{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T04:49:34Z","timestamp":1791521374192,"version":"4.3.4"},"reference-count":49,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2021,2,16]],"date-time":"2021-02-16T00:00:00Z","timestamp":1613433600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Armed Forces Health Surveillance Division (AFHSD) Global Emerging Infections Surveillance Branch (GEIS)","award":["ProMIS ID # P0108_19_AF_03.02."],"award-info":[{"award-number":["ProMIS ID # P0108_19_AF_03.02."]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Background: Next generation sequencing (NGS) technology has been used for a wide range of epidemiological and surveillance studies. Here, we used amplicon-based NGS to species identify Rickettsia and their arthropod hosts from entomological surveillance. Methods: During 2015\u20132016, we screened 1825 samples of rodents and ectoparasites collected from rodents and domestic mammals (dog, cat, and cattle) across Thailand for Rickettsia. The citrate synthase gene was amplified to identify Rickettsia to species, while the Cytochrome Oxidase subunit I (COI) and subunit II (COII) genes were used as target genes for ectoparasite identification. All target gene amplicons were pooled for library preparation and sequenced with Illumina MiSeq platform. Result: The highest percentage of Rickettsia DNA was observed in fleas collected from domestic animals (56%) predominantly dogs. Only a few samples of ticks from domestic animals, rodent fleas, and rodent tissue were positive for Rickettisia DNA. NGS based characterization of Rickettsia by host identified Rickettsia asembonensis as the most common bacteria in positive fleas collected from dogs (83.2%) while \u201cCandidatus Rickettsia senegalensis\u201d was detected in only 16.8% of Rickettsia positive dog fleas. Sequence analysis of COI and COII revealed that almost all fleas collected from dogs were Ctenocephalides felis orientis. Other Rickettsia species were detected by NGS including Rickettsia heilongjiangensis from two Haemaphysalis hystricis ticks, and Rickettsia typhi in two rodent tissue samples. Conclusion: This study demonstrates the utility of NGS for high-throughput sequencing in the species characterization\/identification of bacteria and ectoparasite for entomological surveillance of rickettsiae. A high percentage of C. f. orientis are positive for R. asembonensis. In addition, our findings indicate there is a risk of tick-borne Spotted Fever Group rickettsiosis, and flea-borne murine typhus transmission in Tak and Phangnga provinces of Thailand.<\/jats:p>","DOI":"10.3390\/pathogens10020215","type":"journal-article","created":{"date-parts":[[2021,2,16]],"date-time":"2021-02-16T22:13:38Z","timestamp":1613513618000},"page":"215","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Amplicon-Based Next Generation Sequencing for Rapid Identification of Rickettsia and Ectoparasite Species from Entomological Surveillance in Thailand"],"prefix":"10.3390","volume":"10","author":[{"given":"Suwanna","family":"Chaorattanakawee","sequence":"first","affiliation":[{"name":"Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok 10400, Thailand"},{"name":"Department of Parasitology and Entomology, Faculty of Public Health, Mahidol University, Ratchawithi Road, Bangkok 10400, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Achareeya","family":"Korkusol","sequence":"additional","affiliation":[{"name":"Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok 10400, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bousaraporn","family":"Tippayachai","sequence":"additional","affiliation":[{"name":"Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok 10400, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sommai","family":"Promsathaporn","sequence":"additional","affiliation":[{"name":"Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok 10400, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Betty K.","family":"Poole-Smith","sequence":"additional","affiliation":[{"name":"Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok 10400, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5136-3547","authenticated-orcid":false,"given":"Ratree","family":"Takhampunya","sequence":"additional","affiliation":[{"name":"Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok 10400, Thailand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,2,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5607","DOI":"10.1099\/ijsem.0.004332","article-title":"List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ","volume":"70","author":"Parte","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.idc.2018.10.010","article-title":"The Rickettsioses: A Practical Update","volume":"33","author":"Blanton","year":"2019","journal-title":"Infect. Dis. Clin. N. Am."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"320","DOI":"10.5694\/mja17.00090","article-title":"Tick-borne infectious diseases in Australia","volume":"206","author":"Graves","year":"2017","journal-title":"Med. J. Aust."