scholarly journals Application of metagenomic next-generation sequencing in the diagnosis of severe pneumonia caused by Chlamydia psittaci

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Huan-huan Wu ◽  
Lan-fang Feng ◽  
Shuang-yan Fang
Keyword(s):  
Mechanical Ventilation ◽  
Next Generation Sequencing ◽  
Invasive Mechanical Ventilation ◽  
False Negative ◽  
Clinical Manifestations ◽  
Severe Pneumonia ◽  
Chlamydia Psittaci ◽  
Diagnostic Tools ◽  
Next Generation ◽  
Generation Sequencing

Abstract Purpose Psittacosis is a zoonotic infectious disease caused by the transmission of the bacterium Chlamydia psittaci (C. psittaci) from birds to humans. Infections in humans mainly present as community-acquired pneumonia (CAP). However, most cases are treated without diagnostic testing, and the importance of Chlamydia psittaci infection as a cause of CAP is therefore unclear. Diagnostic tools, including culture, serologic test, and PCR-based methods, are available but prone to false negative results. Metagenomic next-generation sequencing (mNGS) has been increasingly used in the diagnosis of infectious diseases, particularly when conventional diagnostic approaches have limitation. Detection of nucleic acid sequence of C. psittaci in respiratory tract samples by metagenomic next-generation sequencing (mNGS) is effective for early diagnosis of severe C. psittaci pneumonia. Timely treatment based on tetracycline can reduce unnecessary use of antibiotics and improve prognosis of patients with severe C. psittaci pneumonia. Methods Clinical data of thirteen patients with severe C. psittaci pneumonia diagnosed by mNGS were collected. Clinical manifestations, treatment and prognosis of patients were summarized. Results The typical symptoms of pneumonia caused by C. psittaci include fever, headache, myalgia, cough, and dyspnea. In the current study, all patients met the criteria for severe C. psittaci pneumonia and received mechanical ventilation, including noninvasive mechanical ventilation (five/thirteen) and invasive mechanical ventilation (eight/thirteen). The findings showed that patients with C. psittaci pneumonia presented with normal or slightly increased leucocytes and procalcitonin, and high C-reactive protein levels. Computed tomography manifestations included consolidation of lung parenchyma, with air bronchogram and pleural effusion in some patients. mNGS analysis results were obtained within 48–72 h. Eleven patients fully recovered after targeted treatment, however, two patients died from secondary multidrug-resistant Pseudomonas aeruginosa infection. Conclusions The findings of the current study show that mNGS is effective in diagnosis of C. psittaci pneumonia, and has significant diagnosis value in patients with severe infection. Patients responds well to the timely use of appropriate antibiotics.

scholarly journals A case of chlamydia psittaci caused severe pneumonia and meningitis diagnosed by metagenome next-generation sequencing and clinical analysis: a case report and literature review

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yunfeng Shi ◽  
Junxian Chen ◽  
Xiaohan Shi ◽  
Jiajia Hu ◽  
Hongtao Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Fatal Case ◽  
Invasive Mechanical Ventilation ◽  
Clinical Manifestations ◽  
Severe Pneumonia ◽  
Chlamydia Psittaci ◽  
Gene Probe ◽  
Atypical Pneumonia ◽  
Next Generation ◽  
Generation Sequencing

Abstract Background Psittacosis, which is also known as parrot fever, is Chlamydia psittaci (C. psittaci) caused infectious disease. The clinical manifestations vary from asymptomatic infection to severe atypical pneumonia or even fatal meningitis. Early recognition of psittacosis is difficult because of its nonspecific clinical manifestations. Culture and gene probe techniques for C. psittaci are not available for routine clinical use, which makes the diagnosis difficult too. Although psittacosis has increasingly been recognized and reported in recent years, cure of severe pneumonia complicated with meningitis, with etiologic diagnosis aided by the use of metagenomic next-generation sequencing (mNGS), is still uncommon. So, it is necessary to report and review such potentially fatal case. Case presentation This report describes a 54-year-old woman with C. psittaci caused severe atypical pneumonia and meningitis. She presented with symptoms of fever, dry cough and dyspnea, accompanied by prominent headache. Her condition deteriorated rapidly to respiratory failure and lethargy under the treatment of empirical antibacterial agents, and was treated with invasive mechanical ventilation soon. She denied contact with birds, poultry or horses, but unbiased mNGS of both the bronchoalveolar lavage fluid (BALF) and the cerebrospinal fluid (CSF) identified sequence reads corresponding to C. psittaci infection, and there was no sequence read corresponding to other probable pathogens. Combined use of targeted antimicrobial agents of tetracyclines, macrolides and fluoroquinolones was carried out, and the patient’s condition improved and she was discharged home 28 days later. Her status returned close to premorbid condition on day 60 of follow-up. Conclusions When clinicians come across a patient with atypical pneumonia accompanied by symptoms of meningitis, psittacosis should be taken into consideration. mNGS is a promising detection method in such condition and is recommended.

