Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
传染病对人类健康产生巨大威胁。快速准确地检测出病原体对于传染病的诊断和治疗非常重要。宏基因组二代测序技术（mNGS）能无差别检测样本中所有的核酸（DNA和RNA）。随着测序和生物信息学技术的发展，mNGS正从实验室研究向临床应用迈进，为病原体检测开辟了新的途径。大量研究表明，mNGS在感染性疾病的临床应用中具有良好的潜力，尤其适用于难检测、罕见和新型病原。但是，mNGS在临床应用中仍存在一些问题:（1）缺乏通用的、可验证的工作流程和质量保证；（2）对高宿主背景和低生物量的样本不敏感；（3）缺乏对海量数据分析和报告解读的标准化指导。因此，全面了解这项新技术将有助于促进mNGS在感染性疾病中的临床应用。本文简要综述了二代测序技术的发展历史、主流测序平台和mNGS工作流程，并讨论了mNGS在感染性疾病中的临床应用及该技术的优缺点。.

Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
传染病对人类健康产生巨大威胁。快速准确地检测出病原体对于传染病的诊断和治疗非常重要。宏基因组二代测序技术（mNGS）能无差别检测样本中所有的核酸（DNA和RNA）。随着测序和生物信息学技术的发展，mNGS正从实验室研究向临床应用迈进，为病原体检测开辟了新的途径。大量研究表明，mNGS在感染性疾病的临床应用中具有良好的潜力，尤其适用于难检测、罕见和新型病原。但是，mNGS在临床应用中仍存在一些问题:（1）缺乏通用的、可验证的工作流程和质量保证；（2）对高宿主背景和低生物量的样本不敏感；（3）缺乏对海量数据分析和报告解读的标准化指导。因此，全面了解这项新技术将有助于促进mNGS在感染性疾病中的临床应用。本文简要综述了二代测序技术的发展历史、主流测序平台和mNGS工作流程，并讨论了mNGS在感染性疾病中的临床应用及该技术的优缺点。.

UNASSIGNED: Timely and accurate pathogen diagnosis can be challenging in children who contract a respiratory virus following congenital heart surgery (CHS). This often results in suboptimal drug use and treatment delays. Metagenomics next-generation sequencing (mNGS) is a swift, efficient, and unbiased method for obtaining microbial nucleic acid sequences. This technology holds promise as a comprehensive diagnostic tool, especially for pathogens undetectable by traditional methods. However, the efficacy of mNGS in the context of congenital heart disease infections remains uncertain. This study aimed to explore the diagnostic value of mNGS for respiratory virus infections post-CHS.
UNASSIGNED: We conducted a retrospective analysis of patients who developed respiratory tract infections post-CHS and were admitted to our cardiac center between July 2021 and December 2022. The patients were categorized into the following two groups based on the diagnostic method used: (I) the mNGS group (comprising 62 patients); and (II) the conventional microbiological test (CMT) group (comprising 70 patients). Bronchoalveolar lavage fluid (BALF) samples from these patients were tested to identify pathogens.
UNASSIGNED: The mNGS group had significantly higher detection rates for both viral infections and mixed viral infections than the CMT group (56.45% vs. 17.14%, P<0.001, and 80.00% vs. 16.67%, P<0.001, respectively). In the mNGS group, 19.35% of the patients received antiviral therapy, and 61.29% received an anti-infective regimen adjustment. Conversely, in the CMT group, only 4.29% received antiviral therapy, and 28.57% received an anti-infective regimen adjustment. A higher percentage of patients showed improved respiratory symptoms in the mNGS group than the CMT group (74.19% vs. 44.29%, P=0.001). Additionally, the mNGS group had a shorter duration of mechanical ventilation and a reduced length of stay in the cardiac intensive care unit than the CMT group (P=0.012).
UNASSIGNED: Using mNGS for BALF enhances the detection of respiratory viral infections and coexisting viral infections post-CHS. This facilitates more precise treatment strategies and could potentially lead to improved patient outcomes.

