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Minahan NT, Yen TY, Guo YLL, Shu PY, Tsai KH. Concatenated ScaA and TSA56 Surface Antigen Sequences Reflect Genome-Scale Phylogeny of Orientia tsutsugamushi: An Analysis Including Two Genomes from Taiwan. Pathogens 2024; 13:299. [PMID: 38668254 PMCID: PMC11054523 DOI: 10.3390/pathogens13040299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Orientia tsutsugamushi is an obligate intracellular bacterium associated with trombiculid mites and is the causative agent of scrub typhus, a life-threatening febrile disease. Strain typing of O. tsutsugamushi is based on its immunodominant surface antigen, 56-kDa type-specific antigen (TSA56). However, TSA56 gene sequence-based phylogenetic analysis is only partially congruent with core genome-based phylogenetic analysis. Thus, this study investigated whether concatenated surface antigen sequences, including surface cell antigen (Sca) proteins, can reflect the genome-scale phylogeny of O. tsutsugamushi. Complete genomes were obtained for two common O. tsutsugamushi strains in Taiwan, TW-1 and TW-22, and the core genome/proteome was identified for 11 O. tsutsugamushi strains. Phylogenetic analysis was performed using maximum likelihood (ML) and neighbor-joining (NJ) methods, and the congruence between trees was assessed using a quartet similarity measure. Phylogenetic analysis based on 691 concatenated core protein sequences produced identical tree topologies with ML and NJ methods. Among TSA56 and core Sca proteins (ScaA, ScaC, ScaD, and ScaE), TSA56 trees were most similar to the core protein tree, and ScaA trees were the least similar. However, concatenated ScaA and TSA56 sequences produced trees that were highly similar to the core protein tree, the NJ tree being more similar. Strain-level characterization of O. tsutsugamushi may be improved by coanalyzing ScaA and TSA56 sequences, which are also important targets for their combined immunogenicity.
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Affiliation(s)
- Nicholas T. Minahan
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei 100025, Taiwan; (N.T.M.); (Y.-L.L.G.)
| | - Tsai-Ying Yen
- Centers for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei 115210, Taiwan; (T.-Y.Y.); (P.-Y.S.)
| | - Yue-Liang Leon Guo
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei 100025, Taiwan; (N.T.M.); (Y.-L.L.G.)
- Department of Environmental and Occupational Medicine, National Taiwan University (NTU) College of Medicine and NTU Hospital, Taipei 100025, Taiwan
| | - Pei-Yun Shu
- Centers for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei 115210, Taiwan; (T.-Y.Y.); (P.-Y.S.)
| | - Kun-Hsien Tsai
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei 100025, Taiwan; (N.T.M.); (Y.-L.L.G.)
- Global Health Program, College of Public Health, National Taiwan University, Taipei 100025, Taiwan
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Bhandari M, Singh RK, Laishevtcev A, Mohapatra TM, Nigam M, Mori E, Vasconcelos de Lacerda BCG, Coutinho HDM, Mishra AP. Revisiting scrub typhus: A neglected tropical disease. Comp Immunol Microbiol Infect Dis 2022; 90-91:101888. [PMID: 36252451 DOI: 10.1016/j.cimid.2022.101888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 02/08/2023]
Abstract
Scrub typhus is an under diagnosed re-emerging vector borne disease caused by an intracellular gram negative bacteria, Orientia. The disease is commonly prevalent in rural and hilly areas of Tsutsugumashi triangle. The diagnosis of the disease is very challenging due to similarity of its early symptoms with other febrile illnesses, like dengue and COVID 19, as well as non-availability of rapid, reliable and cost-effective methods. Moreover, the diverse clinical presentation in severe cases make it significant health problem. The occupational and behavioral risks responsible for the transmission lead to urgent need of vaccine development against the disease. The complete knowledge about its pathogenesis and the interaction with host's immune cells may help the scientists in developing the appropriate diagnostic methods as well as the vaccines.
