Application of metagenomics next-generation sequencing in the diagnosis and treatment of spinal infection / 实用医学杂志

The incidence of spinal infections,a relatively rare infectious disease,is on the rise due to the empirical use of antibiotics that increases the chances of infection with drug-resistant bacteria,as well as advances in testing technology that have led to an increase in detection rates.Identifying the type of pathogen to target antibi-otics is the key to treatment.However,conventionaldetection methods have low detection rates and are time-consum-ing,which are not conducive to the rapid and accurate diagnosis of spinal infection.Metagenomics next-generation sequencing(mNGS)is a detection technique that can sequence all nucleic acid fragments in samples,the emer-gence of which subverts traditional detection methods and plays an important role in the diagnosis and treatment of spinal infections.This article summarizes the application of mNGS in the diagnosis and treatment of spinal infection.

Epidemiological investigation of the first psittacosis death case in Hangzhou City,China / 中国人兽共患病学报

This study was aimed at performing epidemiologic investigation of the first psittacosis death case in Hangzhou City,to provide a reference for the investigation and disposal of psittacosis cases,as well as prevention and control.Epidemio-logic data were collected through field epidemiologic investigation,and close contacts and environmental samples were collected for pathogenicity testing.The first symptom in the patient was cough,which did not raise concerns at the time.Several days later,the patient developed abdominal distension and black stools,and visited two medical institutions for treatment and hospi-talization.The patient's sputum and peripheral blood were tested for Chlamydia psittaci infection by metagenomic analysis via next-generation sequencing.Samples collected from the patient's family members,close contacts,and home environment test-ed negative with real-time quantitative polymerase chain reaction.The patient later died of gastrointestinal bleeding.This article is the first report of a case of psittacosis contracted from exposure to a sick parrot in Hangzhou City,in a patient who died be-cause of an underlying disease.Operational training should be provided for medical personnel,and early diagnosis with mNGS and treatment of patients with underlying diseases should be performed as early as possible to avoid fatality.In addition,health education should be carried out to raise public awareness of the disease.

Etiological diagnosis value of metagenomic next generation sequencing in the patients with spinal infection / 中华传染病杂志

Objective:To investigate the efficacy of metagenomic next generation sequencing (mNGS) in the etiological diagnosis of patients with spinal infection, so as to provide reference for timely diagnosis and treatment.Methods:A total of 40 patients with suspected spinal infection admitted to the Department of Infectious Diseases in Henan Provincial People′s Hospital from January 2020 to July 2022 were included. The results of tissue culture, histopathological examination and tissue mNGS detection were analyzed retrospectively. According to the clinical diagnose, the patients were divided into the spinal infection group (28 cases) and the non-spinal infection group (12 cases). The positive rate, sensitivity and specificity of mNGS and tissue culture in the pathogen detection of patients with spinal infection were compared. McNemar test was used for statistical analysis.Results:There were 23 males and 17 females in 40 patients. The positive rate of mNGS was higher than that of tissue culture (75.0%(30/40) vs 12.5%(5/40)), and the difference was statistically significant ( χ2=0.08, P<0.001). Based on clinical diagnostic criteria, the sensitivity of mNGS in the diagnosis of spinal infection was higher than that of tissue culture (82.1% vs 17.9%), with a statistically significant difference ( χ2=0.02, P<0.001), while the specificity compared to the tissue culture (33.3% vs 100.0%), the difference was not statistically significant ( P>0.05). Conclusions:mNGS has a high pathogen detection rate and sensitivity in the etiological diagnosis of patients with spinal infection, which could provide clinical guidance for the diagnosis and treatment of patients with spinal infection.

Ureaplasma parvum-induced peritoneal dialysis-associated peritonitis: a case report / 中华肾脏病杂志

Pathogen detection is very important to improve the prognosis of patients with peritoneal dialysis-associated peritonitis. The paper reported a case of peritonitis caused by Ureaplasma parvum diagnosed by metagenomics next-generation sequencing（mNGS）technology. The patient was a middle-aged woman and hospitalized due to abdominal pain and muddy effluent. Anti-infective treatments such as ceftazidime and vancomycin were given but the effect was poor. The result of traditional culture was negative. Ureaplasma parvum was detected by mNGS. After using doxycycline，the patient's inflammation was controlled. It is suggested that mNGS plays an important role in the detection of the pathogens in peritoneal dialysis-associated peritonitis patients with negative culture. Through this case report and literature review，clinical experience is provided for the diagnosis and treatment in such patients.