Blood is a common sample source for metagenomics next-generation sequencing (mNGS) in clinical practice. In this study, we aimed to detect the diagnostic value of blood mNGS in a large real-world cohorts.
Blood mNGS results of 1,046 cases were collected and analyzed along with other laboratory tests. The capabilities and accuracy of blood mNGS were compared with other conventional approaches.
Both the surgical department and the intensive care unit had a positive rate of over 80% in blood mNGS. The positive rate of mNGS was consistent with clinical manifestations. Among the 739 positive samples, 532 were detected as mixed infections. Compared to pathogen cultures, the negative predictive value of blood mNGS for bacteria and fungi detection was 98.9% [95%CI, 96.9%-100%], with an accuracy rate of 89.39%. When compared with polymer chain reaction, the consistency rates of blood mNGS for virus identification were remarkably high.
Blood mNGS have significant advantages in detecting difficult-to-cultivate bacteria or fungi, viruses, and mixed infections, which benefits patients of surgery department the most. Samples other than blood are recommended for mNGS test if a specific infection is suspected. The reporting threshold and reporting criteria of blood mNGS need to be optimized.

BACKGROUND: Cat-scratch disease typically presents with various ocular manifestations such as uveitis, vitritis, retinitis, retinochoroiditis, and optic neuritis. However, fundus nodular lesions was rarely reported. In our study, we reported a case of Cat-Scratch disease with binocular fundus nodular lesions.
METHODS: An 11-year old male presented with uveitis in the right eye and bilateral fundus nodular lesions after indirect contact with unvaccinated cats. Comprehensive ancillary examinations including wide-angle fundus photography, ultrasonography, fluorescein fundus angiography, optical coherence tomography, and orbital magnetic resonance imaging were performed to elucidate the multidimensional features of the binocular lesions. Metagenomics next-generation sequencing was utilized to confirm the diagnosis of Cat-scratch disease. The patient\'s condition showed improvement after a 6-month combination treatment regimen involving systemic administration of doxycycline hyclate and methylprednisolone tablets, as well as local application of mydriatic and corticosteroid eye drops.
CONCLUSIONS: We firstly reported a case of Cat-scratch disease presenting simultaneously with uveitis and fundus nodular lesions caused by Bartonella henselae infection in a child. Timely diagnosis and treatment with antibiotics and corticosteroids showed promising outcomes for the prognosis of these ocular disorders.

A pediatric patient suffered from renal and hepatic abscesses (through hepatorenal space) and recovered by antibiotics and other therapies. By clinical analysis, the multi-organ abscesses might be caused by bloodstream-disseminated infection. In order to identify the pathogen, we collected kidney biopsy tissue, swabs, and plasma samples, and used metagenomics next-generation sequencing (mNGS) and some traditional methods. The results revealed that polymicrobial especially anaerobic bacteremia (Bacteroides fragilis, et al.) contributed to the abscess formation. What is more, systematic human adenovirus C (HAdV-C) infection was shown, and the virus was isolated. The titer of HAdV-2 neutralizing antibodies was 1/4 in the plasma after symptoms onset. Although the exact mechanism of HAdV-2 infection in multiple abscess formation has not been clarified, the case of multi-organ abscesses in the context of polymicrobial especially anaerobic bacteremia and HAdV infection in healthy children is infrequent.

