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Background This study aims to examine the potential link between incomplete immune reconstitution following ART treatment and gut microbiota dysbiosis. Methods We collected clinical data and fecal samples from 50 HIV patients undergoing ART and 30 untreated patients. Based on the observed immune function reconstruction, we further categorized the ART(+) group into a responder group ( n  = 30) and a non-responder group ( n  = 20). The gut microbiota composition differences were assessed using Alpha diversity and Beta diversity analysis, while differential genera were identified through linear discriminant analysis effect size (LEfSe). Subsequently, functional disparities in the gut microbiota were investigated using PICRUSt2 and metagenomeSeq software. Results The results of Alpha diversity and Beta diversity revealed significant differences in the composition of gut microbiota among the three groups. Differential genus analysis identified Morganella as an exclusive genus present only in the Non-responder group, exhibiting a significantly higher relative abundance. Correlation analysis demonstrated a positive association between Morganella and LDL levels. The CAZY analysis revealed that glycosyltransferase 25 (GT25) was significantly expressed in the Non-responder group, whereas it was either undetectable or exhibited extremely low expression levels in both the Responder group and the ART(-) group. Importantly, the correlation analysis indicated a positive association between Morganella and GT25 secretion. Conclusions The ecological imbalance of Morganella might be associated with incomplete immune reconstitution following ART, potentially mediated by GT25 secretions. Consequently, Morganella could serve as a promising biomarker for predicting incomplete immune reconstitution in AIDS patients undergoing ART.

Background Rabies is an acute and lethal zoonotic disease caused by the rabies virus (RABV). After onset, there are no effective drugs or treatment methods. Case presentation A 49-year-old female from Hefei, Anhui Province, China, presented to a local hospital with fever, pruritus, chest distress, and shortness of breath. During the consultation, the patient exhibited agitation and was later admitted to the intensive care unit (ICU) in the local hospital for endotracheal intubation and mechanical ventilation due to worsened agitation and dyspnea. Cerebrospinal fluid (CSF) and blood samples were collected and pathogenic microorganism identification was performed by culture and mNGS. However, all results were negative. In addition, the patient did not display typical rabies-specific symptoms such as aerophobia, hydrophobia or photophobia from onset to admission. Subsequently, saliva samples were collected for mNGS detection following consultation with experts at our hospital. Nucleic acid sequences uniquely aligned to the rabies virus (RABV) were identified in these samples. The result was further confirmed by local Center for Disease Control and Prevention (CDC) through RT-qPCR which detected part of the N gene of RABV in the saliva sample. The patient was then transferred to the ICU for isolation. Unfortunately, the patient died on the 10th day of admission due to multiple organ failure. The detection of human rabies virus IgG antibodies reported positive during the advanced stage of the disease during the hospitalization. We consistently verified with the patient’s family member that there was no clear history of animal bites and no history of RABV vaccination. Furthermore, we performed phylogenetic analysis of partial L and G gene sequences of RABV obtained by mNGS (designated HFG23-L and HFG23-G, respectively), the results showed that both HFG23-L and HFG23-G belonged to the China I lineage, and shared 99.7% similarity with the Fengtai strain isolated from dogs in Beijing. Conclusions The identification of unique RABV sequence through mNGS in the patient’s saliva sample suggested that mNGS could serve as a valuable screening tool for the etiological diagnosis of rabies, especially when timely laboratory testing was unavailable or when patients lacked non-specific prodromal symptom and clear exposure history.