Clinical value of metagenomics next-generation sequencing in the diagnosis of urinary calculi with secondary infection / 中国医师进修杂志

Objective:To explore the clinical value of metagenomics next-generation sequencing (mNGS) in the diagnosis of urinary calculi with secondary infection.Methods:From September 2021 to May 2022, a total of 110 urinary calculi patients from the First People′s Hospital of Zhejiang Province Tonglu County were collected retrospectively, the urine sample of the patients with bacterial meningitis was measured by urine bacterial culture and mNGS respectively. Taking urine bacterial culture as the "gold standard", the sensitivity, specificity, positive predictive value, negative predictive value, and Kappa consistency of mNGS in the diagnosing of urinary calculi with secondary infection were analyzed. Results:The positive of urine bacterial culture were 35 cases and negative were 75 cases; while positive and negative were 39 cases and 71 cases in the mNGS detection. Taking urinary bacterial culture as the "gold standard", the specificity, sensitivity, positive predictive value, negative predictive value and Kappa consistency coefficient of mNGS in the diagnosis of secondary infection of urinary calculi were 89.3%, 88.6%, 79.5%, 94.4% and 0.756 respectively. Compared with urine bacterial culture, the Kappa consistency coefficients of three common pathogens detected by the mNGS of macrogenomics, included escherichia coli, klebsiella pneumoniae and enterococcus faecalis were 0.703, 0.735 and 0.769, respectively. Conclusions:mNGS can improve the detection rate of pathogens of secondary infection of urinary calculi, and has a high consistency with the detection results of urinary bacterial culture.

Diagnosis of 3 pediatric cases of scrub typhus without the eschar by metagenomics next-generation sequencing / 中华实用儿科临床杂志

Objective:To analyze the pathogen of 3 pediatric cases of scrub typhus without the eschar using metagenomics next-generation sequencing (mNGS), and the clinical application value of mNGS.Methods:Clinical data of 3 pediatric cases of severe scrub typhus without the eschar in the Second Affiliated Hospital and Yuying Children′s Hospital of Wenzhou Medical University from June 2018 to October 2019 were analyzed retrospectively.Among them, 2 cases were 5-year-old males and 1 case was 6-year-old female.Peripheral blood samples of 3 children were detected via mNGS technology.Results:Through mNGS detection, all 3 children were diagnosed with Orientia tsutsugamushi infection and were not complicated with other pathogenic infections.Case 1 died, and case 2 and case 3 were cured.Conclusions:Early diagnosis of scrub typhus without the eschar is difficult.Clinical infectious diseases, especially complicated and critical infectious diseases are difficult to be diagnosed at an early stage, mNGS can provide fast and accurate pathogenic diagnosis support for precise treatment.

Clinical application of multiplex nucleic acid detection technologies: advancements and future / 中华检验医学杂志

With the advantage of being capable of detecting multiple targets at the same time, high throughput and cost-effective, multiplex nucleic acid detection technologies meet the need of large-scale nucleic acid screening and quantification. Multiplex polymerase chain reaction has been applied to detect pathogen, methylated DNA, mutated gene, and single nucleotide polymorphism typing. Isothermal amplification technologies, such as loop-mediated isothermal amplification and recombinase polymerase amplification are promising in the field of point-of-care testing. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-based multiplex nucleic acid detection technologies have become a hotspot due to their high sensitivity and specificity. Metagenomics sequencing plays a leading role in the detection of emerging pathogens and their gene mutation monitoring as well as tumor research. In this review, the advancements and future of multiplex acid detection technologies in clinical application are discussed.

Application and development of metagenomics next-generation sequencing technology in diagnosis of bone infection / 国际外科学杂志

Bone infection is a serious infectious disease in clinical practice due to its difficult treatment and poor prognosis. Therefore, early accurate diagnosis of bone infection is the key for successful treatment. The traditional detection methods is time consuming with lower positive rate. Therefore, it is urgent to find better detection techniques to identify the pathogenic microorganisms of bone infection. In recent years, metagenomic second-generation sequencing technology has been widely used in the diagnosis of clinical infectious diseases because of its advantages of accurate, rapid, efficient and comprehensive diagnosis of pathogenic microorganisms, and can be used as an effective tool for the diagnosis of bone infections. This paper mainly reviews the advantages, disadvantages and development direction of metagenomics next-generation sequencing technology in the diagnosis of bone infection.

