Objectives: Staphylococcus aureus infective endocarditis is commonly associated with invasive pathology and is worse in prosthetic valve endocarditis. In this study, we aim to examine S. aureus virulence and pathological features of native and prosthetic valve infective endocarditis. Methods: Between 2002 and 2020, 438 patients underwent surgery for left-sided endocarditis caused by S. aureus at our center (59% native and 41% prosthetic valve endocarditis). Endocarditis registry was queried, and pathological features were based on the echocardiography and operative findings. In addition, vegetation samples were collected from 6 patients undergoing surgery for infective endocarditis (3 native and 3 prosthetic valve endocarditis). Total RNA was extracted from all specimens, and messenger RNA sequencing was executed for transcriptomic analysis. Data were pooled into STAR aligner, and gene expression related to virulence factors was compared between 2 groups. Results: Rates of invasive pathology were higher in prosthetic versus native valve infective endocarditis (76% vs 40%, P < .0001), which impacted the complexity of surgical procedures and perioperative course, but not in-hospital mortality. Transcriptomic analysis has shown differences in gene expression between vegetation specimens of native and prosthetic valve endocarditis, including genes for stress response, biofilm formation, and virulence factors. The gene aur (encodes for aureolysin) was highly upregulated in prosthetic valve vegetations compared with native valve vegetations (P 1/4 .023). Conclusions: Prosthetic valve endocarditis caused by S. aureus is associated with further invasive pathology compared with native valve endocarditis, which could be related to upregulation of genes responsible for biofilm formation and metalloproteinase production. (JTCVS Open 2025;24:156-69)

ABSTRACT The objective of the present study was to evaluate the VITEK 2 antimicrobial susceptibility test (AST) for Gram-negative (GN) plazomicin performance using the VITEK 2 and VITEK 2 Compact Systems in clinical settings and to demonstrate its equivalence to the Clinical and Laboratory Standards Institute (CLSI) broth microdilution (BMD) technique. The clinical study conducted at four external sites followed the requirements detailed in the US Food and Drug Administration (FDA) and International Standards Organization (ISO) guidance documents and included clinical, challenge, quality, and reproducibility studies. In this multisite study, a total of 979 Enterobacterales isolates were tested. The VITEK 2 card minimum inhibitory concentration (MIC) results were compared with the reference BMD MIC results. The performance following ISO criteria indicated Essential Agreement (EA) = 97.8% and showed that VITEK 2 plazomicin MIC results for Enterobacterales tend to be in exact agreement when compared with the CLSI BMD reference method, except for Escherichia coli, when MICs tend to be in exact agreement or at least one doubling dilution lower. The analysis was also performed following the FDA criteria using the breakpoints defined by the FDA: ≤2 susceptible (S), 4 intermediate (I), and ≥8 resistant (R) for Enterobacterales. The analysis showed the following performance: EA = 98.7%, category agreement (CA) = 99.4%, and major errors (ME) = 0.1%, with no very major errors (VME) present. There are three species, Klebsiella pneumoniae , Escherichia coli, and Serratia marcescens, for which the trend is ≥ 30% and therefore addressed as a note in the US label. The plazomicin test met the ISO and FDA criteria of ≥95% reproducibility and ≥95% quality control (QC) results within acceptable ranges for QC organisms. IMPORTANCE The VITEK 2 AST-GN plazomicin test is a new, automated alternative to the BMD reference method for determining minimum inhibitory concentrations (MIC) of Enterobacterales, expanding the range of automatic AST testing.

Clostridioides difficileinfection (CDI) is the leading cause of hospital-acquired infective diarrhea. Current methods for diagnosing CDI have limitations; enzyme immunoassays for toxin have low sensitivity andClostridioides difficilepolymerase chain reaction cannot differentiate infection from colonization. An ideal diagnostic test that incorporates microbial factors, host factors, and host-microbe interaction might characterize true infection. Assessing volatile organic compounds (VOCs) in exhaled breath may be a useful test for identifying CDI. To identify a wide selection of VOCs in exhaled breath, we used thermal desorption-gas chromatography-mass spectrometry to study breath samples from 17 patients with CDI. Age- and sex-matched patients with diarrhea and negativeC.difficiletesting (no CDI) were used as controls. Of the 65 VOCs tested, 9 were used to build a quadratic discriminant model that showed a final cross-validated accuracy of 74%, a sensitivity of 71%, a specificity of 76%, and a receiver operating characteristic area under the curve of 0.72. If these findings are proven by larger studies, breath VOC analysis may be a helpful adjunctive diagnostic test for CDI.

