High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis
Aicui Liu,1,2,* Chao Wang,1,2,* Zhijuan Liang,3 Zhi-Wei Zhou,4 Lin Wang,1,2 Qiaoli Ma,1,2 Guowei Wang,1,2 Shu-Feng Zhou,4 Zhenhai Wang1,2 1Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia; 2Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia; 3Departmen...
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| Format: | Article |
| Language: | English |
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Dove Medical Press
2015-08-01
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| Series: | Drug Design, Development and Therapy |
| Online Access: | http://www.dovepress.com/high-throughput-sequencing-of-16s-rdna-amplicons-characterizes-bacteri-peer-reviewed-article-DDDT |
| _version_ | 1818273176389419008 |
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| author | Liu A Wang C Liang Z Zhou ZW Wang L Ma Q Wang G Zhou SF Wang Z |
| author_facet | Liu A Wang C Liang Z Zhou ZW Wang L Ma Q Wang G Zhou SF Wang Z |
| author_sort | Liu A |
| collection | DOAJ |
| description | Aicui Liu,1,2,* Chao Wang,1,2,* Zhijuan Liang,3 Zhi-Wei Zhou,4 Lin Wang,1,2 Qiaoli Ma,1,2 Guowei Wang,1,2 Shu-Feng Zhou,4 Zhenhai Wang1,2 1Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia; 2Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia; 3Department of Neurology, The First People’s Hospital of Lanzhou, Lanzhou, Gansu, People’s Republic of China; 4Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA *These authors contributed equally to this work Abstract: Purulent meningitis (PM) is a severe infectious disease that is associated with high rates of morbidity and mortality. It has been recognized that bacterial infection is a major contributing factor to the pathogenesis of PM. However, there is a lack of information on the bacterial composition in PM, due to the low positive rate of cerebrospinal fluid bacterial culture. Herein, we aimed to discriminate and identify the main pathogens and bacterial composition in cerebrospinal fluid sample from PM patients using high-throughput sequencing approach. The cerebrospinal fluid samples were collected from 26 PM patients, and were determined as culture-negative samples. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 26 samples of PM were sequenced using the 454 GS FLX system. The results showed that there were 71,440 pyrosequencing reads, of which, the predominant phyla were Proteobacteria and Firmicutes; and the predominant genera were Streptococcus, Acinetobacter, Pseudomonas, and Neisseria. The bacterial species in the cerebrospinal fluid were complex, with 61.5% of the samples presenting with mixed pathogens. A significant number of bacteria belonging to a known pathogenic potential was observed. The number of operational taxonomic units for individual samples ranged from six to 75 and there was a comparable difference in the species diversity that was calculated through alpha and beta diversity analysis. Collectively, the data show that high-throughput sequencing approach facilitates the characterization of the pathogens in cerebrospinal fluid and determine the abundance and the composition of bacteria in the cerebrospinal fluid samples of the PM patients, which may provide a better understanding of pathogens in PM and assist clinicians to make rational and effective therapeutic decisions. Keywords: Bioinformatics, cerebrospinal fluid sample, OTU |
| first_indexed | 2024-12-12T21:53:48Z |
| format | Article |
| id | doaj.art-a36aa6f4da584a29bf277dfe758bd348 |
| institution | Directory Open Access Journal |
| issn | 1177-8881 |
| language | English |
| last_indexed | 2024-12-12T21:53:48Z |
| publishDate | 2015-08-01 |
| publisher | Dove Medical Press |
| record_format | Article |
| series | Drug Design, Development and Therapy |
| spelling | doaj.art-a36aa6f4da584a29bf277dfe758bd3482022-12-22T00:10:43ZengDove Medical PressDrug Design, Development and Therapy1177-88812015-08-012015default4417442923036High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitisLiu AWang CLiang ZZhou ZWWang LMa QWang GZhou SFWang ZAicui Liu,1,2,* Chao Wang,1,2,* Zhijuan Liang,3 Zhi-Wei Zhou,4 Lin Wang,1,2 Qiaoli Ma,1,2 Guowei Wang,1,2 Shu-Feng Zhou,4 Zhenhai Wang1,2 1Neurology Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia; 2Key Laboratory of Brain Diseases of Ningxia, Yinchuan, Ningxia; 3Department of Neurology, The First People’s Hospital of Lanzhou, Lanzhou, Gansu, People’s Republic of China; 4Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA *These authors contributed equally to this work Abstract: Purulent meningitis (PM) is a severe infectious disease that is associated with high rates of morbidity and mortality. It has been recognized that bacterial infection is a major contributing factor to the pathogenesis of PM. However, there is a lack of information on the bacterial composition in PM, due to the low positive rate of cerebrospinal fluid bacterial culture. Herein, we aimed to discriminate and identify the main pathogens and bacterial composition in cerebrospinal fluid sample from PM patients using high-throughput sequencing approach. The cerebrospinal fluid samples were collected from 26 PM patients, and were determined as culture-negative samples. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 26 samples of PM were sequenced using the 454 GS FLX system. The results showed that there were 71,440 pyrosequencing reads, of which, the predominant phyla were Proteobacteria and Firmicutes; and the predominant genera were Streptococcus, Acinetobacter, Pseudomonas, and Neisseria. The bacterial species in the cerebrospinal fluid were complex, with 61.5% of the samples presenting with mixed pathogens. A significant number of bacteria belonging to a known pathogenic potential was observed. The number of operational taxonomic units for individual samples ranged from six to 75 and there was a comparable difference in the species diversity that was calculated through alpha and beta diversity analysis. Collectively, the data show that high-throughput sequencing approach facilitates the characterization of the pathogens in cerebrospinal fluid and determine the abundance and the composition of bacteria in the cerebrospinal fluid samples of the PM patients, which may provide a better understanding of pathogens in PM and assist clinicians to make rational and effective therapeutic decisions. Keywords: Bioinformatics, cerebrospinal fluid sample, OTUhttp://www.dovepress.com/high-throughput-sequencing-of-16s-rdna-amplicons-characterizes-bacteri-peer-reviewed-article-DDDT |
| spellingShingle | Liu A Wang C Liang Z Zhou ZW Wang L Ma Q Wang G Zhou SF Wang Z High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis Drug Design, Development and Therapy |
| title | High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis |
| title_full | High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis |
| title_fullStr | High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis |
| title_full_unstemmed | High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis |
| title_short | High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis |
| title_sort | high throughput sequencing of 16s rdna amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with nbsp purulent meningitis |
| url | http://www.dovepress.com/high-throughput-sequencing-of-16s-rdna-amplicons-characterizes-bacteri-peer-reviewed-article-DDDT |
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