scholarly journals Clinical Application of Metagenomic Next-Generation Sequencing for Suspected Infections in Patients With Primary Immunodeficiency Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjing Tang ◽  
Yu Zhang ◽  
Chong Luo ◽  
Lina Zhou ◽  
Zhiyong Zhang ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Primary Immunodeficiency ◽  
Primary Immunodeficiency Disease ◽  
Next Generation ◽  
Opportunistic Pathogens ◽  
Pathogen Identification ◽  
Conventional Methods ◽  
Immunodeficiency Disease ◽  
Generation Sequencing

BackgroundInfections are the major cause of morbidity and mortality in patients with primary immunodeficiency disease (PID). Timely and accurate microbiological diagnosis is particularly important in these patients. Metagenomic next-generation sequencing (mNGS) has been used for pathogen detection recently. However, few reports describe the use of mNGS for pathogen identification in patients with PID.ObjectiveTo evaluate the utility of mNGS for detecting pathogens in patients with PID, and to compare it with conventional microbiological tests (CMT).MethodsThis single center retrospective study investigated the diagnostic performance of mNGS for pathogens detection in PID patients and compared it with CMT. Sixteen PID patients with suspected infection were enrolled, and medical records were analyzed to extract detailed clinical characteristics such as gene variation, immune status, microbial distribution, time-consuming of mNGS and CMT, treatment, and outcomes.ResultsmNGS identified pathogenic microbe in 93.75% samples, compared to 31.25% for culture and 68.75% for conventional methods, and detected an extra 18 pathogenic microorganisms including rare opportunistic pathogens and Mycobacterium tuberculosis. Pathogen identification by mNGS required 48 hours, compared with bacterial culture for 3-7 days and even longer for fungus and Mycobacterium tuberculosis culture.ConclusionsmNGS has marked advantages over conventional methods for pathogenic diagnosis, particularly opportunistic pathogens and mixed infections, in patients with PID. This method might enable clinicians to make more timely and targeted therapeutic decisions, thereby improving the prognosis of these patients.

scholarly journals Pulmonary coinfection of Mycobacterium tuberculosis and Tropheryma whipplei: a case report

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Binghua Zhu ◽  
Jing Tang ◽  
Rong Fang ◽  
Xuejie Fei ◽  
Qing Wang ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Tropheryma Whipplei ◽  
Diagnostic Methods ◽  
Next Generation ◽  
Computed Tomography Scan ◽  
Chest Computed Tomography ◽  
Tomography Scan ◽  
Generation Sequencing

Abstract Background We diagnosed a clinical case of pulmonary infection involving Mycobacterium tuberculosis and Tropheryma whipplei in a patient with acute respiratory distress syndrome. The diagnosis was assisted by metagenomic next-generation sequencing of bronchoalveolar lavage fluid. Case presentation A 44-year-old Han Chinese inmate was transferred to the emergency department because of dry cough, chest tightness, and shortness of breath. The patient’s body temperature rose to 39.3 °C following empirical cephalosporin treatment for 1 week. The blood CD4+/CD8+ ratio was 0.7, suggesting immunodeficiency. Routine microbiological tests were performed, and tuberculosis interferon gamma release assays were positive. Mycobacterium tuberculosis polymerase chain reaction was also positive. Chest computed tomography scan revealed miliary nodules and ground-glass opacifications, which were in accordance with tuberculosis. To fully examine the etiology, we performed routine laboratory tests and metagenomic sequencing, the results of which indicated the presence of Mycobacterium tuberculosis and Tropheryma whipplei. We administered anti-tuberculosis regimen in combination with trimethoprim/sulfamethoxazole. The patient recovered, with chest computed tomography scan showing absorption of lesions. Conclusions Compared with traditional diagnostic methods such as culture and serology, metagenomic next-generation sequencing has the advantage of detecting a wide array of microorganisms in a single test and therefore can be used for clinical diagnosis of rare pathogens and microbial coinfections. It is particularly useful for immunocompromised patients as they are more prone to infection by opportunistic microorganisms.

scholarly journals Family-Based Next-Generation Sequencing Study Identifies an IL2RG Variant in an Infant with Primary Immunodeficiency

