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Objective:To investigate the pathogen spectrum of acquired immunodeficiency syndrome (AIDS) patients with pulmonary opportunistic infections in the local area, and to evaluate the clinical application of metagenomic next-generation sequencing (mNGS) in these patients.Methods:From January to December 2021, AIDS patients with pulmonary infections admitted to Zhongnan Hospital of Wuhan University were enrolled. Their bronchoalveolar lavage fluid (BALF) was subjected to mNGS and coventional pathogen detection.Routine pathogen detection methods included smear, culture, polymerase chain reaction (PCR), and immunochromatographic colloidal gold. Fisher′s exact probability method was used for statistical analysis.Results:A total of 69 patients were included, and all of them were tested positive for mNGS. Among them, 53 cases (76.8%) were positive for fungi and viruses, 40 cases (58.0%) were positive for bacteria (excluding Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM)), six cases were positive for MTB, 11 cases were positive for NTM, and seven cases were positive for other pathogens. Mixed infections with two or more pathogens were found in 89.9%(62/69) of the patients. Among the conventional pathogen detections of BALF, 79.7%(55/69) of the patients were positive for pathogens, including 42 cases positive for Pneumocystis jirovecii PCR, 16 cases positive for BALF culture, nine cases positive for MTB PCR, and five cases positive for Cryptococcus antigen. The total detection rate of mNGS was 100.0%(69/69), which was higher than that of the conventional pathogen detection rate of 79.7%(55/69), and the difference was statistically significant (Fisher′s exact probability method, P<0.001). The specificity of mNGS detection was 88.4%. Combining clinical and two detection methods, the top five pathogens were Pneumocystis jirovecii (62.3%(43/69)), Candida (29.0%(20/69)), MTB (20.3%(14/69)), NTM and Talaromyces marneffei (15.9%(11/69), each). Fifty-three patients (76.8%) had co-infection with virus. Conclusions:The main cause of pulmonary infection in AIDS patients in this area is mixed infection, and Pneumocystis jirovecii is the most common pathogen. mNGS could significantly improve the pathogen detection rate in AIDS patients with pulmonary infections.
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Objective:To analyze the application value of metagenomic next-generation sequencing (mNGS) in the detection of pathogenic bacteria in brain abscesses.Methods:The data of patients with brain abscess in Tianjin Huanhu Hospital from January 2019 to December 2021 were retrospectively analyzed. All patients underwent stereotaxic abscess puncture and drainage. According to the different methods of pathogen detection, they were divided into bacterial culture group (bacterial culture only) and mNGS group (bacterial culture with mNGS). The clinical symptoms, abscess site, bacterial culture and mNGS results, antibiotic application protocol and prognosis of the patients were analyzed. The bacterial detection results of the two groups were analyzed, and the antibiotic application and prognosis were compared. χ 2 test, exact probability method and Mann Whitney test were used to compare the difference between the two groups. Results:A total of 43 patients with brain abscess were enrolled, including 21 cases in bacterial culture group and 22 cases in mNGS group. The positive rate of bacteria culture group was 42.9% (9/21), the positive rate of bacteria culture group was 45.5% (10/22), and the positive rate of mNGS detection was 100% (22/22). Only 3 cases in the bacterial culture group could have a clear bacterial source, while 17 cases in the mNGS group could have a clear bacterial source according to the bacterial results, showing a significant statistical difference between the two groups (χ 2=19.69, P<0.001). The return time of bacterial culture was 7.0 (4.0,7.0) days, and the average return time of mNGS was 1.5 (1.5,1.5) days, the difference of bacterial return time between the two groups was statistically significant ( Z=0.00, P<0.001). The cost of antibiotic use in bacterial culture group was 24.00 (5.60,31.00) thousands yuan, and the cost of antibiotic use in mNGS group was 12.00 (2.10, 20.00) thousands yuan, and there was significant statistical difference between them ( Z=5.22, P=0.026). Conclusions:MNGS can quickly and accurately identify the types and sources of brain abscess pathogens, guide the clinical application of antibiotics more targeted, reduce the cost of antibiotic use, and is an effective method for the detection of brain abscess pathogenic bacteria.