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1016\/j.ttbdis.2016.03.008","article-title":"Rickettsia massiliae infection and SENLAT syndrome in Romania","volume":"7","author":"Zaharia","year":"2016","journal-title":"Ticks Tick Borne Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1128\/CMR.00032-13","article-title":"Update on tick-borne rickettsioses around the world: A geographic approach","volume":"26","author":"Parola","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1111\/mve.12189","article-title":"Vectorial competence of Amblyomma tonelliae to transmit Rickettsia rickettsii","volume":"30","author":"Tarragona","year":"2016","journal-title":"Med. Vet. Entomol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.3201\/eid2310.170309","article-title":"Fatal Rocky Mountain Spotted Fever along the United States-Mexico Border, 2013\u20132016","volume":"23","author":"Drexler","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.15585\/mmwr.mm6546a6","article-title":"Notes from the Field: Community-Based Prevention of Rocky Mountain Spotted Fever\u2014Sonora, Mexico, 2016","volume":"65","author":"Straily","year":"2016","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1089\/vbz.2011.0684","article-title":"Domestic dogs (Canis familiaris) as reservoir hosts for Rickettsia conorii","volume":"12","author":"Levin","year":"2012","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/S1473-3099(03)00739-4","article-title":"African tick bite fever","volume":"3","author":"Jensenius","year":"2003","journal-title":"Lancet Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e286","DOI":"10.1017\/S0950268819001390","article-title":"Diagnosis of spotted fever group Rickettsia infections: The Asian perspective","volume":"147","author":"Robinson","year":"2019","journal-title":"Epidemiol. Infect."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"682","DOI":"10.4269\/ajtmh.1994.50.682","article-title":"First cases of spotted fever group rickettsiosis in Thailand","volume":"50","author":"Sirisanthana","year":"1994","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.3201\/eid1109.050011","article-title":"Human Infection with Rickettsia honei, Thailand","volume":"11","author":"Jiang","year":"2005","journal-title":"Emerg. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"657","DOI":"10.3201\/eid1304.060585","article-title":"Human infection with Rickettsia sp. related to R. japonica, Thailand","volume":"13","author":"Gaywee","year":"2007","journal-title":"Emerg. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1093\/oxfordjournals.aje.a121485","article-title":"Tick-borne rickettsiae of the spotted fever group in West Pakistan. II. Serological classification of isolates from West Pakistan and Thailand: Evidence for two new species","volume":"97","author":"Robertson","year":"1973","journal-title":"Am. J. Epidemiol."},{"key":"ref_16","first-page":"610","article-title":"Spotted fever group Rickettsia sp. closely related to Rickettsia japonica, Thailand","volume":"15","author":"Takada","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"622","DOI":"10.4269\/ajtmh.18-0407","article-title":"Etiologies of Acute Undifferentiated Febrile Illness in Bangkok, Thailand","volume":"100","author":"Luvira","year":"2019","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Kuo, C.C., Wardrop, N., Chang, C.T., Wang, H.C., and Atkinson, P.M. (2017). Significance of major international seaports in the distribution of murine typhus in Taiwan. PLoS Negl. Trop. Dis., 11.","DOI":"10.1371\/journal.pntd.0005430"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"457","DOI":"10.4269\/ajtmh.16-0197","article-title":"Opossums and Cat Fleas: New Insights in the Ecology of Murine Typhus in Galveston, Texas","volume":"95","author":"Blanton","year":"2016","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Maina, A.N., Fogarty, C., Krueger, L., Macaluso, K.R., Odhiambo, A., Nguyen, K., Farris, C.M., Luce-Fedrow, A., Bennett, S., and Jiang, J. (2016). Rickettsial Infections among Ctenocephalides felis and Host Animals during a Flea-Borne Rickettsioses Outbreak in Orange County, California. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0160604"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1089\/vbz.2010.0174","article-title":"Rickettsia, Ehrlichia, Anaplasma, and Bartonella in ticks and fleas from dogs and cats in Bangkok","volume":"11","author":"Foongladda","year":"2011","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1089\/vbz.2017.2180","article-title":"Molecular Evidence of Rickettsia in Human and Dog Blood in Bangkok","volume":"18","author":"Mongkol","year":"2018","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1089\/vbz.2019.2564","article-title":"Spotted Fever Group Rickettsia Infection of Cats and Cat Fleas in Northeast Thailand","volume":"20","author":"Phomjareet","year":"2020","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.ttbdis.2016.09.011","article-title":"Bacterial pathogens and endosymbionts in ticks","volume":"8","author":"Papa","year":"2017","journal-title":"Ticks Tick Borne Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13071-015-0662-3","article-title":"Investigation of tick-borne bacteria (Rickettsia spp., Anaplasma spp., Ehrlichia spp. and Borrelia spp.) in ticks collected from Andean tapirs, cattle and vegetation from a protected area in Ecuador","volume":"8","author":"Pesquera","year":"2015","journal-title":"Parasit. Vectors"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Kurilshikov, A., Livanova, N.N., Fomenko, N.V., Tupikin, A.E., Rar, V.A., Kabilov, M.R., Livanov, S.G., and Tikunova, N.V. (2015). Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0131413"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Portillo, A., Palomar, A.M., de Toro, M., Santibanez, S., Santibanez, P., and Oteo, J.A. (2019). Exploring the bacteriome in anthropophilic ticks: To investigate the vectors for diagnosis. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0213384"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"319","DOI":"10.3389\/fmicb.2019.00319","article-title":"Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand","volume":"10","author":"Takhampunya","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Galan, M., Razzauti, M., Bard, E., Bernard, M., Brouat, C., Charbonnel, N., Dehne-Garcia, A., Loiseau, A., Tatard, C., and Tamisier, L. (2016). 