Clinical Microbiology Research Articles

Rapid identification (ID) and antibiotic susceptibility testing are vital for the treatment of bloodstream infections (BSIs). The aim of this study was to perform direct identification and rapid antimicrobial susceptibility testing (RAST), from positive blood cultures and to compare the performance of these rapid methods with standard reference methods. Blood cultures (BC) submitted to Marmara University Pendik Training and Research Hospital Clinical Microbiology Laboratory between September 2022 - April 2023, that yielded positive signal and were determined to be monomicrobial by gram staining were selected randomly. ID was performed using MALDI-TOF MS(bioMérieux, France). Based on these results, rapid antimicrobial susceptibility testing (RAST) was applied to 103 bottles that met RAST eligibility criteria. The results of rapid ID and RAST were evaluated by comparing them with the results obtained from colony-grown isolates. Rapid ID showed that out of 306 bottles, 281 (91.8%) were monomicrobial. High rates of correct identification were achieved for gram-negative bacilli (84.3%), gram-positive chain cocci (79.4%), and gram-positive cluster cocci (55.2%), while performance was lower for gram-positive bacilli (27.3%) and yeasts (37.5%). For RAST, the readability of inhibition zone diameters increased progressively with incubation time, reaching 85.2%, 94.5%, 100%, and 100% at 4, 6, 8, and 16-20h, respectively. The categorical agreement of the test remained consistently high across all time points, measuring 98.35% at 4h, 98.49% at 6h, 98.38% at 8h, and 98.84% at 16-20h. Rapid ID of microorganisms directly from positive BC bottles, combined with RAST based on EUCAST RAST criteria, demonstrates high accuracy and reliability compared to conventional methods. These rapid approaches significantly reduce the turnaround time for both identification and susceptibility results-by approximately 16-20h and 32-48h, respectively thereby enabling earlier targeted antimicrobial therapy and improving clinical management of BSIs.

Background: The clinical laboratory has witnessed a paradigm shift with the introduction of mass spectrometry (MS) into its activities, extending its role way beyond the traditional field of toxicology. Aim: This review comprehensively discusses the revolutionizing impact of tandem mass spectrometry (MS/MS) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS on the diagnosis and management of human disease, particularly in endocrinology and microbiology. Methods: Synthesis of concepts, applications, and relative advantages of these MS methods from the current literature between 2015 and 2024 was reviewed. Results: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) emerged as the gold standard in endocrinology with improved specificity for steroid, thyroid hormone, and vitamin measurement, thereby enabling accurate diagnosis of complex disorders. Meanwhile, MALDI-TOF MS has revolutionized clinical microbiology by providing quick, accurate, and cost-effective microbial identification, with an appreciable shortening of the time to effective antimicrobial therapy. Further, MS/MS remains the basis of newborn screening for congenital errors of metabolism. Despite challenges like standardization and cost, newer directions like mass spectrometry imaging and ambient ionization techniques promise further advancements. Conclusion: The findings verify that MS/MS and MALDI-TOF MS lead the path of the modern clinical laboratory's commitment to deliver precise, individualized, and prompt patient treatment.

Rapid, sensitive, and specific detection of pathogenic Escherichia coli serotypes is crucial for food safety and public health. Here, we present a surface-enhanced Raman scattering (SERS) platform utilizing highly ordered silver nanorod (AgNR) arrays functionalized with vancomycin for efficient and selective bacterial capture. The system enables multiplexed, high-throughput analysis using a portable Raman spectrometer, achieving direct molecular fingerprinting of seven clinically relevant E. coli serotypes. Systematic optimization of AgNR length and vancomycin coating maximized SERS enhancement and capture efficiency. Advanced data analysis with linear discriminant analysis (LDA) provided robust discrimination among all serotypes and concentrations, achieving up to 100% classification accuracy in single-concentration models and an overall accuracy of 98.41% when all concentrations and serotypes were evaluated jointly. This integrated SERS approach demonstrates significant promise for rapid, on-site bacterial diagnostics and quantitative pathogen monitoring, paving the way for practical applications in food safety and clinical microbiology.

