1
|
Lu H, Li J, Fan R, Hao G, Sun M, Liang Y. First laboratory-confirmed case of scrub typhus in Shijiazhuang City, Hebei Province. Front Microbiol 2024; 15:1409949. [PMID: 38855771 PMCID: PMC11157097 DOI: 10.3389/fmicb.2024.1409949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/14/2024] [Indexed: 06/11/2024] Open
Abstract
Objective Defining whether a suspected case was due to scrub typhus through laboratory testing, to understand the prevalence of scrub typhus in Shijiazhuang City, Hebei Province. Methods An epidemiological investigation was conducted on the suspected case, utilizing Weil-Felix test and indirect immunofluorescence assay (IFA) to detect specific antibodies against O. tsutsugamushi in serum specimens. Additionally, PCR amplification of the 56-kDa and groEL genes was performed, followed by constructing a phylogenetic tree to identify the genotype. Results The acute phase titer of the Weil-Felix test for the case was 1:160, which increased to 1:320 in the recovery phase. IFA assay revealed IgG titers against O. tsutsugamushi of 1:64 in the acute phase and 1:256 in the recovery phase. Sequence alignment of the PCR amplified fragment showed the highest similarity with the O. tsutsugamushi genotype. Kawasaki sequence, ranging from 99.71 to 100.00%. The strain exhibited the closest genetic relationship with the known O. tsutsugamushi Kawasaki genotype. Conclusion This study confirms the presence of O. tsutsugamushi in Shijiazhuang City, Hebei Province, with the identified strain belonging to the Kawasaki genotype, marking the first diagnosis of this strain in the region.
Collapse
Affiliation(s)
- Huixiu Lu
- Department of Dermatology, Shijiazhuang People’s Hospital, Shijiazhuang City, Hebei, China
| | - Jianying Li
- Department of Dermatology, Shijiazhuang People’s Hospital, Shijiazhuang City, Hebei, China
| | - Rong Fan
- Department of Laboratory Medicine, Shijiazhuang People’s Hospital, Shijiazhuang City, Hebei, China
| | - Gaoyuan Hao
- Department of Dermatology, Shijiazhuang People’s Hospital, Shijiazhuang City, Hebei, China
| | - Meilan Sun
- Department of Dermatology, Shijiazhuang People’s Hospital, Shijiazhuang City, Hebei, China
| | - Yunchuan Liang
- Department of Dermatology, Shijiazhuang People’s Hospital, Shijiazhuang City, Hebei, China
| |
Collapse
|
2
|
Alkathiry HA, Alghamdi SQ, Sinha A, Margos G, Stekolnikov AA, Alagaili AN, Darby AC, Makepeace BL, Khoo JJ. Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia. BMC Genomics 2024; 25:380. [PMID: 38632506 PMCID: PMC11025265 DOI: 10.1186/s12864-024-10301-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear. RESULTS Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin. CONCLUSIONS P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.
Collapse
Affiliation(s)
- Hadil A Alkathiry
- Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Samia Q Alghamdi
- Department of Biology, Faculty of Science, Al-Baha University, P.O.Box1988, Al-Baha, 65799, Saudi Arabia
| | - Amit Sinha
- New England Biolabs, Ipswich, Massachusetts, 01938, USA
| | - Gabriele Margos
- National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Veterinärstr. 2, Oberschleissheim, 85764, Germany
| | - Alexandr A Stekolnikov
- Laboratory of Parasitic Arthropods, Zoological Institute of the Russian Academy of Sciences, Universitetskaya embankment 1, St. Petersburg, 199034, Russia
| | | | - Alistair C Darby
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Benjamin L Makepeace
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Jing Jing Khoo
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Govindarajan R, Sankar SG, Kumar MS, Rajamannar V, Krishnamoorthi R, Anand AAP, Kumar A, Samuel PP. Molecular detection of Orientia tsutsugamushi in ectoparasites & their small mammal hosts captured from scrub typhus endemic areas in Madurai district, India. Indian J Med Res 2024; 159:180-192. [PMID: 38494626 PMCID: PMC11050748 DOI: 10.4103/ijmr.ijmr_3530_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND OBJECTIVES Scrub typhus, caused by Orientia tsutsugamushi present in small mammals harbouring the ectoparasites. A study was undertaken to detect the pathogen present in small mammals and its ectoparasites in the scrub typhus-reported areas. METHODS The small mammals (rodents/shrews) and its ectoparasites were screened for O. tsutsugamushi using nested PCR amplification of the groEL gene. Small mammals were collected by trapping and screened for ectoparasites (mites, ticks and fleas) by combing method. RESULTS All the chigger mites collected were tested negative for O. tsutsugamushi . Interestingly, adult non-trombiculid mites ( Oribatida sp., Dermanyssus gallinae ), fleas ( Xenopsylla astia, X. cheopis, Ctenophalides felis and Ctenophalides sp.) and ticks ( Rhipicephalus sanguineus , R. haemaphysaloides ) screened were found to be positive for O. tsutsugamushi , which the authors believe is the first report on these species globally. Bandicota bengalensis with O. tsutsugamushi infection is reported for the first time in India. The O. tsutsugamushi groEL sequences from the positive samples were similar to the reference strains, Karp and Ikeda and phylogenetically clustered in clade IV with less evolutionary divergence. The blood samples of Rattus rattus , Suncus murinus and B. bengalensis collected from this area were tested positive for O. tsutsugamushi ; interestingly, the sequence similarity was much pronounced with their ectoparasites indicating the transmission of the pathogen to host or vice versa . INTERPRETATION CONCLUSIONS The outcome of the present investigations widened our scope on the pathogens present in ectoparasites and rodents/shrews from this area. This will help to formulate the required vector control methods to combat zoonotic diseases.
