The COVID-19 pandemic has intensified interest in how the infection affects the lung microbiome of critically ill patients and how it contributes to acute respiratory distress syndrome (ARDS). We aimed to characterize the lower respiratory tract mycobiome of critically ill patients with COVID-19 in comparison to patients without COVID-19. We performed an internal transcribed spacer 2 (ITS2) profiling with the Illumina MiSeq platform on 26 respiratory specimens from patients with COVID-19 as well as from 26 patients with non–COVID-19 pneumonia. Patients with COVID-19 were more likely to be colonized with Candida spp. ARDS was associated with lung dysbiosis characterized by a shift to Candida species colonization and a decrease of fungal diversity. We also observed higher bacterial phylogenetic distance among taxa in colonized patients with COVID-19. In patients with COVID-19 not colonized with Candida spp., ITS2 amplicon sequencing revealed an increase of Ascomycota unassigned spp. and 1 Aspergillus spp.–positive specimen. In addition, we found that corticosteroid therapy was frequently associated with positive Galactomannan cell wall component of Aspergillus spp. among patients with COVID-19. Our study underpins that ARDS in patients with COVID-19 is associated with lung dysbiosis and that an increased density of Ascomycota unassigned spp. is present in patients not colonized with Candida spp.

Acute central nervous system (CNS) infections, such as meningitis and encephalitis, represent medical emergencies that require rapid identification of the causative pathogen to guide appropriate therapeutic interventions. The QIAstat-Dx^® Meningitis/Encephalitis (QIA/ME) is a molecular syndromic panel that enables the simultaneous detection of multiple pathogens and provides the visualization of cycle threshold (Ct) values, offering rapid results for prompt clinical management. This study retrospectively tested, with the QIA/ME panel, 170 cerebrospinal fluid (CSF) samples from patients with CNS infections, confirmed through routine diagnostic workflows. The results were compared with those obtained from bacterial culture and singleplex PCR for viral detection. The QIA/ME demonstrated 100% concordance with reference methods for bacterial and yeast infections. For viral infections, the overall detection rate was 85.9%. Specifically, when singleplex PCR results exceeded 250 copies/mL for DNA viruses and 500 copies/mL for the RNA virus, the concordance rate with the QIA/ME was 96.8%. In contrast, when PCR values were below these thresholds, the concordance rate dropped to 43.8%. A strong overall correlation was observed between the viral load measured by singleplex PCR and Ct values from the QIA/ME (ρ = −0.83, p < 0.001). Only for enterovirus a weak correlation was found (ρ = −0.40, p = 0.056). The QIA/ME panel is an effective diagnostic tool for viral CNS infections, allowing for the visualization of Ct values that reflect pathogen load in samples and which could be useful in guiding clinical decision-making and patient management.

Total joint arthroplasty (TJA) and total joint replacement (TJR) are effective treatments for end-stage osteoarthritis, but prosthetic joint infections (PJIs) remain a significant complication. These infections are often associated with bacteria that form biofilms, which contribute to their persistence and resistance to treatment. The aim of this study was to investigate the biofilm-forming ability, cyclic diguanylic acid (c-di-GMP) production, and the presence of biofilm-associated genes in Staphylococcus aureus and coagulase-negative Staphylococci (CoNS) isolates obtained from synovial fluid samples of patients with PJIs following TJA and TJR. A total of 198 samples were analyzed, with bacterial growth detected in 33 samples (16.7%). Among these, 10 strains of S. aureus and 22 strains of CoNS were identified. Biofilm formation was evaluated using the crystal violet assay, and c-di-GMP levels were measured. A statistically significant linear regression was found between biofilm formation and c-di-GMP production (p = 0.016, R² = 0.18). Genetic analysis revealed the presence of biofilm-associated genes, including icaA, clfA, fnbA in S. aureus, and atlE, fbe in CoNS. Furthermore, there was a statistically significant difference in c-di-GMP production between strains harboring the icaA gene and strains without icaA (p = 0.016), while oxacillin resistance was detected more frequently in strains carrying fbe gene (p = 0.031). The study emphasizes the variability in antibiotic resistance profiles among staphylococcal isolates, underscoring the complexity of managing these infections.

At the beginning of the COVID-19 pandemic, SARS-CoV-2-positive donors were not considered eligible for organ donation. The Italian National Transplant Centre has gradually introduced measures to prevent donor-to-recipient transmission of SARS-CoV-2 infection through organ transplantation. The current national screening protocol for deceased SARS-CoV-2-positive donors recommends molecular testing of donor lower respiratory tract (LRT) samples, graft biopsies and organ perfusion fluids. The aim of the study is to describe the 3-year experience of protocol application in a northern region of Italy. From 1 January 2022 to 31 January 2025, a total of 132 samples were analyzed (29 liver biopsies, 35 kidney biopsies, 68 perfusion fluids) from 40 organ donors with an active or resolved SARS-CoV-2 infection. SARS-CoV-2 PCR on LRT samples was positive in 26/40 (65%) donors, negative in 11/40 (27.5%) cases and in the remaining 3 (7.5%) the PCR result was unknown. Overall, 65 organs were transplanted into 60 recipients. All processed graft biopsies and organ perfusion fluid samples tested negative for SARS-CoV-2 RNA. Our data suggest that the utilization of non-lung donors with resolved or active SARS-CoV-2 infections who died of other causes appears justified and safe.

Implant-associated infections (IAIs) caused by Staphylococcus aureus are a major cause of orthopedic implant failure, driven by biofilm formation and chronic inflammation. Macrophages regulate bacterial clearance and tissue repair through polarization into pro-inflammatory (M1) and anti-inflammatory (M2) phenotypes. This systematic review evaluated preclinical in vivo studies according to PICO criteria (Population: IAI animal models; Intervention: functionalized biomaterials; Comparator: non-functionalized controls; Outcome: bacterial burden reduction associated with macrophage reprogramming). A PRISMA-guided search of PubMed, Scopus, Web of Science, and Embase (January 2015–December 2025) identified 23 eligible studies, assessed using SYRCLE’s risk-of-bias tool. Due to heterogeneity, a narrative synthesis was performed without meta-analysis. Effect measures included bacterial CFU reduction, macrophage polarization markers, cytokine expression, and histological outcomes. In 87.5% of studies, macrophage modulation was associated with reduced bacterial load, biofilm disruption, and improved peri-implant tissue repair and bone integration. These findings support immunomodulatory biomaterials as promising strategies to manage IAIs through combined antibacterial and immune-regulatory mechanisms. However, further validation in larger animal models is required, particularly for nanomaterials. The protocol of this systematic review was registered on the Open Science Framework.