title: An efficient strategy of screening for pathogens in wild-caught ticks and mosquitoes by reusing small RNA deep sequencing data.
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.
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Lu
authors.initials: L
authors.lastname: Zhuang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: An
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Hang
authors.initials: H
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Maijuan
authors.initials: M
authors.lastname: Ma
authors.affiliation: College of Public Health and Health Professions, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Anderson
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Jiafu
authors.initials: J
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Wuchun
authors.initials: W
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Fengtai District, Beijing, P. R. China.
authors.forename: Yigang
authors.initials: Y
authors.lastname: Tong
mesh_terms: D000818:Animals; D001179:Arthropod Vectors / Q000382:microbiology; D002681:China; D019295:Computational Biology; D009033:Culicidae / Q000382:microbiology*; D005843:Geography; D054892:Metagenome; D056186:Metagenomics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013987:Ticks / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S