Collapse
Affiliation(s)
- R. Govindarajan
- Division of Vector Borne Zoonotic Diseases, ICMR-Vector Control Research Centre Field Station, Madurai, Tamil Nadu, India
| | - S. Gowri Sankar
- Division of Vector Borne Zoonotic Diseases, ICMR-Vector Control Research Centre Field Station, Madurai, Tamil Nadu, India
| | - M. Senthil Kumar
- Division of Vector Borne Zoonotic Diseases, ICMR-Vector Control Research Centre Field Station, Madurai, Tamil Nadu, India
| | - V. Rajamannar
- Division of Vector Borne Zoonotic Diseases, ICMR-Vector Control Research Centre Field Station, Madurai, Tamil Nadu, India
| | | | | | - Ashwani Kumar
- ICMR-Vector Control Research Centre, Puducherry, India
| | - P. Philip Samuel
- Division of Vector Borne Zoonotic Diseases, ICMR-Vector Control Research Centre Field Station, Madurai, Tamil Nadu, India
| |
Collapse
|
5
|
Thiriot JD, Liang Y, Gonzales C, Sun J, Yu X, Soong L. Differential cellular immune responses against Orientia tsutsugamushi Karp and Gilliam strains following acute infection in mice. PLoS Negl Trop Dis 2023; 17:e0011445. [PMID: 38091346 PMCID: PMC10752558 DOI: 10.1371/journal.pntd.0011445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/27/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023] Open
Abstract
Scrub typhus is a leading cause of febrile illness in endemic countries due to infection with Orientia tsutsugamushi (Ot), a seriously understudied intracellular bacterium. Pulmonary involvement associated with vascular parasitism in patients is common and can develop into life threatening interstitial pneumonia. The diverse antigenicity of Ot genotypes and inter-strain differences in genome content are connected to varied virulence and clinical outcomes; however, detailed studies of strain-related pulmonary immune responses in human patients or small animal models of infection are lacking. In this study, we have used two clinically prevalent bacterial strains (Karp and Gilliam) to reveal cellular immune responses in inflamed lungs and potential biomarkers of disease severity. The results demonstrate that outbred CD-1 mice are highly susceptible to both Karp and Gilliam strains; however, C57BL/6 (B6) mice were susceptible to Karp, but resistant to Gilliam (with self-limiting infection), corresponding to their tissue bacterial burdens and lung pathological changes. Multicolor flow cytometric analyses of perfused B6 mouse lungs revealed robust and sustained influx and activation of innate immune cells (macrophages, neutrophils, and NK cells), followed by CD4+ and CD8+ T cells, during Karp infection, but such responses were greatly attenuated during Gilliam infection. The robust cellular responses in Karp-infected B6 mice positively correlated with significantly early and high levels of serum cytokine/chemokine protein levels (CXCL1, CCL2/3/5, and G-CSF), as well as pulmonary gene expression (Cxcl1/2, Ccl2/3/4, and Ifng). In vitro infection of B6 mouse-derived primary macrophages also revealed bacterial strain-dependent immune gene expression profiles. This study provided the lines of evidence that highlighted differential tissue cellular responses against Karp vs. Gilliam infection, offering a framework for future investigation of Ot strain-related mechanisms of disease pathogenesis vs. infection control.
Collapse
Affiliation(s)
- Joseph D. Thiriot
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yuejin Liang
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Casey Gonzales
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jiaren Sun
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Xiaoying Yu
- Department of Biostatistics & Data Science, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Lynn Soong
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| |
Collapse
|
6
|
Panda S, Swain SK, Sahu BP, Sarangi R. Insights into genome plasticity and gene regulation in Orientia tsutsugamushi through genome-wide mining of microsatellite markers. 3 Biotech 2023; 13:366. [PMID: 37840877 PMCID: PMC10575825 DOI: 10.1007/s13205-023-03795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Microsatellite markers are being used for molecular identification and characterization as well as estimation of evolution patterns due to their highly polymorphic nature. The repeats hold 40% of the entire genome of Orientia tsutsugamushi (OT), but not yet been characterized. Thus, we investigated the genome-wide presence of microsatellites within nine complete genomes of OT and analyzed their distribution pattern, composition, and complexity. The in-silico study revealed that the genome of OT enriched with microsatellites having a total of 126,187 SSRs and 10,374 cSSRs throughout the genome, of which 70% and 30% are represented within the coding and non-coding regions, respectively. The relative density (RD) and relative abundance (RA) of SSRs were 42-44.43/kb and 6.25-6.59/kb, while for cSSRs this value ranged from 7.06 to 8.1/kb and 0.50 to 0.55/kb, respectively. However, RA and RD were weakly correlated with genome size and incidence of microsatellites. The mononucleotide repeats (54.55%) were prevalent over di- (33.22%), tri- (11.88%), tetra- (0.27%), penta- (0.02%), hexanucleotide (0.04%) repeats, with poly (A/T) richness over poly (G/C). The motif composition of cSSRs revealed that maximum cSSRs were made up of two microsatellites having unique duplication patterns such as AT-x-AT and CG-x-CG. To our knowledge, this is the first study of microsatellites in the OT genome, where characterization of such variations in repeat sequences would be important in deciphering the origin, rate of mutation, and role of repeat sequences in the genome. More numbers of microsatellites represented within the coding region provide an insight into the genome plasticity that may interfere with gene regulation to mitigate host-pathogen interaction and evolution of the species.