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Objective:To analyze the viral genome sequence of novel coronavirus infected persons in Baotou City, understand the mutation characteristics of novel coronavirus genome in the process of transmission among cases, and explore the transmission rule of novel coronavirus in the clustered populations.Methods:Nine throat swabs samples (No. 1 - 7, No. 9, and No. 10), two sputum samples (No. 8, No. 11, and No. 11 sample was from No. 10 case), and one surface smear sample (No.12, and No. 12 sample was from No. 10 case) were collected from 10 confirmed cases of novel coronavirus infection in Baotou City from January 25 to February 21, 2020. Samples 1 and 3 were from single cases, and the rest were from clustered cases. The virus genome was sequenced by metagenomic next-generation sequencing (mNGS), and single nucleotide polymorphism (SNP) mutation sites were screened by comparing with NC_045512, a reference strain of novel coronavirus. Combined with relevant epidemiological information, gene mutation, virus typing, and evolutionary traceability analysis were carried out.Results:The results of viral genome mNGS showed that 76 SNP mutation sites were detected in 12 samples compared with the reference strain NC_045512, including 3 (3.95%) transitions and 73 (96.05%) reversals. There were 19 (25.00%) synonymous mutations and 57 (75.00%) non-synonymous mutations. The analysis of nucleotide and amino acid variation sites showed that mutations were found at five sites (T2821C, C6548T, T16464C, G16858A and T251C) in all the clustered cases (cases 2, 4 - 10). In the single cases, sample 1 had mutations at C9245T and A15340T, and sample 3 had mutation at C13T. The virus typing analysis showed that the samples 1 and 3 belonged to the L type of novel coronavirus, while the rest belonged to the S type of novel coronavirus. The results of genomic evolutionary relationship analysis showed that all the samples could be divided into two branches. The branches of sample 1 and 3 belonged to single cases, and the rest belonged to family clustered cases.Conclusion:The genomic characteristics of the clustered cases of novel coronavirus infection in Baotou City are basically consistent with the epidemiological investigation results, and the transmission of the virus is mainly related to close contact and family gathering.
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ObjectiveTo identify causal factors of a case of severe Chlamydia psittaci pneumonia in Yangpu District and provide a scientific basis for effective prevention and control. MethodsBasic information and epidemiological data of the patient were collected through telephone interviews and field epidemiological surveys. Specimens from the patient， close contacts and the environment were collected for pathogen detection. Metagenomics next-generation sequencing （mNGS） was used to identify unknown pathogens. ResultsA 65-year-old male patient with a history of hypertension and diabetes was admitted to the hospital with symptoms of fatigue， poor appetite for a week， fever and cough for four days. A chest computer tomography （CT） scan showed scattered inflammation in the left lung with infiltration of multiple lobes. Blood gas analysis showed type I respiratory failure. The results of mNGS on the bronchoalveolar lavage fluid of the patient indicated that he was infected with Chlamydia psittaci. Epidemiological investigation showed a clear history of avian exposure， with an incubation period of 30 days. ConclusionThis serious pneumonia is a zoonotic disease caused by Chlamydia psittaci. A clear history of avian exposure and the use of mNGS technology can help in the timely diagnosis of this disease.
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@#Abstract: Objective To analyze the clinical characteristics of Chlamydia psittaci pneumonia and improve the diagnosis and treatment skills of clinicians on this disease. Methods The clinical data of thirty-nine Chlamydia psittaci pneumonia cases detected by metagenomic next-generation sequencing (mNGS) from September 2020 to January 2022 at the Affiliated Hospital of Southwest Medical University were retrospectively analyzed. Results There was a history of poultry exposure in 89.7%(35 cases) of the patients. The most common clinical manifestations were high fever (92.3%, 36), cough (76.9%,30), muscle soreness (48.7%,19), headache (38.5%,15), etc. Laboratory examinations showed 76.9% of patients had a normal leukocyte count, and 76.9% had decreased lymphocyte count, often accompanied by elevated C-reactive protein (100%), procalcitonin (97.4%), interleukin-6 (95.8%), interleukin-10 (95.8%), alanine aminotransferase (74.4%), and aspartate aminotransferase (84.6%). Univariate analysis indicated that there were statistically significant differences in the levels of aspartate transaminase, blood urea nitrogen, C-reactive protein, and procalcitonin between severe pneumonia patients and non-severe pneumonia patients（P<0.05）. Multivariate logistic regression analysis showed that an elevated blood urea nitrogen (OR=4.899) had guiding significance for predicting the occurrence of severe pneumonia. Bronchoscopy examination showed no abnormalities in 53.6% of the patients. The imaging manifestations of pulmonary lesions were mainly lobar pneumonia (61.5%) and air bronchograms (94.9%). Therapeutically, it was sensitive to tetracyclines, macrocyclic lactones, and fluoroquinolones. A total of 84.6%(33 cases) of the patients were cured and discharged from the hospital at the end of the treatment. Conclusion Chlamydia psittaci pneumonia is a zoonotic disease that can be detected by mNGS. An elevated blood urea nitrogen level has guiding significance for predicting the occurrence of severe pneumonia. Empirically-selected regimens based on doxycycline are effective for the treatment of Chlamydia psittaci pneumonia.
