NL63 (5.3 × 10⁴ copies/mL). The quantitative performance was demonstrated by the linear correlations between Ct values and input concentrations for all pathogen targets, with 24 of them demonstrating coefficients of correlation (r) greater than 0.9. The POCm assay was subsequently evaluated in 283 clinical samples. A high level of agreement (98.2–100%) was achieved for pathogen detection results between POCm and standard diagnostic methods. The POCm result was also fully concordant with the result of another commercial POC multiplex platform. For positive clinical samples, pairwise Ct values measured by POCm closely correlated with those of the bench-top reference method (r = 0.70). The feasibility of mutation genotyping of the viral subtype was further demonstrated. Conclusions: This study demonstrated the practicality of POCm for routine testing in clinical laboratories. Further clinical trials are being conducted to evaluate the clinical performance of the system. Full article

Chicken coccidiosis is a major parasitic disease in poultry that causes substantial economic losses worldwide. The accurate and simultaneous diagnosis of mixed infections with multiple Eimeria species remains challenging using conventional methods. In this study, we developed a multiplex TaqMan-MGB qPCR assay targeting the ITS1 region for simultaneous detection and quantification of four major pathogenic species: E. acervulina, E. necatrix, E. maxima, and E. tenella. The assay exhibited high specificity without cross-reactivity and achieved a sensitivity 100-fold greater than conventional PCR, with detection limits ranging from 10¹ to 10² copies/μL. Standard curves demonstrated strong linearity (R² ≥ 0.95) and amplification efficiency (95–113%). Repeatability was robust, with intra- and inter-assay CVs below 2%. Applied to 165 clinical samples collected from poultry farms in Fujian Province, China (2022–2024), the assay detected an overall Eimeria infection rate of 93.3%, higher than conventional PCR (89.7%). Epidemiological analysis revealed E. tenella (78.8%, [130/165]) and E. necatrix (78.8%, [130/165]) were dominant, while mixed infections were frequent (83.3%, [136/154]), including dual (45.5%, [70/154]), triple (31.2%, [48/154]), and quadruple (11.7%, [18/154]) infections. This multiplex TaqMan-MGB qPCR provides a rapid, sensitive, and quantitative tool for detecting multiple Eimeria species, greatly improving diagnostic efficiency and supporting clinical diagnosis, surveillance, and control strategies. Full article

Acute Oak Decline (AOD) is a progressive disease affecting oaks across Europe and is increasingly recognised as a threat to the health of forests and urban trees. While the occurrence of this disease has been documented in forest ecosystems, its presence in urban landscapes is still poorly understood. In this study, the occurrence of AOD-associated bacteria (Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana, Lonsdalea quercina) was investigated in Quercus robur and Q. rubra growing in urban areas of Wrocław, Poland. Multiplex real-time PCR analyses confirmed the pathogens in 11 trees, with B. goodwinii being the most common species. Importantly, we provide the first confirmed detection of B. goodwinii in Q. rubra under urban conditions, possibly the first such detection in Europe. The results show the occurrence of AOD-associated pathogens in urban environments, suggesting that such habitats may provide favourable conditions for their occurrence. However, further investigations, including epidemiological and spatial analyses, are needed to clarify whether urban areas contribute to the persistence or spread of these pathogens. Beyond local documentation, our results emphasise the need to include urban ecosystems in AOD surveillance and highlight potential pathways for pathogen adaptation and spread in cities. This work provides new insights into the ecology of AOD in anthropogenically modified habitats and has direct implications for urban tree health monitoring, biodiversity conservation, and the development of integrated management strategies. Full article

Background: This study investigated the epidemiology of Mycoplasma pneumoniae (MP) in children with acute respiratory tract infections (ARTIs) and explored the risk factors for severe mycoplasma pneumoniae pneumonia (SMPP) in children. Methods: A retrospective analysis was conducted on 36,380 children with acute respiratory infections who underwent multiplex real-time polymerase chain reaction (RT-PCR) assays for nine respiratory pathogens from September 2021 to November 2024. Results: A total of 36,380 children with ARTIs were enrolled in this study. The co-detection rate of MP with other pathogens was significantly higher in the post-NPIs period than in the NPIs period (36.5% vs. 25.7%, p < 0.01). Multivariate regression identified the detection of influenza A virus (InfA), InfB, human parainfluenza virus (HPIV), human bocaparvovirus (HBoV), human rhinovirus (HRV), adenovirus (ADV), human respiratory syncytial virus (HRSV), and human metapneumovirus (HMPV) as protective factors against MP epidemics (p < 0.01); meanwhile, older age, the cancellation of NPIs, and summer–autumn seasons were found to be risk factors. After adjusting for sex, age, period, season, and pathogens, InfB (OR: 3.009, 95%CI: 1.041–8.697, p = 0.042), HPIV (OR: 2.226, 95%CI: 1.170–4.235, p = 0.015), and ADV (OR: 2.035, 95%CI: 1.105–3.750, p = 0.023) were identified as independent risk factors for SMPP. Conclusions: These findings highlight post-NPI shifts in MP epidemiology and identify ADV, InfB, and HPIV as early warning markers for SMPP. Full article

