Objective To investigate a suspected outbreak of hospital-acquired infections caused by Mycobacterium chelonae related to flexible bronchoscope (hereinafter referred to as “bronchofibroscope”) and apply targeted high-throughput sequencing (tNGS) technology for etiological analysis, providing references for controlling hospital infection outbreaks. Methods A retrospective survey of patients who were detected with Mycobacterium chelonae through tNGS testing of bronchoalveolar lavage fluid (BALF) after bronchofibroscopy at the Zhengdong District, People’s Hospital of Henan University of Chinese Medicine, People’s Hospital of Zhengzhou between May 1, 2018 and March 18, 2024. The causes were investigated through comprehensive measures including on-site epidemiological surveys and environmental health assessments, and intervention measures were developed and evaluated for effectiveness. Results A total of 52 patients were included. Mycobacterium chelonae was detected in 30 patients, nosocomial infection was excluded in all cases. The suspicious contaminated bronchofibroscope lavage fluid and its cleaning and disinfection equipment, environment and other samples were collected. The traditional microbial culture results were negative. The tNGS results showed that Mycobacterium chelonae was detected in bronchofibroscope lavage fluid (sequence number 156), and all the patients with Mycobacterium chelonae detected in BALF used the bronchofibroscope. It was judged that this event was a pseudo-outbreak of nosocomial infection caused by the contamination of bronchofibroscope with the patient’s BALF. After three months of continuous follow-up after the comprehensive control measures were taken, Mycobacterium chelonae was not detected by tNGS in bronchofibroscope lavage fluid or patients’ BALF. All patients in the hospital improved and discharged without any new cases. The pseudo-outbreak of nosocomial infection was effectively controlled. Conclusions There are many links in the reprocessing of bronchofibroscope, which is easy to cause pollution, and the management needs to be strengthened. tNGS detection has the characteristics of high efficiency, few background bacteria and clear pathogen spectrum, which can be used as a supplementary means for the investigation of nosocomial infection outbreaks, and is of great significance for identifying the source of infection and determining the transmission route.
ObjectiveTo explore the influence of enhanced recovery after surgery (ERAS) on intestinal flora in patients with colorectal cancer.MethodsBy convenient sampling method, 60 patients with colorectal cancer were selected from August 2018 to December 2019 in the Department of Gastrointestinal Surgery of West China Hospital of Sichuan University and randomly divided into ERAS group and traditional treatment group (traditional group). Among them, the perioperative clinical management was carried out according to the ERAS management and traditional treatment process in the the ERAS group and in the traditional group, respectively. The fresh fecal samples were collected within 24 h after admission and the first natural defecation after operation. The bacterial 16 Sr DNA V3–V4 region was sequenced by Illumina MiSeq sequencer, and the results were analyzed by bioinformatics.ResultsA total of 60 patients with colorectal cancer were included, 30 cases in the traditional group and 27 cases in the ERAS group (3 people temporarily withdrew from the study). There were no significant differences in the basic informations between the two groups (P>0.05). ① Before or after operation, there were no significant differences in Shannon index and Simpson index between the two groups. The difference between preoperative and postoperative comparison in the same group was also not statistically significant (P>0.05). ② Beta diversity analysis showed that there was no significant difference in community composition between the traditional group and the ERAS group before operation, and there was a clear boundary between the traditional group and the ERAS group after operation. ③ At the phylum level, compared with the preoperative abundance, the postoperative abundance Firmicutes decreased by 26.5% and 5.5% in the traditional and ERAS group, respectively; Bacteroidetes increased by 21.6% and 4.7% in the traditional and ERAS group, respectively; Proteobacteria increased by 7.2% and 2.2% in the traditional and ERAS group, respectively. At the genus level, compared with the preoperative abundance, the postoperative abundance of Bacteroides in the traditional group increased by 17.6% and in the ERAS group decreased by 1.6%; Bifidobacterium decreased by 1.8% and 1.3% in the traditional group and in the ERAS group, respectively.ConclusionsERAS does not affect species diversity of intestinal flora. Although ERAS has some damage to structure of intestinal flora, it is weaker than traditional process, so it is more conducive to reconstruction and restoration of intestinal microecological environment.