Aim A consensus‑driven definition of prosthetic joint infection (PJI) outcomes is essential for unified data collection, cross‑study comparisons, and evidence‑based guidelines. Such consistency refines treatment strategies, informs decisions, and enhances patient care. We systematically summarized the evidence — using a rigorous meta‑epidemiological approach — on how PJI outcomes are defined, building on analyses of native vertebral osteomyelitis and postoperative spinal infection definitions. Methods We searched Cochrane, Embase, Medline, and Scopus without date or language limits for publications that provided a specific PJI outcome definition. Eligible randomized controlled trials and cohort studies reported at least ten PJI cases. Following meta‑epidemiological guidelines adapted from PRISMA, we extracted verbatim definitions of PJI outcomes and categorized them into thematic criteria using a saturation approach. A network plot displayed the frequency and co‑occurrence of criteria across studies (Figure 1). Results Of 7,584 screened studies, 552 (7.3 %) met inclusion criteria. This pilot analysis covers 49 randomly selected studies (8,162 patients), mostly retrospective (48/49, 98 %), concerning mixed joint replacements (25/49, 51 %), two‑stage exchanges (15/49, 31 %), or mixed surgeries (24/49, 49 %). 25/49 studies (51 %) exceeded two-years follow-up. Only 6/49 (12.2 %) used a society‑endorsed definition, and 13/49 (26.5 %) cited a reference. Overall, 32/49 (65.3 %) defined “success”, 35/49 (71.4 %) “failure”, and 16/49 (32.7 %) both. Patient‑reported outcomes appeared in 14/49 (28.6 %), employing 14 PROMs, most frequently UCLA, HHS, and KSS; 13/49 (26.5 %) assessed functional outcomes. Sixteen outcome criteria clustered into seven domains: clinical signs, microbiology, imaging, histopathology, antibiotics‑related, surgical‑related, and mortality. Network analysis revealed strong links among clinical, microbiology, surgical, imaging, and mortality domains, whereas histopathology and antibiotics‑related criteria were infrequent. Conclusion Substantial heterogeneity in PJI outcome definitions and limited uptake of standardized criteria remain. Reliance on clinical and microbiological measures impedes comparability, particularly given underused histopathology, antibiotic‑related endpoints, and patient‑reported measures, whose perspectives may diverge from clinical parameters. A unified, consensus‑driven approach would enhance evidence synthesis and ultimately improve patient care in prosthetic joint infections. For any figures or tables, please contact the authors directly.

Respiratory sepsis: a 12-year prospective observational study in critically ill patients.

Executive summary of the consensus document of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC: GEPI, GeSIDA, GESITRA-IC, GEIRAS) on screening for imported infectious diseases in immunocompromised patients.

Tricuspid vs Bicuspid Aortic Valve Endocarditis: Delayed Symptom-Onset-to-Diagnosis Time in Bicuspid Patients Increases Their Complication Burden.

Implementation of Artificial Intelligence in Food, Laboratory, Agricultural, Medical and Environmental Microbiology

Attitudes to phage therapy among Australian infectious diseases physicians.

This study evaluated the reliability of different laboratory methods for detecting resistance to glycopeptide antibiotics-vancomycin and teicoplanin-in clinical Staphylococcus aureus and coagulase-negative staphylococci (CoNS) isolates. While automated systems are widely used in clinical microbiology laboratories due to their efficiency and ease of use, they may yield inaccurate results when assessing glycopeptide susceptibility. A total of 87 previously collected clinical isolates (22 S. aureus and 65 CoNS), initially identified as resistant to at least one of the vancomycin or teicoplanin by an automated system, were retrospectively analyzed. All isolates were stored at -80 °C and retested using three methods: the same automated system (following the manufacturer's protocol), the gradient diffusion method, and the reference broth microdilution (BMD) method. Interpretations were made according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. Upon re-evaluation, all isolates were found to be susceptible to vancomycin and teicoplanin using the BMD method. The automated system yielded 100% concordance with BMD for vancomycin and 77% for teicoplanin, while the gradient method produced similar findings. Notably, five S. aureus isolates (23%) remained resistant to teicoplanin according to both the automated system and the gradient method but were susceptible by BMD. These results emphasize that automated systems, although practical, may lead to overestimation of glycopeptide resistance. Therefore, when resistance is suspected, especially to teicoplanin, confirmatory testing with the BMD reference method is essential to ensure accurate interpretation and avoid misclassification.

Laboratory testing plays an important role in diagnosis and clinical management of Lyme borreliosis (LB). While external quality assessments (EQAs) evaluate the technical quality of laboratory diagnostics, the clinical interpretation of laboratory results often remains unassessed. Although specific guidelines are available, different interpretation can result in variations in clinical diagnosis and subsequent management of LB patients. This study aimed to evaluate variations in interpretating LB laboratory diagnostics in relation to the clinical history of the patient. An EQA was organized for medical microbiological laboratories (MMLs) in the Netherlands using a web-based survey. The survey consisted of twenty LB case descriptions including laboratory findings. Participants were asked to (i) interpret each case according to their protocols (open-ended), and (ii) rate the likelihood of the case being active LB (multiple-choice). Six LB diagnostics experts determined the baseline and scored participants' answers on a 1-10 scale. Of the 50 invited MMLs, 38 (76.0%) completed the survey. The overall mean score was 8.8 (range: 7.2 - 9.8). For the multiple-choice questions, the mean score was 9.6 (range: 8.4 - 10) and for open-ended questions this was 8.0 (range: 5.6 - 9.6). Lower scores were obtained for low-incidence manifestations. This EQA showed that interpreting LB laboratory results in relation to the clinical information was good and increased awareness among participants to challenges of LB diagnosis and treatment. Training and education could improve interpretation skills. This EQA might be exemplary for future harmonization efforts for (pan-European) clinical evaluation of LB diagnostics. As a potential future approach, supplementing guidelines with an artificial intelligence-based clinical support system could aid medical microbiologists and physicians in decision making, especially for rare manifestations.

