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1.
Am J Transl Res ; 15(1): 47-62, 2023.
Article in English | MEDLINE | ID: mdl-36777850

ABSTRACT

OBJECTIVE: Timely and precise etiology diagnosis is crucial for optimized medication regimens and better prognosis in central nervous system infections (CNS infections). We aimed to analyze the impact of mNGS tests on the management of patients with CNS infections. METHODS: We conducted a single-center retrospective cohort study to analyze the value of mNGS in clinical applications. Three hundred sixty-nine patients with a CNS infection diagnosis were enrolled, and their clinical data were collected. CDI and DDI were defined in our study to describe the intensity of drug use in different groups. We used LOH and mRS to evaluate if the application of mNGS can benefit CNS infected patients. RESULTS: mNGS reported a 91.67% sensitivity in culture-positive patients and an 88.24% specificity compared with the final diagnoses. Patients who participated with the mNGS test had less drug use, both total (58.77 vs. 81.18) and daily (22.6 vs. 28.12, P < 0.1, McNemar) intensity of drug use, and length of hospitalization (23.14 vs. 24.29). Patients with a consciousness grading 1 and 3 had a decrease in CDI (Grade 1, 86.49 vs. 173.37; Grade 3, 48.18 vs. 68.21), DDI (Grade 1, 1.52 vs. 2.72; Grade 3, 2.3 vs. 2.45), and LOH (Grade 1, 32 vs. 40; Grade 3, 21 vs. 23) with the application of mNGS. Patients infected with bacteria in the CNS had a reduced CDI, DDI, and LOH in the mNGS group. This was compared with the TraE group that had 49% of patients altered medication plans, and 24.7% of patients reduced drug intensity four days after mNGS reports. This was because of the reduction of drug types. CONCLUSION: mNGS showed its high sensitivity and specificity characteristics. mNGS may assist clinicians with more rational medication regimens and reduce the drug intensity for patients. The primary way of achieving this is to reduce the variety of drugs, especially for severe patients and bacterial infections. mNGS has the ability of improving the prognosis of CNS infected patients.

3.
J Infect Public Health ; 15(4): 450-454, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35349863

ABSTRACT

BACKGROUND: Sepsis is a severe and acute disease associated with high mortality, for those who survive, long-term morbidity. In-time detection of pathogen for proper and optimized treatment in the early stage of sepsis is crucial. METHODS: We performed droplet digital PCR (ddPCR) on two cases of sepsis. The clinical information, laboratory test results, and the therapeutic regimen was detailed recorded. RESULTS: ddPCR showed its clinical value of sepsis ultra-early diagnosis and the guidance of medication in both cases we provided. CONCLUSIONS: ddPCR has potential for rapid and precise diagnose in ultra-early stage of sepsis for its high sensitivity and short turn-around-time, thus benefiting in optimal and timely treatment of sepsis.


Subject(s)
Sepsis , Early Diagnosis , Humans , Polymerase Chain Reaction/methods , Sepsis/diagnosis
4.
Open Forum Infect Dis ; 8(2): ofaa442, 2021 Feb.
Article in English | MEDLINE | ID: mdl-33553466

ABSTRACT

BACKGROUND: Public health interventions have been implemented to contain the outbreak of coronavirus disease 2019 (COVID-19) in New York City. However, the assessment of those interventions-for example, social distancing and cloth face coverings-based on real-world data from published studies is lacking. METHODS: The Susceptible-Exposed-Infectious-Removed (SEIR) compartmental model was used to evaluate the effect of social distancing and cloth face coverings on the daily culminative laboratory confirmed cases in New York City (NYC) and COVID-19 transmissibility. The latter was measured by Rt reproduction numbers in 3 phases that were based on 2 interventions implemented during this timeline. RESULTS: Transmissibility decreased from phase 1 to phase 3. The initial R0 was 4.60 in phase 1 without any intervention. After social distancing, the Rt value was reduced by 68%, while after the mask recommendation, it was further reduced by ~60%. CONCLUSIONS: Interventions resulted in significant reduction of confirmed case numbers relative to predicted values based on the SEIR model without intervention. Our findings highlight the effectiveness of social distancing and cloth face coverings in slowing down the spread of severe acute respiratory syndrome coronavirus 2 in NYC.

