1
|
Drews SJ, Kjemtrup AM, Krause PJ, Lambert G, Leiby DA, Lewin A, O'Brien SF, Renaud C, Tonnetti L, Bloch EM. Transfusion-transmitted Babesia spp.: a changing landscape of epidemiology, regulation, and risk mitigation. J Clin Microbiol 2023; 61:e0126822. [PMID: 37750699 PMCID: PMC10595070 DOI: 10.1128/jcm.01268-22] [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] [Indexed: 09/27/2023] Open
Abstract
Babesia spp. are tick-borne parasites with a global distribution and diversity of vertebrate hosts. Over the next several decades, climate change is expected to impact humans, vectors, and vertebrate hosts and change the epidemiology of Babesia. Although humans are dead-end hosts for tick-transmitted Babesia, human-to-human transmission of Babesia spp. from transfusion of red blood cells and whole blood-derived platelet concentrates has been reported. In most patients, transfusion-transmitted Babesia (TTB) results in a moderate-to-severe illness. Currently, in North America, most cases of TTB have been described in the United States. TTB cases outside North America are rare, but case numbers may change over time with increased recognition of babesiosis and as the epidemiology of Babesia is impacted by climate change. Therefore, TTB is a concern of microbiologists working in blood operator settings, as well as in clinical settings where transfusion occurs. Microbiologists play an important role in deploying blood donor screening assays in Babesia endemic regions, identifying changing risks for Babesia in non-endemic areas, investigating recipients of blood products for TTB, and drafting TTB policies and guidelines. In this review, we provide an overview of the clinical presentation and epidemiology of TTB. We identify approaches and technologies to reduce the risk of collecting blood products from Babesia-infected donors and describe how investigations of TTB are undertaken. We also describe how microbiologists in Babesia non-endemic regions can assess for changing risks of TTB and decide when to focus on laboratory-test-based approaches or pathogen reduction to reduce TTB risk.
Collapse
Affiliation(s)
- Steven J. Drews
- Microbiology, Donation Policy and Studies, Canadian Blood Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, Division of Diagnostic and Applied Microbiology, University of Alberta, Edmonton, Alberta, Canada
| | - Anne M. Kjemtrup
- California Department of Public Health, Vector-Borne Disease Section, Sacramento, California, USA
| | - Peter J. Krause
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Yale School of Medicine, New Haven, Connecticut, USA
| | - Grayson Lambert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Yale School of Medicine, New Haven, Connecticut, USA
| | - David A. Leiby
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, USA
| | - Antoine Lewin
- Epidemiology, Surveillance and Biological Risk Assessment, Medical Affairs and Innovation, Héma-Québec, Montréal, Quebec, Canada
- Département d'Obstétrique et de Gynécologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sheila F. O'Brien
- Epidemiology and Surveillance, Canadian Blood Services, Donation Policy and Studies, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Christian Renaud
- Department of Microbiology, CHU Sainte-Justine, Université de Montréal, Montréal, Quebec, Canada
| | - Laura Tonnetti
- American Red Cross, Scientific Affairs, Holland Laboratories for the Biomedical Sciences, Rockville, Maryland, USA
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
2
|
Lin H, Zhao S, Ye Y, Shao L, Jiang N, Yang K. A Fluorescent Recombinase Aided Amplification Assay for Detection of Babesia microti. THE KOREAN JOURNAL OF PARASITOLOGY 2022; 60:201-205. [PMID: 35772739 PMCID: PMC9256288 DOI: 10.3347/kjp.2022.60.3.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022]
Abstract
Babesia microti is one of the most common causative agents of babesiosis. A sensitive and rapid detection is necessary for screening potentially infected individuals. In this study, B. microti cytochrome c oxidase subunit I (cox1) was selected as the target gene, multiple primers were designed, and optimized by a recombinase-aided amplification (RAA) assay. The optimal primers and probe were labeled with fluorescein. The sensitivity of fluorescent RAA (fRAA) was evaluated using gradient diluents of the cox1 recombinant plasmid and genomic DNA extracted from whole blood of B. microti infected mice. The specificity of fRAA was assessed by other transfusion transmitted parasites. The analytical sensitivity of the fRAA assay was 10 copies of recombinant plasmid per reaction and 10 fg/μl B. microti genomic DNA. No cross-reaction with any other blood-transmitted parasites was observed. Our results demonstrated that the fRAA assay would be rapid, sensitive, and specific for the detection of B. microti.