Evaluation of sulbactam-durlobactam disk diffusion and broth microdilution methods for Acinetobacter baumannii.

Accurate and rapid pathogen identification is critical for modern diagnostics, driving the need for technologies that combine speed, specificity, and functional insight. In this context, mass spectrometry (MS)-based proteomics is rapidly emerging as a transformative approach in clinical microbiology, offering comprehensive characterization of microorganisms and direct identification of protein biomarkers relevant to infectious disease diagnostics. While MS1-based approaches such as MALDI-TOF Biotyper have revolutionized species-level microbial identification through rapid and cost-effective workflows, they remain fundamentally limited in resolving strain-level differences and in detecting antimicrobial resistance (AMR) determinants. In contrast, so-called proteotyping enables the identification of organisms and resistance-associated proteins based on peptide sequence information obtained by tandem mass spectrometry (MS/MS), most commonly using shotgun proteomics. However, the clinical utility of proteotyping depends on the availability of efficient and accurate bioinformatics tools capable of handling large databases, disambiguating shared peptide sequences, and providing taxonomic and functional assignments with clinical relevance. This perspective highlights the diagnostic potential of MS/MS proteotyping and argues that advances in bioinformatics pipelines are needed for moving from microbial identification to actionable clinical insight.

The article presents the results of the development and clinical application of the domestic Raman fluorescence therapeutic and diagnostic technology (RFD), implemented on the basis of the hardware and software complex "InSpectr M". High analytical sensitivity and specificity of the method are shown in comparison with traditional fluorescence and microbiological diagnostic methods. The possibilities of using RFD in clinical microbiology, dentistry, as well as in the diagnosis of benign and malignant neoplasms of the oral organs and maxillofacial region are considered. Particular attention is paid to the digitalization of diagnostic and treatment processes in dental clinics, which meets the modern requirements of personalized and express medicine. The technique allows for express assessment of microbial association, mineralization of hard dental tissues, selection of antimicrobial drugs and monitoring of the effectiveness of treatment "on site". The work presents experimental and clinical data confirming the effectiveness and prospects of introducing RFD into medical practice. Objectives. To develop and implement a highly sensitive Raman fluorescence diagnostic and treatment technology for express diagnostics, monitoring and optimization of treatment of dental diseases in a polyclinic setting. Methodology. The study included the development of the hardware and software complex "InSpectr M", implementing RFD-technology using laser radiation at wavelengths of 405, 532 and 637 nm and the use of SERS substrates to increase sensitivity. The objects of the study were microbial suspensions (Pseudomonas aeruginosa, Morganella morganii, Staphylococcus aureus, etc.), hard tissues of teeth of patients with caries and fluorosis, as well as tissues of oral organs with neoplasms. Results. The developed RFD technology based on the InSpectr M complex is an innovative, highly sensitive and specific method of express diagnostics and treatment of dental diseases and pathologies of oral tissues. Its integration into the digital infrastructure of polyclinics contributes to a significant improvement in the quality and speed of medical care, and also opens up new opportunities for diagnosing oncological diseases.

This study evaluated the characteristics of patients receiving prophylactic antiviral therapy against hepatitis B virus (HBV) infection due to immunosuppressive treatment and assessed the occurrence of HBV reactivation. Between January 2015 and January 2025, 199 adult patients followed in the Infectious Diseases and Clinical Microbiology outpatient clinic who had received prophylactic oral antiviral therapy were retrospectively analyzed. Demographic characteristics, underlying diseases, immunosuppressive treatment history, HBV serological results, biochemical and virological findings, and prophylactic antiviral regimens were recorded. Patients were stratified into low-, moderate-, and high-risk groups according to the American Gastroenterological Association (AGA) 2025 classification. The mean age was 60.4 years; 50.3% of patients were male. Serologically, 26.6% were HBsAg- and anti-HBc-positive, 33.2% showed isolated anti-HBc positivity, and 40.2% had dual anti-HBc/anti-HBs positivity. The risk of HBV reactivation was low in 41.2%, moderate in 22.1%, and high in 36.7% of patients. Prophylaxis consisted of entecavir in 76.4%, tenofovir alafenamide in 13.1%, and tenofovir disoproxil fumarate in 10.5%. HBV reactivation occurred in only one patient, who had discontinued treatment. These findings emphasize the importance of HBV screening and timely prophylactic antiviral therapy in patients undergoing immunosuppression to effectively prevent HBV reactivation.