5.
Respir Res ; 22(1): 23, 2021 Jan 20.
Article in English | MEDLINE | ID: mdl-33472618

ABSTRACT

BACKGROUND: When infected with Mycobacterium tuberculosis, only a small proportion of the population will develop active TB, and the role of host genetic factors in different TB infection status was not fully understood. METHODS: Forty-three patients with active tuberculosis and 49 with latent tuberculosis were enrolled in the prospective cohort. Expressing levels of 27 candidate mRNAs, which were previously demonstrated to differentially expressed in latent and active TB, were measured by dual color reverse transcription multiplex ligation dependent probe amplification assay (dcRT-MLPA). Using expression levels of these mRNAs as quantitative traits, associations between expression abundance and genome-wild single nucleotide polymorphisms (SNPs) were calculated. Finally, identified candidate SNPs were further assessed for their associations with TB infection status in a validation cohort with 313 Chinese Han cases. RESULTS: We identified 9 differentially expressed mRNAs including il7r, il4, il8, tnfrsf1b, pgm5, ccl19, il2ra, marco and fpr1 in the prospective cohort. Through expression quantitative trait loci mapping, we screened out 8 SNPs associated with these mRNAs. Then, CG genotype of the SNP rs62292160 was finally verified to be significantly associated with higher transcription levels of IL4 in LTBI than in TB patients. CONCLUSION: We reported that the SNP rs62292160 in Chinese Han population may link to higher expression of il4 in latent tuberculosis. Our findings provided a new genetic variation locus for further exploration of the mechanisms of TB and a possible target for TB genetic susceptibility studies, which might aid the clinical decision to precision treatment of TB.


Subject(s)
Asian People/genetics , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study/methods , Quantitative Trait Loci/genetics , RNA-Directed DNA Polymerase/genetics , Tuberculosis/genetics , Adult , China/epidemiology , Cohort Studies , Female , Gene Expression , Gene Regulatory Networks/genetics , Genetic Predisposition to Disease/epidemiology , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide/genetics , Prospective Studies , Tuberculosis/diagnosis , Tuberculosis/epidemiology
6.
Clin Infect Dis ; 73(3): 376-385, 2021 08 02.
Article in English | MEDLINE | ID: mdl-32463434

ABSTRACT

BACKGROUND: The recent identification of a novel coronavirus, also known as severe acute respiratory syndrome coronavirus 2, has caused a global outbreak of respiratory illnesses. The rapidly developing pandemic has posed great challenges to diagnosis of this novel infection. However, little is known about the metatranscriptomic characteristics of patients with coronavirus disease 2019 (COVID-19). METHODS: We analyzed metatranscriptomics in 187 patients (62 cases with COVID-19 and 125 with non-COVID-19 pneumonia). Transcriptional aspects of 3 core elements, pathogens, the microbiome, and host responses, were evaluated. Based on the host transcriptional signature, we built a host gene classifier and examined its potential for diagnosing COVID-19 and indicating disease severity. RESULTS: The airway microbiome in COVID-19 patients had reduced alpha diversity, with 18 taxa of differential abundance. Potentially pathogenic microbes were also detected in 47% of the COVID-19 cases, 58% of which were respiratory viruses. Host gene analysis revealed a transcriptional signature of 36 differentially expressed genes significantly associated with immune pathways, such as cytokine signaling. The host gene classifier built on such a signature exhibited the potential for diagnosing COVID-19 (area under the curve of 0.75-0.89) and indicating disease severity. CONCLUSIONS: Compared with those with non-COVID-19 pneumonias, COVID-19 patients appeared to have a more disrupted airway microbiome with frequent potential concurrent infections and a special trigger host immune response in certain pathways, such as interferon-gamma signaling. The immune-associated host transcriptional signatures of COVID-19 hold promise as a tool for improving COVID-19 diagnosis and indicating disease severity.