Clostridioides difficile infection (CDI) is the leading cause of hospital-acquired infective diarrhea. Current methods for diagnosing CDI have limitations; enzyme immunoassays for toxin have low sensitivity and Clostridioides difficile polymerase chain reaction cannot differentiate infection from colonization. An ideal diagnostic test that incorporates microbial factors, host factors, and host-microbe interaction might characterize true infection. Assessing volatile organic compounds (VOCs) in exhaled breath may be a useful test for identifying CDI. To identify a wide selection of VOCs in exhaled breath, we used thermal desorption-gas chromatography-mass spectrometry to study breath samples from 17 patients with CDI. Age- and sex-matched patients with diarrhea and negative C.difficile testing (no CDI) were used as controls. Of the 65 VOCs tested, 9 were used to build a quadratic discriminant model that showed a final cross-validated accuracy of 74%, a sensitivity of 71%, a specificity of 76%, and a receiver operating characteristic area under the curve of 0.72. If these findings are proven by larger studies, breath VOC analysis may be a helpful adjunctive diagnostic test for CDI.

Polyoma viruses are genomically small, nonenveloped DNA viruses that are ubiquitous among humans. Primary infection is still poorly understood, since patients are either asymptomatic or disease is subclinical. The most important polyoma viruses in human medicine are the BK and JC viruses. Symptomatic infections caused by the BK and JC polyoma viruses present exclusively in immunocompromised patients. Both of these viruses replicate in the urothelium of urinary tract, but have been detected in other sites of latency. The principal diseases caused by the BK virus are nephropathy in patients that have undergone renal transplanation and hemorrhagic cystitis in patients undergoing hematopoietic stem cell transplantation. Although the JC virus replicates in the lower urinary tract, the most important disease caused by this virus is progressive multifocal leukoencephalopathy, which occurs predominantly in patients with altered T-cell immunity. The diagnosis and/or monitoring of patients with these diseases relies heavliy on quantitative polymerase chain reaction (PCR), and occasionally other diagnostic methods. A variety of other polyoma viruses have been described and will be discussed briefly. Among these, the Merkel cell polyoma virus is the most important, which is a cause of Merkel cell carcinoma.

Abstract Background Four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants predominated in the United States since 2021. Understanding disease severity related to different SARS-CoV-2 variants remains limited. Method Viral genome analysis was performed on SARS-CoV-2 clinical isolates circulating March 2021 through March 2022 in Cleveland, Ohio. Major variants were correlated with disease severity and patient outcomes. Results In total 2779 patients identified with either Alpha (n = 1153), Gamma (n = 122), Delta (n = 808), or Omicron variants (n = 696) were selected for analysis. No difference in frequency of hospitalization, intensive care unit (ICU) admission, and death were found among Alpha, Gamma, and Delta variants. However, patients with Omicron infection were significantly less likely to be admitted to the hospital, require oxygen, or admission to the ICU (χ2 = 12.8, P < .001; χ2 = 21.6, P < .002; χ2 = 9.6, P = .01, respectively). In patients whose vaccination status was known, a substantial number had breakthrough infections with Delta or Omicron variants (218/808 [26.9%] and 513/696 [73.7%], respectively). In breakthrough infections, hospitalization rate was similar regardless of variant by multivariate analysis. No difference in disease severity was identified between Omicron subvariants BA.1 and BA.2. Conclusions Disease severity associated with Alpha, Gamma, and Delta variants is comparable while Omicron infections are significantly less severe. Breakthrough disease is significantly more common in patients with Omicron infection.

