Microbiology spectrum最新文献

Pathogen whole-genome sequencing (WGS) has significant potential for improving healthcare-associated infection (HAI) outcomes. However, methods for integrating WGS with epidemiologic data to quantify risks for pathogen spread remain underdeveloped. To identify analytic strategies for conducting WGS-based HAI surveillance in high-burden settings, we modeled patient- and facility-level transmission risks of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a long-term acute care hospital (LTACH). Using rectal surveillance data collected over 1 year, we fit three pairwise regression models with three different metrics of genomic relatedness for pairs of case isolates, a proxy for transmission linkage: (i) single-nucleotide variant genomic distance, (ii) closest genomic donor, and (iii) common genomic cluster. To assess the performance of these approaches under real-world conditions defined by passive surveillance, we conducted a sensitivity study including only cases detected by admission surveillance or clinical symptoms. Genomic relatedness between pairs of isolates was associated with room sharing in two of the three models and overlapping stays on a high-acuity unit in all models, echoing previous findings from LTACH settings. In our sensitivity analysis, qualitative findings were robust to the exclusion of cases that would not have been identified with a passive surveillance strategy; however, uncertainty in all estimates also increased markedly. Taken together, our results demonstrate that pairwise regression models combining relevant genomic and epidemiologic data are useful tools for identifying HAI transmission risks.IMPORTANCEWhole-genome sequencing of healthcare-associated infections (HAIs) is becoming more common, and new methods are necessary to integrate these data with epidemiologic risk factors to quantify transmission drivers. We demonstrate how pairwise regression models, in which the outcome of a regression model represents genomic similarity between a pair of isolates, can identify known transmission risk factors of carbapenem-resistant Klebsiella pneumoniae in a long-term acute care facility. Such pairwise regression models could be used with rich epidemiologic data in other settings to identify important risk factors of endemic HAI transmission.

Pneumonia is the most common complication of influenza virus infection and is associated with a high mortality rate in immunocompromised individuals. Currently, neither vaccination nor antiviral therapy has achieved satisfactory therapeutic outcomes. Unlike other organs, the lungs harbor a distinct microbial community due to their unique exposure patterns to airborne particulates and pathogens. However, the characteristic alterations of the pulmonary microbiota and its metabolic products, as well as their potential association with immune suppression in influenza pneumonia, remain inadequately investigated. Mice were rendered immunocompromised through administration of the immunosuppressant cyclophosphamide. Mouse models of influenza pneumonia were established under both immunocompetent and immunosuppressed conditions. Body weight was routinely monitored, and lung histopathology was assessed via hematoxylin and eosin staining. Viral load in lung tissue, serum inflammatory cytokine levels, pulmonary microbiota composition, and lung metabolites were analyzed using RT-qPCR, enzyme-linked immunosorbent assay, 16S rRNA gene sequencing, and untargeted metabolomics, respectively. Spearman correlation analysis was performed to evaluate significant associations between pulmonary microbial taxa and specific metabolites. Influenza virus infection led to a marked reduction in body weight and significantly increased viral load in lung tissue, as well as elevated serum levels of inflammatory cytokines (IL-1β, IL-6, and TNF-α). These effects were more pronounced in immunosuppressed mice, which also exhibited more severe inflammatory and pathological changes in lung tissues. Characteristic shifts in the pulmonary microbiota were observed in the immunosuppressed influenza pneumonia model, particularly involving increased abundance of Bacteroides and Agathobacter. In addition, key metabolites such as adenosine, adenosine 5'-monophosphate, and xanthine were significantly altered, indicating perturbations in the purine metabolism pathway. Immunosuppressed influenza pneumonia results in more severe inflammatory and pathological lung damage. The observed characteristic changes in the pulmonary microbiota and associated metabolites provide potential microbial and metabolic targets that may contribute to the pathogenesis of severe lung injury in immunocompromised individuals following influenza virus infection.IMPORTANCETaking lung tissue as the entry point, this study directly observes the microbial and metabolite changes in the lungs, distinguishing the effects of different immune states. From this novel perspective, it aims to identify new targets for the treatment of influenza pneumonia.