The identification of filamentous fungi in clinical microbiology laboratories remains a challenging task. Although matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized microbial diagnostics by enabling rapid and accurate species-level identification, its application to molds is still evolving. This study aims to evaluate the performance of two Bruker MALDI-TOF MS systems, Sirius One and Microflex 3.1, for the identification of filamentous fungi using different extraction protocols and database configurations. A total of 68 filamentous fungal isolates, including clinically significant species, were analyzed. Fungal cultures were processed under standardized conditions using two protein extraction methods: a detailed in-tube extraction with ethanol, formic acid, and acetonitrile, and a direct on-plate extraction. Spectra were acquired using both Sirius One and Microflex 3.1 systems, and identifications were performed using manufacturer-provided databases and the MSI-2.0 database. The Sirius One system outperformed Microflex 3.1, achieving a 92.6% correct identification rate with the MSI-2 database compared to 70.6% for Microflex (p < 0.01). When using manufacturer-provided databases, identification rates were lower: 51.5% for Sirius One and 41.2% for Microflex. Notably, the on-plate extraction method performed comparably to the in-tube method, achieving 94.1% accuracy with Sirius One and the MSI-2 database. The combination of the Sirius One system, MSI-2.0 database, and on-plate extraction method provides a highly effective and time-efficient workflow for the identification of filamentous fungi in routine clinical diagnostics, reaching 94.1% accuracy. This approach is recommended for implementation in clinical mycology laboratories, though further optimization of manufacturer-supplied databases remains necessary.

Abstract Not Available Bangladesh Journal of Infectious Diseases, June 2025;12(1):195-197

Development of two methods for detecting Streptococcus mitis/oralis-related species with meropenem-non-susceptibility.

Aims: This study retrospectively evaluates the serological (CMV IgM and IgG) and molecular (CMV DNA PCR) test results of patients admitted to İstanbul Faculty of Medicine Hospital between 2021 and 2023 due to suspected cytomegalovirus (CMV) infection. The aim is to assess the diagnostic value of combining serological and molecular methods and to analyze CMV positivity across age and gender groups. Methods: This cross-sectional observational study included 1.649 patients who underwent CMV testing (CMV IgM, CMV IgG, and/or CMV DNA PCR) at the Medical Microbiology Laboratory of İstanbul Faculty of Medicine between January 1, 2021, and December 31, 2023. Serological tests were performed using ELISA (Vircell, Spain), and CMV DNA was quantified using real time PCR (QIAsymphony/Artus CMV QS-RGQ and cobas® 6800). Data were anonymized and analyzed statistically using SPSS v26.0. Mann-Whitney U, Chi-square, McNemar, and ROC tests were applied; p0.05), CMV DNA positivity varied significantly across age groups (p

Timely reporting of microbiological results is critical for clinical decision-making, particularly in pediatric hospitals where delays can significantly impact outcomes. Despite advances in laboratory automation, workflow inefficiencies and resistance to change remain barriers to improvement in Latin America. This study aimed to evaluate the effect of implementing a Kaizen-based change management strategy on reducing turnaround time (TAT) in the microbiology laboratory of Hospital Roberto del Río, Santiago, Chile. We conducted a prospective, pre–post intervention study focusing on blood culture processing. The baseline period (July 2022) included 961 cultures processed with the BacT/ALERT® 3D system. A Kaizen/LEAN intervention was designed, comprising workflow redesign, staff training, and installation of the BACT/ALERT® Virtuo® (bioMerieux, Marcy l’Etoile, France) continuous-loading blood culture system. The intervention engaged all technical and professional staff in a five-day Kaizen immersion, followed by eight months of monitoring. Outcomes were assessed by comparing TAT for positive blood cultures before and after implementation (June 2023, 496 samples). Statistical analysis was performed using the Mann–Whitney U test, with p &lt; 0.05 considered significant. The intervention achieved a median reduction in TAT from 68.22 h (IQR 56.14–88.59) pre-intervention to 51.52 h (IQR 41.17–66.57) post-intervention, corresponding to a 24.48% improvement (p &lt; 0.001), surpassing the 20% target. Time to preliminary Gram reporting also decreased, and workflow standardization enhanced staff productivity and culture validation frequency. Implementation of Kaizen principles in a pediatric microbiology laboratory significantly reduced blood culture TAT and improved workflow efficiency. Beyond technological upgrades, active staff engagement and structured change management were key to success. These findings support the applicability of Kaizen-based interventions to optimize laboratory performance in resource-constrained public healthcare systems.