This study proposes a region of interest (ROI) setting method to improve the accuracy and efficiency of fluorescence detection in a compact real-time multiplex fluorescence PCR system. Conventional commercial real-time PCR systems are limited in point-of-care (POC) environments due to their high cost and complex optical structures. To address this issue, we developed a low-cost, compact system using an open-platform camera and a Fresnel lens. However, in such a simply structured system, variations between the wells of the polymerase chain reaction (PCR) plate may affect the accuracy of fluorescence detection. In this study, after capturing images with a CMOS camera, we propose two ROI image processing algorithms. The proposed algorithms reliably extract fluorescence signals and compare ROI deviations caused by variations between wells to determine whether physical correction is necessary. To validate the system, we performed comparative analysis of real-time DNA amplification images and fluorescence dye images collected over multiple periods. Based on evaluations using manual detection as a reference, it was confirmed that even a simple algorithm can achieve stable fluorescence detection while minimizing ROI distortion. This study presents an efficient method for enhancing the accuracy of quantitative fluorescence analysis in small PCR systems and is expected to contribute to improving the performance of point-of-care diagnostics, thereby increasing accessibility to on-site diagnostics in the future. Full article

Background: Differentiating between bacterial and viral infections in pediatric emergency care is challenging, often leading to unnecessary antibiotic use. The MeMed BV (MMBV) test is a host-response assay designed to differentiate bacterial from viral infections, but real-world data in pediatric settings remain limited. Methods: We conducted a pragmatic, single-center, prospective cohort study to assess the clinical utility of MMBV in children with acute respiratory infections or fever without source. Patients were assigned to standard of care (SOC) or MMBV testing (SOC+MMBV) based on time of presentation to the emergency department. The primary outcome was antibiotic prescribing. Secondary outcomes included diagnostic test utilization, hospitalization rates, and length of stay. Analyses were stratified by hospitalization status, clinical severity [National Institute for Health and Care Excellence (NICE) traffic light system], and patient age. Results: From July 2023 to April 2024, 343 patients were enrolled (171 SOC, 172 SOC+MMBV). In the SOC+MMBV arm, reduced antibiotic prescribing was observed among outpatients and those with non-severe signs and symptoms. Antibiotic prescribing was significantly reduced in children under five years with a low-risk profile, according to the NICE traffic light system (26.3% vs. 7.5%; p = 0.034). Multiplex PCR testing was significantly reduced in the SOC+MMBV group (28.7% vs. 16.3%; p = 0.006) compared to SOC for both inpatients and outpatients. No significant differences were observed in overall diagnostic test use or length of stay. Conclusions: MMBV improved antibiotic and diagnostic stewardship in a real-world pediatric ED setting, significantly reducing unnecessary antibiotic use among low-risk children under five and minimizing unnecessary multiplex PCR testing across the cohort. Full article

Background/Objectives. Multi-drug-resistant (MDR) microorganisms pose a significant challenge in healthcare settings, particularly with beta-lactam-resistant Gram-negative bacteria and glycopeptide-resistant enterococci. Culture represents the most reliable technique in determining their presence within surveillance swabs. However, it requires a long time-to-result (TTR) and shows low sensitivity. Molecular techniques integrate diagnostic procedures, allowing TTR reduction and precise identification of genes. Methods. During our usual surveillance campaign, we had the opportunity to evaluate the Allplex Entero-DR assay (Seegene Inc., Seoul, Republic of Korea) and the Entero-DR Plus assay (Arrow Diagnostics srl, Genova, Italy) molecular kits for the detection of extended-β-lactamases (ESBL), carbapenem- and vancomycin-resistant genes, as well as Acinetobacter spp. and Pseudomonas aeruginosa spp. identification directly from rectal swabs. A comparison between these tests and the culture-based routine completed the study. Results. The analysis included 300 rectal swabs from the University Hospital Policlinico (Catania, Italy). One hundred and eighty-eight samples (62.6%) resulted as positive for at least one Allplex™ target, reaching optimal sensitivity and negative predictive value (100%). Our results underlined the ubiquitous blaCTX-M and van genes presence and demonstrated the diffusion of double-carbapenemases genes and metallo-β-lactamases-producing strains. In our epidemiological setting, few data were collected about carbapenem-resistant P. aeruginosa and Acinetobacter spp., which require further evaluations on simultaneous respiratory colonization and higher sample numbers. Conclusions. Our analysis highlighted the importance of combining conventional and advanced diagnostic methods in investigating MDR pathogens. The right approach should be based on the prevalence and variability of resistance mechanisms within a specific epidemiological area. Remarkably, molecular screenings may exclude negative samples within high-risk areas due to a significant negative predictive value. Full article