Collapse
Affiliation(s)
- Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Subrat Kumar Swain
- Medical Research Laboratory, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Basanta Pravas Sahu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| |
Collapse
|
7
|
Fisher DJ, Beare PA. Recent advances in genetic systems in obligate intracellular human-pathogenic bacteria. Front Cell Infect Microbiol 2023; 13:1202245. [PMID: 37404720 PMCID: PMC10315504 DOI: 10.3389/fcimb.2023.1202245] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/22/2023] [Indexed: 07/06/2023] Open
Abstract
The ability to genetically manipulate a pathogen is fundamental to discovering factors governing host-pathogen interactions at the molecular level and is critical for devising treatment and prevention strategies. While the genetic "toolbox" for many important bacterial pathogens is extensive, approaches for modifying obligate intracellular bacterial pathogens were classically limited due in part to the uniqueness of their obligatory lifestyles. Many researchers have confronted these challenges over the past two and a half decades leading to the development of multiple approaches to construct plasmid-bearing recombinant strains and chromosomal gene inactivation and deletion mutants, along with gene-silencing methods enabling the study of essential genes. This review will highlight seminal genetic achievements and recent developments (past 5 years) for Anaplasma spp., Rickettsia spp., Chlamydia spp., and Coxiella burnetii including progress being made for the still intractable Orientia tsutsugamushi. Alongside commentary of the strengths and weaknesses of the various approaches, future research directions will be discussed to include methods for C. burnetii that should have utility in the other obligate intracellular bacteria. Collectively, the future appears bright for unraveling the molecular pathogenic mechanisms of these significant pathogens.
Collapse
Affiliation(s)
- Derek J. Fisher
- School of Biological Sciences, Southern Illinois University, Carbondale, IL, United States
| | - Paul A. Beare
- Rocky Mountain Laboratory, National Institute of Health, Hamilton, MT, United States
| |
Collapse
|
8
|
Gillespie JJ, Salje J. Orientia and Rickettsia: different flowers from the same garden. Curr Opin Microbiol 2023; 74:102318. [PMID: 37080115 DOI: 10.1016/j.mib.2023.102318] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/22/2023]
Abstract
Recent discoveries of basal extracellular Rickettsiales have illuminated divergent evolutionary paths to host dependency in later-evolving lineages. Family Rickettsiaceae, primarily comprised of numerous protist- and invertebrate-associated species, also includes human pathogens from two genera, Orientia and Rickettsia. Once considered sister taxa, these bacteria form distinct lineages with newly appreciated lifestyles and morphological traits. Contrasting other rickettsial human pathogens in Family Anaplasmataceae, Orientia and Rickettsia species do not reside in host-derived vacuoles and lack glycolytic potential. With only a few described mechanisms, strategies for commandeering host glycolysis to support cytosolic growth remain to be discovered. While regulatory systems for this unique mode of intracellular parasitism are unclear, conjugative transposons unique to Orientia and Rickettsia species provide insights that are critical for determining how these obligate intracellular pathogens overtake eukaryotic cytosol.
Collapse
Affiliation(s)
- Joseph J Gillespie
- Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, USA.
| | - Jeanne Salje
- Department of Biochemistry, Department of Pathology, and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
| |
Collapse
|
9
|
Multiple Orientia clusters and Th1-skewed chemokine profile: a cross-sectional study in patients with scrub typhus from Nepal. Int J Infect Dis 2023; 128:78-87. [PMID: 36566774 DOI: 10.1016/j.ijid.2022.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Scrub typhus is an emerging infectious disease in Asia caused by Orientia tsutsugamushi (Ot). From Nepal, only scant data on the genetic epidemiology of this agent is available, and determinants of immunoregulation are poorly understood. METHODS Patients (n = 238) referred to the National Public Health Laboratory (Kathmandu, Nepal) from all over Nepal for suspected scrub typhus were enrolled upon positive immunoglobulin (Ig)M testing between July and October 2015. From Ot 16S and 47 kD polymerase chain reaction (PCR)-positive samples, the variable domain I of the 56 kD gene was sequenced and phylogenetically analyzed. T helper (Th) cell-associated cytokines (n = 13) and chemokines (n = 12) were quantified by multiplex bead arrays. RESULTS In 93/238 (39.1%) IgM-positive samples, Ot DNA was detected by quantitative PCR. Phylogenetic analysis of 56 kD sequences revealed seven distinct clusters, six of them with high homologies to strains detected in other countries. The Th1-related cytokines interferon-γ and C-X-C motif chemokine ligand 10 were strongly upregulated and correlated with bacteremia, while levels of Th2-associated chemokines were reduced. Bacteremia also correlated with concentrations of interleukin (IL)-6 and IL-10 but not tumor necrosis factor-α. CONCLUSION We identified a considerable genetic heterogeneity of human-pathogenic Ot strains circulating in Nepal. Acute Nepalese scrub typhus patients showed strong Th1 but impaired Th2 responses, especially on the chemokine level.
Collapse
|
10
|
Ali A, Waris A, Khan MA, Asim M, Khan AU, Khan S, Zeb J. Recent advancement, immune responses, and mechanism of action of various vaccines against intracellular bacterial infections. Life Sci 2023; 314:121332. [PMID: 36584914 DOI: 10.1016/j.lfs.2022.121332] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Emerging and re-emerging bacterial infections are a serious threat to human and animal health. Extracellular bacteria are free-living, while facultative intracellular bacteria replicate inside eukaryotic host cells. Many serious human illnesses are now known to be caused by intracellular bacteria such as Salmonella enterica, Escherichia coli, Staphylococcus aureus, Rickettsia massiliae, Chlamydia species, Brucella abortus, Mycobacterium tuberculosis and Listeria monocytogenes, which result in substantial morbidity and mortality. Pathogens like Mycobacterium, Brucella, MRSA, Shigella, Listeria, and Salmonella can infiltrate and persist in mammalian host cells, particularly macrophages, where they proliferate and establish a repository, resulting in chronic and recurrent infections. The current treatment for these bacteria involves the application of narrow-spectrum antibiotics. FDA-approved vaccines against obligate intracellular bacterial infections are lacking. The development of vaccines against intracellular pathogenic bacteria are more difficult because host defense against these bacteria requires the activation of the cell-mediated pathway of the immune system, such as CD8+ T and CD4+ T. However, different types of vaccines, including live, attenuated, subunit, killed whole cell, nano-based and DNA vaccines are currently in clinical trials. Substantial development has been made in various vaccine strategies against intracellular pathogenic bacteria. This review focuses on the mechanism of intracellular bacterial infection, host immune response, and recent advancements in vaccine development strategies against various obligate intracellular bacterial infections.