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Objective To investigate clinical and epidemiological features of pneumocystis jirovecii pneumonia (PJP) in kidney transplant recipients. Methods Clinical data of 68 kidney transplant recipients admitted from July, 2021 to December, 2021 were collected. All patients were divided into the PJP group (n=11), common pulmonary infection group (n=24) and non-pneumonia group (n=33) according to the status of pulmonary infection. The incidence and treatment of PJP after kidney transplantation were analyzed. Basic characteristics and laboratory parameters of the recipients were compared among all groups. The genotyping and transmission map of PJP patients were evaluated. Results Among 64 kidney transplant recipients, 11 cases were definitely diagnosed with PJP. The most common clinical manifestations included elevated body temperature, and dry cough complicated with progressive dyspnea. Chest CT scan showed diffuse interstitial inflammation and ground glass-like lesions of bilateral lungs in all patients. After diagnosis, all patients were orally given with compound sulfamethoxazole for 3-4 weeks. Two patients received non-invasive ventilator-assisted ventilation due to severe lung infection and dyspnea, and the remaining patients were given with nasal cannula oxygenation. One patient experienced elevated serum creatinine level upon discharge, and developed renal allograft failure. The remaining 10 recipients with PJP obtained normal renal allograft function, and no recipient died. Compared with the non-pneumonia group, the rejection rate was higher, the length of hospital stay was longer, the lymphocyte count was less, the lymphocyte proportion was lower, the levels of C-reactive protein, serum creatinine and lactate dehydrogenase were higher, and the levels of serum albumin was lower and CD4+T cell count was less in the PJP group (all P < 0.05). Compared with common pulmonary infection group, the lymphocyte count was less, the lymphocyte proportion was lower, the CD4+T cell count was less and 1, 3-β-D- glucan (BDG) level was higher in the PJP group (all P < 0.05). No new genotype was detected in 10 of the 12 testing samples. It was considered that PJP mainly depended on two transmission chains and two independent transmission individuals. Conclusions Kidney transplant recipients are prone to pneumocystis jirovecii (PJ) infection due to impaired cellular immune function. The most common clinical manifestations consist of elevated body temperature and dry cough complicated with progressive dyspnea, accompanied by headache and fatigue in partial patients. Chest CT scan shows diffuse interstitial inflammation and ground glass-like lesion of bilateral lungs. PJ may be transmitted through respiratory tract. Small-scale PJP might occur in the follow-up outpatient of kidney transplant recipients. Preventive measures should be delivered in a timely manner.
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Objective:To study the clinical features and treatment strategy of neonatal ureaplasma meningitis.Methods:During 2021, the clinical data of 2 neonates with ureaplasma meningitis treated in Children's Hospital of Hunan Province were retrospectively analyzed. Literature on this subject were searched in the following databases: CNKI, Wanfang Database, Chinese Medical Journal Full-Text Database, CQVIP database, SinoMed, PubMed, Embase and Web of Science (up to March 2022). The key words included “infant”, “neonate”, “newborn”, “ureaplasma”, “mycoplasma urealytium”, “meningitis”, “central nervous system infection”, “brain”. The clinical data, treatment and prognosis of patients from the literature were summarized.Results:Case 1, female, gestational age(GA) 33 +3 weeks, intracranial hemorrhage (ICH) and ventricular dilatation were found on 2 d after birth. The cerebrospinal fluid (CSF) routine and biochemistry tests indicated meningitis, but the CSF culture was negative. No improvement after antibiotic treatment. CSF metagenomic next-generation sequencing (mNGS) and 23S rRNA showed Ureaplasma urealyticum on 30 d after birth. The patient was treated with doxycycline (DOX) for 21 d until mNGS turned negative and DOX was discontinued. However, the disease recurred 23 d later and erythromycin was added with DOX as combined therapy. The patient was followed up until 6 months without neurodevelopmental disabilities. Case 2, male, GA 26 weeks, ICH and ventricular dilatation were found on 10 d after birth. The CSF routine and biochemistry tests indicated meningitis, but the CSF culture was negative. No improvement after antibiotic treatment. CSF mNGS and 23S rRNA showed Ureaplasma parvum. The patient received erythromycin therapy for 32 d and had normal neurodevelopment at 5 months. According to the literature, 43 cases were reported including the 2 cases descirbed above, 17 cases were full-term infants and 26 cases were preterm infants. The median CSF leukocytes, glucose and proteins were 566 cells/mm 3, 0.2 mmol/L and 2.2 g/L. 27 cases were diagnosed based on CSF culture, 6 cases using mNGS, 4 cases with both CSF culture and PCR method and 6 cases with other methods. Macrolides alone were used in 14 cases, macrolides combined with another antibiotic were used in 8 cases, non-macrolide antibiotics were used in 9 cases and 12 cases didn't receive any anti-ureaplasma therapy. All 17 term infants survived, however, 8 cases with hydrocephalus. Among the 26 preterm infants, 8 patients died, 18 patients had periventricular-intraventricular hemorrhage and 15 patients had hydrocephalus. Conclusions:Neonatal ureaplasma meningitis has significantly lower CSF glucose level with hydrocephalus as the common complication. For intracranial infections of unknown etiology and no response to treatment, mNGS is helpful in determining the pathogen.Neonatal ureaplasma meningitis should be treated with macrolides alone or as add-on therapy.