Diagnostic value of detection of pathogens in bronchoalveolar lavage fluid by metagenomics next-generation sequencing in organ transplant patients with pulmonary infection / 中华危重病急救医学

Objective:To evaluate the diagnostic value of metagenomics next-generation sequencing (mNGS) in detecting pathogens in bronchoalveolar lavage fluid (BALF) for pulmonary infection in solid organ transplant patients in intensive care unit (ICU).Methods:A retrospective study was conducted, the BALF samples from 46 patients with post organ transplant pneumonia/suspected pneumonia admitted to the Department of Critical Care Medicine of the First Affiliated Hospital of University of Science and Technology of China from August 2018 to August 2021 were collected, all tested by simultaneous mNGS and conventional comprehensive microbial test (CMT), and the results of CMT were used as the reference standard to compare the differences in the diagnostic value of mNGS and CMT for pulmonary infections in solid organ transplant patients, and to analyze the diagnostic value of mNGS for mixed infections.Results:① Pneumonia pathogens: a total of 31 pathogens were detected in 35 patients, including bacteria (16 species), fungi (9 species) and viruses (6 species). Among them, 25 pathogens were detected by mNGS and CMT, and only 19 pathogens were detected by mNGS. Among the microorganisms isolated by mNGS method, the detection rates of Pseudomonas aeruginosa, Acinetobacter baumannii and Klebsiella pneumoniae were higher [51.4%(18/35), 42.9% (15/35), 31.4% (11/35), respectively]; Candida albicans, Aspergillus and Pneumocystis carinii were the most commonly detected fungi [31.4% (11/35), 22.9% (8/35), 22.9% (8/35), respectively]; 20 patients were positive for the virus, and the most commonly detected viruses were cytomegalovirus, herpesvirus and EB virus [28.6% (10/35), 20.0% (7/35), 17.1% (6/35), respectively]. In addition, one case of Brucella was detected by mNGS.② Diagnostic efficiency: as far as bacterial detection is concerned, 20 cases of negative results were obtained by CMT detection of 35 samples included in the study, and a total of 10 cases of positive results were obtained by mNGS detection of negative samples; the percentage of mNGS positive samples was significantly higher than that of CMT positive samples [odds ratio ( OR) = 5.5, 95% confidence interval (95% CI) = 1.2-24.8, P = 0.02]. When compared with CMT, the sensitivity and specificity of mNGS were 93.3% and 50.0%, and the positive predictive value (PPV) and negative predictive value (NPV) were 58.3%, 91.1%. As far as fungal detection was concerned, there was no significant difference in the percentage of positive samples between the two methods ( OR = 1.5, 95% CI = 0.5-4.2, P = 0.60); the sensitivity and specificity of mNGS were 72.2% and 64.7%, and the PPV and NPV were 68.4%, 68.8%; CMT test of the 35 included samples produced 17 negative results, and mNGS test of the negative samples produced 6 positive results. A total of 20 patients tested positive for the virus by mNGS. In addition, 23 patients (65.7%) were diagnosed with pulmonary mixed infection. Conclusion:The use of mNGS to detect pathogens in BALF can improve the sensitivity and specificity of bacterial identification of pulmonary infection in critically ill organ transplant patients, and mNGS has obvious advantages in detecting virus and identifying mixed infections.

Etiological analysis of the immunosuppressed children with severe pneumonia by metagenomics next generation sequencing / 中国小儿急救医学

Objective:To explore the application of metagenomics next generation sequencing(mNGS)in the immunosuppressed children with severe pneumonia and to understand the distribution of pathogens in order to provide reference for early prevention and treatment.Methods:We performed a retrospective analysis of the immunosuppressed children with severe pneumonia who had mNGS reports admitted to PICU according with the enrollment condition from July 2019 to July 2020.The records included general clinical data, traditional detection method report and mNGS results.We evaluated the consistency of the mNGS with the clinical microbiology reports and clinical judgment.Results:Twenty-three patients were enrolled, 15 were male and 8 were female, aging from 28 days to 10 years old, with an average age of(3.67±3.20)years old.Seven cases were cured, 2 were improved, and 14 died.A total of 23 samples were obtained, including 21 blood specimens and 2 bronchoal-veolar lavage fluid specimens.Among the 23 cases, 5 were single infected and 15 were mixed infected.Fungi were detected in 15 cases(65.22%), including 12 cases of Pneumocystis jirovecii, 2 cases of Aspergillus fumigatus and 2 cases of Candida albicans.Virus were detected in 14 cases(60.87%), including cytomegalovirus(CMV) in 10 cases(8 cases with pneumocystis infection), Herpes virus in 3 cases and fine ring virus in 2 cases(1 case with herpes virus infection). Bacteria were detected in 10 cases, including 3 cases of Acinetobacter, 1 case of Klebsiella pneumoniae, 1 case of Stenotrophomonas maltophilia, 1 case of Pinocytogenes, 4 cases of Staphylococcus and 1 case of Bacillus licheniformis.There were Mycoplasma in 3 cases with mixed infection.The positive rate and coincidence rate of mNGS were significantly higher than that of the traditional test group( P<0.05). A total of 19 cases were treated with hormone or immunosuppressive agents, and 17 cases were treated for 1 to 6 months when severe pneumonia occurred. Conclusion:Most immunosuppressed children with severe pneumonia are mixed infection.The common pathogens are Pneumocystis jirovecii and CMV.The use of mNGS can significantly improve the pathogen detection rate, effectively guiding the treatment.