Collapse
Affiliation(s)
- Asmat Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong.
| | - Muhammad Ajmal Khan
- Division of Life Sciences, Center for Cancer Research and State Key Laboratory of Molecular Neurosciences, The Hong Kong University of Science and Technology, Hong Kong
| | - Muhammad Asim
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong
| | - Atta Ullah Khan
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China
| | - Sahrish Khan
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jehan Zeb
- Department of Infectious Diseases and Public Health, City University of Hong Kong, Hong Kong
| |
Collapse
|
11
|
Panda S, Swain SK, Sahu BP, Sarangi R. Gene expression and involvement of signaling pathways during host-pathogen interplay in Orientia tsutsugamushi infection. 3 Biotech 2022; 12:180. [PMID: 35860421 PMCID: PMC9295102 DOI: 10.1007/s13205-022-03239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/18/2022] [Indexed: 11/22/2022] Open
Abstract
Scrub typhus is a neglected tropical disease that affects one-third of the world’s population. The disease is caused by Orientia tsutsugamushi (OT), an obligate intracellular Gram-negative bacterium. OT efficiently escapes from the endosomal pathway after entering the host cell and replicates inside cytosol. OT infection promotes cellular autophagy, the autonomous defense mechanism unlike other bacteria. This study has discussed the bacterial invasion process through the extracellular matrix and the immune response activated by the bacterium within the hosts. Furthermore, we have emphasized the importance of extracellular matrix and their cross-talk with the immune cells, such as, macrophages, neutrophils, and dendritic cells followed by their inflammatory response. We have also put an insight into the host factors associated with signaling pathways during scrub typhus disease with a special focus on the OT-induced stress response, autophagy, apoptosis, and innate immunity. Multiple cytokines and chemokines play a significant role in activating different immune-related signaling pathways. Due to the presence of high antigenic diversity among strains, the signaling pathways during the host–pathogen interplay of OT with its host is very complicated. Thus, it hinders to mitigate the severity of the pandemic occurred by the respective pathogen. Our investigation will provide a useful guide to better understand the virulence and physiology of this intracellular pathogen which will lead towards a better therapeutic diagnosis and vaccine development.
Collapse
Affiliation(s)
- Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha 'O' Anusandhan Deemed to be University, K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Subrat Kumar Swain
- Centre for Genomics and Biomedical Informatics, IMS and SUM Hospital, Siksha 'O' Anusandhan Deemed to be University, K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Basanta Pravas Sahu
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552 India
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha 'O' Anusandhan Deemed to be University, K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| |
Collapse
|
12
|
Atwal S, Wongsantichon J, Giengkam S, Saharat K, Pittayasathornthun YJ, Chuenklin S, Wang LC, Chung T, Huh H, Lee SH, Sobota RM, Salje J. The obligate intracellular bacterium Orientia tsutsugamushi differentiates into a developmentally distinct extracellular state. Nat Commun 2022; 13:3603. [PMID: 35739103 PMCID: PMC9226355 DOI: 10.1038/s41467-022-31176-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Orientia tsutsugamushi (Ot) is an obligate intracellular bacterium in the family Rickettsiaceae that causes scrub typhus, a severe mite-borne human disease. Its mechanism of cell exit is unusual amongst Rickettsiaceae, as Ot buds off the surface of infected cells enveloped in plasma membrane. Here, we show that Ot bacteria that have budded out of host cells are in a distinct developmental stage compared with intracellular bacteria. We refer to these two stages as intracellular and extracellular bacteria (IB and EB, respectively). These two forms differ in physical properties: IB is both round and elongated, and EB is round. Additionally, IB has higher levels of peptidoglycan and is physically robust compared with EB. The two bacterial forms differentially express proteins involved in bacterial physiology and host-pathogen interactions, specifically those involved in bacterial dormancy and stress response, and outer membrane autotransporter proteins ScaA and ScaC. Whilst both populations are infectious, entry of IB Ot is sensitive to inhibitors of both clathrin-mediated endocytosis and macropinocytosis, whereas entry of EB Ot is only sensitive to a macropinocytosis inhibitor. Our identification and detailed characterization of two developmental forms of Ot significantly advances our understanding of the intracellular lifecycle of an important human pathogen. Orientia tsutsugamushi (Ot) the causing agent of scrub typhus exits infected cells using a unique mechanism that involves budding off the surface of infected cells. Here, Atwal et al. report that Ots that have budded from their host cells are in a distinct developmental stage than intracellular bacteria and provide the first characterization of this extracellular stage. Both forms are infectious but differ in their physical properties, proteome, and entry mechanism into host cells.