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Objective:To analyze the clinical features and etiological results of neonatal central nervous system(CNS) infection and provide basis for optimization of pathogen detection strategy for CNS infection.Methods:We collected the clinical and laboratory data of hospitalized neonates with clinical diagnosis of CNS infection in the neonatal department at Hebei Provincial Children′s Hospital, from January 1, 2020 to August 31, 2021.The clinical manifestations of the enrolled neonates, as well as the cerebrospinal fluid(CSF)pathogens detected by conventional and molecular biological detection techniques were analyzed.Laboratory characteristics of different kinds of pathogen were compared.Results:A total of 101 eligible neonates were enrolled.The median gestational age was 38.8(36.2, 39.6)weeks, with a prematurity rate 26.7%.There were 68 boys.The median age of onset was 9(2, 14)days.Blood culture was positive in 19(18.8%) cases, including 17 cases of bacteria and two cases of fungus.Positive findings were found in CSF specimens of 33(32.7%)cases by various methods including 13 bacteria, 19 viruses and one fungi.Streptococcus group B and Escherichia coli were the first two bacteria in CSF.Enterovirus was the most common virus in CSF.In terms of detection methods of CSF pathogens, seven cases(7/101, 6.9%) were detected by CSF culture, two cases(2/21, 9.5%)by smear, 22 cases(22/45, 48.9%)by single-virus targeted/multiplex polymerase chain reaction and four cases(4/7, 57.1%)by metagenomic next-generation sequencing.The CSF white blood cell counts, protein levels and blood C-reactive protein levels were higher in the cases with bacteria/fungi detection from CNS infection than in those with virus detection( P<0.05). Almost all neonates(98/101, 97.0%)were clinically cured or significantly improved before discharge.Two neonates were discharged against medical advice and one neonate was transferred to the other hospital after clinical improvement. Conclusion:Combined use of conventional and molecular biological detection techniques can significantly improve the etiological positive rate of neonatal CNS infection.Viral infection is not rare in the neonatal population.Our study demonstrated the spectrum of organism causing neonatal CNS infection, which provided a basis for the optimization of pathogen detection strategy.
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OBJECTIVES@#To explore the value of metagenomic next-generation sequencing (mNGS) in the pathogen identification in children with hematological malignancies complicated with infections.@*METHODS@#A retrospective analysis was conducted on clinical data and pathogenic test results of 43 children with hematological malignancies who underwent microbial culture and mNGS due to infections in the Third Xiangya Hospital of Central South University between June 2020 and July 2022. Differences in detection rates and characteristics of pathogenic microorganisms detected by mNGS and microbial culture were compared.@*RESULTS@#A total of 54 specimens were examined, and the overall detection rate of pathogen by mNGS (80%, 43/54) was significantly higher than that by microbial culture (30%, 16/54) (P<0.001). The most commonly detected infection type by mNGS was viral infection, followed by fungal infection combined viral infection, while that by microbial culture was bacterial infection, followed by fungal infection. The detection rate of fungi by mNGS (33%, 18/54) was higher than that by microbial culture (6%, 3/54) (P<0.001). The detection rate of two or more pathogenic microorganisms by mNGS was higher at 48% compared to microbial culture at 9% (P<0.05). The detection rate of two or more types of pathogenic microorganisms by mNGS was also significantly higher at 33% compared to microbial culture at 2% (P<0.05). The most commonly detected bacteria and fungi by mNGS were Pseudomonas aeruginosa and Candida tropicalis, respectively, in peripheral blood, while Streptococcus pneumoniae and Pneumocystis jirovecii were most commonly detected in bronchoalveolar lavage fluid. Treatment adjustments based on mNGS results were beneficial for 35% (15/43) of the cases.@*CONCLUSIONS@#mNGS has a higher detection rate than microbial culture and has obvious advantages in diagnosing mixed and fungal infections, making it a useful supplementary diagnostic method to microbial culture.
