scholarly journals Metagenomic Next-Generation Sequencing in Diagnosis of a Case of Pneumocystis jirovecii Pneumonia in a Kidney Transplant Recipient and Literature Review

2020 ◽  
Vol Volume 13 ◽  
pp. 2829-2836 ◽  
Author(s):  
Jie Chen ◽  
Ting He ◽  
Xiujun Li ◽  
Xue Wang ◽  
Li Peng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Literature Review ◽  
Transplant Recipient ◽  
Kidney Transplant ◽  
Kidney Transplant Recipient ◽  
Pneumocystis Jirovecii ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals 645. Rapid Diagnosis of Disseminated Mycobacterium kansasii infection in Renal Transplant Recipients Using Plasma Microbial Cell Free DNA Next Generation Sequencing

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S424-S425
Author(s):  
Tosin Ogunsiakan ◽  
Kristen D Fajgenbaum ◽  
Gautam Phadke ◽  
Thomas Montgomery ◽  
Kiran Gajurel
Keyword(s):  
Next Generation Sequencing ◽  
Transplant Recipient ◽  
Kidney Transplant ◽  
Kidney Transplant Recipient ◽  
Rapid Diagnosis ◽  
Mycobacterium Kansasii ◽  
Transplant Recipients ◽  
Next Generation ◽  
Free Dna ◽  
Generation Sequencing

Abstract Background Disseminated Mycobacterium kansasii infection is rare in kidney transplant recipients. The diagnosis may not be suspected readily due to non-specific clinical presentation. The diagnosis and treatment can be further delayed due to poor sensitivity of culture (especially of extra-pulmonary sites) and slow growth in culture media. Accurate and rapid diagnosis of disseminated M. kansasii infections in transplant recipients is important for antimicrobial management. Methods Two cases of disseminated M. kansasii infections with unusual presentation in which rapid diagnosis was made using the Karius test (KT) are presented. The KT is a CLIA certified/CAP-accredited next-generation sequencing (NGS) plasma test that detects microbial cell-free DNA (mcfDNA). After mcfDNA is extracted and NGS performed, human reads are removed, and remaining sequences are aligned to a curated database of >1400 organisms. Organisms present above a statistical threshold are reported. Results Case 1: A 31-year female kidney transplant recipient presented with a thyroglossal duct cyst, as well as swelling of her right metacarpophalangeal joint and left 3rd finger. AFB culture of the thyroglossal cyst aspiration done on post admission day (PAD) 2 took 27 days to be identified as M. kansasii (on PAD 29) whereas plasma sent for KT on PAD 5 reported a positive test for M. kansasii at 284 molecules/microliter (MPM) in 4 days (on PAD 9). Case 2: A 59-year male kidney transplant recipient presented with generalized weakness, arthralgia, pericardial effusion, cytopenia, weight loss and intermittent fevers. Plasma sent for KT on PAD 12 was reported positive for M. kansasii at 1314 MPM in 3 days (on PAD 15). PET CT done simultaneously was consistent with an infection of an old AV graft in the left upper extremity. The AFB culture of the resected graft was confirmed as M. kansasii in 22 days on PAD 36. After the KT was available (before confirmation of M. kansasii on culture), the first patient underwent modification of empiric treatment and the second patient was started on specific treatment for M. kansasii. Table of M. kansasii cases Rapid diagnosis of disseminated M. kansasii infection Conclusion Open-ended NGS plasma testing for mcfDNA identified disseminated M kansasii infection much earlier than standard microbiology and thus helped in initiation and modification of pathogen directed treatment. Disclosures All Authors: No reported disclosures

scholarly journals Next Generation Sequencing for the Prediction of the Antibiotic Resistance in Helicobacter pylori: A Literature Review

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 437
Author(s):  
Ilaria Maria Saracino ◽  
Matteo Pavoni ◽  
Angelo Zullo ◽  
Giulia Fiorini ◽  
Tiziana Lazzarotto ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Next Generation Sequencing ◽  
Literature Review ◽  
Molecular Mechanisms ◽  
World Health ◽  
Next Generation ◽  
Culture Methods ◽  
Phenotypic Resistance ◽  
H Pylori ◽  
Generation Sequencing