Collapse
Affiliation(s)
- Sharanjeet Atwal
- Public Health Research Institute, Rutgers the State University of New Jersey, Newark, NJ, USA
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Suparat Giengkam
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kittirat Saharat
- Public Health Research Institute, Rutgers the State University of New Jersey, Newark, NJ, USA
| | | | - Suthida Chuenklin
- Public Health Research Institute, Rutgers the State University of New Jersey, Newark, NJ, USA.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Loo Chien Wang
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,SingMass-National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Taerin Chung
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA
| | - Hyun Huh
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA
| | - Sang-Hyuk Lee
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA.,Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, USA
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,SingMass-National Mass Spectrometry Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jeanne Salje
- Public Health Research Institute, Rutgers the State University of New Jersey, Newark, NJ, USA. .,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
13
|
Swain SK, Sahu BP, Panda S, Sarangi R. Molecular characterization and evolutionary analysis of Orientia tsutsugamushi in eastern Indian population. Arch Microbiol 2022; 204:221. [PMID: 35338394 PMCID: PMC8956147 DOI: 10.1007/s00203-022-02823-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 01/13/2023]
Abstract
Scrub typhus is a bacterial zoonotic acute febrile illness (AFI) caused by the obligate intracellular bacterium Orientia tsutsugamushi, which is an antigenically diverse strain frequently observed in the tropical region of Southeast Asian countries. The recent investigation was conducted to delineate the genotype identification of Orientia tsutsugamushi predominating in the eastern zone of India such as Odisha to decipher its strain type, and evaluate its diversity as well as evolutionary pattern based on the nucleotide analysis of the immune dominant 56 KDa gene. During this study, we have investigated 100 clinical samples (2014-2018), out of which 28 were positive for scrub typhus followed by its molecular characterization and phylogenetic analysis utilizing 56 KDa partial genes. Population genetic parameters showed the presence of 287 polymorphic sites within the analyzed 56 KDa gene. The gene diversity (Hd) and sequence diversity (π) was estimated 0.638 and 0.280, respectively. Selection pressure analysis (θ = dN/dS) having the value 0.222 suggests that the gene lied under purifying selection. The present study suggested a high rate of genetic diversity within the isolates. This research study sheds light on the hereditary and evolutionary relationships of Orientia strains found in the eastern Indian population. Understanding regional genetic variation is critical for vaccine development and sero-diagnostics methods. A significant level of genetic variability was observed during this study. This information has a way to understand more about antigen diversity that leads to develop an effective vaccine candidate for this pathogen.
Collapse
Affiliation(s)
- Subrat Kumar Swain
- Department of Pediatrics, IMS and SUM Hospital, Siksha "O" Anusandhan Deemed to be University, Bhubaneswar, Odisha, 751003, India
| | - Basanta Pravas Sahu
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India
| | - Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha "O" Anusandhan Deemed to be University, Bhubaneswar, Odisha, 751003, India
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha "O" Anusandhan Deemed to be University, Bhubaneswar, Odisha, 751003, India.
| |
Collapse
|
14
|
Basharat Z, Akhtar U, Khan K, Alotaibi G, Jalal K, Abbas MN, Hayat A, Ahmad D, Hassan SS. Differential analysis of Orientia tsutsugamushi genomes for therapeutic target identification and possible intervention through natural product inhibitor screening. Comput Biol Med 2022; 141:105165. [PMID: 34973586 DOI: 10.1016/j.compbiomed.2021.105165] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022]
Abstract
Orientia tsutsugamushi (Ott) is a causative agent of scrub typhus, and one of the emerging pathogens that could affect a large human population. It is one of the misdiagnosed and under-reported, febrile illnesses that infects various body organs (skin, heart, lung, kidney, and brain). The control of this infection is hampered due to the lack of drugs or vaccine against it. This study was undertaken to identify potential drug targets from the core genome of Ott and investigate novel natural product inhibitors against them. Hence, the available genomes for 22 strains of Ott were downloaded from the PATRIC database, and pan-genomic analysis was performed. Only 202 genes were present in the core region. Among these, 94 were identified as essential, 32 non-homologous to humans, nine non-homologous to useful gut flora and a single gene dapD as a drug target. Product of this gene (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase) was modeled and docked against traditional Indian (Ayurvedic) and Chinese phytochemical libraries, with best hits selected for docking, based on multiple target-drug/s interactions and minimum energy scores. ADMET profiling and molecular dynamics simulation was performed for top three compounds from each library to assess the toxicity and stability, respectively. We presume that these compounds (ZINC8214635, ZINC32793028, ZINC08101133, ZINC85625167, ZINC06018678, and ZINC13377938) could be successful inhibitors of Ott. However, in-depth experimental and clinical research is needed for further validation.
Collapse
Affiliation(s)
- Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Umaima Akhtar
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi, 75270, Pakistan
| | - Ghallab Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Al-Dawadmi Campus, Shaqra University, Shaqra, 15571, Saudi Arabia
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Science University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Naseer Abbas
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Pakistan
| | - Ajmal Hayat
- Department of Pharmacy, Abdul Wali Khan University Mardan, 23200, Khyber Pakhtunkhwa, Pakistan
| | - Diyar Ahmad
- HEJ Research Institute of Chemistry International Center for Chemical and Biological Science University of Karachi, Karachi, 75270, Pakistan
| | - Syed Shah Hassan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| |
Collapse
|
15
|
Sharma D, Sharma A, Singh B, Kumar S, Verma S. Neglected scrub typhus: An updated review with a focus on omics technologies. ASIAN PAC J TROP MED 2022. [DOI: 10.4103/1995-7645.364003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
16
|
Hayashi T. [Genome analysis-based studies on bacterial genetic diversity]. Nihon Saikingaku Zasshi 2022; 77:145-160. [PMID: 36418109 DOI: 10.3412/jsb.77.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
There are a huge number of bacterial species on earth, and a huge intra-species genomic diversity are also observed in many bacteria. The high ability of bacteria to acquire foreign DNA and the presence of various mobile genetic elements contribute the generation of such genomic diversity. During the biochemical and genetic analysis of a Pseudomonas aeruginosa toxin, called cytotoxin, and its converting phage, which I first engaged in my research carrier, I became very interested in the genetic diversity of bacteria and mobile genetic elements such as bacteriophages, and realized the usefulness and power of genome analysis. Since then, I have been involved in genome analyses of various pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC), commensal bacteria of human and other animals, and bacteria or bacterial communities in natural environments. I was so lucky that I jumped in this research field at the very begging of genome analyses and experienced a very exciting time of surprisingly rapid advance in genome sequencing technologies which revolutionized a wide range of biology. In this article, I first review the main findings which our group obtained from the genome analyses on the P. aeruginosa cytotoxin converting phage and those on the evolution and genomic diversity of EHEC and related bacteria. The results of our analyses of Rickettsiaceae family genomes, which show surprisingly very low genomic diversity, and genome sequence-based analyses of an intrahospital bacterial outbreak and within-host genomic diversity are also summarized.