Adenosma buchneroides Bonati, also known as fleagrass, is an important medicinal plant used by the Akha (Hani) people of China for treating inflammation-related skin swelling, acne, and diarrhoea, among other conditions. In this study, we aimed to evaluate the anti-inflammatory activities and explore the molecular mechanisms of fleagrass on treating skin swelling and acne. The results demonstrated that fleagrass inhibited the enzymatic activities of 5-LOX and COX-2 in vitro, and decreased the release of NO, IL-6, TNF-α, and IL-10 in the LPS-induced RAW264.7 macrophages. The levels of proteins associated with the nuclear factor-kappa B (NF-κB) pathway were examined by western blotting and immunofluorescence, demonstrating that fleagrass downregulated the expression of TLR4, MyD88, NF-κB/p65, and iNOS and blocked the nuclear translocation of NF-κB/p65. Furthermore, fleagrass exhibited acute anti-inflammatory activity in paw oedema models. The results confirm that fleagrass exhibits remarkable anti-inflammatory activity and can be used in alleviating inflammation, suggesting that fleagrass has the potential to be a novel anti-inflammatory agent. Graphical Abstract

Background: Community-acquired central nervous system infections (CA-CNS infections) have the characteristics of acute onset and rapid progression, and are associated with high levels of morbidity and mortality worldwide. However, there have been only limited studies on the etiology of this infections. Here, metagenomic next-generation sequencing (mNGS), a comprehensive diagnosis method, facilitated us to better understand the etiology of CA-CNS infections.Methods: We conducted a single-center retrospective study between September 2018 and July 2021 in which 606 cerebrospinal fluid (CSF) samples were collected from suspected CNS infectious patients for mNGS testing, and all positive samples were included in this analysisResults: After the exclusion criteria, a total of 131 mNGS-positive samples were finally enrolled. Bacterial, viral, fungal, parasitic, specific pathogen and mixed infections were accounted for 32.82% (43/131), 13.74% (18/131), 0.76% (1/131), 2.29% (3/131) and 6.87% (9/131), respectively. A total of 41 different pathogens were identified, including 16 bacteria, 12 viruses, 10 fungi, and 1 parasite and 3 specific pathogens. The most frequent infecting pathogens are Epstein-Barr virus (n = 14), Herpes simplex virus 1 (n = 14), Mycobacterium tuberculosis (n = 13), Streptococcus pneumoniae (n = 13), and Cryptococcus neoformans (n = 8). Some difficult-to-diagnose pathogen infections were also detected by mNGS, such as Streptococcus suis, Pseudorabies virus, Bunyavirus, Orientia tsutsugamushi and Toxoplasma gondii.Conclusion: In this study, mNGS identified a wide variety of pathogens of CA-CNS infections and many of which could not be detected by conventional methods. Our data provide a better understanding of the etiology of CA-CNS infections and show that mNGS represents a comparative screening of CSF in an unbiased manner for a broad range of human pathogens.

Background As one of the oldest traditional dyes, people worldwide have used natural indigo for centuries. Local people have unique knowledge about indigo identification, which is crucial for indigo quality control and determining the dyeing effects. However, such traditional knowledge is rarely documented and explained. Therefore, the aims of this study were to document and assess the traditional knowledge used by local people when identifying natural indigo paste as well as quantitatively explore the characteristics and material basis of such traditional knowledge. Method Three field surveys were conducted between 2019 and 2020. A total of 283 traditional indigo-paste artisans were interviewed in Guizhou, Yunnan, and Fujian Provinces. The frequency of citation, mention index, and fidelity level of each indigo-paste quality criterion were calculated to determine the most commonly used, recognized, and important quality criteria. To explore the characteristics and material basis of the traditional knowledge, we analyzed 21 indigo-paste samples using high-performance liquid chromatography with diode-array detection (HPLC-DAD), pH, and particle size analyses. Results Local people possess unique knowledge to identify natural indigo. Based on this knowledge accumulated over thousands of years, four criteria (color, taste, touch, and dyeing ability) were chosen by local people, and using these criteria, nature indigo was divided into five quality grades. The best quality indigo paste was judged according to the following folk criteria: dark blue in color with a purple-red luster; smooth and difficult to wipe off; having a sweet, bitter or spicy taste; and easy cloth dyeing. Additionally, the higher the contents of indigo and indirubin—especially indirubin—the better is the quality of the indigo paste. Within the pH range of 9–12, high-quality indigo-paste was more acidic. There was no significant relationship between particle size and quality. Conclusion The ancient methods used by local people for identifying natural indigo are comprehensive and unique. By documenting the various folk quality criteria and conducting quantitative analyses, this study revealed the importance of indirubin and pH for assessing the quality of indigo paste. These findings differ from existing quality standards for synthetic indigo. Amid rapid modernization, traditional knowledge remains invaluable as a world heritage of humanity that warrants preservation.