Subject(s)
COVID-19 , Microbiota , COVID-19 Testing , Humans , Microbiota/genetics , Pandemics , SARS-CoV-2
7.
Front Cell Infect Microbiol ; 11: 745156, 2021.
Article in English | MEDLINE | ID: mdl-35127548

ABSTRACT

INTRODUCTION: The diagnosis of infection-caused fever of unknown origin (FUO) is still challenging, making it difficult for physicians to provide an early effective therapy. Therefore, a novel pathogen detection platform is needed. Metagenomic next-generation sequencing (mNGS) provides an unbiased, comprehensive technique for the sequence-based identification of pathogenic microbes, but the study of the diagnostic values of mNGS in FUO is still limited. METHODS: In a single-center retrospective cohort study, 175 FUO patients were enrolled, and clinical data were recorded and analyzed to compare mNGS with culture or traditional methods including as smears, serological tests, and nucleic acid amplification testing (NAAT) (traditional PCR, Xpert MTB/RIF, and Xpert MTB/RIF Ultra). RESULTS: The blood mNGS could increase the overall rate of new organisms detected in infection-caused FUO by roughly 22.9% and 19.79% in comparison to culture (22/96 vs. 0/96; OR, ∞; p = 0.000) and conventional methods (19/96 vs. 3/96; OR, 6.333; p = 0.001), respectively. Bloodstream infection was among the largest group of those identified, and the blood mNGS could have a 38% improvement in the diagnosis rate compared to culture (19/50 vs. 0/50; OR, ∞; p = 0.000) and 32.0% compared to conventional methods (16/50 vs. 3/50; OR, 5.333; p = 0.004). Among the non-blood samples in infection-caused FUO, we observed that the overall diagnostic performance of mNGS in infectious disease was better than that of conventional methods by 20% (9/45 vs. 2/45; OR, 4.5; p = 0.065), and expectedly, the use of non-blood mNGS in non-bloodstream infection increased the diagnostic rate by 26.2% (8/32 vs. 0/32; OR, ∞; p = 0.008). According to 175 patients' clinical decision-making, we found that the use of blood mNGS as the first-line investigation could effectively increase 10.9% of diagnosis rate of FUO compared to culture, and the strategy that the mNGS of suspected parts as the second-line test could further benefit infectious patients, improving the diagnosis rate of concurrent infection by 66.7% and 12.5% in non-bloodstream infection, respectively. CONCLUSION: The application of mNGS in the FUO had significantly higher diagnostic efficacy than culture or other conventional methods. In infection-caused FUO patients, application of blood mNGS as the first-line investigation and identification of samples from suspected infection sites as the second-line test could enhance the overall FUO diagnosis rate and serve as a promising optimized diagnostic protocol in the future.


Subject(s)
Fever of Unknown Origin , Adult , Fever of Unknown Origin/diagnosis , High-Throughput Nucleotide Sequencing/methods , Humans , Metagenome , Metagenomics/methods , Retrospective Studies , Sensitivity and Specificity
8.
Emerg Microbes Infect ; 9(1): 1864-1868, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32757712

ABSTRACT

Infective endocarditis caused by Neisseria macacae in humans is extremely rare. We presented here a case of N. macacae infective endocarditis in a 61-year-old man with a native aortic valve infection. N. macacae was isolated from blood culture and was detected by nanopore-based metagenomic sequencing in the vegetations. Finally, the patient recovered completely after surgery and antibiotic therapy.


Subject(s)
Endocarditis, Bacterial/diagnosis , Endocarditis, Bacterial/therapy , Neisseria/isolation & purification , Sequence Analysis, DNA/methods , Anti-Bacterial Agents/therapeutic use , Blood Culture , Endocarditis, Bacterial/blood , Heart Valve Prosthesis Implantation , Humans , Male , Middle Aged , Nanopore Sequencing , Neisseria/genetics , Neisseria/growth & development , Treatment Outcome
9.
Emerg Microbes Infect ; 9(1): 1869-1877, 2020 Dec.
Article in English | MEDLINE | ID: mdl-32795143