Collapse
Affiliation(s)
- Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| |
Collapse
|
17
|
Schmidt WP, Devamani CS, Elangovan D, Alexander N, Rose W, Prakash JAJ. Clinical characteristics of and antibody response to spotted fever group rickettsial infections in South India: Case series and serological cohort study. Trop Med Int Health 2021; 26:1616-1623. [PMID: 34597443 DOI: 10.1111/tmi.13682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The clinical and serological characteristics of spotted fever group rickettsial (SFGR) infections in South Asia are poorly understood. We studied the clinical presentation and the IgM/IgG response in cases enrolled at two health care centres in South India. METHOD We enrolled 77 patients. Fifty-seven of these patients were recruited at a tertiary care centre, the remaining 20 at a community hospital (secondary care level). Diagnostic tests included IgM and IgG enzyme-linked immunosorbent assay and polymerase chain reaction. Over a period of 1 year, 41 cases were followed up for repeated sero-analysis. RESULTS Median age was 9 years (range 1-79). A rash was present in 74% of cases (57/77). In cases aged <15 years, rash was present in 94% (44/47) vs. 43% (13/30) in cases aged ≥15 years. An eschar was found in two cases (3%). Severe infection or complications occurred in 10 cases (13%). These included central nervous system infection (6/77, 8%), kidney injury (3/77, 4%), shock (3/77, 4%), lung involvement (2/77, 3%) and peripheral gangrene (2/77, 3%). IgM antibody levels increased faster after fever onset than IgG antibodies, peaking at 50 and 60 days, respectively. After the peak, IgM and IgG levels showed a slow decline over one year with less than 50% of cases showing persistent IgG antibody levels. CONCLUSION Spotted fever group rickettsial infections in South India may be under-diagnosed, as many cases may not develop a rash. The proportion of cases developing severe infection seems lower than for scrub typhus in this region. IgG seroprevalence may substantially underestimate the proportion in a population with past SFGR infection.
Collapse
Affiliation(s)
- Wolf-Peter Schmidt
- Department of Emergency Medicine, Christian Medical College, Vellore, India.,Department for Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - Carol S Devamani
- Rural Unit for Health & Social Affairs, Christian Medical College, Vellore, India
| | - Divyaa Elangovan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Neal Alexander
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Winsley Rose
- Department of Pediatrics and Pediatric Infectious Diseases, Christian Medical College, Vellore, India
| | - John A J Prakash
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| |
Collapse
|
18
|
Elliott I, Thangnimitchok N, de Cesare M, Linsuwanon P, Paris DH, Day NPJ, Newton PN, Bowden R, Batty EM. Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans. INFECTION GENETICS AND EVOLUTION 2021; 91:104818. [PMID: 33771726 PMCID: PMC8164161 DOI: 10.1016/j.meegid.2021.104818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
Abstract
Scrub typhus is a febrile disease caused by Orientia tsutsugamushi, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of O. tsutsugamushi in chiggers, small mammals and humans remains poorly understood. To combat the limitations imposed by the low relative quantities of pathogen DNA in typical O. tsutsugamushi clinical and ecological samples, along with the technical, safety and cost limitations of cell culture, a novel probe-based target enrichment sequencing protocol was developed. The method was designed to capture variation among conserved genes and facilitate phylogenomic analysis at the scale of population samples. A whole-genome amplification step was incorporated to enhance the efficiency of sequencing by reducing duplication rates. This resulted in on-target capture rates of up to 93% for a diverse set of human, chigger, and rodent samples, with the greatest success rate in samples with real-time PCR Ct values below 35. Analysis of the best-performing samples revealed phylogeographic clustering at local, provincial and international scales. Applying the methodology to a comprehensive set of samples could yield a more complete understanding of the ecology, genomic evolution and population structure of O. tsutsugamushi and other similarly challenging organisms, with potential benefits in the development of diagnostic tests and vaccines.
Collapse
Affiliation(s)
- Ivo Elliott
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Neeranuch Thangnimitchok
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | | | - Piyada Linsuwanon
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Daniel H Paris
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Nicholas P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Division of Advanced Technology and Biology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Elizabeth M Batty
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
19
|
Salje J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat Rev Microbiol 2021; 19:375-390. [PMID: 33564174 DOI: 10.1038/s41579-020-00507-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 01/01/2023]
Abstract
The Rickettsiales are a group of obligate intracellular vector-borne Gram-negative bacteria that include many organisms of clinical and agricultural importance, including Anaplasma spp., Ehrlichia chaffeensis, Wolbachia, Rickettsia spp. and Orientia tsutsugamushi. This Review provides an overview of the current state of knowledge of the biology of these bacteria and their interactions with host cells, with a focus on pathogenic species or those that are otherwise important for human health. This includes a description of rickettsial genomics, bacterial cell biology, the intracellular lifestyles of Rickettsiales and the mechanisms by which they induce and evade the innate immune response.
Collapse
Affiliation(s)
- Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Public Health Research Institute, Rutgers University, Newark, NJ, USA.
| |
Collapse
|
20
|
Leguia M, Vila-Sanjurjo A, Chain PSG, Berry IM, Jarman RG, Pollett S. Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing. J Infect Dis 2021; 221:S289-S291. [PMID: 31751454 DOI: 10.1093/infdis/jiz424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This brief report serves as an introduction to a supplement of the Journal of Infectious Diseases entitled "Next-Generation Sequencing (NGS) Technologies to Advance Global Infectious Disease Research." We briefly discuss the history of NGS technologies and describe how the techniques developed during the past 40 years have impacted our understanding of infectious diseases. Our focus is on the application of NGS in the context of pathogen genomics. Beyond obvious clinical and public health applications, we also discuss the challenges that still remain within this rapidly evolving field.