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Humans , Child , Retrospective Studies , Hematologic Neoplasms/complications , High-Throughput Nucleotide Sequencing , Bronchoalveolar Lavage Fluid , Hospitals , Sensitivity and SpecificityABSTRACT
ObjectiveTo summarize the clinical features and prognosis of pulmonary mucormycosis （PM） in southern China， and to explore the diagnostic value of metagenomic next generation sequencing （mNGS） in PM. MethodsThe clinical manifestations， diagnosis， treatment and prognosis of patients diagnosed with PM in The First Affiliated Hospital of Sun Yat-sen University from January 1， 2019 to January 31， 2022 who had undergone mNGS detection in lung tissue or alveolar lavage fluid were collected retrospectively. A total of 14 patients with PM were included， including 4 patients with confirmed diagnosis and 10 patients with clinical diagnosis. ResultsAll patients had underlying medical conditions， with hematological malignancies and diabetes being the most common. The most common symptoms were fever （n = 10）， cough （n = 9） and shortness of breath （n = 9）. Consolidation was the most common sign of chest CT， followed by mass， mostly with cavity. On laboratory tests， decreased CD4+T lymphocytes， elevated CD8+T lymphocytes， and decreased CD4+/CD8+ ratio， and presentation with pleural effusion indicate poor prognosis. The positive rate of mNGS diagnosis was 78.5%， which was significantly higher than that of histopathology （50%）， fungus rapid fluorescence staining （61.5%） and fungal culture （23.1%） of bronchoalveolar lavage fluid. ConclusionsPulmonary mucormycosis is more likely to occur in patients with underlying diseases or who are immunocompromised. The clinical manifestations lack specificity. The low CD4/CD8 ratio and presentation of pleural effusion on CT imaging indicate poor prognosis of patients. mNGS is a rapid， convenient and sensitive method for the diagnosis of PM， which has advantages in the diagnosis of pulmonary mucormycosis.
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@#Abstract：Objective To investigate the morphological features of the Pneumocystis jirovecii, in order to facilitate early detection and rapid diagnosis of this rare pathogen from a morphology point of view by laboratory technicians. By analyzing the laboratory features and application value of different pathogen detection methods in the diagnosis of Pneumocystis jirovecii pneumonia, we aim to provide the most reliable diagnostic basis for rapid diagnosis of Pneumocystis jirovecii pneumonia.Methods A retrospective analysis was conducted on the test results of bronchoalveolar lavage fluid samples from a comprehensive hospital in Zhangqiu District, Jinan City, Shandong Province, and a hospital in Changde City from April 2022 to October 2022. Five confirmed cases of Pneumocystis jirovecii pneumonia were detected. Its clinical manifestations, laboratory results, and morphological characteristics of pathogens under different stains were analyzed to discuss the advantages and disadvantages of different detection methods. Results Cytological examination of bronchoalveolar lavage fluid found the trophozoites and cysts of Pneumocystis jirovecii by Wright's-Giemsa staining in 4 cases (80%), and the cysts of Pneumocystis jirovecii by Silver hexamine staining in 4 cases (80%), while the metagenomic next-generation sequencing confirmed all the 5 positive results. All 5 patients had different degrees of reduction in the absolute count of peripheral blood lymphocytes, and the serum lactic dehydrogenase and (1-3)-β-D-Glucan were increased. Among the 5 patients in this study, 4 were treated with sulfamethoxazole combined with caspofungin, and 1 was treated with sulfamethoxazole. Three patients were cured and discharged from hospital after treatment, but two died. Conclusions The method of Wright's-Giemsa staining for the cytological examination of bronchoalveolar lavage fluid to find Pneumocystis jirovecii has the unique and irreplaceable advantages as silver staining. Metagenomic next-generation sequencing can further increase the positive detection rate of Pneumocystis jirovecii. The combination of cytological examination of bronchoalveolar lavage fluid with metagenomic nextgeneration sequencing is a powerful diagnostic method for rapid diagnosis of Pneumocystis jirovecii pneumonia, which can diagnose accurately and reduce missed diagnosis.
