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An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data
- Source :
- PLoS ONE, PLoS ONE, Vol 9, Iss 3, p e90831 (2014)
- Publication Year :
- 2013
-
Abstract
- This paper explored our hypothesis that sRNA (18 ∼ 30 bp) deep sequencing technique can be used as an efficient strategy to identify microorganisms other than viruses, such as prokaryotic and eukaryotic pathogens. In the study, the clean reads derived from the sRNA deep sequencing data of wild-caught ticks and mosquitoes were compared against the NCBI nucleotide collection (non-redundant nt database) using Blastn. The blast results were then analyzed with in-house Python scripts. An empirical formula was proposed to identify the putative pathogens. Results showed that not only viruses but also prokaryotic and eukaryotic species of interest can be screened out and were subsequently confirmed with experiments. Specially, a novel Rickettsia spp. was indicated to exist in Haemaphysalis longicornis ticks collected in Beijing. Our study demonstrated the reuse of sRNA deep sequencing data would have the potential to trace the origin of pathogens or discover novel agents of emerging/re-emerging infectious diseases.
- Subjects :
- Small RNA
China
Infectious Disease Control
Sequence analysis
Epidemiology
Science
Computational biology
Microbiology
Mosquitoes
Deep sequencing
Vector Biology
Infectious Disease Epidemiology
law.invention
Ticks
law
Phylogenetics
RNA, Ribosomal, 16S
RNA, Ribosomal, 18S
Animals
Genome Sequencing
Biology
Microbial Pathogens
Polymerase chain reaction
Phylogeny
Multidisciplinary
biology
Geography
Arthropod Vectors
Computational Biology
Reproducibility of Results
Vectors and Hosts
Sequence Analysis, DNA
Genomics
Ribosomal RNA
biology.organism_classification
Molecular biology
Culicidae
Infectious Diseases
Metagenomics
Metagenome
Medicine
Public Health
Haemaphysalis longicornis
Sequence Analysis
Research Article
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 9
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- PloS one
- Accession number :
- edsair.doi.dedup.....f10387fb41c733e1763d399aeb3a8eb1