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Metataxonomics of Internal Transcribed Spacer amplicons in cerebrospinal fluid for diagnosing and genotyping of cryptococcal meningitis

Authors :
Ji-Ting Zhu
Han Lin
Xuan Wu
Zhi-Wen Li
Ai-Yu Lin
Xin Chen and Li-Min Chen
Source :
Chinese Medical Journal, Vol 132, Iss 23, Pp 2827-2834 (2019)
Publication Year :
2019
Publisher :
Wolters Kluwer, 2019.

Abstract

Abstract. Background:. Cryptococcal meningitis is a severe infectious disease associated with high morbidity and mortality. Rapidity and accuracy of diagnosis contribute to better prognosis, but readily available tools, such as microscopy, culture, and antigens do not perform well all the time. Our study attempted to diagnose and genotype cryptococcus in the cerebrospinal fluid (CSF) samples from patients with cryptococcal meningitis using the approach of metataxonomics of Internal Transcribed Spacer (ITS) amplicons. Methods:. The CSF samples were collected from 11 clinically suspected cryptococcal meningitis patients and four non-infectious controls. Samples were recruited from the First Affiliated Hospital of Fujian Medical University Hospital, Fuzhou Fourth Hospital and the 476th Hospital of Chinese People's Liberation Army from December 2017 to December 2018. ITS1 ribosomal deoxyribonucleic acid (rDNA) genes of 15 whole samples were amplified by universal forward primer ITS1 (CTTGGTCATTTAGAGGAAGTAA) and reverse primer ITS2 (GCTGCGTTCTTCATCGATGC), sequenced by Illumina MiSeq Benchtop Sequencer. The results were confirmed by sanger sequencing of ITS1 region and partial CAP59 gene of microbial isolates from 11 meningitic samples. Pair-wise comparison between infectious group and control group was conducted through permutational multivariate analysis (PERMANOVA) in R software. Results:. The 30,000 to 340,000 high-quality clean reads were obtained from each of the positively stained or cultured CSF samples and 8 to 60 reads from each control. The samples from 11 infected patients yielded detectable cryptococcal-specific ITS1 DNA with top abundance (from 95.90% to 99.97%), followed by many other fungal groups (each

Subjects

Subjects :
Medicine

Details

Language :
English
ISSN :
03666999, 25425641, and 00000000
Volume :
132
Issue :
23
Database :
Directory of Open Access Journals
Journal :
Chinese Medical Journal
Publication Type :
Academic Journal
Accession number :
edsdoj.32a6541803f24c4aa76ab16c54a56d55
Document Type :
article
Full Text :
https://doi.org/10.1097/CM9.0000000000000541