Collapse
Affiliation(s)
- Mariana Leguia
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú, Lima
| | - Anton Vila-Sanjurjo
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade de A Coruña, Spain
| | | | | | | | - Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics (Uniformed Services University of the Health Sciences), Bethesda, Maryland
| |
Collapse
|
21
|
Driscoll TP, Verhoeve VI, Brockway C, Shrewsberry DL, Plumer M, Sevdalis SE, Beckmann JF, Krueger LM, Macaluso KR, Azad AF, Gillespie JJ. Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas. PeerJ 2020; 8:e10646. [PMID: 33362982 PMCID: PMC7750005 DOI: 10.7717/peerj.10646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.
Collapse
Affiliation(s)
| | - Victoria I Verhoeve
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | | | | | - Mariah Plumer
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Spiridon E Sevdalis
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - John F Beckmann
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Laura M Krueger
- Orange County Mosquito and Vector Control District, Garden Grove, CA, USA
| | - Kevin R Macaluso
- Microbiology and Immunology, University of South Alabama, Mobile, AL, USA
| | - Abdu F Azad
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Joseph J Gillespie
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| |
Collapse
|
22
|
Paris DH, Kelly DJ, Fuerst PA, Day NPJ, Richards AL. A Brief History of the Major Rickettsioses in the Asia-Australia-Pacific Region: A Capstone Review for the Special Issue of TMID. Trop Med Infect Dis 2020; 5:tropicalmed5040165. [PMID: 33121158 PMCID: PMC7709643 DOI: 10.3390/tropicalmed5040165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/19/2022] Open
Abstract
The rickettsioses of the "Far East" or Asia-Australia-Pacific region include but are not limited to endemic typhus, scrub typhus, and more recently, tick typhus or spotted fever. These diseases embody the diversity of rickettsial disease worldwide and allow us to interconnect the various contributions to this special issue of Tropical Medicine and Infectious Disease. The impact of rickettsial diseases-particularly of scrub typhus-was substantial during the wars and "police actions" of the last 80 years. However, the post-World War II arrival of effective antibiotics reduced their impact, when recognized and adequately treated (chloramphenicol and tetracyclines). Presently, however, scrub typhus appears to be emerging and spreading into regions not previously reported. Better diagnostics, or higher population mobility, change in antimicrobial policies, even global warming, have been proposed as possible culprits of this phenomenon. Further, sporadic reports of possible antibiotic resistance have received the attention of clinicians and epidemiologists, raising interest in developing and testing novel diagnostics to facilitate medical diagnosis. We present a brief history of rickettsial diseases, their relative importance within the region, focusing on the so-called "tsutsugamushi triangle", the past and present impact of these diseases within the region, and indicate how historically, these often-confused diseases were ingeniously distinguished from each another. Moreover, we will discuss the importance of DNA-sequencing efforts for Orientia tsutsugamushi, obtained from patient blood, vector chiggers, and rodent reservoirs, particularly for the dominant 56-kD type-specific antigen gene (tsa56), and whole-genome sequences, which are increasing our knowledge of the diversity of this unique agent. We explore and discuss the potential of sequencing and other effective tools to geographically trace rickettsial disease agents, and develop control strategies to better mitigate the rickettsioses.
Collapse
Affiliation(s)
- Daniel H. Paris
- Department of Medicine, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland
- Department of Clinical Research, University of Basel, 4051 Basel, Switzerland
- Correspondence: ; Tel.: +41-61-284-8111
| | - Daryl J. Kelly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA; (D.J.K.); (P.A.F.)
| | - Paul A. Fuerst
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA; (D.J.K.); (P.A.F.)
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Programme, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithee Road, Bangkok 10400, Thailand;
- Center for Tropical Medicine, Nuffield Department of Clinical Medicine, Churchill Hospital, Old Road, Headington, Oxford OX3 7LJ, UK
| | - Allen L. Richards
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA;
| |
Collapse
|
23
|
Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen. Nat Commun 2020; 11:3363. [PMID: 32620750 PMCID: PMC7335160 DOI: 10.1038/s41467-020-17094-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Studying emerging or neglected pathogens is often challenging due to insufficient information and absence of genetic tools. Dual RNA-seq provides insights into host-pathogen interactions, and is particularly informative for intracellular organisms. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium that causes the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning to study the transcriptional architecture of Ot, we find evidence for wide-spread post-transcriptional antisense regulation. Comparing the host response to two clinical isolates, we identify distinct immune response networks for each strain, leading to predictions of relative virulence that are validated in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.
Collapse
|
24
|
Liu Y, Jin X, Wu C, Zhu X, Liu M, Call DR, Zhao Z. Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897. Front Microbiol 2020; 11:1404. [PMID: 32670245 PMCID: PMC7326809 DOI: 10.3389/fmicb.2020.01404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/29/2020] [Indexed: 01/06/2023] Open
Abstract
The genus Vibrio is a genetically and metabolically versatile group of heterotrophic bacteria that are important contributors to carbon cycling within marine and estuarine ecosystems. HN897, a Vibrio strain isolated from the coastal seawater of South China, was shown to be agarolytic and capable of catabolizing D-galactose. Herein, we used Illumina and PacBio sequencing to assemble the whole genome sequence for the strain HN897, which was comprised of two circular chromosomes (Vas1 and Vas2). Genome-wide phylogenetic analysis with 140 other Vibrio sequences firmly placed the strain HN897 into the Marisflavi clade, with Vibrio astriarenae strain C7 being the closest relative. Of all types of carbohydrate-active enzyme classes, glycoside hydrolases (GH) were the most common in the HN897 genome. These included eight GHs identified as putative β-agarases belonging to GH16 and GH50 families in equal proportions. Synteny analysis showed that GH16 and GH50 genes were tandemly arrayed on two different chromosomes consistent with gene duplication. Gene knockout and complementation studies and phenotypic assays confirmed that Vas1_1339, a GH16_16 subfamily gene, exhibits an agarolytic phenotype of the strain. Collectively, these findings explained the agar-decomposing of strain HN897, but also provided valuable resources to gain more detailed insights into the evolution and physiological capability of the strain HN897, which was a presumptive member of the species V. astriarenae.