ABSTRACT

Critically ill patients with coronavirus diseases 2019 (COVID-19) are of grave concern. Those patients usually underwent a stage of excessive inflammation before developing acute respiratory distress syndrome. In this study, we test the hypothesis that short-term, low-to-moderate-dose corticosteroids would benefit patients when used in the early phase of excessive inflammation, namely, the therapeutic window. Among a Shanghai cohort and a validation cohort, we enrolled COVID-19 patients showing marked radiographic progression. Short-term, low-to-moderate-dose corticosteroids were considered for them. After identifying the possible markers for the therapeutic window, we then divided the patients, based on whether they were treated with corticosteroids within the therapeutic window, into the early-start group and control group. We identified that the therapeutic window for corticosteroids was characterized by a marked radiographic progression and lactase dehydrogenase (LDH) less than two times the upper limit of normal (ULN). The Shanghai cohort comprised of 68 patients, including 47 in the early-start group and 21 in the control group. The proportion of patients requiring invasive mechanical ventilation was significantly lower in the early-start group than in the control group (10.6% vs. 33.3%, difference, 22.7%, 95% confidence interval 2.6-44.8%). Among the validation cohort of 51 patients, similar difference of the primary outcome was observed (45.0% vs. 74.2%, P = 0.035). Among COVID-19 patients with marked radiologic progression, short-term, low-to-moderate-dose corticosteroids benefits patients with LDH levels of less than two times the ULN, who may be in the early phase of excessive inflammation.


Subject(s)
Adrenal Cortex Hormones/therapeutic use , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Adrenal Cortex Hormones/administration & dosage , Biomarkers , COVID-19 , Cohort Studies , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/pathology , Coronavirus Infections/therapy , Disease Progression , Humans , Inflammation/prevention & control , L-Lactate Dehydrogenase/blood , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/pathology , Pneumonia, Viral/therapy , Radiography , Reproducibility of Results , Respiration, Artificial , Respiratory Distress Syndrome/etiology , Treatment Outcome
10.
BMC Med ; 18(1): 168, 2020 06 03.
Article in English | MEDLINE | ID: mdl-32493370

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) has infected more than 4 million people within 4 months. There is an urgent need to properly identify high-risk cases that are more likely to deteriorate even if they present mild diseases on admission. METHODS: A multicenter nested case-control study was conducted in four designated hospitals in China enrolling confirmed COVID-19 patients who were mild on admission. Baseline clinical characteristics were compared between patients with stable mild illness (stable mild group) and those who deteriorated from mild to severe illness (progression group). RESULTS: From Jan 17, 2020, to Feb 1, 2020, 85 confirmed COVID-19 patients were enrolled, including 16 in the progression group and 69 in the stable mild group. Compared to stable mild group (n = 69), patients in the progression group (n = 16) were more likely to be older, male, presented with dyspnea, with hypertension, and with higher levels of lactase dehydrogenase and c-reactive protein. In multivariate logistic regression analysis, advanced age (odds ratio [OR], 1.012; 95% confidence interval [CI], 1.020-1.166; P = 0.011) and the higher level of lactase dehydrogenase (OR, 1.012; 95% CI, 1.001-1.024; P = 0.038) were independently associated with exacerbation in mild COVID-19 patients. CONCLUSION: Advanced age and high LDH level are independent risk factors for exacerbation in mild COVID-19 patients. Among the mild patients, clinicians should pay more attention to the elderly patients or those with high LDH levels.


Subject(s)
Betacoronavirus , Coronavirus Infections/enzymology , L-Lactate Dehydrogenase/metabolism , Pneumonia, Viral/enzymology , Adolescent , Adult , Aged , Aged, 80 and over , C-Reactive Protein/metabolism , COVID-19 , Case-Control Studies , China , Coronavirus Infections/complications , Coronavirus Infections/diagnosis , Disease Progression , Disease Susceptibility , Female , Humans , Hypertension/complications , Male , Middle Aged , Pandemics , Pneumonia, Viral/complications , Pneumonia, Viral/diagnosis , Risk Factors , SARS-CoV-2 , Young Adult
11.
Hepatobiliary Pancreat Dis Int ; 19(4): 358-364, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32571745