Background and aims: Only a few antimicrobials are effective against H. pylori, and antibiotic resistance is an increasing problem for eradication therapies. In 2017, the World Health Organization categorized clarithromycin resistant H. pylori as a “high-priority” bacterium. Standard antimicrobial susceptibility testing can be used to prescribe appropriate therapies but is currently recommended only after the second therapeutic failure. H. pylori is, in fact, a “fastidious” microorganism; culture methods are time-consuming and technically challenging. The advent of molecular biology techniques has enabled the identification of molecular mechanisms underlying the observed phenotypic resistance to antibiotics in H. pylori. The aim of this literature review is to summarize the results of original articles published in the last ten years, regarding the use of Next Generation Sequencing, in particular of the whole genome, to predict the antibiotic resistance in H. pylori.Methods: a literature research was made on PubMed. The research was focused on II and III generation sequencing of the whole H. pylori genome. Results: Next Generation Sequencing enabled the detection of novel, rare and complex resistance mechanisms. The prediction of resistance to clarithromycin, levofloxacin and amoxicillin is accurate; for other antimicrobials, such as metronidazole, rifabutin and tetracycline, potential genetic determinants of the resistant status need further investigation.

Disseminated Rhinocladiella mackenziei infection in a kidney transplant recipient: A case report and literature review

2021 ◽  
pp. 101196
Author(s):  
Torki M AlOtaibi ◽  
Osama A Gheith ◽  
Khaled Alobaid ◽  
Prasad Nair ◽  
Sohair M Zein Eldein ◽  
...  
Keyword(s):  
Case Report ◽  
Literature Review ◽  
Transplant Recipient ◽  
Kidney Transplant ◽  
Kidney Transplant Recipient

Simultaneous coccidioidomycosis and phaeohyphomycosis in a kidney transplant recipient: A case report and literature review

2020 ◽  
Vol 22 (6) ◽  
Author(s):  
Alfredo G. Puing ◽  
Antoine Couture‐Cossette ◽  
Aileen X. Wang ◽  
Corinna C. Zygourakis ◽  
Xingxing Cheng ◽  
...  
Keyword(s):  
Case Report ◽  
Literature Review ◽  
Transplant Recipient ◽  
Kidney Transplant ◽  
Kidney Transplant Recipient

scholarly journals COVID-19 pneumonia presenting as a single pulmonary nodule in a kidney transplant recipient: A case report and literature review

2020 ◽  
Vol 15 (9) ◽  
pp. 1587-1590 ◽  
Author(s):  
Alireza Rasekhi ◽  
Meisam Hoseinyazdi ◽  
Saeid Esmaeilian ◽  
Arash Teimouri ◽  
Akbar Safaei ◽  
...  
Keyword(s):  
Case Report ◽  
Literature Review ◽  
Transplant Recipient ◽  
Kidney Transplant ◽  
Pulmonary Nodule ◽  
Kidney Transplant Recipient ◽  
Single Pulmonary Nodule

scholarly journals Severe pulmonary co-infection with varicella-zoster virus, Pneumocystis jirovecii and Cytomegalovirus: a case report

2022 ◽  
Vol 50 (1) ◽  
pp. 030006052110707
Author(s):  
Zhijiang Qi ◽  
Yanting Sun ◽  
Jun Li ◽  
Yingjie Wang ◽  
Haining Lu ◽  
...  
Keyword(s):  
Case Report ◽  
Next Generation Sequencing ◽  
Varicella Zoster Virus ◽  
Pneumocystis Jirovecii ◽  
Imaging Features ◽  
Severe Respiratory Failure ◽  
Next Generation ◽  
Varicella Zoster ◽  
Immunosuppressed Patients ◽  
Generation Sequencing

Pneumocystis jirovecii, Cytomegalovirus and varicella-zoster virus are all opportunistically infective pathogens, but pulmonary co-infection with these pathogens is rare. Herein, this case report describes a patient with autoimmune haemolytic anaemia treated with methylprednisolone and cyclosporine that presented with rapidly progressive severe respiratory failure. Analysis of microbial nucleic acid sequences in both blood and sputum using next-generation sequencing revealed pulmonary co-infection with Pneumocystis jirovecii, varicella-zoster virus, and possibly Cytomegalovirus. After timely targeted and supportive treatments, the patient recovered. This case report highlights the imaging features of co-infection with these pathogens, the importance of next-generation sequencing for early diagnosis in immunosuppressed patients, and the effects of corticosteroid therapy.

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