Journal of Clinical Microbiology最新文献

Timely initiation of appropriate antimicrobial therapy is crucial for patients with Gram-negative (GN) blood stream infections. In this study, the performance of VITEK REVEAL (bioMérieux, USA), an FDA cleared in vitro diagnostic automated system for antimicrobial susceptibility testing (AST) directly from positive blood culture (BC), was compared to that of Accelerate Pheno (Accelerate Diagnostics, USA), as standard of care method. 128 GN positive BCs were analyzed according to manufacturer recommendations, comparing time to result (TTR) and AST results. The categorical agreement (CA) rate between VITEK REVEAL and Accelerate Pheno was 94.3% and the essential agreement (EA) rate was 96.0%. Very major discrepancies (VMD), major discrepancies (MD), and minor discrepancies (miD) rates between the systems were 7.5%, 0.5%, and 4.1%, respectively. Lastly, we observed a mean sequential TTR (reporting of AST results per antibiotic in real-time) on VITEK REVEAL of 6.1 h (3.0-8.2) and mean final TTR of 7.9 h (6.5-8.2), compared to Accelerate Pheno, with a significantly shorter mean final TTR of 7.1 h (6.8-7.7). Sequential TTR on VITEK REVEAL was significantly shorter for resistant isolates (those with ≥1 'Resistant' antimicrobial-organism combination interpretation, using FDA STIC 2024 or CLSI M100 criteria) compared to susceptible/intermediate ones, with a mean difference of 1.4 h (P  <  0.001). Overall, compared to Accelerate Pheno, VITEK REVEAL displayed high %CA and %EA for AST of GN bacteria directly from positive BC. Also, unlike Accelerate Pheno, VITEK REVEAL reports MIC results in real time, allowing an earlier release of actionable information useful for antimicrobial stewardship.

Importance: Previous studies have compared the performance of the VITEK REVEAL, system for fast antimicrobial susceptibility testing (AST) to conventional, non-rapid microbiology methods. To evaluate how the VITEK REVEAL correlates to similarly available fast, direct-from-blood culture AST technologies, this study aimed to compare it to the Accelerate Pheno system, as standard of care method. High categorical agreement (94.3%) and essential agreement (96.0%) between the two systems were observed, underscoring their reliability. The VITEK REVEAL has the advantage of real-time AST reporting, unlike the Accelerate Pheno. Ultimately, this study supports the need for and continued optimization of fast diagnostic technologies for AST, contributing to the goal of advancing antimicrobial stewardship-focused treatment strategies and improving the prognosis of patients with bloodstream infections.

Formulating safe and effective diagnostic stewardship guidance for blood cultures in immunocompromised patients is challenging due to limited data and high risk of infectious complications. A 2024 global shortage in blood culture bottles (BD Diagnostics) necessitated the implementation of blood culture stewardship, including at our tertiary care cancer center. This was a retrospective pre-post intervention study of the effects of diagnostic stewardship at a stand-alone cancer center during a 5-month period of the 2024 blood culture bottle shortage compared to the same 5-month unaffected period in 2023. Interventions included discontinuation of an ordering set for persistent fever, modification of an ordering set for new fever to recommend two sets of blood cultures for initial workup, and issuing revised blood culture ordering guidance to providers, phlebotomists, and nurses with repeated educational efforts. Stewardship interventions led to decreased blood culture utilization by 36.3% (from 14,021 to 8,932), while the number of patients tested remained similar. Greatest reductions in utilization occurred in inpatient encounters and with follow-up blood cultures. There was a trend toward increasing blood culture positivity following intervention, excluding potential contaminants (7.1% vs 7.6%, P = 0.08). The frequency of sepsis-coded encounters and 30-day mortality rate were similar between the two time periods. No adverse outcomes related to blood culture stewardship were reported. A significant reduction in blood culture utilization is achievable in a high-complexity cancer patient population without negative clinical impact through limiting the number of initial blood cultures and eliminating pre-emptive ordering of blood culture orders for persistent fever.IMPORTANCECancer and transplant patient populations are frequently excluded from experimental studies on decreasing blood culture utilization, but a recent global supply shortage in blood culture bottles provided a valuable opportunity to evaluate the effects of stewardship interventions on a large scale. This study, centered on a high-complexity cancer patient population, found that a significant 36.3% reduction in blood culture utilization was achievable, safe, and effective through multidisciplinary diagnostic stewardship efforts.