Collapse
Affiliation(s)
- Yupeng Liu
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Chao Wu
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Xinyuan Zhu
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Min Liu
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Douglas R Call
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, United States
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| |
Collapse
|
25
|
Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, Rodrigues JFM, von Mering C, Pedro Coelho L, Huerta-Cepas J, Sunagawa S, Bork P. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. THE ISME JOURNAL 2020; 14:1247-1259. [PMID: 32047279 PMCID: PMC7174425 DOI: 10.1038/s41396-020-0600-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/04/2022]
Abstract
Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.
Collapse
Affiliation(s)
- Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Daniel R Mende
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Mechthild Luetge
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Institute of Immunobiology, Kantonsspital St. Gallen, 9007, St. Gallen, Switzerland
| | - Falk Hildebrand
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Simone S Li
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - João F Matias Rodrigues
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, CH-8057, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, CH-8057, Zurich, Switzerland
| | - Luis Pedro Coelho
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Jaime Huerta-Cepas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
- Department of Biology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| |
Collapse
|
26
|
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: 24] [Impact Index Per Article: 6.0] [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.
Collapse
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;
| |
Collapse
|
27
|
Wongsantichon J, Jaiyen Y, Dittrich S, Salje J. Orientia tsutsugamushi. Trends Microbiol 2020; 28:780-781. [PMID: 32781029 DOI: 10.1016/j.tim.2020.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/30/2020] [Accepted: 02/24/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yanin Jaiyen
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sabine Dittrich
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jeanne Salje
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Public Health Research Institute, Rutgers University, Newark, NJ, USA; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
28
|
Molina-Mora JA, Campos-Sánchez R, Rodríguez C, Shi L, García F. High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers. Sci Rep 2020; 10:1392. [PMID: 31996747 PMCID: PMC6989561 DOI: 10.1038/s41598-020-58319-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/06/2020] [Indexed: 12/14/2022] Open
Abstract
Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. To assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.
Collapse
Affiliation(s)
- José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Leming Shi
- Human Phenome Institute of Fudan University, Shanghai, China
| | - Fernando García
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| |
Collapse
|
29
|
Sharma D, Sharma A, Singh B, Verma SK. Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi. Front Genet 2019; 10:797. [PMID: 31608099 PMCID: PMC6769048 DOI: 10.3389/fgene.2019.00797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/30/2019] [Indexed: 12/21/2022] Open
Abstract
Metal ions are involved in many essential biological processes and are crucial for the survival of all organisms. Identification of metal-binding proteins (MBPs) of human affecting pathogens may provide the blueprint for understanding biological metal usage and their putative roles in pathogenesis. This study is focused on the analysis of MBPs from Orientia tsutsugamushi (Ott), a causal agent of scrub typhus in humans. A total of 321 proteins were predicted as putative MBPs, based on sequence search and three-dimensional structure analysis. Majority of proteins could bind with magnesium, and the order of metal binding was Mg > Ca > Zn > Mn > Fe > Cd > Ni > Co > Cu, respectively. The predicted MBPs were functionally classified into nine broad classes. Among them, gene expression and regulation, metabolism, cell signaling, and transport classes were dominant. It was noted that the putative MBPs were localized in all subcellular compartments of Ott, but majorly found in the cytoplasm. Additionally, it was revealed that out of 321 predicted MBPs 245 proteins were putative bacterial toxins and among them, 98 proteins were nonhomologous to human proteome. Sixty putative MBPs showed the ability to interact with drug or drug-like molecules, which indicate that they may be used as broad-spectrum drug targets. These predicted MBPs from Ott could play vital role(s) in various cellular activities and virulence, hence may serve as plausible therapeutic targets to design metal-based drugs to curtail its infection.
Collapse
Affiliation(s)
- Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Shailender Kumar Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| |
Collapse
|
30
|
Kelly DJ, Fuerst PA, Richards AL. Origins, Importance and Genetic Stability of the Prototype Strains Gilliam, Karp and Kato of Orientia tsutsugamushi. Trop Med Infect Dis 2019; 4:E75. [PMID: 31052283 PMCID: PMC6631653 DOI: 10.3390/tropicalmed4020075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 11/16/2022] Open
Abstract
Scrub typhus, a chigger-borne febrile illness, occurs primarily in countries of the Asia-Pacific rim and islands of the Western Pacific. The etiologic agent is the obligate intracellular rickettsial bacterium Orientia tsutsugamushi. Research on O. tsutsugamushi has relied on the availability of several prototype strains, which were isolated from human cases of scrub typhus in the 1940s and 1950s. We review the history of the three original, and most important, prototype strains, Gilliam, Karp and Kato, including information on their isolation, their culture history, their clinical characteristics, their importance within the research literature on scrub typhus, and recent advances in elucidating their molecular genomics. The importance of these strains to the research and development of clinical tools related to scrub typhus is also considered. Finally, we examine whether the strains have been genetically stable since their isolation, and whether prototype strains maintained in separate laboratories are identical, based on pairwise comparisons of several sequences from four genes. By using genetic information archived in international DNA databases, we show that the prototype strains used by different laboratories are essentially identical, and that the strains have retained their genetic integrity at least since the 1950s. The three original prototype strains should remain a standard by which new diagnostic procedures are measured. Given their fundamental position in any comparative studies, they are likely to endure as a critical part of present and future research on scrub typhus and Orientia.
Collapse
Affiliation(s)
- Daryl J Kelly
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA, and Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Paul A Fuerst
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Allen L Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA, and Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
| |
Collapse
|
31
|
Lalchhandama K. Orientia tsutsugamushi, the agent of scrub typhus. WIKIJOURNAL OF MEDICINE 2019. [DOI: 10.15347/wjm/2019.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|