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Objective:To explore the clinical utility of metagenomic next-generation sequencing (mNGS) for patients with critically ill atypical rickettsial infections in the early diagnosis and therapy.Methods:From Jan 2020 to Aug 2022, clinical features, blood biochemical results, imaging data and mNGS results in patients with unexplained critical illnesses were collected and analyzed retrospectively. Fisher's exact test was used to compare the positive rate of mNGS and weil felix reaction.Results:All 15 patients with rickettsial disease had fever, 12 cases had headache, but only 3 had a typical rash or scab of diagnostic significance, 6 had septic shock and all had multi-organ dysfunction; blood mNGS tests were positive in 15 cases, of which 10 had Orientia tsutsugamushi detected in their blood and the remaining five had Rickettsia moschata detected in their blood. The positive rate of mNGS was significantly higher than that of the weil felix reaction (15/15 vs 0, P<0.001). All patients were given doxycycline and other treatments after diagnosis, of which 14 improved and were discharged, and one died 1 week after discharge due to critical condition and abandonment of treatment. Conclusion:mNGS can improve the detection rate of atypical rickettsiae in patients with negative routine test results, which can provide valuable reference basis for early diagnosis and early anti-infection treatment of patients with critical rickettsial disease.
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Objective:To explore the etiological diagnostic value of metagenomic next-generation sequencing (mNGS) in peritoneal dialysis (PD)-related peritonitis.Methods:The study was a retrospective cohort study. The clinical data of patients with PD-related peritonitis who were treated and underwent microbial cultivation and mNGS test at the same time from June 2020 to July 2021 in the Affiliated Drum Tower Hospital, Medical School of Nanjing University were analyzed. The positive rate, detection time and consistency between mNGS test and traditional microbial culture were compared.Results:A total of 18 patients with age of (50.4±15.4) years old and median dialysis time of 34.0 (12.4, 62.0) months were enrolled in the study, including 11 males and 7 females. Pathogenic microorganisms were isolated in 17 patients by mNGS test, with a positive rate of 17/18, which was higher than 13/18 of microbial culture, but the difference was not statistically significant ( P=0.219). Both mNGS test and microbial culture isolated positive pathogenic bacteria in 12 patients, and mNGS test isolated the same types of pathogenic bacteria as microbial cultivation did in 11 patients. In five patients with negative microbial culture, mNGS test also isolated pathogenic microorganisms, including 3 cases of Staphylococcus epidermidis, 1 case of Mycobacterium tuberculosis and 1 case of Ureaplasma urealyticum. In 1 patient, microbial culture isolated pathogenic bacteria ( Escherichia coli) whereas mNGS test did not. The detection time of mNGS was 25.0 (24.0, 27.0) h, which was significantly shorter than 89.0 (72.8, 122.0) h of microbial culture ( Z=3.726, P<0.001). Conclusions:mNGS test can improve the detection rate of pathogenic microorganisms in PD-related peritonitis and greatly shorten the detection time, and has good consistency with microbial culture. mNGS may provide a new approach for pathogen identification of PD-related peritonitis, especially refractory peritonitis.
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Objective:To investigate the urinary virology and clinical characteristics of female overactive bladder (OAB) patients.Methods:Catheterized urine samples were collected from 55 women with OAB and 18 control individuals between January 2021 and August 2021. Inclusion criteria were: female with age>18, diagnosed as OAB, OABSS total score≥3 and item Urgency score≥2, informed consent signed. Exclusion criteria were: Urine culture positive, urinary catheter indwelling status, antibiotic usage in recent 30 days, other disease leading to OAB-like symptoms, pelvic organ prolapse and current pregnancy, immunosuppressive therapy or status. Clinical characteristic and history were collected. OAB symptoms were assessed via both OABSS (overactive bladder symptom score) and OAB-V8 (8-item overactive bladder questionnaire). The urine specimens were analyzed using mNGS for identifying viral infections. The correlation between the disease and JC virus infection was analyzed by t test, chi-square test, binary logistic regression analysis and Spearman correlation matrix, and the Nomogram map for predicting the risk of viral infection was constructed. Results:In total, 55 women with OAB and 18 healthy controls were recruited in the study. There are significant difference in terms of UTI history, pelvic surgery history and the habit of holding urine [60.0%(n=33)to 16.7%(n=3), P=0.002; 43.6%(n=24)to 0.0%(n=0), P<0.01; 36.4%( n=20)to 5.6%( n=1), P=0.015]. Based on mNGS results, OAB patients were identified with more positive viral infection [47.3%(n=26)to 33.3%(n=6)] and more JC virus infection. In the OAB group, subtype 7B of JCV ( n=8) was identified, while in the control group, subtype 7A(n=2) was identified. Pairwise Spearman correlation analysis indicated high correlations between viral infection and OABSS ( r=0.58), age and pausimenia ( r=0.68), hypertension and age ( r=0.53), respectively. Estimates from binary logistic regression model indicated risk factors for virus infection in OAB patients including age ( OR=1.99, 95% CI 0.02-2.61), holding urine habit( OR=2.16, 95% CI 0.18-3.85) and pelvic surgery ( OR=2.53, 95% CI 0.54-4.27). Conclusions:Urinary viral infections appear to be associated with more severe OAB symptoms and JC virus may be a potential therapeutic target for OAB.