Mycoplasma pneumoniae is a major cause of community-acquired pneumonia and increasingly exhibits macrolide resistance due to the A2063G and A2064G mutations in the 23S rRNA gene. We developed a loop-mediated isothermal amplification (LAMP) assay with hybridization-based TaqMan-style probes (HyTaq) to simultaneously detect M. pneumoniae wild-type strains and macrolide resistance mutations (A2063G and A2064G) within a single reaction (hereafter referred to as the MP-R HyTaq-LAMP assay). Analytical performance was evaluated using plasmid standards, and clinical validation was conducted with 224 nasopharyngeal swab samples. The MP-R HyTaq-LAMP assay detected wild-type strains and the A2063G and A2064G mutations with a limit of detection of 1 × 10³ copies/μL. In clinical samples, the assay demonstrated 95.79% sensitivity for A2063G and 100% sensitivity for wild-type strains, along with 100% specificity against 103 non-infection samples. Additionally, no cross-reactivity was observed with 16 other common respiratory pathogens. The MP-R HyTaq-LAMP assay provides rapid, multiplex detection of M. pneumoniae and associated macrolide resistance mutations without thermal cycling, demonstrating its strong potential as a point-of-care diagnostic tool.

Importance: Macrolide-resistant Mycoplasma pneumoniae is a significant cause of treatment failure in community-acquired respiratory infections, particularly in children and adolescents. Early and accurate detection of resistance-associated mutations, such as A2063G and A2064G, is essential for guiding effective antibiotic therapy. In this study, we developed an MP-R HyTaq-based loop-mediated isothermal amplification assay capable of simultaneously detecting and discriminating wild-type strains and macrolide resistance mutations (A2063G and A2064G) in a single-tube, isothermal reaction. Its high specificity, rapid turnaround time, and minimal equipment requirements make this assay suitable for point-of-care testing in diverse clinical settings.

Effective tuberculosis (TB) management relies on prompt diagnosis of Mycobacterium tuberculosis complex (MTBC) and associated drug resistance. The Sanity 2.0 assay is a high-resolution melting assay designed for direct respiratory sample testing, enabling simultaneous detection of MTBC and resistance to rifampicin (RIF), isoniazid (INH), and fluoroquinolones (FQ) in a single step. This study evaluated its diagnostic performance in two registered multicenter trials among bacteriologically confirmed TB patients. Diagnostic performance was evaluated for MTBC detection, as well as for the identification of resistance to RIF, INH, and FQ, using phenotypic drug susceptibility testing, whole-genome sequencing, and a composite reference standard. Agreement analyses were conducted between the Sanity 2.0 assay and Xpert MTB/RIF and Xpert MTB/XDR. Among 611 patients, the Sanity 2.0 assay detected MTBC in 563 patients, exhibiting a sensitivity of 92.1% (95% CI: 89.7-94.0). For detecting resistance to RIF, INH, and FQ, sensitivities exceeded 90%, with specificities of 95.8% (95% CI: 88.5-98.6), 100.0% (95% CI: 96.4-100.0), and 97.8% (95% CI: 93.8-99.3) against the composite reference standard, respectively. The agreement with Xpert MTB/RIF for RIF detection was 98.6% (95% CI: 96.9-99.3). For INH and FQ resistance, the agreement with Xpert MTB/XDR was 92.0% (95% CI: 88.5-94.5) and 94.3% (95% CI: 91.2-96.3), respectively. The Sanity 2.0 assay is a rapid and user-friendly platform capable of detecting both MTBC and key drug resistance. It demonstrated good diagnostic performance and could potentially be an effective alternative to guide individualized anti-TB treatment, especially in resource-limited settings.