Objective To investigate the clinical manifestations, diagnosis, treatment and prognosis of psittacosis patients. Methods The clinical features, treatment and prognosis of severe pneumonia caused by Chlamydia psittaci were analyzed and relevant literatures were reviewed. Results An 83-year-old male with a history of type 2 diabetes mellitus was admitted to the hospital for "fever, cough for 5 days and dyspnea for 3 days". Chest CT showed a large mass of increased density in the right lung; CD4+ T lymphocytes had an absolute value of 23 cells/μL; Blood gas analysis showed type Ⅰ respiratory failure; Chlamydia psittaci was detected by metagenomic next-generation sequencing. The patient was diagnosed of severe pneumonia (Chlamydia psittaci), type 2 diabetes mellitus, suspected central nervous system infection. This patient was treated with doxycycline and macrolides antibiotics and discharged from hospital after complete recovery. Literature review showed that patients got infected from contacting sick bird, manifested with multiple system involvement. Respiratory symptoms were common, while central nervous system infection seemed to be rare. The diagnosis of psittacosis depended on serology, nucleic acid detection, pathogen isolation and culture. Metagenomic next-generation sequencing had superiority in the diagnosis of psittacosis. Tetracyclines were the preferable treatment, such as doxycycline or tetracycline, with a duration of at least 10 to 14 days. The prognosis of psittacosis was well, and most of the severe and even life-threatening cases were caused by unclear diagnosis and delayed treatment, and the overall mortality rate was about 1%. Conclusions Psittacosis is one kind of zoonoses. History of poultry exposure is helpful in diagnosis, and metagenomic next-generation sequencing has advantages in diagnosing psittacosis. Tetracyclines are preferred with adequate course of treatment. The overall prognosis is good.
ObjectiveTo detect the differentially expressed circular RNA (circRNA) in rotator cuff tendinopathy and analyze the potential molecular mechanism of these parental genes.MethodsTen supraspinatus tendons donated from patients who underwent tendon repair surgery between June 2018 and June 2019 were used for RNA-sequence. All rotator cuff tendinopathy and normal tendon samples were confirmed by MRI, histological staining, and observation by arthroscopy. All pathological tendons were matched with tendon samples for patients’ age, gender, body mass index, and Bonar score. The bioinformatic analysis was performed based on the differentially expressed circRNA and their parental genes, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and competing endogenous RNA (ceRNA) network construction.ResultsThere were 94 differentially expressed circRNAs, including 31 up-regulated and 63 down-regulated, detected between the rotator cuff tendinopathy and normal tendon samples with |log2 fold change (FC)| >2, P<0.05. GO analysis showed that the genes were mostly enriched in response to cyclic adenosine monophosphate (cAMP). KEGG pathway analysis showed that the most genes were enriched in extracellular matrix-receptor interaction, protein digestion and absorption, cell cycle, and nuclear factor κB signaling pathway. ceRNA networks showed the interactions among circRNAs, mRNAs, and miRNAs. And circRNA.8951-has-miR-6089-DNMT3B was the most sum max energy.ConclusionThis bioinformatic study reveals several potential therapeutic targets for rotator cuff tendinopathy, which paves the way to better treatment and prevention of this disorder.
In recent years, pathogenic metagenomic next-generation sequencing (mNGS) technology has become more and more widely used in the field of clinical infection. Driven by clinical needs, mNGS technology is constantly being optimized and developed. From manual operation to automated process, from simple qualitative detection to quantitative monitoring, from infection identification to multi-dimensional diagnosis of “infection+tumor”, certain research results have been achieved. Of course, there are still some limitations in clinical application of this technology. For example, there are many mNGS detection related reagents in China, but a systematic and complete quality management control and evaluation system has not been established. Further research is needed. This article summarizes the development and application of pathogen metagenomic sequencing technology in recent years, as well as the standardization and normalized process of mNGS detection, in order to provide a reference for pathogen mNGS sequencing to better assist clinical infection diagnosis.
ObjectiveTo summarize the research progress of the relationship between biliary flora and cholangiocarcinoma.MethodThe literatures on the relationship between biliary flora and cholangiocarcinoma were collected and reviewed.ResultsBiliary flora was closely related to the occurrence and development of biliary tract diseases. The inflammatory environment of the biliary tract was an important factor in the occurrence and development of cholangiocarcinoma. Microbes might induce chronic inflammation of the host tissue, leading to cell proliferation and genetic mutation, and ultimately leading to the occurrence of cholangiocarcinoma. Bacterial infection might play an important role in the pathogenesis of cholangiocarcinoma.ConclusionThe study of the role of biliary flora in the development of cholangiocarcinoma may open up a new direction for the prevention and treatment of cholangiocarcinoma.