ABSTRACT

BACKGROUND: Infections still represent the main factors influencing morbidity and mortality following liver transplantation. This study aimed to evaluate the incidence and risk factors for infection and survival after liver transplantation. METHODS: We retrospectively examined medical records in 210 liver recipients who underwent liver transplantation between April 2015 and October 2017 in our hospital. Clinical manifestations and results of pathogen detection test were used to define infection. We analyzed the prevalence, risk factors and prognosis of patients with infection. RESULTS: The median follow-up was 214 days; the incidence of infection after liver transplantation was 46.7% (n = 98) which included pneumonia (43.4%), biliary tract infection (21.9%), peritonitis (21.4%) and bloodstream infection (7.6%). Among the pathogens in pneumonia, the most frequently isolated was Acinetobacter baumanii (23.5%) and Klebsiella pneumoniae (21.2%). Model for end-stage liver disease (MELD) score (OR = 1.083, 95% CI: 1.045-1.123; P < 0.001), biliary complication (OR = 4.725, 95% CI: 1.119-19.947; P = 0.035) and duration of drainage tube (OR = 1.040, 95% CI: 1.007-1.074; P = 0.017) were independent risk factors for posttransplant infection. All-cause mortality was 11.0% (n = 23). The prognostic factors for postoperative infection in liver recipients were prior-transplant infection, especially pneumonia within 2 weeks before transplantation. Kaplan-Meier curves of survival showed that recipients within 2 weeks prior infection had a significantly lower cumulative survival rate compared with those without infection (65.2% vs. 90.0%; hazard ratio: 4.480; P < 0.001). CONCLUSIONS: Infection, especially pneumonia within 2 weeks before transplantation, complication with impaired renal function and MELD score after 7 days of transplantation was an independent prognostic factor for postoperative infection in liver transplant recipients.


Subject(s)
End Stage Liver Disease/surgery , Infections/etiology , Liver Transplantation/adverse effects , Adolescent , Adult , Aged , Child , Child, Preschool , China , End Stage Liver Disease/complications , Female , Humans , Incidence , Infant , Infections/microbiology , Infections/virology , Male , Middle Aged , Prognosis , Retrospective Studies , Risk Factors , Young Adult
12.
J Transl Med ; 18(1): 199, 2020 05 13.
Article in English | MEDLINE | ID: mdl-32404108

ABSTRACT

BACKGROUND: Accurate etiology diagnosis is crucial for central nervous system infections (CNS infections). The diagnostic value of metagenomic next-generation sequencing (mNGS), an emerging powerful platform, remains to be studied in CNS infections. METHODS: We conducted a single-center prospective cohort study to compare mNGS with conventional methods including culture, smear and etc. 248 suspected CNS infectious patients were enrolled and clinical data were recorded. RESULTS: mNGS reported a 90.00% (9/10) sensitivity in culture-positive patients without empirical treatment and 66.67% (6/9) in empirically-treated patients. Detected an extra of 48 bacteria and fungi in culture-negative patients, mNGS provided a higher detection rate compared to culture in patients with (34.45% vs. 7.56%, McNemar test, p < 0.0083) or without empirical therapy (50.00% vs. 25.00%, McNemar test, p > 0.0083). Compared to conventional methods, positive percent agreement and negative percent agreement was 75.00% and 69.11% separately. mNGS detection rate was significantly higher in patients with cerebrospinal fluid (CSF) WBC > 300 * 106/L, CSF protein > 500 mg/L or glucose ratio ≤ 0.3. mNGS sequencing read is correlated with CSF WBC, glucose ratio levels and clinical disease progression. CONCLUSION: mNGS showed a satisfying diagnostic performance in CNS infections and had an overall superior detection rate to culture. mNGS may held diagnostic advantages especially in empirically treated patients. CSF laboratory results were statistically relevant to mNGS detection rate, and mNGS could dynamically monitor disease progression.


