ObjectiveTo explore application value of next-generation sequencing (NGS) technology in diagnosis of pathogenic microorganism infection through two cases report and literature review.MethodsThe NGS technology was used to make clear diagnosis of two cases of suspected pulmonary tuberculosis and pulmonary nontuberculous mycobacterial diseases. Bronchoalveolar lavage fluid of these two patients was collected for gene detection of pathogens using the NGS technology. A systematic literature review was performed for similar published cases in WanFang and CNKI database, using the keywords (next-generation sequencing) OR (NGS) AND (microorganism OR infection) from January 2000 to January 2018, using the PubMed database to retrieve the English literature before January 2018 with the " NGS, infectious diseases, China” as keywords.ResultsOne case of Mycobacterium tuberculosis and one case of non-tuberculous Mycobacteria were detected respectively. A total of 221 Chinese literatures and 3 English literatures were retrieved, excluding dissertations, conferences and newspapers. Finally, 10 articles were published in the infectious diseases and respiratory diseases subjects. The role of NGS technology in the diagnosis and study of related pathogens is proposed.ConclusionThe NGS method is expected to achieve precision medical purposes, such as early diagnosis of infectious diseases, transmission control, accurate treatment, good prognosis and so on.
ObjectiveTo analyze the effects of alcohol consumption on oral flora of middle-aged and elderly men from the core area of southwestern China, and explore the relationship between excessive-alcohol-consumption-related flora and alcohol-related cancer.MethodsFrom March to June 2018, saliva samples of target subjects were collected for 16S ribosomal RNA gene sequencing, and a questionnaire survey which took drinking history of each participant as the target variable was conducted. According to the amount of alcohol consumed, the subjects were divided into non-drinking group, moderate-drinking group, and excessive-drinking group. The microbial analysis of α diversity, analysis of group difference of oral flora abundance, bacterial function prediction, and receiver operating characteristic (ROC) curve model prediction were carried out.ResultsA total of 59 subjects were included. There were 23 cases (39.0%) in the non-drinking group, 23 cases (39.0%) in the moderate-drinking group, and 13 cases (22.0%) in the excessive-drinking group. The average age was (61.90±8.85) years. Excessive drinking increased the abundance of oral flora (P<0.05), and could change the abundance of specific genus such as Peptostreptococcus and TM7［G-6］ (P<0.05) and regulate cancer-related pathways (P<0.05). ROC analysis found that a panel of three genus oral bacteria such as TM7［G-6］ might effectively distinguish the non-drinking group from the excessive-drinking group (area under curve=0.915).ConclusionsGenus of Peptostreptococcus and TM7_［G-6］ are the potential oral flora biomarkers for the excessive-drinking of target subjects. Some excessive drinking-related flora are closely related to oral cancer.
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.
ObjectiveTo analyze the microbiological characteristics of airway bacteria in adult patients with bronchiectasis and to analyze their correlation with the clinical features. MethodsPatients diagnosed with bronchiectasis in the Department of Respiratory and Critical Care Medicine of West China Hospital of Sichuan University from October 2017 to April 2018 were classified into the bronchiectasis group, while the control group was those who were found to have pulmonary nodules (diameter less than 10 mm) requiring bronchoscopy by physical examination. All subjects in both groups had not used antibiotics or hormones within 4 weeks and had no other respiratory diseases. Bronchoalveolar lavage fluid (BALF) from the lesion site of the branchial expansion group was collected, and BALF from the basal segment of the contralateral inferior bronchial lobe of the pulmonary nodule was collected in the control group. Bacterial culture and 16S rRNA gene sequencing were performed in both groups. ResultsSeventeen cases and six controls were enrolled in this study and the BALF specimens were collected. Eight cases were in stable period and nine cases were in acute period. The case group was divided into the bacteria-positive group and negative group based on bacterial culture of BALF. Shannon index in the bacteria-positive group was significantly lower than the bacteria-negative group and the control group. And Shannon index showed a negative correlation with positive bacterial culture in BALF. When Shannon index ≤4.5 was used to predict positive bacterial culture, the sensitivity and specificity were 83.3% and 90.9% respectively. The average relative abundance of bacteria was higher and the average sample distribution uniformity was lower in patients with acute period, compared with those in patients with stable period. Shannon index was negatively correlated with the acute exacerbation in patients. When Shannon index <5.0 was used to predict acute exacerbation, the sensitivity and specificity were 77.8% and 100.0%, respectively. ConclusionsShannon index in 16S rRNA gene sequencing results has certain predictive value for acute exacerbation stage. 16S rRNA gene sequencing combined with bacterial culture results can help guide clinicians to provide more precise treatment plans.
Objective To explore the relationship between nasopharyngeal microecology and diseases in children with bronchial asthma. Methods A total of 41 children with asthma who were treated in Hainan Provincial Hospital of Traditional Chinese Medicine between November 2020 and March 2023 were retrospectively included in the study, and 26 healthy children undergoing adenoid examination in the same period were selected as the control group. Samples of nasal mucosa were collected from the anterior and medial side of inferior turbinate, and the expression of DEFB2, IL17A, TSLP, IL13, IL5 and T1R3 genes was analyzed by polymerase chain reaction. Nasal swabs were collected from the children, and the bacterial composition was analyzed by 16S ribosomal RNA gene sequencing. Results Compared with the control group, the rate of atopy cases in the asthma group increased significantly (53.7% vs. 19.2%, P<0.05). At the phylum level, compared with the control group, the phylum Chloroflexi, the phylum Patescibacteria, the phylum Tenericutes and the phylum Nitrospirae in the asthma group increased significantly (P<0.05), and the phylum Elusimicrobia decreased significantly (P<0.05). At the genus level, compared with the control group, the members of Bacillus (Fimnicutes), Ruminococcus (Fimnicutes), Rhodococcus (Actinobacteria), Acinetobacter (Proteobacteria), Moraxella (Proteobacteria) and Asaia (Proteobacteria) in the asthma group increased significantly (P<0.05), and the members of Enterococcus (Fimnicutes), Alkanindiges (Proteobacteria), Rickettsia (Proteobacteria), and Rhizobium (Proteobacteria) in the asthma group decreased significantly (P<0.05). Compared with the control group, the Shannon index of the asthma group decreased significantly (2.63±1.45 vs. 3.90±1.44; t=2.708, P=0.010). According to receiver operating characteristic curve analysis, the optimal cut-off point of Shannon index was 3.10. In all study populations, compared with children whose Shannon index was higher than the cut-off point, children whose Shannon index was lower than the cut-off point were characterized by increased expression of IL17A and T1R3 (P<0.05) and decreased expression of TSLP (P<0.05). Conclusion The composition and abundance of nasopharyngeal microbiota are significantly different between children with asthma and healthy control children.