scholarly journals Clinical Analysis of Metagenomic Next-generation Sequencing Confirmed Chlamydia psittaci Pneumonia: A Case Series and Literature Review

2021 ◽  
Author(s):  
Xin-Qi Teng ◽  
Wen-Cheng Gong ◽  
Ting-Ting Qi ◽  
Guo-Hua Li ◽  
Qiang Qu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Literature Review ◽  
Clinical Characteristics ◽  
Pathogenic Bacteria ◽  
False Negative ◽  
False Negative Rate ◽  
Case Series ◽  
Chlamydia Psittaci ◽  
Next Generation ◽  
Generation Sequencing

Abstract Introduction: Chlamydia psittaci infection is a zoonotic infectious disease, which mainly inhaled through the lungs when exposed to the secretions of poultry that carry pathogenic bacteria. The traditional respiratory specimens or serological antibody testing is slow and the false-negative rate is high. Metagenomic next-generation sequencing gives a promising rapid diagnosis tool. Methods: We retrospective summarized the clinical characteristics of five C. psittaci pneumonia patients diagnosed by mNGS, conducted a literature review summarizing the clinical characteristics of patients with C. psittaci pneumonia reported since 2010.Results: Five C. psittaci. pneumonia patients confirmed by mNGS aged from 36 to 66 years with three males. 60% of patients had type 2 diabetes mellitus. And 60% of patients had a history of contact with avian or poultry. All patients had a high fever over 38.5 °C, cough, hypodynamia, hypoxemia, and dyspnea on admission. Two patients had invasive ventilator support and Extracorporeal Membrane Oxygenation support. The levels of C-reactive protein, procalcitonin, and erythrocyte sedimentation rate on admission and follow-up were all higher than normal values. Doxycycline or moxifloxacin monotherapy was accounted for 1/5 (20%) and 2/5 (40%) patients, and combination therapy was accounted for 2/5(40%) patients. Four patients improved and were discharged, and one patient died due to multiple organ failure and disseminated intravascular coagulation.Conclusions: mNGS can increase the detection rate of C. psittaci, shorten the diagnosis time of C. psittaci pneumonia and improve the prognosis of patients.

scholarly journals Clinical diagnostic application of metagenomic next-generation sequencing in children with severe pneumonia

2019 ◽  
Author(s):  
Heping Wang ◽  
Zhiwei Lu ◽  
Yaomin Bao ◽  
Yonghong Yang ◽  
Ronald de Groot ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mycoplasma Pneumoniae ◽  
Severe Pneumonia ◽  
Clinical Diagnostics ◽  
Nucleic Acid Amplification ◽  
Direct Immunofluorescence ◽  
Specific Information ◽  
Next Generation ◽  
Blood Tests ◽  
Generation Sequencing