Subject(s)
Central Nervous System Infections , Metagenomics , Adult , Central Nervous System Infections/diagnosis , High-Throughput Nucleotide Sequencing , Humans , Prospective Studies , Sensitivity and Specificity
13.
Article in English | MEDLINE | ID: mdl-32133300

ABSTRACT

In this original study, we retrospectively reviewed the cases of nocardiosis diagnosed through culture and next-generation sequencing (NGS) methods between 2014 and 2018 in Huashan Hospital and found out that the latter way can not only improve the detection rate of Nocardia spp. but also greatly reduce the turnaround time. In addition, by comparing nocardiosis and non-nocardiosis patients both of whose samples had Nocardia spp. detected by NGS, we found that Nocardia's specific reads ranking among top two might be a satisfactory cutoff value for clinical diagnosis of the disease. Our study introduced the promising value of the NGS method in the rapid diagnosis of nocardiosis.


Subject(s)
High-Throughput Nucleotide Sequencing , Nocardia Infections/diagnosis , Nocardia/isolation & purification , Sequence Analysis, DNA , Female , Humans , Male , Nocardia/genetics , Nocardia Infections/microbiology , Retrospective Studies
14.
Emerg Microbes Infect ; 9(1): 597-600, 2020.
Article in English | MEDLINE | ID: mdl-32174267

ABSTRACT

Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT-PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , COVID-19 Vaccines , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Humans , Molecular Diagnostic Techniques , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , SARS-CoV-2
15.
Front Cell Infect Microbiol ; 10: 567615, 2020.
Article in English | MEDLINE | ID: mdl-33585263

ABSTRACT

Pulmonary infections are among the most common and important infectious diseases due to their high morbidity and mortality, especially in older and immunocompromised individuals. However, due to the limitations in sensitivity and the long turn-around time (TAT) of conventional diagnostic methods, pathogen detection and identification methods for pulmonary infection with greater diagnostic efficiency are urgently needed. In recent years, unbiased metagenomic next generation sequencing (mNGS) has been widely used to detect different types of infectious pathogens, and is especially useful for the detection of rare and newly emergent pathogens, showing better diagnostic performance than traditional methods. There has been limited research exploring the application of mNGS for the diagnosis of pulmonary infections. In this study we evaluated the diagnostic efficiency and clinical impact of mNGS on pulmonary infections. A total of 100 respiratory samples were collected from patients diagnosed with pulmonary infection in Shanghai, China. Conventional methods, including culture and standard polymerase chain reaction (PCR) panel analysis for respiratory tract viruses, and mNGS were used for the pathogen detection in respiratory samples. The difference in the diagnostic yield between conventional methods and mNGS demonstrated that mNGS had higher sensitivity than traditional culture for the detection of pathogenic bacteria and fungi (95% vs 54%; p<0.001). Although mNGS had lower sensitivity than PCR for diagnosing viral infections, it identified 14 viral species that were not detected using conventional methods, including multiple subtypes of human herpesvirus. mNGS detected viruses with a genome coverage >95% and a sequencing depth >100× and provided reliable phylogenetic and epidemiological information. mNGS offered extra benefits, including a shorter TAT. As a complementary approach to conventional methods, mNGS could help improving the identification of respiratory infection agents. We recommend the timely use of mNGS when infection of mixed or rare pathogens is suspected, especially in immunocompromised individuals and or individuals with severe conditions that require urgent treatment.


Subject(s)
High-Throughput Nucleotide Sequencing , Metagenomics , Aged , China , Humans , Phylogeny , Sensitivity and Specificity
17.
Article in English | MEDLINE | ID: mdl-31681628