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife. mSystems, 1.","DOI":"10.1128\/mSystems.00032-16"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.meegid.2017.09.022","article-title":"Microbial sequence typing in the genomic era","volume":"63","author":"Arenas","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"ref_31","first-page":"447","article-title":"Echidnophaga gallinacea infestation in dogs","volume":"165","author":"Kalkofen","year":"1974","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1186\/s13071-015-0781-x","article-title":"Evidence for a specific host-endosymbiont relationship between \u2018Rickettsia sp. genotype RF2125\u2019 and Ctenocephalides felis orientis infesting dogs in India","volume":"8","author":"Hii","year":"2015","journal-title":"Parasit. Vectors"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"334","DOI":"10.3389\/fvets.2018.00334","article-title":"Worldwide Presence and Features of Flea-Borne Rickettsia asembonensis","volume":"5","author":"Maina","year":"2018","journal-title":"Front. Vet. Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1128\/JCM.41.4.1600-1608.2003","article-title":"Detection of Ehrlichia spp., Anaplasma spp., Rickettsia spp., and other eubacteria in ticks from the Thai-Myanmar border and Vietnam","volume":"41","author":"Parola","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_35","unstructured":"Rodkvamtook, W., Pholpetch, S., Yokanit, W., Thongphun, A., Somsri, M., Somsri, K., Boonsom, V., Thimhaipol, C., Siriwatthanakul, K., and Amradee, B. (2018, January 16\u201319). Rickettsia asembonensis causing febrile disease in southern Thailand, 2016\u20132018. Proceedings of the 29th Meeting of the American Society for Rickettsiology, Milwaukee, WI, USA."},{"key":"ref_36","first-page":"630","article-title":"Rickettsial species in human cases with non-specific acute febrile syndrome in Peru","volume":"35","year":"2018","journal-title":"Rev. Peru Med. Exp. Salud. Publica"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"765","DOI":"10.4269\/ajtmh.16-0199","article-title":"Spotted Fever Group Rickettsioses and Murine Typhus in a Malaysian Teaching Hospital","volume":"95","author":"Kho","year":"2016","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1089\/vbz.2015.1849","article-title":"Molecular Detection of Zoonotic Rickettsiae and Anaplasma spp. in Domestic Dogs and Their Ectoparasites in Bushbuckridge, South Africa","volume":"16","author":"Kolo","year":"2016","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"545","DOI":"10.3201\/eid2103.141457","article-title":"Rickettsial infections in monkeys, Malaysia","volume":"21","author":"Tay","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1186\/s13071-016-1764-2","article-title":"Characterization of rickettsiae in ticks in northeastern China","volume":"9","author":"Liu","year":"2016","journal-title":"Parasit. Vectors"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1594","DOI":"10.1016\/j.ttbdis.2018.07.015","article-title":"Genetic variability of Rickettsia spp. in Dermacentor and Haemaphysalis ticks from the Russian Far East","volume":"9","author":"Igolkina","year":"2018","journal-title":"Ticks Tick Borne Dis."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"241","DOI":"10.2307\/1379792","article-title":"Lekagul, Boonsong, Jeffrey, A. McNeely. Mammals of thailand. Association for the Conservation of Wildlife*, Bangkok, Thailand","volume":"60","author":"Muul","year":"1979","journal-title":"J. Mammal."},{"key":"ref_43","unstructured":"Fleas, B.M.R.C.O., Hopkins, G.H.E., Siphonaptera, B.M.D.O.E., Collection, B.M.R., Rothschild, M., Mardon, D.K., and Smit, F.G.A.M. (1966). An Illustrated Catalogue of the Rothschild Collection of Fleas (Siphonaptera) in the British Museum (Natural History): With Keys and Short Descriptions for the Identification of Families, Genera, Species and Subspecies of the Order. Hystrichopsyllidae (Ctenophthalminae, Dinopsyllinae, Doratopsyllinae and Listropsyllinae), Trustees of the British Museum (Natural History)."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/jmedent\/26.6.573","article-title":"Keys to the adult ticks of Haemaphysalis Koch, 1844, in Thailand with notes on changes in taxonomy (Acari: Ixodoidea: Ixodidae)","volume":"26","author":"Tanskull","year":"1989","journal-title":"J. Med. Entomol."},{"key":"ref_45","first-page":"1","article-title":"The sucking lice (Insecta, Anoplura) of the world: A taxonomic checklist with records of mammalian hosts and geographical distributions","volume":"218","author":"Durden","year":"1994","journal-title":"Bull. AMNH"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1046\/j.0300-3256.2001.00095.x","article-title":"Mecoptera is paraphyletic: Multiple genes and phylogeny of Mecoptera and Siphonaptera","volume":"31","author":"Whiting","year":"2002","journal-title":"Zool. Scr."},{"key":"ref_47","first-page":"294","article-title":"DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates","volume":"3","author":"Folmer","year":"1994","journal-title":"Mol. Mar. Biol. Biotechnol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: Molecular Evolutionary Genetics Analysis version 6.0","volume":"30","author":"Tamura","year":"2013","journal-title":"Mol. Biol. Evol."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/10\/2\/215\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T05:24:57Z","timestamp":1760160297000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/10\/2\/215"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,16]]},"references-count":49,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2]]}},"alternative-id":["pathogens10020215"],"URL":"https:\/\/doi.org\/10.3390\/pathogens10020215","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,16]]}}}