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Affiliation(s)
- Munni Bhandari
- Department of Microbiology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar (Garhwal) 246174, India.
| | - Rahul Kunwar Singh
- Department of Microbiology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar (Garhwal) 246174, India.
| | - Alexey Laishevtcev
- Federal Research Center - All-Russian Scientific Research Institute of Experimental Veterinary Medicine named after K.I. Skryabin and Y.R. Kovalenko of the Russian Academy of Sciences, Moscow, Russia; Laboratory of Biocontrol and Antimicrobial Resistance, Orel State, University Named After I.S. Turgenev, Orel, Russia.
| | - Tribhuvan Mohan Mohapatra
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
| | - Manisha Nigam
- Department of Biochemistry, Hemvati Nandan Bahuguna Garhwal University, Srinagar Garhwal-246174, Uttarakhand, India.
| | - Edna Mori
- CECAPE - College of Dentistry, Av. Padre Cícero, 3917, Juazeiro do Norte, São José CE 63024-015, Brazil.
| | | | | | - Abhay Prakash Mishra
- Department of Pharmacology, Faculty of Health Science, University of Free State, Bloemfontein 9300, South Africa.
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Inthawong M, Sunyakumthorn P, Wongwairot S, Anantatat T, Dunachie SJ, Im-Erbsin R, Jones JW, Mason CJ, Lugo LA, Blacksell SD, Day NPJ, Sonthayanon P, Richards AL, Paris DH. A time-course comparative clinical and immune response evaluation study between the human pathogenic Orientia tsutsugamushi strains: Karp and Gilliam in a rhesus macaque (Macaca mulatta) model. PLoS Negl Trop Dis 2022; 16:e0010611. [PMID: 35925895 PMCID: PMC9352090 DOI: 10.1371/journal.pntd.0010611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Scrub typhus is a vector-borne febrile illness caused by Orientia tsutsugamushi transmitted by the bite of Trombiculid mites. O. tsutsugamushi has a high genetic diversity and is increasingly recognized to have a wider global distribution than previously assumed. METHODOLOGY/PRINCIPLE FINDINGS We evaluated the clinical outcomes and host immune responses of the two most relevant human pathogenic strains of O. tsutsugamushi; Karp (n = 4) and Gilliam (n = 4) in a time-course study over 80 days post infection (dpi) in a standardized scrub typhus non-human primate rhesus macaque model. We observed distinct features in clinical progression and immune response between the two strains; Gilliam-infected macaques developed more pronounced systemic infection characterized by an earlier onset of bacteremia, lymph node enlargement, eschar lesions and higher inflammatory markers during the acute phase of infection, when compared to the Karp strain. C-reactive protein (CRP) plasma levels, interferon gamma (IFN-γ, interleukin-1 receptor antagonist (IL-1ra), IL-15 serum concentrations, CRP/IL10- and IFN-γ/IL-10 ratios correlated positively with bacterial load in blood, implying activation of the innate immune response and preferential development of a T helper-type 1 immune response. The O. tsutsugamushi-specific immune memory responses in cells isolated from skin and lymph nodes at 80 dpi were more markedly elevated in the Gilliam-infected macaques than in the Karp-infected group. The comparative cytokine response dynamics of both strains revealed significant up-regulation of IFN-γ, tumor necrosis factor (TNF), IL-15, IL-6, IL-18, regulatory IL-1ra, IL-10, IL-8 and granulocyte-colony-stimulating factor (G-CSF). These data suggest that the clinical outcomes and host immune responses to scrub typhus could be associated with counter balancing effects of pro- and anti-inflammatory cytokine-mediated responses. Currently, no data on characterized time-course comparisons of O. tsutsugamushi strains regarding measures of disease severity and immune response is available. Our study provides evidence for the strain-specificity of host responses in scrub typhus, which supports our understanding of processes at the initial inoculation site (eschar), systemic disease progression, protective and/or pathogenic host immune mechanisms and cellular immune memory function. CONCLUSIONS/SIGNIFICANCE This study characterised an improved intradermal rhesus macaque challenge model for scrub typhus, whereby the Gilliam strain infection associated with higher disease severity in the rhesus macaque model than the previous Karp strain infection. Difficulties associated with inoculum quantitation for obligate-intracellular bacteria were overcome by using functional inoculum titrations in outbred mice. The Gilliam-based rhesus macaque model provides improved endpoint measurements and contributes towards the identification of correlates of protection for future vaccine development.