ABSTRACT

Background: Tuberculosis (TB) is now the leading cause of death from infectious disease. Rapid screening and diagnostic methods for TB are urgently required. Rapid development of metagenomics next-generation sequencing (mNGS) in recent years showed promising and satisfying application of mNGS in several kinds of infectious diseases. However, research directly evaluating the ability of mNGS in TB infection is still scarce. Methods: We conducted an adult prospective study in mainland China to evaluate the diagnostic performance of mNGS for detection of Mycobacterium tuberculosis complex (MTB) in multiple forms of direct clinical samples compared with GeneXpert MTB/RIF assay (Xpert), traditional diagnostic methods, and the clinical final diagnosis. Results: Of 123 patients presenting with suspected active TB infection between June 1, 2017, and May 21, 2018, 105 patients underwent synchronous tuberculous testing with culture, Xpert, and mNGS on direct clinical samples including sputum, cerebrospinal fluids, pus, etc. During follow-up, 45 of 105 participants had clinical final diagnosis of active TB infection, including 13 pulmonary TB cases and 32 extrapulmonary TB cases. Compared to clinical final diagnosis, mNGS produced a sensitivity of 44% for all active TB cases, which was similar to Xpert (42%) but much higher than conventional methods (29%). With only one false-positive result, mNGS had a specificity of 98% in our study. mNGS yielded significantly much higher sensitivity in pre-treatment samples (76%) than post-treatment ones (31%) (P = 0.005), which was also true for Xpert and conventional methods. Combining Xpert and mNGS together, the study identified 27 of 45 active TB cases (60%), including all 13 conventional method-identified cases, and the result reached statistical significance compared to conventional methods (McNemar-test P < 0.001). Conclusions: mNGS had a similar diagnostic ability of MTB compared with Xpert and showed potential for a variety of clinical samples. Combined mNGS and Xpert showed an overall superior advantage over conventional methods and significantly improved the etiology diagnosis of both MTB and other pathogens. The result that anti-TB treatment significantly reduced diagnostic efficacy of culture, Xpert, and mNGS highlighted the importance of collecting samples before empirical treatment.


Subject(s)
High-Throughput Nucleotide Sequencing , Metagenomics , Mycobacterium tuberculosis/genetics , Tuberculosis/diagnosis , Tuberculosis/microbiology , Computational Biology , High-Throughput Nucleotide Sequencing/methods , High-Throughput Nucleotide Sequencing/standards , Humans , Metagenomics/methods , Metagenomics/standards , Molecular Diagnostic Techniques , Sensitivity and Specificity , Tuberculosis, Pulmonary/diagnosis , Tuberculosis, Pulmonary/microbiology
18.
Emerg Microbes Infect ; 8(1): 1361-1369, 2019.
Article in English | MEDLINE | ID: mdl-31522608

ABSTRACT

Rapid and simple-to-use diagnostic methods for tuberculosis are urgently needed. Recent development has unveiled the diagnostic power of the CRISPR system in the detection of viral infections. However, its potential use in detecting the Mycobacterium tuberculosis complex (MTB) remained unexplored. We developed a rapid CRISPR-based assay for TB detection and conducted a retrospective cohort study of 179 patients to evaluate the CRISPR-MTB test for identifying MTB in various forms of direct clinical samples. Its diagnostic performance was compared, in parallel with culture and the GeneXpert MTB/RIF assay (Xpert). The CRISPR-MTB test is highly sensitive with a near single-copy sensitivity, demands less sample input and offers shorter turnaround time than Xpert. When evaluated in the clinical cohort of both pulmonary and extra-pulmonary tuberculosis, the CRISPR-MTB test exhibited an overall improved sensitivity over both culture (79% vs 33%) and Xpert (79% vs 66%), without comprise in specificity (62/63, 98%). The CRISPR-MTB test exhibits an improved overall diagnostic performance over culture and Xpert across a variety of sample types, and offers great potential as a new diagnostic technique for both pulmonary and extra-pulmonary tuberculosis.


Subject(s)
Clustered Regularly Interspaced Short Palindromic Repeats , Molecular Diagnostic Techniques , Mycobacterium tuberculosis/isolation & purification , Tuberculosis, Pulmonary/diagnosis , Tuberculosis/diagnosis , Humans , Mycobacterium tuberculosis/genetics , Reagent Kits, Diagnostic/standards , Retrospective Studies , Sensitivity and Specificity , Sputum/microbiology , Tuberculosis/microbiology , Tuberculosis, Pulmonary/microbiology
19.
J Infect ; 79(5): 419-425, 2019 11.
Article in English | MEDLINE | ID: mdl-31442461