Importance: Rapid and accurate detection of both Mycobacterium tuberculosis complex (MTBC) and key drug resistance is critical to improving tuberculosis treatment outcomes and reducing transmission. However, current molecular diagnostic workflows often require sequential testing, which can delay the initiation of effective and individualized therapy. We evaluated the Sanity 2.0 assay, an integrated high-resolution melting test that simultaneously detects MTBC and resistance to rifampicin, isoniazid, and fluoroquinolone resistance directly from respiratory samples in about 2-3 hours. The assay demonstrated excellent performance, with MTBC detection sensitivity of 92.1% and drug resistance sensitivities exceeding 90% and specificities over 95% against a composite reference standard, as well as strong concordance with World Health Organization-endorsed molecular assays. Implementation of the Sanity 2.0 assay could streamline TB diagnostic workflows; enable rapid, single-step resistance profiling; and facilitate timely, individualized treatment-particularly in resource-limited settings where rapid and comprehensive resistance testing remains a critical unmet need.

Lower respiratory tract infections (LRTIs) place a substantial burden on emergency departments (EDs) during winter outbreaks. Their microbiological diagnosis is currently based on either broad-spectrum molecular techniques performed in laboratory, with turnaround times incompatible with ED workflows, or point-of-care systems, restricted to SARS-CoV-2, influenza A/B, and RSV (quadriplex panel). The Spotfire combines rapid result and syndromic approach (10 respiratory viruses and 4 atypical bacteria), but its added value in EDs remains unassessed. During the 2023 winter, trained nurses collected nasopharyngeal swabs from adult patients with LRTI symptoms and operated the Spotfire in the ED of the Poitiers University Hospital. We described the viral epidemiology and evaluated the impact and efficacy of this rapid broad-spectrum diagnosis by comparing the management of patients with or without respiratory pathogen detected. From 15 December 2023 to 15 March 2024, 1,320 samples were analyzed with Spotfire, with a median turnaround time of 37 min and 10 uninterpretable results. A total of 540 (41%) were positive. Influenza A (30.9%), rhinovirus/enterovirus (21.1%), and SARS-CoV-2 (18.7%) were the main viruses detected, while atypical bacteria represented 8% of all pathogens. Overall, a pathogen not represented on the quadriplex panel was detected in 43% samples. Positive test results were associated with faster medical decision (380 ± 234 vs 431 ± 238 min; P < 0.001), fewer hospital admissions (65% vs 78%; P < 0.001), and shorter hospital stay (10 ± 9 vs 12 ± 14 days; P = 0.006) than negative test results. Antibiotic therapy was administered to 42 of 43 of Mycoplasma pneumoniae-positive patients (98%) compared with 110 of 1,265 (9%) negative patients. This study validated the feasibility of this new diagnostic tool in high-volume EDs improving patient flow, antimicrobial decisions, and isolation strategies.IMPORTANCEThis study provides the first real-world evidence supporting the use of a broad multiplex PCR platform for respiratory pathogens directly at the point of care in a high-volume emergency department. By enabling the simultaneous detection of 14 viruses and atypical bacteria within 20 min, this system bridges a critical gap between laboratory diagnostics and bedside clinical decision-making. Its implementation proved feasible and reliable, improving patient flow, antimicrobial stewardship, and infection control measures. Nearly half of the pathogens identified would have been missed by conventional quadriplex assays, highlighting the added diagnostic value of broader syndromic coverage. These findings are of interest to both clinicians and microbiologists, as they provide pragmatic evidence to guide the integration of advanced molecular diagnostics into acute-care workflows and to optimize patient management during respiratory infection surges.

Although artificial intelligence-particularly large-language models-receives daily attention, the application of AI to image-recognition challenges in clinical microbiology has been under development for several years. In the accompanying article, B. A. Mathison, K. Knight, J. Potts, B. Black, et al. (J Clin Microbiol 63:e01062-25, 2025, https://doi.org/10.1128/jcm.01062-25) (in collaboration with ARUP Laboratories and TechCyte) describe a trained convolutional neural network (CNN) that reviews wet-mount parasitology smears with accuracy and analytical sensitivity exceeding that of a cohort of highly trained medical technologists. The impressive results were enabled by an extensive, globally sourced training set. These findings constitute Part II of the authors' earlier Journal of Clinical Microbiology publication on CNN-based diagnosis of trichrome-stained smears and provide a robust proof-of-concept for integrating AI into clinical microbiology workflows. We comment on the translatability of this technology to routine clinical laboratories.