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Affiliation(s)
- Manutsanun Inthawong
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piyanate Sunyakumthorn
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Sirima Wongwairot
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tippawan Anantatat
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Susanna J. Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Rawiwan Im-Erbsin
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - James W. Jones
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Carl J. Mason
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Luis A. Lugo
- Department of Veterinary Medicine, United States Army Medical Directorate, Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Stuart D. Blacksell
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
| | - Piengchan Sonthayanon
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Allen L. Richards
- Viral & Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, United States of America
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Daniel H. Paris
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Department of Medicine, Swiss Tropical and Public Health Institute, Faculty of Medicine, University of Basel, Switzerland
- Department of Clinical Research, Faculty of Medicine, University of Basel, Switzerland
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Ernieenor FCL, NorJaiza MJ, Fadillah A, Canedy J, Mariana A. Screening and genotyping of Orientia tsutsugamushi from field-collected on-host chiggers (Acari: Prostigmata) recovered from a positive scrub typhus locality in Kelantan, Malaysia. EXPERIMENTAL & APPLIED ACAROLOGY 2021; 84:171-182. [PMID: 33826009 DOI: 10.1007/s10493-021-00609-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Orientia tsutsugamushi is the causative agent of scrub typhus vectored by larval stages of trombiculid mites (chiggers) that occur in most tropical regions of Southeast Asia. A total of 242 chiggers extracted from eight small mammals captured from a positive scrub typhus locality in Kelantan, Malaysia, were screened for the presence of O. tsutsugamushi. The chiggers were grouped in 16 pools for extraction of DNA prior to screening of O. tsutsugamushi based on the nucleotide sequence of 56-kDa type specific antigen (TSA) gene using nested polymerase chain reaction. Two species of on-host chiggers were identified, the one, Leptotrombidium deliense, much more dominant (94.8%) than the other, Ascoshoengastia sp. (5.2%). The pathogen was detected in two pools (12.5%) of L. deliense recovered from Rattus rattus and Tupaia sp. The 56-kDa TSA gene sequence analysis revealed the O. tsutsugamushi harboured in those chiggers were Karp prototype strain with high similarity (99.3%). Findings of this study strongly supported the existence of scrub typhus infections in certain parts of Malaysia which agrees with previous local reports. Moreover, this study highlighted the pressing need of a large-scale close observation of O. tsutsugamushi DNA sequences from chiggers that can probably be collected from other positive scrub typhus localities to precisely provide the distribution and prevalence of this zoonotic pathogen.
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Affiliation(s)
- F C L Ernieenor
- Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Acarology Unit, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170, Shah Alam, Selangor, Malaysia.
| | - M J NorJaiza
- Disease Control Division, Entomology and Pest Unit, Kelantan State Health Department, Ministry of Health Malaysia, Jalan Mahmood, 15200, Kota Bharu, Kelantan, Malaysia
| | - A Fadillah
- Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Acarology Unit, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170, Shah Alam, Selangor, Malaysia
| | - J Canedy
- Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Acarology Unit, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170, Shah Alam, Selangor, Malaysia
| | - A Mariana
- Infectious Diseases Research Centre, Institute for Medical Research (IMR), National Institutes of Health, Ministry of Health Malaysia, Acarology Unit, Jalan Setia Murni U13/52, Seksyen U13, Setia Alam, 40170, Shah Alam, Selangor, Malaysia
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Roumia AF, Tsirigos KD, Theodoropoulou MC, Tamposis IA, Hamodrakas SJ, Bagos PG. OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:646581. [PMID: 36303794 PMCID: PMC9581022 DOI: 10.3389/fbinf.2021.646581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families. The database has been updated continuously using a collection of characteristic profile Hidden Markov Models able to discriminate between the different families of prokaryotic transmembrane β-barrels. The number of families has increased ultimately to a total of 129 families in the current, second major version of OMPdb. New additions have been made in parallel with efforts to update existing families and add novel families. Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.