We present the first performance evaluation results for omadacycline on the VITEK 2 and VITEK 2 Compact Systems (bioMérieux, Inc.). The trial was conducted at four external sites and one internal site.

ABSTRACT The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

The carbapenem/beta-lactamase inhibitor meropenem-vaborbactam (MEV) used to treat complicated urinary tract infections and pyelonephritis in adults was approved in 2017 by the U.S. Food and Drug Administration (FDA). Here, we evaluated Vitek 2 MEV (bioMérieux, Durham, NC) compared to the reference broth microdilution (BMD) method.

Phaeohyphomycosis is a spectrum of subcutaneous and systemic infections caused by a variety of dematiaceous fungi. It is an opportunistic disease with an increased incidence in immunocompromised patients. We report a case of a pedal phaeohyphomycotic cyst in an immunocompetent adult male immigrant with the goal of highlighting its clinical presentation, diagnosis, and optimal treatment. A 57-year-old male immigrant from Panama presented with a painless, gradually increasing, large cystic lesion in his left foot, first intermetatarsal space, which had been present for many years. The patient was treated with surgical excision without antifungal therapy. Histologic analysis showed multiple granulomas composed of fibrin and necrosis in the centers surrounded by proliferative palisading fibroblasts admixed with heavily infiltrated neutrophils, plasma cells, macrophages, lymphocytes, and eosinophils. Periodic acid-Schiff and Fontana-Masson stains revealed sporadic, scattered dematiaceous fungal hyphae and pseudohyphae among granulomatous tissues. The mass was diagnosed as a phaeohyphomycotic cyst. Polymerase chain reaction-based sequencing failed to identify the fungal species because of the rarity of the fungal elements in the granulomatous tissues. The patient had no recurrence at a follow-up of 2 years. A phaeohyphomycotic cyst is a rare entity that needs to be differentiated from other benign and malignant lesions. Multiple modalities, including clinical evaluation, radiography, histologic analysis, microbiological culture, and nucleic acid sequencing, should be used for the final diagnosis. Surgical excision is an optimal treatment. Antifungal therapy should be considered based on the patient's clinical manifestation, surgical excision, and immune functional status.

Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time- of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.

A retrospective review of salient features of the early-to-mid phases COVID-19 pandemic is provided from the perspective of the clinical laboratory. Lessons learned and possible improvements are opined. These include the importance of maintaining a robust laboratory infrastructure, increased public health funding, the partnership between public health and hospital/commercial laboratories, and the critical importance of sound scientific assessment even during a pandemic crisis.

Objectives To clarify the clinical significance and degree of resolution (ie, grade) of Histoplasma granulomas in routinely reviewed surgical pathology specimens and the clinical outcomes of patients with this diagnosis, with an emphasis on those not receiving antifungal therapy. Methods We performed a retrospective medical record, laboratory data, and surgical pathology slide review of patients with Histoplasma granulomas following institutional review board approval. Results Clinical, pathologic, and laboratory data from 62 patients with Histoplasma granulomas were available for review. Of these, 1 of 19 (5%) fungal cultures, 4 of 12 (33%) fungal serologic studies, 0 of 9 Histoplasma urinary antigen tests, and 0 of 2 Histoplasma serum antigen tests were positive. All but 3 of the Histoplasma granulomas were either in the resolving (grade 2) or resolved (grade 3) stage of resolution. None of the patients, including those who did not receive antifungal therapy after the histologic diagnosis, developed progressive or disseminated histoplasmosis. Conclusions These findings, which are supportive of clinical guidelines, suggest that patients with old, hyalinized Histoplasma granulomas do not benefit from further laboratory studies or antifungal therapy. The proposed grading of Histoplasma granulomas informs clinicians of the stage of resolution of an excised lesion, which informs therapeutic decisions and thus is recommended.

The authors review the rationale behind and approaches to testing for COVID-19, the quality of currently available tests, the role of data analytics in strategizing testing, and using the electronic medical record and other programs designed to steward COVID-19 testing and follow-up of patients.