Integrating whole-genome sequencing into antimicrobial resistance surveillance: methodologies, challenges, and perspectives.

SUMMARYAntimicrobial resistance (AMR) poses a significant threat to global public health. Surveillance is a fundamental method for controlling AMR and guiding clinical decisions, public health interventions, and policymaking. Whole-genome sequencing (WGS) provides a comprehensive and accurate understanding of AMR mechanisms, gene profiling, and transmission dynamics.

Differences in the Clinical Characteristics of Campylobacteriosis between Immunocompromised and Immunocompetent Patients: a Single-Center Retrospective Cohort Study in Japan.

Background: Despite growing concerns about the invasiveness of infections in patients with comorbidities, the clinical features of campylobacteriosis in immunocompromised hosts remain unclear.

Methods: We conducted a retrospective cohort study on campylobacteriosis to investigate the clinical features of patients with immunosuppressive conditions in a university hospital in Japan between 2010 and 2023. The patients were classified into immunocompetent and immunocompromised groups.

An 11-year multicentre clinical and genomic surveillance of listeriosis across Japan.

Objectives: We conducted a multicenter retrospective study to characterize the clinical features of listeriosis and the genomic characteristics of causative Listeria monocytogenes isolates across Japan.

Methods: In this retrospective observational cohort study, we enrolled all microbiologically confirmed listeriosis cases between Jan 1, 2011, and Dec 31, 2021. We collected the causative isolates and performed whole genome sequencing.

Brown adipose tissue, anthropometric traits, and metabolic profiles in women with normal weight obesity.

Emerging evidence indicates that individuals with normal-weight obesity (NWO), characterized by a normal body mass index (BMI) but high body fat (BF) percentage, are at increased risk of cardiometabolic diseases. Brown adipose tissue (BAT) is crucial for cardiometabolic health. However, the connection between adipose tissue density and NWO remains elusive.

Characteristics of febrile seizure after the end of the COVID-19 global health emergency.

Objective: This study aimed to clarify the characteristics of febrile seizures (FSs) before and after the coronavirus disease 2019 (COVID-19) global health emergency.

Methods: This study was a retrospective study conducted at a single institution in Japan. Clinical data were retrospectively collected from 797 children with FS, aged <16 years, between January 2018 and July 2024.

Relationship between clinical and pathologic findings and the presence of genetic variants in patients with steroid-resistant nephrotic syndrome.

Background: Genetic analysis, crucial in determining treatment strategies for steroid-resistant nephrotic syndrome (SRNS), can be performed in limited facilities and requires a long time. Predicting the presence or absence of genetic variants by clinical and pathologic features is preferable.

Methods: In this multicenter, retrospective study, we compared the clinical or pathologic features between the patients with and without genetic variants in children with SRNS and evaluated the efficacy of immunosuppressive treatment and long-term kidney outcomes.

Reduction of post-bronchoscopy pneumonia by working channel irrigation with sterile saline before diagnostic procedures.

Background: After transbronchial biopsy with flexible bronchoscopy, pneumonia sometimes occurs as a complication. The goal of our study was to determine whether irrigation of the working channel before diagnostic procedures can reduce the frequency of post-bronchoscopy pneumonia.

Methods: Initially, we examined the effect of working channel irrigation with 100 mL of sterile saline to reduce the number of bacteria attached to the working channel.

Machine Learning Model for Predicting Coronary Heart Disease Risk: Development and Validation Using Insights From a Japanese Population-Based Study.

Background: Coronary heart disease (CHD) is a major cause of morbidity and mortality worldwide. Identifying key risk factors is essential for effective risk assessment and prevention. A data-driven approach using machine learning (ML) offers advanced techniques to analyze complex, nonlinear, and high-dimensional datasets, uncovering novel predictors of CHD that go beyond the limitations of traditional models, which rely on predefined variables.

Efficacy and safety of intrapleural administration of sodium bicarbonate in patients with acute empyema and complicated parapneumonic effusion: protocol for a prospective, single-arm, interventional study.

Background: The standard treatment for acute empyema/complicated parapneumonic effusion (CPPE) is antibiotic administration and continuous chest drainage. However, adequate drainage becomes impossible in multichambered pleural effusion and some patients may require surgery or may die. In Japan, intrapleural urokinase is frequently used to restore drainage effects; however, its supply was suspended in 2022 owing to difficulties in procuring the raw materials.

Structural analysis shows the mode of inhibition for Staphylococcus aureus lipase by antipsychotic penfluridol.