Background Historically, indigo-yielding plant species were important cash crops from Central Asia to the southern United States and Central America. Indigo-dyed textiles were widely traded along the legendary Silk Road that linked China to Europe. Today, due to the labor-intensive nature of indigo extraction at the household level, lifestyle changes and the widespread availability of commercially produced indigo paste, traditional indigo extraction methods have declined in villages. Yet Li textile weavers on Hainan Island are internationally recognized as producers of indigo-dyed textile using warp ikat techniques. In contrast, Hainan Miao weavers produce indigo-dyed textiles using batik (wax resist) techniques. The aim of this study was to document the indigenous knowledge on indigo-yielding plant species used by both Hainan Miao and Li people on Hainan Island, China. Method Ethnic uses were documented during three field surveys, through a questionnaire survey of 193 respondents, comprising 144 Hainan Miao and 49 Li traditional dyers. Mention index (QI), Availability index (AI), and Preference ranking (PR) of each indigo-yielding plant species were calculated to screen out plant resources with potential development value. Results Five indigo-yielding plant species (from four plant families and four genera) were historically used by Hainan Miao and Li dyers. However, just four species are still in use. Strobilanthes cusia was the main indigo source for Hainan Miao dyers. Li dyers also commonly use Indigofera species ( I. tinctoria and I. suffruticosa ) for indigo extraction. Wrightia laevis is less commonly used as a contemporary indigo source. Indigo extraction by steeping in water to which lime is added to increase the pH is sharing by the five indigo-yielding plant species. Strobilanthes cusia had the highest QI, AI and PR values in Hainan Miao villages. Indigofera tinctoria had the highest QI and AI values, but Indigofera suffruticosa was preferred by Li dyers. Conclusion In the process of modernization and urbanization, some Hainan Miao and Li dyers retain the traditional indigo extraction methods. We found that Strobilanthes cusia and Indigofera tinctoria have the most potential for sustainable indigo production in the future. Furthermore, this study documents the details of extraction method from Wrightia laevis for the first time and the use of Ricinus communis seeds in that process. As one of the last places globally where Wrightia laevis is still used for indigo production, the may also be a nice market among textile collectors and museums that keeps the tradition of Wrightia laevis production and use for indigo extraction alive.

Bartonella species are fastidious, aerobic bacteria that are transmitted by blood-sucking arthropods. Bartonella spp. are responsible for cat scratch disease, Carrion's disease, bacillary angiomatosis and trench fever. On the other hand, Bartonella vinsonii is rarely reported in the literature and there exist a few reports of systemic infection caused by Bartonella vinsonii in patients with acquired immunodeficiency syndrome. A 31-year-old male (diagnosed with AIDS six years ago) had persistent fever and ulceration in the right knee. The elevated levels of inflammatory markers suggested an infectious aetiology. Despite the negative findings of blood culture, metagenomic Next-Generation Sequencing of plasma detected Bartonella vinsonii. The polymerase chain reaction of whole blood and Sanger sequencing confirmed the mNGS findings. Immunohistochemical staining had later suggested bacillary angiomatosis, which was consistent with Bartonella infection. Following antibiotic treatment, the ulcers subsided significantly, but a high fever persisted. The patient died due to sudden respiratory failure.