Historically, LpxC inhibitors, which target the UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase catalyzing the rate-limiting step in lipid A biosynthesis, have a hydroxamate zinc-chelating head group that targets the active site and can participate in non-specific metal chelation. We synthesized novel molecules with a 2-(1S-hydroxymethyl)-imidazole head group to target the Neisseria gonorrhoeae LpxC enzyme. The gonococcal LpxC structure was generated with AlphaFold, and relative affinities of PF-04753299, CHIR-090, and our novel inhibitors were compared in docking simulations. The MIC of the most potent novel inhibitor for human challenge and multidrug-resistant N. gonorrhoeae was less than 1 μg/mL, intermediate to PF-04753299 and CHIR-090 MICs. Potency in bactericidal assays, which were designed to reflect in vivo conditions, and the ability to inhibit induction of TNF-α in THP-1 monocytes infected with gonococci, reflected relative MIC values. Cytotoxicity of the inhibitors was minimal in hemolysis and lactate dehydrogenase release assays. We showed that treating gonococci with the most potent novel inhibitor reduced lipooligosaccharide expression. Alternatives to differences in affinity for LpxC that could affect potency, including iron binding via the hydroxamate moieties and variable permeability, were explored utilizing synergism experiments and mutational analyses. We isolated spontaneous mutants resistant to the inhibitors and demonstrated that this resistance could be transferred by DNA-mediated transformation. DNA sequence analysis indicated that resistance was not due to lpxC alterations. Overall, the non-hydroxamate inhibitors exhibited high efficacy and low cytotoxicity. Furthermore, exploration of multiple antibacterial mechanisms led us to develop a promising dual therapy approach that could inform strategies to combat multidrug resistance.IMPORTANCENeisseria gonorrhoeae is a major pathogen worldwide and the second most commonly reported cause of sexually transmitted infection in the USA. A total of 601,319 cases of gonorrhea were reported to the Centers for Disease Control and Prevention (CDC) in 2023. The bacteria typically infect the urogenital tract, but infections also occur in the eye, throat, and rectum. The CDC has classified gonorrhea as an urgent public health threat, as there is no vaccine and the bacteria have developed resistance to all but one class of antibiotic. We developed novel inhibitors of an enzyme that plays a critical role in the synthesis of lipooligosaccharide, an important bacterial cell surface toxin, that have high efficacy and low cytotoxicity. Importantly, we found that the inhibitors may have relatively low propensity to engender resistance and, furthermore, we identified a potential dual therapy approach utilizing the novel inhibitors that could have clinical applicability.

Traditional antifouling mechanisms primarily prevent biofouling by inhibiting the initial adhesion of microorganisms to material surfaces. Conversely, the antifouling effect of cicada wings arises from their microstructured or nanostructured surface. These structures trap and rupture adherent microorganisms, which prevent biofilm formation and enable effective antifouling. This study used two typical gram-positive pathogenic strains-the rod-shaped Bacillus cereus and the coccus-shaped Staphylococcus aureus-as model microorganisms. The bactericidal efficacy of the nanopillar array on Pomponia linearis cicada wings against surface-adhered gram-positive bacteria was quantitatively evaluated using live/dead staining. Additionally, the interfacial morphological evolution during bacteria-structure interaction was visualized via scanning electron microscopy/transmission electron microscopy, aiming to elucidate how physical disruption compromises bacterial cellular integrity. The results show that the nanopillar surface exhibits potent bactericidal activity against both gram-positive species, with B. cereus consistently showing higher killing efficiency. This bactericidal effect is not mediated by chemical composition but rather follows a purely physical "adhere-deform-rupture" mechanism. This mechanism has revolutionized the design paradigm of antibiofilm materials, enabling a shift from passive exclusion to an active "capture-and-kill" dual-function strategy.IMPORTANCEThe colonization and spread of bacteria pose significant biosafety threats to several key industries, including healthcare, food, pharmaceuticals, and biotechnology. To mitigate these risks, the current industry commonly employs intervention measures such as the addition of antibiotics, treatment with chemical disinfectants, and application of antibacterial chemical coatings. However, these chemical sterilization methods may potentially have adverse effects on human health. In contrast, the cicada wing surface, with its natural micro- and nanostructures, exhibits physical antibacterial properties that achieve efficient sterilization while avoiding the health risks associated with chemical agents, thus offering a new approach to safe antibacterial strategies.

Given the current global challenges posed by antimicrobial resistance, the early and accurate identification of carbapenem-resistant Gram-negative bacilli (CR-GNB) is crucial for patient outcomes. This study evaluates the combined diagnostic performance of Xpert Carba-R and Loop-mediated isothermal amplification (LAMP) in the early detection of CR-GNB in patients with hospital-acquired pneumonia (HAP) or ventilator-associated pneumonia (VAP) and investigates the effect of early treatment based on detection results on the prognosis of these patients. In this single-center prospective study, 250 HAP/VAP patients were enrolled. Respiratory specimens underwent bacterial culture, antimicrobial susceptibility testing, Xpert Carba-R, and LAMP. Diagnostic performance (sensitivity, specificity, positive predictive value [PPV], negative predictive value [NPV]) of the combined test to detect CR-GNB was assessed. Clinical utility in guiding early antibiotic therapy was evaluated. The combined method demonstrated 64.87% sensitivity (95% CI: 52.89%-75.61%) and 94.32% specificity (95% CI: 89.80%-97.24%), with perfect 100% sensitivity and specificity for detecting CR-GNB in Klebsiella pneumoniae. Patients testing positive were randomized to early or non-early treatment groups. For severe patients, the early treatment group showed significantly improved clinical outcomes, including lower acute physiology and chronic health evaluation-II (APACHE-II) scores (P < 0.05) and sequential organ failure assessment (SOFA) scores (P < 0.01) at 15 days post-treatment, along with reduced 30-day hospitalization costs (P < 0.05). Notably, among the critically ill patients, compared with the non-early treatment group, the early treatment group achieved a clinical improvement rate of 81.25% and a microbiological eradication rate of 56.25%, showing a clear advantage.

