Based on the pharmacogenomics theory, this study developed a software system for interpretation of drug gene loci and guidance on clinical safe medication with the purpose of providing clinical guidance on the safety and effectiveness of drug use through accurate and efficient detection and interpretation of drug gene loci. The system infrastructure was built on a service-oriented architecture (SOA) design and Docker container virtualization approach to achieve a rapid and automatic interpretation of genetic results and best available drugs. The front end was established on HTML5 and JavaScript to realize visualization of analysis results and user interaction. The system was tested and validated to show robust performance which is reliable in clinical use. It will show high impact on the development of pharmacogenomics and clinical practice of patients with personalized medicine.
Objective To analysis and explore the value of metagenomics next-generation sequencing (mNGS) and clinical characteristics of Chlamydia psittaci (C. psittaci) pneumonia. Methods Totally 5 patients who were diagnosed with C. psittaci pneumonia and were treated in the Department of Respiratory and Critical Care Medicine and the Department of Infectious Diseases of Huazhong University of Science and Technology Union Shenzhen Hospital from Febuary 2021 to March 2021 were enrolled in the study. The clinical data of the patients were analyzed, and the clinical characteristics of the disease and treatment experience were summarized. Results The main symptoms of the 5 patients were high fever and cough, 4 of them had a history of raising parrots. The white blood cell and the neutrophils were mostly normal or slightly increased, the C reactive protein and erythrocyte sedimentation rate were significantly increased. The chest CT showed exudation and consolidation of one or several lung lobes. The serious patients might develop respiratory failure, if they were not treated by effective antibiotics. The diagnosis was based on clinical manifestations, contact history and alveolar lavage fluid that were detected by mNGS technology of C. psittaci nucleic acid sequence. The accuracy of detecting pathogens in alveolar lavage fluid by mNGS was high. In addition, mNGS could also identify other bacteria or viruses. After the timely adjustment of treatment, the condition of the patients was improved relied on tetracycline drugs or quinolone drugs, which shortened the diagnosis time and course of C. psittaci pneumnonia and reduced the use of unnecessary antibacterial drugs. Conclusions mNGS is of great significance in diagnosing C. psittaci pneumonia. The timely use of appropriate antibacterial drugs can achieve favorable therapeutic effect.
With the exacerbation of aging population in China, the number of patients with Alzheimer's disease (AD) is increasing rapidly. AD is a chronic but irreversible neurodegenerative disease, which cannot be cured radically at present. In recent years, in order to intervene in the course of AD in advance, many researchers have explored how to detect AD as early as possible, which may be helpful for effective treatment of AD. Imaging genomics is a kind of diagnosis method developed in recent years, which combines the medical imaging and high-throughput genetic omics together. It studies changes in cognitive function in patients with AD by extracting effective information from high-throughput medical imaging data and genomic data, providing effective guidance for early detection and treatment of AD patients. In this paper, the association analysis of magnetic resonance image (MRI) with genetic variation are summarized, as well as the research progress on AD with this method. According to complexity, the objects in the association analysis are classified as candidate brain phenotype, candidate genetic variation, genome-wide genetic variation and whole brain voxel. Then we briefly describe the specific methods corresponding to phenotypic of the brain and genetic variation respectively. Finally, some unsolved problems such as phenotype selection and limited polymorphism of candidate genes are put forward.
Gut microbiota plays an important role in development of diabetes with frailty. Therefore, it is of great significance to study the structural and functional characteristics of gut microbiota in Chinese with frailty. Totally 30 middle-aged and the aged participants in communities with diabetes were enrolled in this study, and their feces were collected. At the same time, we developed a metagenome analysis to explore the different of the structural and functional characteristics between diabetes with frailty and diabetes without frailty. The results showed the alpha diversity of intestinal microbiota in diabetes with frailty was lower. Collinsella and Butyricimonas were more abundant in diabetes with frailty. The functional characteristics showed that histidine metabolism, Epstein-Barr virus infection, sulfur metabolism, and biosynthesis of type Ⅱ polyketide products were upregulated in diabetes with frailty. Otherwise, butanoate metabolism and phenylalanine metabolism were down-regulated in diabetes with frailty. This research provides theoretical basic for exploring the mechanism of the gut microbiota on the occurrence and development of diabetes with frailty, and provides a basic for prevention and intervention of it.
Epigenetics has been very hot in the research of biomedicine. In addition to genetic factors, the occurrence of a disease is also influenced by environmental factors. Retinal vascular diseases are a type of irreversible blind eye disease, such as age-related macular degeneration and diabetic retinopathy. The retinal vessel changes are the major features of retinal vascular diseases, which are the result of interaction of multiple environmental factors and genes. Epigenetic modification mainly includes DNA methylation, histone modification, and non-coding RNA regulation. Epigenetic mechanisms mediate the effects of environmental factors on genes related to retinal vascular diseases, and affect the eventual development of the diseases. Therefore, ophthalmologists should keep eyes close on the role of epigenetics in retinal vascular diseases, track the progress of epigenetic methods in the treatment of retinal vascular diseases, and pay attention to the application prospects of epigenetics. Finding the epigenetic regulators of these diseases can not only deepen the understanding of the pathological mechanism of these diseases, but also provide new ideas for the diagnosis and treatment of these diseases.