Abstract Background: Pneumonia is one of the most important causes of morbidity and mortality in children. Identification and characterization of pathogens that cause infections are crucial for accurate treatment and accelerated recovery of the patients. However, in most cases the causative agent cannot be identified partly due to the limited spectrum covered by current diagnostics based on nucleic acid amplification. Therefore, in this study we explored the application of metagenomic next-generation sequencing (mNGS) for the diagnosis of children with severe pneumonia. Methods: From April to July 2017, 32 children were hospitalized with severe pneumonia in Shenzhen Children’s Hospital. Blood tests were conducted immediately after hospitalization to assess infection, oropharygeal swabs were collected to identify common pathogens. After bronchoscopy, bronchoalveolar lavage fluids (BALFs) were collected for further pathogen identification using standardized laboratory and mNGS. Results: Blood tests were normal in 3 of the 32 children. In oropharygeal swabs from 5 patients Mycoplasma pneumoniae by qPCR, 27 cases showed negative results for common pathogens. In BALFs we detected 6 cases with Mycoplasma pneumoniae with qPCR, 9 patients with adenovirus by using a Direct Immunofluorescence Assay (DFA) and 4 patients with bacterial infections, as determined by culture, In 3 of the cases a co-infection was detected. In 15 cases no common pathogens were found in BALF samples, using the current diagnostics, while in all the 32 BALFS pathogens were identified using mNGS, including adenovirus, Mycoplasma pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, cytomegalovirus andbocavirus. Conclusions: mNGS can increase the sensitivity of detection of the causative pathogens in children with severe pneumonia. In addition, mNGS will give more strain specific information, will help to identify new pathogens and could potentially help to trace and control outbreaks. In this study we have shown that it is feasible to have the results within 24 hours, making the application of mNGS feasible for clinical diagnostics.

scholarly journals Detection of Listeria monocytogenes in a patient with meningoencephalitis using next-generation sequencing: a case report

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zi-Wei Lan ◽  
Min-Jia Xiao ◽  
Yuan-lin Guan ◽  
Ya-Jing Zhan ◽  
Xiang-Qi Tang
Keyword(s):  
Listeria Monocytogenes ◽  
Next Generation Sequencing ◽  
Mammalian Cells ◽  
Clinical Manifestations ◽  
Bacterial Pathogen ◽  
Next Generation ◽  
Accurate Treatment ◽  
The Central Nervous System ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Listeria monocytogenes (L. monocytogenes) is a facultative intracellular bacterial pathogen which can invade different mammalian cells and reach to the central nervous system (CNS), leading to meningoencephalitis and brain abscesses. In the diagnosis of L. monocytogenes meningoencephalitis (LMM), the traditional test often reports negative owing to the antibiotic treatment or a low number of bacteria in the cerebrospinal fluid. To date, timely diagnosis and accurate treatment remains a challenge for patients with listeria infections. Case presentation We present the case of a 66-year-old woman whose clinical manifestations were suspected as tuberculous meningoencephalitis, but the case was finally properly diagnosed as LMM by next-generation sequencing (NGS). The patient was successfully treated using a combined antibacterial therapy, comprising ampicillin and trimethoprim-sulfamethoxazole. Conclusion To improve the sensitivity of LMM diagnosis, we used NGS for the detection of L. monocytogenes. Hence, the clinical utility of this approach can be very helpful since it provides quickly and trust results.

Balamuthia mandrillaris-Related Primary Amoebic Encephalitis in China Diagnosed by Next Generation Sequencing and a Review of the Literature

2019 ◽  
Author(s):  
Yinan Yang ◽  
Xiaobin Hu ◽  
Li Min ◽  
Xiangyu Dong ◽  
Yuanlin Guan
Keyword(s):  
Next Generation Sequencing ◽  
Inflammatory Diseases ◽  
Clinical Manifestations ◽  
Infectious Agent ◽  
Disease Diagnosis ◽  
Rapid Identification ◽  
Next Generation ◽  
Balamuthia Mandrillaris ◽  
Granulomatous Amoebic Encephalitis ◽  
Generation Sequencing

Abstract Background Encephalitis is caused by infection, immune mediated diseases, or primary inflammatory diseases. Of all the causative infectious pathogens, 90% are viruses or bacteria. Granulomatous amoebic encephalitis (GAE), caused by Balamuthia mandrillaris, is a rare but life-threatening disease. Diagnosis and therapy are frequently delayed due to the lack of specific clinical manifestations. Method A healthy 2 year old Chinese male patient initially presented with a nearly 2 month history of irregular fever. We present this case of granulomatous amoebic encephalitis caused by B. mandrillaris. Next generation sequencing of the patient’s cerebrospinal fluid (CSF) was performed to identify an infectious agent. Result The results of next generation sequencing of the CSF showed that most of the mapped reads belonged to Balamuthia mandrillaris. Conclusion Next generation sequencing (NGS) is an unbiased and rapid diagnostic tool. The NGS method can be used for the rapid identification of causative pathogens. The NGS method should be widely applied in clinical practice and help clinicians provide direction for the diagnosis of diseases, especially for rare and difficult cases.