UNASSIGNED: To screen the related genes of community-acquired pneumonia (CAP) by bioinformatics technology, and to analyze the clinical value of key genes.
UNASSIGNED: Gene chip data sets containing CAP patients and normal controls were screened from the Gene Expression Omnibus (GEO) database. The downregulated differentially expressed genes (DEGs) were screened using a gene expression analysis tool (GEO2R). Simultaneously, gene set enrichment analysis (GSEA) was used to explore the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and core genes related to CAP. The candidate genes were then intersected with the genes reported in Online Mendelian Inheritance in Man (OMIM), and the clinical value of these candidate genes was examined based on a literature search. Finally, the clinical data of the CAP patients were retrospectively analyzed. Detect the type of pathogenic bacteria in bronchial-alveolar lavage fluid (BALF) using metagenomics next-generation sequencing (mNGS) high throughput sequencing technology, and detect the expression of key genes through liquid based cell immunohistochemistry to analyze the correlation between pathogenic bacteria and key genes.
UNASSIGNED: Through the intersection of Venn diagrams, 175 co-expressed downregulated DEGs related to CAP were identified. A total of 4 candidate genes, including ICOS, IL7R, ITK, and ZAP70, were obtained by constructing the protein mutual aid network and conducting a module analysis of the common differentially expressed genes. The core genes in the GSEA enrichment pathways were intersected with the CAP-related genes reported in the relevant literature retrieved from the OMIM database. In the Venn diagram, two genes that coexist with OMIM include IL7R and PIK3R1. After considering our findings and the relevant literature, we determined that the key gene related to the occurrence and development of CAP was IL7R. The mNGS detected 13 kinds of bacteria, 4 kinds of fungi, and 2 kinds of viruses. Based on immunohistochemical results, it was found that there were relatively more bacteria detected in the IL7R high expression group.
UNASSIGNED: The identification of the key gene IL7R and the related signaling pathways extend understanding of the pathogenesis of CAP and provide a theoretical basis for clinical targeted therapy research.

UNASSIGNED: To explore the value of metagenomic next-generation sequencing (mNGS) in diagnosing pneumocystis jiroveciipneumonia (PJP) in the immunocompromised patients.
UNASSIGNED: Data of 122 patients with PJP in an immunosuppressed state and 67 non-PJP patients were collected. The diagnostic efficacy of mNGS was compared with the conventional methods, including Gomori methenamine silver (GMS) staining and serum (1,3)-β-D-glucan (BDG). Changes of anti-microbial therapy for patients with PJP based on mNGS results were also reviewed.
UNASSIGNED: The diagnostic sensitivity of mNGS to PJP was higher than that of GMS and BDG (100% vs. 15 and 74.5%, p < 0.001). The diagnostic specificity (91.%) was lower than that of GMS (100%), and similar with BDG (89.6%). In addition to P. jirovecii, mNGS revealed co-pathogens like human β-herpesvirus 5, human γ-pesvirus 4, and some other opportunistic pathogens. The reads of mNGS were remarkably higher in BALF than in blood samples. Initial antimicrobial treatment was modified in 89.3% patients based on the mNGS results, and 74 cases (60.7%) were treated with anti-P. jirovecii therapy.
UNASSIGNED: mNGS is highly efficient in diagnosing PJP and good at identifying pathogens in mixed infections.

Metagenomics next-generation sequencing (mNGS) has been increasingly used in the clinic, which provides a powerful tool for the etiological diagnosis of infectious diseases. Precise treatment can be carried out according to the positive mNGS results. However, the role of negative results of mNGS remains poorly defined in clinical practice.
The results of 1,021 samples from patients who received the mNGS test at Zhongshan Hospital, Fudan University, between January 2019 and December 2019 were analyzed.
There were 308 samples (30.17%) of negative results included in the current study. The top 2 types of negative samples were blood (130/308) and tissue (63/308), which also accounted for the highest negative proportion in diseases. Sputum and bronchoalveolar lavage fluid (BALF) were more likely to have positive results. In false-negative results (defined as negative in mNGS test but reported positive in other sample types or assays), 118 samples were found when compared to regular microbiological assays. The negative predictive value (NPV) of mNGS was 95.79% [95%CI, 93.8%-97.8%] as compared to culture and smear. Mycobacterium, Aspergillus, and Mycoplasma ranked as the top 3 microorganisms on the undetected pathogen list.
The present data indicate that when the mNGS test is negative, the negative prediction accuracy rate of the original specimen is significant. However, other laboratory assays results and clinical presentations should always be carefully considered prior to drawing a diagnosis.