Importance: An urgent clinical need exists for rapid detection of carbapenem-resistant Gram-negative bacilli (CR-GNB) in respiratory specimens to facilitate early and precise antibiotic therapy. To address this gap, we developed an innovative dual-method assay: Xpert Carba-R to detect five major carbapenemases, and loop-mediated isothermal amplification (LAMP) to identify common Gram-negative respiratory pathogens. Integration of these methods enables simultaneous and early determination of bacterial species and their resistance profiles. We validated this assay against conventional culture-based antimicrobial susceptibility testing (AST) and assessed its clinical impact on patient outcomes. Results indicate that this integrated approach provides clinically actionable data, serving as a viable alternative to conventional diagnostic workflows.This study is registered with the Chinese Clinical Trial Registry as ChiCTR2400090694.

Candida auris is an emerging fungal pathogen linked to healthcare-associated infections, necessitating rapid and accurate detection for effective infection control. This study evaluated the analytical and clinical performance of the Diasorin Simplexa C. auris Direct IVD assay compared to traditional culture as the reference standard and also to two lab-developed tests (LDTs) already validated in our laboratory: one using DSQ Alert primers/probes on the Roche Cobas 5800 and another on the DiaSorin LIAISON MDX platform. Clinical accuracy was assessed using deidentified residual axillary/groin surveillance specimens from 20 culture-positive and 20 culture-negative patients. Analytical specificity was tested against 14 microbial species commonly found in the axilla/groin. Analytical sensitivity was determined using ZeptoMetrix C. auris strain Z485. Specimen stability was examined at various temperatures. Environmental swabbing was also conducted before and after sample handling. The Diasorin Simplexa C. auris IVD assay demonstrated 100% sensitivity and 90% specificity relative to culture and showed 100% positive agreement with both LDTs and 100% negative percent agreement with the DSQ Alert LDT. The assay also achieved 100% analytical specificity, with no cross-reactivity observed, and an analytical sensitivity of 702 CFU/mL. Specimen integrity remained stable for up to 30 days under all storage conditions. No environmental contamination was detected. The DiaSorin Simplexa C. auris IVD assay demonstrated strong analytical and clinical performance while offering advantages in speed, ease of use, and flexible batch size. It may serve as a practical solution for institutions seeking timely C. auris screening in support of infection prevention protocols.

Importance: Candida auris is an important yeast notable for its ability to easily colonize people as well as its drug resistance. Colonized patients who become immunocompromised may ultimately become infected with C. auris, without many options for treatment. Many health care facilities mandate screening patients for colonization with this yeast to help prevent transmission. This work evaluates the recently FDA approved Diasorin Simplexa C. auris PCR based screening assay and compares its performance to cultures, as well as two existing lab-developed assays. It is the first assay performance evaluation outside of the FDA submission.

Mammalian orthoreovirus (reovirus) is a well-established model for studying viral pathogenesis. Although studies of reovirus have largely been focused on central nervous system disease, reoviruses can also cause myocarditis. Reovirus strain type 1 Lang (T1L) causes mild myocarditis in neonatal mice. However, many highly myocarditic reoviruses are reassortants between T1L and the serotype 3 (T3) Dearing strain that is non-myocarditic. Although cardiac immune responses to T1L are well described, many open questions remain regarding cardiac immune responses to T3 reoviruses. To better understand the effects of T3 reoviruses on the heart, we investigated the long-term cardiac impact of reovirus strain T3 Dearing (T3D) in neonatal C57BL/6 mice. Oral infection with T3D resulted in subclinical myocarditis that was non-lethal but still produced persistent histological myocardial alterations. Echocardiographic analysis revealed a mild decrease in diastolic left ventricular anterior wall thickness in mice infected with 10⁴ PFU, though no consistent dose-dependent functional impairments were observed. Histological examination identified myocardial lesions characterized as replacement fibrosis that developed independently of the inoculating dose. Flow cytometry showed an early immune response at 8 days post-infection, with increased CD4 T cells, CD8 T cells, B cells, and innate immune cells. By 26 days post-infection, the inflammation had largely resolved, but low-level immune infiltration persisted, characterized by CD4 T cells, CD8 T cells, and B cells. These findings suggest that T3D induces subclinical myocarditis with lasting histopathological changes. The presence of fibrosis raises concerns about potential long-term cardiac effects, emphasizing the need for further research into the myocardial impact of non-myocarditic reoviruses.IMPORTANCEViral infections that cause myocarditis are a significant cause of morbidity and mortality worldwide, particularly in children and young adults. Mammalian orthoreoviruses (reoviruses) are an established model for studying viral myocarditis in mice and are also under development as a cancer therapeutic due to their capacity to kill cancer cells. Here, we describe the long-term myocardial effects of the type 3 Dearing (T3D) reovirus strain, which is classically considered neurotropic. Our findings indicate that T3D causes subclinical myocarditis that is non-lethal but produces histopathological changes indicative of fibrosis. Thus, although T3D does not cause overt acute cardiac pathology, it can have long-term effects on the myocardium. This work will inform future studies on reovirus tropism and is relevant to ongoing efforts to harness the oncolytic properties of reoviruses for therapeutic applications.