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Aggregatibacter aphrophilus is a member of the normal flora of the human oral cavity and pharynx, a Gram-negative fastidous bacteria, belonging to agglomerates, which is a normal mixed oropharyngeal flora in humans, most commonly colonized on the surface of oral mucosa. This bacterial infection is rare in clinical practice, and it is difficult to culture and identify the bacteria, which is easy to be missed. A patient with intracranial infection was admitted to Huaihe Hospital, who showed fever and headache as the main clinical manifestations, and Aggregatibacter aphrophilus was detected by the metagenomic next-generation sequencing of cerebrospinal fluid. The patient′s symptoms were significantly improved after anti-infection treatment.
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Objective:To study the clinical application of metagenomic next-generation sequencing (mNGS) on pathogen diagnosis and clinical management in neonatal sepsis.Methods:From January 2019 to February 2021, neonates suspected of sepsis receiving both mNGS and blood culture in our hospital were retrospectively reviewed. The effects of mNGS on pathogen detection, antibiotic choice and clinical management were analyzed.Results:A total of 35 neonates were included. Sepsis was confirmed in 24 neonates. 12 neonates had positive microbiology results (both mNGS and blood culture were positive in 3 cases, only mNGS positive in 8 cases and only blood culture positive in 1 case). mNGS showed higher positive rate than blood culture in patients with neonatal sepsis (45.8% vs. 16.7%, P=0.049). The concordance of mNGS and blood culture was 74.3%. 21 cases (60.0%) had antibiotics before testing and the positive rate showed no significant difference between mNGS and blood culture [19.0% (4/21) vs. 4.8% (1/21), P=0.343] in these patients. 14 cases didn't receive antibiotics before testing and the positive rate also showed no significant difference between mNGS and blood culture [28.6%(4/14) vs.21.4% (3/14), P=1.000]. 8.6% patients changed clinical treatment based on the mNGS results. Conclusions:mNGS increases pathogen detection in neonatal sepsis and is well consistent with blood culture. mNGS is useful in clinical practice.
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OBJECTIVES@#To study the application value of metagenomic next-generation sequencing (mNGS) in children with severe infectious diseases.@*METHODS@#An analysis was performed on the clinical data and laboratory test results of 29 children with severe infection who were admitted to the Second Affiliated Hospital of Wenzhou Medical University from June 2018 to December 2020. Conventional pathogen culture was performed for the 29 specimens (27 peripheral blood specimens and 2 pleural effusion specimens) from the 29 children, and mNGS pathogen detection was performed at the same time.@*RESULTS@#Among the 29 children, 2 tested positive by conventional pathogen culture with 2 strains of pathogen, and the detection rate was 7% (2/29); however, 20 children tested positive by mNGS with 38 strains of pathogen, and the detection rate was 69% (20/29). The pathogen detection rate of mNGS was significantly higher than that of conventional pathogen culture (P<0.05), and mNGS could detect the viruses, fungi, and other special pathogens that conventional pathogen culture failed to detect, such as Orientia tsutsugamushi. The univariate analysis showed that gender, routine blood test results, C-reactive protein, procalcitonin, D-dimer, radiological findings, and whether antibiotics were used before admission did not affect the results of mNGS (P>0.05).@*CONCLUSIONS@#Compared with conventional pathogen culture, mNGS is more sensitive for pathogen detection, with fewer interference factors. Therefore, it is a better pathogenic diagnosis method for severe infectious diseases in children.
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Child , Humans , Anti-Bacterial Agents , Communicable Diseases , High-Throughput Nucleotide Sequencing/methods , Metagenomics/methods , Sensitivity and SpecificityABSTRACT
Infectious diseases are commonly seen in clinical practice, and pathogen diagnosis is the key link in diagnosis and treatment; however, conventional pathogen detection methods cannot meet clinical needs due to time-consuming operation and low positive rate. As a new pathogen detection method, metagenomic next-generation sequencing (mNGS) has a wide detection range and can detect bacteria, viruses, fungi, parasites, rare pathogens, and even unknown pathogens. The technique of mNGS is unbiased and can rapidly, efficiently, and accurately obtain all nucleic acid information in test samples, analyze pathogens, and guide clinical diagnosis and treatment, thereby playing an important role in complicated infectious diseases. This article reviews the diagnostic advantages and clinical value of mNGS in bacterial, fungal, viral, and parasitic infections.