It is now well-established that Staphylococcus aureus can produce a range of toxin proteins, resulting in a spectrum of pathological conditions when it infects individuals with pre-existing medical conditions or immunocompromised. Among these, MRSA is one of the most prominent antimicrobial-resistant organisms and a significant cause of mortality in many patients. It has been demonstrated that Staphylococcus aureus lipase (SAL) is a vital factor in the proliferation of this bacterium.

Effect of prevaccination blood and T-cell phenotypes on antibody responses to a COVID-19 mRNA vaccine.

Despite the high effectiveness of the coronavirus disease 2019 (COVID-19) mRNA vaccines, both immunogenicity and reactogenicity show substantial interindividual variability. One key challenge is predicting high and low responders using easily measurable parameters. In this study, we performed multivariate linear regression analysis, which allows adjustment for confounding, to explore independent predictive factors for antibody responses.

XFEL crystallography reveals catalytic cycle dynamics during non-native substrate oxidation by cytochrome P450BM3.

Cytochrome P450s are haem-containing enzymes, catalysing the regio- and stereospecific oxidation of non-activated hydrocarbons. Among these, the bacterial P450BM3 is a promising biocatalyst due to its high enzymatic activity. Given the significant conformational flexibility of this enzyme, understanding protein-substrate interactions and associated structural dynamics are crucial for designing P450BM3-based biocatalysts.

Molecular epidemiology and β-lactam resistance mechanisms of complex isolates obtained from bloodstream infections, Kyoto, Japan.

The complex (ECC) comprises multiple species that require genomic analysis for precise identification. They produce inducible AmpC β-lactamase and may carry acquired β-lactamases, which are responsible for cefotaxime and cefepime resistance. To determine the molecular epidemiology, antimicrobial resistance, and β-lactam resistance mechanisms of the ECC, we conducted whole-genome sequencing analysis, antimicrobial susceptibility testing, and mutation analysis on bloodstream ECC isolates from patients in Kyoto, Japan.

Macromolecular crystallography at SPring-8 and SACLA.

Since the groundbreaking determination of the first protein crystal structure by J. C. Kendrew in 1959, macromolecular crystallography (MX) has remained at the forefront of structural biology, driven by continuous technological advancements.

Prediction of depressive disorder using machine learning approaches: findings from the NHANES.

Background: Depressive disorder, particularly major depressive disorder (MDD), significantly impact individuals and society. Traditional analysis methods often suffer from subjectivity and may not capture complex, non-linear relationships between risk factors. Machine learning (ML) offers a data-driven approach to predict and diagnose depression more accurately by analyzing large and complex datasets.

Epidemiology of respiratory viruses according to age group, 2023-24 winter season, Kyoto, Japan.

The seasonality and epidemiology of viral acute respiratory infections (ARIs) have changed since the coronavirus disease 2019 pandemic. However, molecular-based ARI surveillance has not been conducted in Japan. We developed a regional surveillance program to define the local epidemiology of ARIs.

Booster COVID-19 mRNA vaccination ameliorates impaired B-cell but not T-cell responses in older adults.

Age-associated differences in the effect of repetitive vaccination, particularly on memory T-cell and B-cell responses, remain unclear. While older adults (aged ≥65 years) exhibited enhanced IgG responses following COVID-19 mRNA booster vaccination, they produced fewer spike-specific circulating follicular helper T cells-1 than younger adults. Similarly, the cytotoxic CD8 T-cell response remained diminished with reduced PD-1 expression even after booster vaccination compared with that in younger adults, suggesting impaired memory T-cell activation in older adults.

Congenital extraventricular neurocytoma with atypical features in a 3-day-old neonate.

Extraventricular neurocytoma (EVN) is a rare neuronal tumor with a marked tendency towards ganglionic or glial differentiation. Although EVN commonly occurs in young adults, congenital cases are extremely rare, and standardized therapeutic strategies remain undetermined. The presence of atypical features such as increased mitotic activity on histological analysis is correlated with a higher rate of recurrence and poor prognosis.

Total baseline tumor size predicts survival among patients with advanced small-cell lung cancer receiving chemotherapy plus programmed death-ligand 1 inhibitor as first-line therapy: a multicenter retrospective observational study.

Introduction: Total baseline tumor size (BTS) is a prognostic factor for programmed death 1 and programmed death-ligand 1 (PD-L1) inhibitor treatments. However, the prognostic value of total BTS for patients with small-cell lung cancer (SCLC) who receive chemotherapy plus PD-L1 inhibitor remains unknown. Thus, in this study, we aimed to determine whether total BTS is associated with prognosis in patients with SCLC who receive chemotherapy plus PD-L1 inhibitor as first-line therapy.