(Mtb) survives inside a human host for a long time in the form of latent tuberculosis infection (LTBI). Latent infection of tuberculosis has the opportunity of developing into active tuberculosis (ATB), which has greatly endangered human health. The existing diagnostic methods cannot effectively distinguish LTBI from ATB. Therefore, more effective diagnostic biomarkers and methods are urgently needed. Here, we screened the GEO data set, conducted joint differential analysis and target gene enrichment analysis, after filtering the disease-related database, we screened the differential miRNA related to TB. The qPCR was used to verify the miRNAs in 84 serum samples. Different combinations of biomarkers were evaluated by logistic regression to obtain a biomarker panel with good performance for diagnosing LTBI. A panel with two miRNAs (hsa-let-7d-5p, hsa-miR-140-5p) was established to differentiate LTBI from ATB. Receiver operating characteristic (ROC) curve showed that the area under the curve (AUC) are 0.930 (sensitivity = 100%, specificity = 88.5%) and 0.923 (sensitivity = 100%, specificity = 92.3%) with the biomarker panel for the training set and test set respectively. The findings indicated that the logistic regression model built by let-7d-5p and miR-140-5p has the ability to distinguish LTBI from active TB patients.

Background Infectious diseases are a serious threat to human especially since the COVID-19 outbreak has proved the importance and urgency of their diagnosis and treatment again. Metagenomic next-generation sequencing (mNGS) has been widely used and recognized in clinical and carried out localized testing in hospitals. Increasing the training of mNGS detection technicians can enhance their professional quality and more effectively realize the application value of the hospital platform. Methods Based on the initial theoretical understanding and practice of the mNGS platform for localization construction, we have designed a training program to enhance the ability of technicians to detect pathogens by utilizing mNGS, and hence to conduct training practices nationwide. Results Until August 30, 2022, the page views of online classes have reached 51,500 times and 6 of offline small-scale training courses have been conducted. A total of 67 trainees from 67 hospitals have participated in the training with a qualified rate of 100%. After the training course, the localization platform of 1 participating hospital has been put into use, 2 have added the mNGS localization platform for admission, among which 3 have expressed strong intention of localization. Conclusions This study focuses on the training procedures and practical experience of the project which is the first systematic standardized program of mNGS in the world. It solves the training difficulties in the current industry, and effectively promotes the localization construction and application of mNGS in hospitals. It has great development potential in the future and is worth further promotion.

Purpose: To explore the clinical value of detecting pathogens in pus samples by metagenomic next-generation sequencing (mNGS). Methods: The 25 pus samples from infected patients were collected in this research. The positive rate and consistency of pathogenic bacteria detected by mNGS and conventional methods were compared. The pathogen types detected by the two methods were analyzed. Furthermore, the modifications of antibiotic treatment therapy were also evaluated based on mNGS results. Results: The sensitivity of mNGS method in detecting pathogenic bacteria in pus samples was better than that of conventional method (96% vs 40%; P < 0.01). Only 10 samples were detected pathogens by conventional methods, but 24 samples were detected by mNGS method. In specific, the results of conventional methods showed 10 samples had 11 kinds of pathogenic bacteria, of which 9 samples were single pathogen and 1 sample had two kinds of pathogenic bacteria. The results of mNGS method showed 24 samples were detected with 54 kinds of pathogenic bacteria, of which 15 samples were detected with single pathogen, and 9 samples were detected with two or more kinds of pathogenic bacteria. The two methods had 9(36%) consistent results, 14 (56%) completely different results, and 2 (8%) partially consistent results, and the kappa value was 0.19. Notably, mNGS could detect viruses, anaerobic bacteria, and other uncommon pathogens simultaneously. Conclusion: The application of mNGS in the detection of pus specimens from different parts not only have high accuracy rate and also reduce the turnaround time of diagnosis. In addition, the performance of mNGS detection of anaerobic bacteria and caustic bacteria is better than conventional methods. The mNGS diagnosis in pus sample may play an important role in clinical diagnosis and treatment strategy decisions. Keywords: mNGS, pus specimens, pathogen