2019 ◽  
Vol 23 (5) ◽  
pp. 285-290
Author(s):  
Aravind K. Bandari ◽  
Sunil Bhat ◽  
MV Archana ◽  
Sunita Yadavalli ◽  
Krishna Patel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Primary Immunodeficiency ◽  
Next Generation ◽  
Family Based ◽  
Generation Sequencing

scholarly journals Outcomes of Next-Generation Sequencing Panel Testing for Primary Immunodeficiency

2019 ◽  
Vol 143 (2) ◽  
pp. AB110
Author(s):  
Nurcicek Padem ◽  
Alexander Ing ◽  
Kai Lee Yap ◽  
Asma Mustafa ◽  
Jessica Shank ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Primary Immunodeficiency ◽  
Next Generation ◽  
Panel Testing ◽  
Generation Sequencing

scholarly journals Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates

2015 ◽  
Vol 53 (12) ◽  
pp. 3779-3783 ◽  
Author(s):  
Nontuthuko E. Maningi ◽  
Luke T. Daum ◽  
John D. Rodriguez ◽  
Matsie Mphahlele ◽  
Remco P. H. Peters ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Detection Sensitivity ◽  
Next Generation ◽  
Resistance Mutations ◽  
Coding Region ◽  
Content Type ◽  
Mdr Tb ◽  
Generation Sequencing

The technical limitations of common tests used for detecting pyrazinamide (PZA) resistance inMycobacterium tuberculosisisolates pose challenges for comprehensive and accurate descriptions of drug resistance in patients with multidrug-resistant tuberculosis (MDR-TB). In this study, a 606-bp fragment (comprising thepncAcoding region plus the promoter) was sequenced using Ion Torrent next-generation sequencing (NGS) to detect associated PZA resistance mutations in 88 recultured MDR-TB isolates from an archived series collected in 2001. These 88 isolates were previously Sanger sequenced, with 55 (61%) designated as carrying the wild-typepncAgene and 33 (37%) showing mutations. PZA susceptibility of the isolates was also determined using the Bactec 460 TB system and the Wayne test. In this study, isolates were recultured and susceptibility testing was performed in Bactec 960 MGIT. Concordance between NGS and MGIT results was 93% (n= 88), and concordance values between the Bactec 460, the Wayne test, orpncAgene Sanger sequencing and NGS results were 82% (n= 88), 83% (n= 88), and 89% (n= 88), respectively. NGS confirmed the majority ofpncAmutations detected by Sanger sequencing but revealed several new and mixed-strain mutations that resolved discordancy in other phenotypic results. Importantly, in 53% (18/34) of these isolates,pncAmutations were located in the 151 to 360 region and warrant further exploration. In these isolates, with their known resistance to rifampin, NGS ofpncAimproved PZA resistance detection sensitivity to 97% and specificity to 94% using NGS as the gold standard and helped to resolve discordant results from conventional methodologies.

scholarly journals Molekuláris genetikai vizsgálatok primer immundefektusokban

2018 ◽  
Vol 159 (49) ◽  
pp. 2095-2112
Author(s):  
Melinda Erdős
Keyword(s):  
Next Generation Sequencing ◽  
Primary Immunodeficiency ◽  
Molecular Genetic ◽  
Primary Immunodeficiencies ◽  
Genetic Diagnostics ◽  
Next Generation ◽  
Advantages And Disadvantages ◽  
Whole Exome ◽  
Molecular Genetic Diagnostics ◽  
Generation Sequencing

Abstract: Next generation sequencing methods represent the latest era of molecular genetic diagnostics. After a general introduction on primary immunodeficiencies, the author summarizes the importance of molecular genetic studies, especially next generation sequencing in the diagnosis of primary immunodeficiencies. Another purpose of the manuscript is to give a brief summary on the methodological basis of next generation sequencing. The author analyzes the advantages and disadvantages of primary immunodeficiency gene-panel sequencing and whole-exome and whole-genome sequencing. Primary immunodeficiency genes and diseases recognized by next generation sequencing is also summarized. Finally, the author emphasizes the indispensability of gene level diagnostics in primary immunodeficiencies and presents the results achieved in this field in Hungary. Orv Hetil. 2018; 159(49): 2095–2112.

Sign in / Sign up

Export Citation Format

Share Document