Next generation sequencing uncovers unexpected bacterial pathogens in ticks in western Europe

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Vayssier Taussat, Muriel ^a   Moutailler, Sara ^a   Michelet, Lorraine ^a   Devillers, Elodie ^a   Bonnet, Sarah ^a   Cheval, Justine ^b   Hébert, Charles ^b   Eloit, Marc ^b,c,d  

^a INRA   (France)

^b PathoQuest   (France)

^c ECOLE NATIONALE VÉTÉRINAIRE D ALFORT   (France)

^d INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; BACTERIAL RNA; RNA 16S;

ADULT; ARTICLE; BACTERIAL TRANSMISSION; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; CONTIG MAPPING; DNA EXTRACTION; FEMALE; FRANCE; HUMAN; IXODES RICINUS; MAJOR CLINICAL STUDY; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; NYMPH; PREVALENCE; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA EXTRACTION; SEQUENCE ANALYSIS; TAXONOMY; TICK; TICK BORNE DISEASE; WESTERN EUROPE; ANIMAL; BACTERIA; EUROPE; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; MICROBIOLOGY; MICROFLORA;

ANIMALS; BACTERIA; EUROPE; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROBIOTA; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; TICKS;

EID: 84896705912     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081439     Document Type: Article

References (49)

1. Githeko AK, Lindsay SW, Confalonieri UE, Patz JA (2000) Climate change and vector-borne diseases: a regional analysis. Bull World Health Organ 78: 1136-1147.
2. Parola P, Raoult D (2001) Ticks and tickborne bacterial diseases in humans: an emerging infectious threat. Clin Infect Dis 32: 897-928.
3. Andersson M, Raberg L (2011) Wild rodents and novel human pathogen candidatus Neoehrlichia mikurensis, Southern Sweden. Emerg Infect Dis 17: 1716-1718.
4. Haselbarth K, Tenter AM, Brade V, Krieger G, Hunfeld KP (2007) First case of human babesiosis in Germany - Clinical presentation and molecular characterisation of the pathogen. Int J Med Microbiol 297: 197-204.
5. Parola P, Raoult D (2001) Tick-borne bacterial diseases emerging in Europe. Clin Microbiol Infect 7: 80-83.
6. Hubalek Z (2009) Epidemiology of lyme borreliosis. Curr Probl Dermatol 37: 31-50.
7. Piesman J, Eisen L (2008) Prevention of tick-borne diseases. Annu Rev Entomol 53: 323-343.
8. Kik M, Nijhof AM, Balk JA, Jongejan F (2011) Babesia sp. EU1 infection in a forest reindeer, The Netherlands. Emerg Infect Dis 17: 936-938.
9. Mayne PJ (2011) Emerging incidence of Lyme borreliosis, babesiosis, bartonellosis, and granulocytic ehrlichiosis in Australia. Int J Gen Med 4: 845-852.
10. Feder HM, Jr., Johnson BJ, O'Connell S, Shapiro ED, Steere AC, et al. (2007) A critical appraisal of "chronic Lyme disease". N Engl J Med 357: 1422-1430.
11. Sauvage V, Cheval J, Foulongne V, Gouilh MA, Pariente K, et al. (2011) Identification of the first human Gyrovirus, a virus related to chicken anemia virus. J Virol.
12. Sauvage V, Foulongne V, Cheval J, Ar Gouilh M, Pariente K, et al. (2011) Human polyomavirus related to African green monkey lymphotropic polyomavirus. Emerg Infect Dis 17: 1364-1370.
13. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, et al. (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318: 283-287.
14. Buckwalter MR, Nga PT, Gouilh MA, Fiette L, Bureau JF, et al. (2011) Identification of a Novel Neuropathogenic Theiler's Murine Encephalomyelitis Virus. J Virol 85: 6893-6905.
15. Nakamura S, Maeda N, Miron IM, Yoh M, Izutsu K, et al. (2008) Metagenomic diagnosis of bacterial infections. Emerg Infect Dis 14: 1784-1786.
16. Nakamura S, Nakaya T, Iida T (2011) Metagenomic analysis of bacterial infections by means of high-throughput DNA sequencing. Exp Biol Med (Maywood) 236: 968-971.
17. Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, et al. (2011) Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 49: 3268-3275.
18. Hoffmann B, Scheuch M, Hoper D, Jungblut R, Holsteg M, et al. (2012) Novel orthobunyavirus in cattle, europe, 2011. Emerg Infect Dis 18: 469-472.
19. Carpi G, Cagnacci F, Wittekindt NE, Zhao F, Qi J, et al. (2011) Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks. PLoS One 6: e25604.
20. Nakao R, Abe T, Nijhof AM, Yamamoto S, Jongejan F, et al. (2013) A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks. ISME J 7: 1003-1015.
21. Reis C, Cote M, Paul RE, Bonnet S (2011) Questing ticks in suburban forest are infected by at least six tick-borne pathogens. Vector Borne Zoonotic Dis 11: 907-916.
22. Reis C, Cote M, Le Rhun D, Lecuelle B, Levin ML, et al. (2011) Vector competence of the tick Ixodes ricinus for transmission of Bartonella birtlesii. PLoS Negl Trop Dis 5: e1186.
23. Hauck WW (1991) Confidence intervals for seroprevalence determined from pooled sera. Ann Epidemiol 1: 277-281.