ABSTRACT

OBJECTIVES: Microbiological diagnosis is essential during clinical management of focal infections. Metagenomic next generation sequencing (mNGS) has been reported as a promising diagnostic tool in infectious diseases. However, little is known about the clinical utility of mNGS in focal infections. METHODS: We conducted a single-center retrospective study to investigate impact of mNGS on focal infection diagnosis and compared it with conventional methods, including culture, pathological examination, Xpert MTB/RIF, etc. 98 suspected focal infections cases were enrolled, and medical records were reviewed to determine their rates of detection, time-to-identification, and clinical outcomes. RESULTS: mNGS showed a satisfying diagnostic positive percent agreement of 86.30% (95% CI: 75.79-92.88%) in a variety of tissues, compared to 45.21% (95% CI: 33.68-57.24%) for culture and 57.53% (95% CI: 45.43-68.84%)f for conventional methods (p < 0.0125), and detected an extra 34 pathogenic microorganisms. Time requirement for pathogen identification using mNGS ranges from 31 h to 55 h, which showed an advantage over culture. (82.36 h; 95%CI: 65.83, 98.89; P < 0.05) CONCLUSIONS: mNGS showed promising potential in pathogenic diagnosis during focal infections and might enable clinicians to make more timely and targeted therapeutic decisions.


Subject(s)
Focal Infection/diagnosis , High-Throughput Nucleotide Sequencing/methods , Metagenomics/methods , Molecular Diagnostic Techniques/methods , Adolescent , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Retrospective Studies , Sensitivity and Specificity , Treatment Outcome , Young Adult
20.
Endocrine ; 65(2): 327-337, 2019 08.
Article in English | MEDLINE | ID: mdl-31056722

ABSTRACT

BACKGROUND: Thyroid stimulating hormone (TSH) suppression therapy after differentiated thyroid carcinoma surgery causes cognitive impairment. However, data on naming difficulties (anomia)-related specific cognitive impairment are lacking. METHODS: A prospective cohort study was conducted, in which, patients with differentiated thyroid carcinoma and benign thyroid nodules were given oral L-T4 therapy after surgery, after meeting the criteria of TSH suppression therapy and thyroxine replacement therapy, respectively, the patients were continually given L-T4 therapy for 6 and 12 months, and then, the neuropsychological test was performed. RESULTS: Of the 255 subjects, 212 cases (83.13%) completed all the tests, including 33 cases in the normal control group (NC group), 110 cases in the TSH suppression therapy group (TS group), and 69 cases in the thyroxine replacement therapy group (TR group). There was no significant difference in background data among the three groups (P > 0.05). The scores of mini-mental state examination, clock drawing test, digit symbol substitution test, personal history, temporal and spatial orientation, digit order relation, visual object recognition, associative learning, and color naming in the TS and TR groups were not significantly different from those in the NC group after 6 and 12 months of L-T4 therapy (P > 0.05); the scores of picture recall, visual recall, comprehension memory, and digit span forward in the TS and TR groups were notably lower than those in the NC group (P < 0.01); the scores of confrontation naming and listing the names in the TS group were significantly lower than those in the NC and TR groups, and the scores decreased with the prolongation of TSH suppression therapy (P < 0.01). CONCLUSION: TSH suppression therapy after differentiated thyroid carcinoma surgery could lead to short-term memory impairment, attention impairment, word selection anomia, and depression, of which, word selection anomia was aggravated with the prolongation of TSH suppression therapy. Therefore, we suggested that optimal TSH goals for individual patients must balance the potential benefit of TSH suppression therapy with the possible harm from subclinical hyperthyroidism especially in low risk differentiated thyroid carcinoma patients (ClinicalTrials.gov Protocol Registration System: ClinicalTrials.gov ID NCT0266532, Registered on 21 June 2016).


Subject(s)
Anomia/chemically induced , Carcinoma/drug therapy , Thyroid Neoplasms/drug therapy , Thyrotropin/antagonists & inhibitors , Thyroxine/adverse effects , Adult , Carcinoma/surgery , Cognitive Dysfunction/chemically induced , Female , Hormone Replacement Therapy/adverse effects , Humans , Male , Middle Aged , Mood Disorders/chemically induced , Neuropsychological Tests , Prospective Studies , Thyroid Neoplasms/surgery , Thyroidectomy , Thyrotropin/blood , Thyroxine/administration & dosage
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