scholarly journals Hidden biases in germline structural variant detection

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Michael M. Khayat ◽  
Sayed Mohammad Ebrahim Sahraeian ◽  
Samantha Zarate ◽  
Andrew Carroll ◽  
Huixiao Hong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
False Negative ◽  
False Negative Rate ◽  
Next Generation Sequencing Data ◽  
Chinese Family ◽  
Next Generation ◽  
Sequencing Data ◽  
Structural Variations ◽  
The Impact ◽  
Generation Sequencing

Abstract Background Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging. Results In this study, DNA from a Chinese family quartet is sequenced at three different sequencing centers in triplicate. A total of 288 derivative data sets are generated utilizing different analysis pipelines and compared to identify sources of analytical variability. Mapping methods provide the major contribution to variability, followed by sequencing centers and replicates. Interestingly, SV supported by only one center or replicate often represent true positives with 47.02% and 45.44% overlapping the long-read SV call set, respectively. This is consistent with an overall higher false negative rate for SV calling in centers and replicates compared to mappers (15.72%). Finally, we observe that the SV calling variability also persists in a genotyping approach, indicating the impact of the underlying sequencing and preparation approaches. Conclusions This study provides the first detailed insights into the sources of variability in SV identification from next-generation sequencing and highlights remaining challenges in SV calling for large cohorts. We further give recommendations on how to reduce SV calling variability and the choice of alignment methodology.

scholarly journals 667. Next Generation Sequencing of Microbial Cell Free DNA in the Diagnosis and Treatment of Infectious Disease in Children: When Does the Result Justify the Cost?

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S436-S436
Author(s):  
Rachel Downey Quick ◽  
Kelli A Martinez ◽  
Susan M Russo ◽  
Sarah E McGwier ◽  
Rachel A Quirt ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
False Negative ◽  
Next Generation ◽  
Cell Free Dna ◽  
Negative Results ◽  
Free Dna ◽  
False Negative Results ◽  
The Cost ◽  
Generation Sequencing

Abstract Background Pathogen testing using next-generation sequencing of microbial cell-free DNA (NGS cfDNA) is a promising diagnostic tool to identify pathogens that might not be detected using conventional lab evaluation. Considering the cost of this test, it is important to determine when it is most useful to the plan of care (POC). Figure 1. Unit of admission among cases Figure 2. Patient characteristics in cases determined to be valuable and not valuable to the plan of care (POC) Methods In this retrospective study, we collected data from the medical charts of 50 consecutive NGS cfDNA tests in a free-standing children’s hospital. We evaluated patients for demographics, underlying conditions, diagnosis at time of testing, conventional laboratory testing and timing, medical treatment, and NGS cfDNA test results for clinical relevance or false negative results compared to conventional testing. The primary goal was to identify patients for whom the NGS cfDNA testing affected the POC. Charts were reviewed, and determinations regarding whether the result influenced the POC were confirmed by a provider. Results We were unable to differentiate patients with clinically valuable NGS cfDNA results (Fig 1 & 2). Among those with NGS cfDNA results valuable to the POC (n=22), both negative and positive testing guided POC (13 valuable negative vs. 9 diagnostic cases). In the total sample, 5 cases (10%) had a clinically relevant pathogen identified through conventional testing, but not through NGS cfDNA and 2 cases had antimicrobial resistance on culture, which is not detected by NGS cfDNA. Conclusion While we did not find a specific clinical profile for NGS cfDNA use, positive results were essential to the diagnosis in 18% of cases with otherwise negative laboratory evaluation for the pathogen identified in NGS cfDNA. Negative tests affected the POC in 26% of cases by avoiding unnecessary antimicrobials in high risk immunocompromised patients and patients that presented with low-risk of infection, but unclear disease process. Caution must be exercised with reliance on this test with respect to antimicrobial resistance and risk of false negative results. Disclosures All Authors: No reported disclosures

scholarly journals Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Talaromycosis of an Immunocompetent Patient