24. Cowling DW, Gardner IA, Johnson WO (1999) Comparison of methods for estimation of individual-level prevalence based on pooled samples. Prev Vet Med 39: 211-225.
25. Socolovschi C, Mediannikov O, Raoult D, Parola P (2009) Update on tick-borne bacterial diseases in Europe. Parasite 16: 259-273.
26. McKiel JA, Bell EJ, Lackman DB (1967) Rickettsia canada: a new member of the typhus group of rickettsiae isolated from Haemaphysalis leporispalustris ticks in Canada. Can J Microbiol 13: 503-510.
27. Brouqui P, Parola P, Fournier PE, Raoult D (2007) Spotted fever rickettsioses in southern and eastern Europe. FEMS Immunol Med Microbiol 49: 2-12.
28. Welinder-Olsson C, Kjellin E, Vaht K, Jacobsson S, Wenneras C (2010) First case of human "Candidatus Neoehrlichia mikurensis" infection in a febrile patient with chronic lymphocytic leukemia. J Clin Microbiol 48: 1956-1959.
29. Vayssier-Taussat M, Le Rhun D, Buffet JP, Maaoui N, Galan M, et al. (2012) Candidatus Neoehrlichia mikurensis in Bank Voles, France. Emerg Infect Dis 18: 2063-2065.
30. Doyle CK, Labruna MB, Breitschwerdt EB, Tang YW, Corstvet RE, et al. (2005) Detection of medically important Ehrlichia by quantitative multicolor TaqMan real-time polymerase chain reaction of the dsb gene. J Mol Diagn 7: 504-510.
31. Chomel BB, Boulouis HJ, Breitschwerdt EB, Kasten RW, Vayssier-Taussat M, et al. (2009) Ecological fitness and strategies of adaptation of Bartonella species to their hosts and vectors. Vet Res 40: 29.
32. Janecek E, Mietze A, Goethe R, Schnieder T, Strube C (2012) Bartonella spp. infection rate and B. grahamii in ticks. Emerg Infect Dis 18: 1689-1690.
33. Dietrich F, Schmidgen T, Maggi RG, Richter D, Matuschka FR, et al. (2010) Prevalence of Bartonella henselae and Borrelia burgdorferi sensu lato DNA in ixodes ricinus ticks in Europe. Appl Environ Microbiol 76: 1395-1398.
34. Marsot M, Sigaud M, Chapuis JL, Ferquel E, Cornet M, et al. (2011) Introduced Siberian chipmunks (Tamias sibiricus barberi) harbor more-diverse Borrelia burgdorferi sensu lato genospecies than native bank voles (Myodes glareolus). Appl Environ Microbiol 77: 5716-5721.
35. Platonov AE, Karan LS, Kolyasnikova NM, Makhneva NA, Toporkova MG, et al. (2011) Humans infected with relapsing fever spirochete Borrelia miyamotoi, Russia. Emerg Infect Dis 17: 1816-1823.
36. Geller J, Nazarova L, Katargina O, Jarvekulg L, Fomenko N, et al. (2012) Detection and genetic characterization of relapsing fever spirochete Borrelia miyamotoi in Estonian ticks. PLoS One 7: e51914.
37. Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, Ferrera I, et al. (2013) Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol.
38. Li H, Jiang J, Tang F, Sun Y, Li Z, et al. (2013) Wide distribution and genetic diversity of "Candidatus Neoehrlichia mikurensis" in rodents from China. Appl Environ Microbiol 79: 1024-1027.
39. Li H, Jiang JF, Liu W, Zheng YC, Huo QB, et al. (2012) Human infection with Candidatus Neoehrlichia mikurensis, China. Emerg Infect Dis 18: 1636-1639.
40. Fukunaga M, Koreki Y (1995) The flagellin gene of Borrelia miyamotoi sp. nov. and its phylogenetic relationship among Borrelia species. FEMS Microbiol Lett 134: 255-258.
41. Fukunaga M, Takahashi Y, Tsuruta Y, Matsushita O, Ralph D, et al. (1995) Genetic and phenotypic analysis of Borrelia miyamotoi sp. nov., isolated from the ixodid tick Ixodes persulcatus, the vector for Lyme disease in Japan. Int J Syst Bacteriol 45: 804-810.
42. Fraenkel CJ, Garpmo U, Berglund J (2002) Determination of novel Borrelia genospecies in Swedish Ixodes ricinus ticks. J Clin Microbiol 40: 3308-3312.
43. Richter D, Schlee DB, Matuschka FR (2003) Relapsing fever-like spirochetes infecting European vector tick of Lyme disease agent. Emerg Infect Dis 9: 697-701.
44. Scoles GA, Papero M, Beati L, Fish D (2001) A relapsing fever group spirochete transmitted by Ixodes scapularis ticks. Vector Borne Zoonotic Dis 1: 21-34.
45. Sarksyan DS, Platonov AE, Karan LS, Malinin IE, Khalitova LI, et al. (2012) [Clinical presentation of "new" tick-borne borreliosis caused by Borrelia miyamotoi]. Ter Arkh 84: 34-41.
46. Cotte V, Bonnet S, Le Rhun D, Le Naour E, Chauvin A, et al. (2008) Transmission of Bartonella henselae by Ixodes ricinus. Emerg Infect Dis 14: 1074-1080.
47. Klee SR, Tyczka J, Ellerbrok H, Franz T, Linke S, et al. (2006) Highly sensitive real-time PCR for specific detection and quantification of Coxiella burnetii. BMC Microbiol 6: 2.
48. Versage JL, Severin DD, Chu MC, Petersen JM (2003) Development of a multitarget real-time TaqMan PCR assay for enhanced detection of Francisella tularensis in complex specimens. J Clin Microbiol 41: 5492-5499.
49. Socolovschi C, Pages F, Raoult D (2012) Rickettsia felis in Aedes albopictus mosquitoes, Libreville, Gabon. Emerg Infect Dis 18: 1687-1689.