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Affiliation(s)
- Ahmed F. Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | | | - Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- *Correspondence: Pantelis G. Bagos
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Jiang J, Farris CM, Yeh KB, Richards AL. International Rickettsia Disease Surveillance: An Example of Cooperative Research to Increase Laboratory Capability and Capacity for Risk Assessment of Rickettsial Outbreaks Worldwide. Front Med (Lausanne) 2021; 8:622015. [PMID: 33738293 PMCID: PMC7960665 DOI: 10.3389/fmed.2021.622015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
Cooperative research that addresses infectious disease surveillance and outbreak investigations relies heavily on availability and effective use of appropriate diagnostic tools, including serological and molecular assays, as exemplified by the current COVID-19 pandemic. In this paper, we stress the importance of using these assays to support collaborative epidemiological studies to assess risk of rickettsial disease outbreaks among international partner countries. Workforce development, mentorship, and training are important components in building laboratory capability and capacity to assess risk of and mitigate emerging disease outbreaks. International partnerships that fund cooperative research through mentoring and on-the-job training are successful examples for enhancing infectious disease surveillance. Cooperative research studies between the Naval Medical Research Center's Rickettsial Diseases Research Program (RDRP) and 17 institutes from nine countries among five continents were conducted to address the presence of and the risk for endemic rickettsial diseases. To establish serological and molecular assays in the collaborative institutes, initial training and continued material, and technical support were provided by RDRP. The laboratory methods used in the research studies to detect and identify the rickettsial infections included (1) group-specific IgM and IgG serological assays and (2) molecular assays. Twenty-six cooperative research projects performed between 2008 and 2020 enhanced the capability and capacity of 17 research institutes to estimate risk of rickettsial diseases. These international collaborative studies have led to the recognition and/or confirmation of rickettsial diseases within each of the partner countries. In addition, with the identification of specific pathogen and non-pathogen Rickettsia species, a more accurate risk assessment could be made in surveillance studies using environmental samples. The discoveries from these projects reinforced international cooperation benefiting not only the partner countries but also the scientific community at large through presentations (n = 40) at international scientific meetings and peer-reviewed publications (n = 18). The cooperative research studies conducted in multiple international institutes led to the incorporation of new SOPs and trainings for laboratory procedures; biosafety, biosurety, and biosecurity methods; performance of rickettsia-specific assays; and the identification of known and unknown rickettsial agents through the introduction of new serologic and molecular assays that complemented traditional microbiology methods.
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Affiliation(s)
- Ju Jiang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Christina M. Farris
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD, United States
| | | | - Allen L. Richards
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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Richards AL, Jiang J. Scrub Typhus: Historic Perspective and Current Status of the Worldwide Presence of Orientia Species. Trop Med Infect Dis 2020; 5:E49. [PMID: 32244598 PMCID: PMC7344502 DOI: 10.3390/tropicalmed5020049] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Scrub typhus and its etiological agents, Orientia species, have been around for a very long time. Historical reference to the rickettsial disease scrub typhus was first described in China (313 AD) by Hong Ge in a clinical manual (Zhouhofang) and in Japan (1810 AD) when Hakuju Hashimoto described tsutsuga, a noxious harmful disease in the Niigata prefecture. Other clinicians and scientists in Indonesia, Philippines, Taiwan, Australia, Vietnam, Malaysia, and India reported on diseases most likely to have been scrub typhus in the early 1900s. All of these initial reports about scrub typhus were from an area later designated as the Tsutsugamushi Triangle-an area encompassing Pakistan to the northwest, Japan to the northeast and northern Australia to the south. It was not until the 21st century that endemic scrub typhus occurring outside of the Tsutsugamushi Triangle was considered acceptable. This report describes the early history of scrub typhus, its distribution in and outside the Tsutsugamushi Triangle, and current knowledge of the causative agents, Orientia species.
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Affiliation(s)
- Allen L. Richards
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Ju Jiang
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA;
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