Objective To investigate the characteristics of micro-biology in the respiratory tract in the patients who were suffering acute exacerbation of chronic obstructive pulmonary disease (AECOPD) with/without their respiratory failures as well as with the high/low frequency of exacerbation. MethodsSixty confirmed subjects in the Department of Respiratory and Critical Care in Guizhou Provincial Hospital from Nov. 2021 to Mar. 2022 were chosen and then divided them into two pairs of sub-groups randomly. Sub-group pairs one were based on the frequency of AECOPD: higher frequency and lower frequency. Sub-group pairs two were based on whether the patients were once with respiratory failure or not. 16S rRNA high-throughput sequencing method was used to detect sputum microecology. The Alpha and Beta diversity of each subgroup, and the differences in bacterial composition and relative abundance, were compared. Results For the AECOPD group with low-frequent of exacerbation, its diversity and abundance of microbiology were higher than those group with high-frequent of exacerbation. The group of AECOPD with respiratory failure had lower bacteria micro diversity but abundancy was higher than those group without respiratory failure. ConclusionThe frequency of AECOPD and whether it is with respiratory failure is related to the change of micro-biology in respiratory tract, so such change plays a great role in this disease.
Objective To analyze the differences in distribution of traditional Chinese medicine (TCM) syndrome elements and salivary microbiota between the individuals with pulmonary nodules and those without, and to explore the potential correlation between the distribution of TCM syndrome elements and salivary microbiota in patients with pulmonary nodules. Methods We retrospectively recruited 173 patients with pulmonary nodules (PN) and 40 healthy controls (HC). The four diagnostic information was collected from all participants, and syndrome differentiation method was used to analyze the distribution of TCM syndrome elements in both groups. Saliva samples were obtained from the subjects for 16S rRNA high-throughput sequencing to obtain differential microbiota and to explore the correlation between TCM syndrome elements and salivary microbiota in the evolution of the pulmonary nodule disease. Results The study found that in the PN group, the primary TCM syndrome elements related to disease location were the lung and liver, and the primary TCM syndrome elements related to disease nature were yin deficiency and phlegm. In the HC group, the primary TCM syndrome elements related to disease location were the lung and spleen, and the primary TCM syndrome elements related to disease nature were dampness and qi deficiency. There were differences between the two groups in the distribution of TCM syndrome elements related to disease location (lung, liver, kidney, exterior, heart) and disease nature (yin deficiency, phlegm, qi stagnation, qi deficiency, dampness, blood deficiency, heat, blood stasis) (P<0.05). The species abundance of the salivary microbiota was higher in the PN group than that in the HC group (P<0.05), and there was significant difference in community composition between the two groups (P<0.05). Correlation analysis using multiple methods, including Mantel test network heatmap analysis and Spearman correlation analysis and so on, the results showed that in the PN group, Prevotella and Porphyromonas were positively correlated with disease location in the lung, and Porphyromonas and Granulicatella were positively correlated with disease nature in yin deficiency (P<0.05). ConclusionThe study concludes that there are notable differences in the distribution of TCM syndrome elements and the species abundance and composition of salivary microbiota between the patients with pulmonary nodules and the healthy individuals. The distinct external syndrome manifestations in patients with pulmonary nodules, compared to healthy individuals, may be a cascade event triggered by changes in the salivary microbiota. The dual correlation of Porphyromonas with both disease location and nature suggests that changes in its abundance may serve as an objective indicator for the improvement of symptoms in patients with yin deficiency-type pulmonary nodules.
Objective To investigate specific changes of T cell repertoire in convalescent patients infected by influenza A (H7N9) virus. Methods Peripheral blood samples from 8 convalescent patients infected by H7N9 virus and 10 healthy donors were collected. After extracting whole DNA from these samples, arm-PCR were performed and the products were submitted to Illumina HiSeq2000 platform to produce deep sequencing data of the nucleotide sequences of complementary determining region 3 of T cell receptor β chain (TRB). Differences were compared in TRB diversity and V-D-J gene usage and similarities of sequences between the patients and the healthy donors. Results Frequency of V-D-J gene usage was different between the H7N9 patient group and the healthy group, such as TRBV30, TRBV27, and TRBV18 (Student's t test, P < 05). Main component analysis showed V-J pairing pattern was significantly different between two groups, which may have potential in identifying patients from healthy people. A considerable number of shared CDR3s were found in patient-patient pairs and normal-normal pairs, while seldom were found in patient-normal pairs. The similarity between patients was also confirmed by overlap distance analysis. Indexes for assessing diversity of immune repertoires, Shannon-Weiner index and Simpson index, were both lower in the patients (Student's t test, P < 05), suggesting that the immune system of the patients had not recovered 6 months after H7N9 infection. Compared with the healthy donors, the number of hyper-expression clones increased in the patient group, and some of them showed similarity among patients. Conclusions TRB repertoires are less diverse in patients with increased hyper-expressed clones and identifiable V-J usage pattern, which is identifiable from normal population. These results suggest that there are H7N9-specific changes in TRB repertoires of H7N9 infected patients in convalescent phase, which have potential implication in diagnosis and therapeutic T cell development.