Subject(s)
Humans , Bacteria , Communicable Diseases/diagnosis , High-Throughput Nucleotide Sequencing/methods , Metagenomics/methods , Sensitivity and SpecificityABSTRACT
OBJECTIVES@#To study the application value of metagenomic next-generation sequencing (mNGS) for pathogen detection in childhood agranulocytosis with fever.@*METHODS@#A retrospective analysis was performed on the mNGS results of pathogen detection of 116 children with agranulocytosis with fever who were treated from January 2020 to December 2021. Among these children, 38 children with negative mNGS results were enrolled as the negative group, and 78 children with positive results were divided into a bacteria group (n=22), a fungal group (n=23), and a viral group (n=31). Clinical data were compared between groups.@*RESULTS@#For the 116 children with agranulocytosis and fever, the median age was 8 years at diagnosis, the median turnaround time of mNGS results was 2 days, and the positive rate of mNGS testing was 67.2% (78/116). Compared with the negative group, the bacterial group had a higher procalcitonin level (P<0.05), the fungal group had higher level of C-reactive protein and positive rate of (1,3)-β-D glucan test/galactomannan test (P<0.05), and the fungal group had a longer duration of fever (P<0.05). Among the 22 positive microbial culture specimens, 9 (41%) were consistent with the mNGS results. Among the 17 positive blood culture specimens, 8 (47%) were consistent with the mNGS results. Treatment was adjusted for 28 children (36%) with the mNGS results, among whom 26 were cured and discharged.@*CONCLUSIONS@#The mNGS technique has a shorter turnaround time and a higher sensitivity for pathogen detection and can provide evidence for the pathogenic diagnosis of children with agranulocytosis and fever.
Subject(s)
Child , Humans , Agranulocytosis/diagnosis , Bacteria , Fever/diagnosis , High-Throughput Nucleotide Sequencing/methods , Metagenomics/methods , Retrospective Studies , Sensitivity and SpecificityABSTRACT
Objective:To evaluate the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of osteoarticular infection.Methods:The clinical data of 37 inpatients aged 32-90 year with osteoarticular infection admitted in the Department of Spine Surgery of Qingdao Chest Hospital from January to December 2019 were retrospectively analyzed. There were 31 cases of spine infection and 6 cases of other joint infection. The tissue samples were obtained from the infected sites through puncture or surgical approach in all patients. The tissue samples were subjected to routine culture of mycobacteria, aerobic bacteria and anaerobic bacteria, respectively. The gene amplification and mNGS were performed for detection of mycobacterium tuberculosis DNA (MTB-DNA). The chi-square test or Fisher’s exact test were used to compare the detection rates of pathogen and simple bacterial infection between mNGS and conventional culture. The conventional culture, mNGS and MTB-DNA amplification detection were performed for all samples; with clinical diagnosis as the gold standard, the diagnostic values of 3 methods were evaluated with receiver operating characteristic curve (ROC). Paired sample t test was used to compare white blood cell(WBC) count, erythrocyte sedimentation rate, C-reactive protein of patients before and after treatment. P<0.05 was considered statistically significant. Results:The pathogens were detected by mNGS for 42 times: bacteria for 39 times (92.8%), fungi for twice (4.8%) and Kirks body for once (2.4%). Among 37 patients there were 29 cases of pure bacterial infection (78.4%), 2 cases of pure fungi infection (5.4%), 1 case of pure Kirks body infection (2.7%), and 5 cases of mixed infection of two or more pathogens (13.5%). The detection rates of mNGS and conventional culture were 100.0% (37/37) and 67.6% (25/37), respectively ( χ2=13.987, P<0.05). The detection rates of mNGS and conventional culture in 29 patients with pure bacterial infection were 100.0% (29/29) and 69.0% (20/29), respectively ( χ2=16.913, P<0.05). The area under the ROC curve (AUC) of conventional culture, mNGS, and MTB-DNA in the diagnosis of osteoarticular tuberculosis infection was 0.958 (95% CI: 0.866-1.000, P<0.05), 1.000 (95% CI: 1.000-1.000, P<0.05) and 0.958 (95% CI: 0.866-1.000, P<0.05). All the 37 patients were treated with anti-infective drugs according to the results of mNGS and conventional culture. Among them, 28 patients received surgical intervention. The patients were followed up until April 30, 2020, 1 patient died. After 3 months of follow-up, the WBC count, erythrocyte sedimentation rate and C-reactive protein were (5.5±1.5)×10 9/L, (41±38)mm/h and (5.0±4.6) mg/L, respectively, which were lower than those before anti-infection treatment [(8.0±2.9)×10 9/L, (79±42)mm/h and(63±52)mg/L] ( t=6.536, 8.302 and 6.373, all P<0.05). Conclusion:The metagenomic next-generation sequencing may have important clinical value in the differential diagnosis of osteoarticular infection.