In recent years, with the wide application of metagenomics next-generation sequencing, more and more rare pathogens have been detected in our clinical work, including non-tuberculous Mycobacterium, Corynebacterium, Fusarium, Cryptococcus pneumoniae, human herpes virus, torque teno virus, parvovirus, Tropheryma whipplei, Bartonella, Chlamydia psittaci, etc. It is difficult to determine whether these rare pathogens are clinically significant and need treatment. This article puts forward some suggestions and discussions on the diagnosis and treatment of pulmonary infections with some rare pathogens.
ObjectiveTo improve the understanding of psittacosis, the clinical data of 8 cases are reviewed. The application of pathogen metagenomics next-generation sequencing (mNGS) in the diagnosis of nocardiosis is also investigated.MethodsThe clinical data of eight patients with psittacosis diagnosed by mNGS in Nanjing Drum Tower Hospital from January 2018 to May 2020 were reviewed. The clinical characteristics, laboratory examination characteristics and imaging changes were analyzed, and the treatment outcome was followed-up.ResultsAmong the eight cases, there were six males and two females, aged 43～83 years old, with an average age of 64±12 years old. Six of them had a clear history of poultry exposure. The major clinical manifestations were fever, cough, dyspnea, etc. Chest high-resolution computed tomography (HRCT) may have solid shadow, ground glass like shadow. Chlamydia psittaci was detected by mNGS in eight patients’ bronchoalveolar lavage fluid. Minocycline or moxifloxacin were administrated, six patients were discharged after their condition improved, and two patients died.ConclusionsThe incidence of psittacosis is low, and its clinical manifestations lack specificity. In the course of the disease, there may be different degrees of fever, cough, sputum, dyspnea and other symptoms. The lungs can be heard with wet rales, chest HRCT can be seen ground glass shadow, consolidation shadow, accompanied by air bronchogram. Chlamydia psittaci can be detected in alveolar lavage fluid by mNGS. The patients need to be treated for a long time, lasting at least 10 to 14 days. Tetracycline drugs should be the first choice, and can be combined with other antibiotics with activity against gram-positive and gram-negative bacteria in critical patients.
Objective To analyse the clinical and pathological characteristics of Chlamydia psittaci pneumonia, and increase the comprehensive understanding of the Chlamydia psittaci pneumonia. Methods Five patients diagnosed with Chlamydia psittaci pneumonia were selected in this hospital from November 2021 to November 2022, and their clinical and pathological characteristics were analysed. Results Out of these five patients, 2 patients were male and 3 were female, with a mean age (65±9) years and length of hospital stay (11 - 13) d. The first symptom of all five patients was fever; 3 patients were complicated with hypoxemia; there were several accompanying symptoms, including chilly, shiver, fatigue, headache, cough, muscle soreness, hearing loss and so on. In the laboratory indicators, white blood cell count was not significantly abnormal, the C-reactive protein and procalcitonin were high. In the chest CT, the diseased regions were mostly located in unilateral lesions, 3 cases were on the right side; the forms included pulmonary consolidation, lung glass opacity, pleural effusion, pleural thickening, etc.; the mNGS results of bronchoalveolar lavage fluid showed the Chlamydia psittaci; the pathology of lung biopsy showed significant proliferation of fibers in the interstitial lung and partly fibrosis, with histiocytic reaction and minimal lymphocyte infiltration. Conclusion Clearly diagnosing patients with pneumonia which are suspected being infected Chlamydia psittaci as soon as earlier can prompt anti-infection treatment, and avoid further damage to the lung interstitium, eventually decrease the deterioration of lung function and progression to severe pneumonia.
Objective To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice. Methods The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7±1) and (14±1); for the AF group, preoperatively and on postoperative day (7±1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm). Results Analysis of gut microbiota diversity showed that the preoperative α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7±1), the α-diversity indices in the PJI group on postoperative day (7±1) were lower, but the difference was not significant (P>0.05); by postoperative day (14±1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the α-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group. Conclusion Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.
The precision diagnosis and treatment of chest wall tumors heavily rely on imaging assessment, which is limited by the subjectivity of conventional methods and their insensitivity to microscopic features. Artificial intelligence (AI) technologies, particularly radiomics and deep learning, offer new opportunities to overcome these bottlenecks. It is important to note, however, that direct AI research focused specifically on chest wall tumors remains scarce. Most current insights are derived from methodological borrowing and conceptual extrapolation of studies on other solid tumors, such as lung, breast, and esophageal cancers. This review systematically outlines the potential application framework of AI in the management of chest wall tumors, encompassing benign-malignant differentiation, non-invasive pathological subtyping, early treatment response prediction, and prognosis stratification based on multi-modal imaging. It discusses the core model-building strategies and validation processes centered on data fusion, and critically analyzes the unique challenges in this field, including data scarcity, model interpretability, and clinical translation. Moving forward, key directions for translating the potential of AI into clinical reality include fostering the development of dedicated chest wall tumor datasets, conducting prospective validation studies, and exploring "imaging-genomics" integration as well as dynamic decision-support systems.