2021 ◽  
Vol 8 ◽  
Author(s):  
Jiejun Shi ◽  
Naibin Yang ◽  
Guoqing Qian
Keyword(s):  
Next Generation Sequencing ◽  
Pathogenic Bacteria ◽  
Clinical Decision Making ◽  
Fungal Infections ◽  
Clinical Manifestations ◽  
Whole Body ◽  
Recurrent Fever ◽  
Next Generation ◽  
Generation Sequencing ◽  
Immunocompetent Patients

Background: Talaromycosis is a serious fungal infection which is rare in immunocompetent people. Since its clinical manifestations lack specificity, it is easy to escape diagnosis or be misdiagnosed leading to high mortality and poor prognosis. It is necessary to be alert to the disease when broad-spectrum antibiotics do not work well in immunocompetent patients.Case Presentation: A 79-year-old man was admitted to our Infectious Diseases Department for recurrent fever and cough. Before admission he has been treated with piperacillin-tazobactam, moxifloxacin followed by antituberculous agents in other hospitals while his symptoms were not thoroughly eased. During the first hospitalization in another hospital, he has been ordered a series of examination including radionuclide whole body bone imaging, transbronchial needle aspiration for subcarinal nodes. However, the results were negative showing no neoplasm. After being admitted to our hospital, he underwent various routine examinations. The initial diagnosis was bacterial pneumonia, and he was given meropenem injection and tigecycline injection successively, but there were no improvement of symptoms and inflammatory indicators. In the end, the main pathogen Talaromyces marneffei was confirmed using Metagenomic Next-Generation Sequencing (mNGS), and his clinical symptoms gradually relieved after targeted antifungal treatment using voriconazole.Conclusion: When empirical anti-infective treatment is ineffective, it is necessary to consider the possibility of opportunistic fungal infections on immunocompetent patients. mNGS, as a new generation of pathogenic testing methods, can often detect pathogenic bacteria faster than traditional methods, providing important help for clinical decision-making.

scholarly journals Disseminated Strongyloides Stercoralis Hyperinfection in An Immunocompetent Patient First Diagnosed by Metagenomic Next-Generation Sequencing in Cerebrospinal Fluid: A Case Report

2021 ◽  
Author(s):  
Junyan Qu ◽  
Zhiyong Zong
Keyword(s):  
Cerebrospinal Fluid ◽  
Abdominal Pain ◽  
Next Generation Sequencing ◽  
Clinical Manifestations ◽  
Good Health ◽  
Strongyloides Stercoralis ◽  
Next Generation ◽  
Diagnostic Dilemma ◽  
Disseminated Strongyloidiasis ◽  
Generation Sequencing

Abstract Background Disseminated Strongyloides stercoralis hyperinfection is rarely described in immunocompetent individuals and can lead to fatal outcomes if not recognized and diagnosed early. Non-specific clinical manifestations, such as pneumonia and gastroenteritis, pose a diagnostic dilemma. Case presentation: We report a case of a 67-year-old Chinese male who presented with two months of abdominal pain, fever, headache, vomiting, constipation, and slight cough with sputum. He had been in good health and had no history of glucocorticoid use. He was diagnosed with enterococcal meningitis and intestinal obstruction at a local hospital and improved after treatment with vancomycin, but symptoms of headache and abdominal pain soon recurred. The metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid using Illumina X10 sequencer revealed 7 sequence reads matching Strongyloides stercoralis. Disseminated strongyloidiasis was suspected. Next, microscopic examination of gastric fluid revealed Larvae of S. stercoralis. DNA extracted of larvae, the presence of both S. stercoralis ribosomal DNA gene and mitochondrial cytochrome c oxidase subunit 1 gene was identified. Disseminated strongyloidiasis was diagnosed. Albendazole (400 mg, twice daily) was used and the patient recovered gradually. Conclusions S. stercoralis hyperinfection can occur in immunocompetent individuals, imposing challenges for diagnosis. mNGS may be a useful tool for detecting rare infectious disease. The case would help clinicians to raise awareness of strongyloidiasis in non-endemic areas and reduce fatality.

Sign in / Sign up

Export Citation Format

Share Document