Collapse
Affiliation(s)
| | - Song Zhao
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064,
PR China
| | - Yuying Ye
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064,
PR China
| | - Lei Shao
- Jiangsu Province Blood Center, Nanjing 210042,
PR China
| | - Nizhen Jiang
- Jiangsu Province Blood Center, Nanjing 210042,
PR China
| | - Kun Yang
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064,
PR China
- Corresponding authors (, )
| |
Collapse
|
3
|
A Multi-copy Nucleic Acid-Based Diagnostic Test for Bovine Tropical Theileriosis. Acta Parasitol 2022; 67:504-510. [PMID: 34146240 DOI: 10.1007/s11686-021-00428-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Bovine tropical theileriosis (BTT) is a haemoprotozoan tick-borne disease that implicates huge losses to livestock in terms of considerable mortality and morbidity in tropical and subtropical regions of the globe. Currently available diagnostic methods have less specificity and sensitivity towards the detection of Theileria species. Therefore, an attempt was made to diagnose Theileria annulata by targeting a multi-copy gene, viz. mitochondrially encoded cytochrome b (MT-CYB) gene via polymerase chain reaction (PCR) in different agro-zones of India. METHODS AND RESULTS 129 cattle blood samples were collected from major livestock rearing regions of India and processed for both molecular and microscopic techniques. Screening of Giemsa-stained thin blood smears was able to detect 14 samples (10.85%) as positive for T. annulata. However, the MT-CYB gene-based PCR assay detected 107 samples (82.94%) positive for T. annulata out of 129 samples. Furthermore, the MT-CYB gene-based PCR assay was standardized in terms of its sensitivity and specificity. Specificity of PCR assay was evaluated against other common haemoprotozoan parasites of tropical countries viz. Babesia bigemina, Anaplasma marginale and Trypanosoma evansi. The multi-copy MT-CYB gene-based PCR assay provided an optimum level of sensitivity (up to the level of 10 femtogram) and high specificity. Haematological examination (Hb, PCV and TLC) of 113 samples revealed significantly (p < 0.05) decreased Hb and PCV levels in positive animals in comparison with the control group of healthy animals. However, the control group had significantly higher (p < 0.001) TLC levels than the positive group. CONCLUSION The MT-CYB gene-based PCR assay was found to be highly sensitive that can accurately detect the occurrence of T. annulata infection in carrier animals which are potential infection sources to healthier populations in naive demographic locations through infected ticks.
Collapse
|
4
|
Berná L, Rego N, Francia ME. The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now? Front Microbiol 2021; 12:751775. [PMID: 34721355 PMCID: PMC8554336 DOI: 10.3389/fmicb.2021.751775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.
Collapse
Affiliation(s)
- Luisa Berná
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María E Francia
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
5
|
Puri A, Bajpai S, Meredith S, Aravind L, Krause PJ, Kumar S. Babesia microti: Pathogen Genomics, Genetic Variability, Immunodominant Antigens, and Pathogenesis. Front Microbiol 2021; 12:697669. [PMID: 34539601 PMCID: PMC8446681 DOI: 10.3389/fmicb.2021.697669] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/30/2021] [Indexed: 12/30/2022] Open
Abstract
More than 100 Babesia spp. tick-borne parasites are known to infect mammalian and avian hosts. Babesia belong to Order Piroplasmid ranked in the Phylum Apicomplexa. Recent phylogenetic studies have revealed that of the three genera that constitute Piroplasmida, Babesia and Theileria are polyphyletic while Cytauxzoon is nested within a clade of Theileria. Several Babesia spp. and sub-types have been found to cause human disease. Babesia microti, the most common species that infects humans, is endemic in the Northeastern and upper Midwestern United States and is sporadically reported elsewhere in the world. Most infections are transmitted by Ixodid (hard-bodied) ticks, although they occasionally can be spread through blood transfusion and rarely via perinatal transmission and organ transplantation. Babesiosis most often presents as a mild to moderate disease, however infection severity ranges from asymptomatic to lethal. Diagnosis is usually confirmed by blood smear or polymerase chain reaction (PCR). Treatment consists of atovaquone and azithromycin or clindamycin and quinine and usually is effective but may be problematic in immunocompromised hosts. There is no human Babesia vaccine. B. microti genomics studies have only recently been initiated, however they already have yielded important new insights regarding the pathogen, population structure, and pathogenesis. Continued genomic research holds great promise for improving the diagnosis, management, and prevention of human babesiosis, and in particular, the identification of lineage-specific families of cell-surface proteins with potential roles in cytoadherence, immune evasion and pathogenesis.
Collapse
Affiliation(s)
- Ankit Puri
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Surabhi Bajpai
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, India
| | - Scott Meredith
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Peter J Krause
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Yale School of Medicine, New Haven, CT, United States
| | - Sanjai Kumar
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| |
Collapse
|
6
|
Namasivayam S, Baptista RP, Xiao W, Hall EM, Doggett JS, Troell K, Kissinger JC. A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia. Genome Res 2021; 31:852-865. [PMID: 33906963 PMCID: PMC8092004 DOI: 10.1101/gr.266403.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
Mitochondrial genome content and structure vary widely across the eukaryotic tree of life, with protists displaying extreme examples. Apicomplexan and dinoflagellate protists have evolved highly reduced mitochondrial genome sequences, mtDNA, consisting of only three cytochrome genes and fragmented rRNA genes. Here, we report the independent evolution of fragmented cytochrome genes in Toxoplasma and related tissue coccidia and evolution of a novel genome architecture consisting minimally of 21 sequence blocks (SBs) totaling 5.9 kb that exist as nonrandom concatemers. Single-molecule Nanopore reads consisting entirely of SBs ranging from 0.1 to 23.6 kb reveal both whole and fragmented cytochrome genes. Full-length cytochrome transcripts including a divergent coxIII are detected. The topology of the mitochondrial genome remains an enigma. Analysis of a cob point mutation reveals that homoplasmy of SBs is maintained. Tissue coccidia are important pathogens of man and animals, and the mitochondrion represents an important therapeutic target. The mtDNA sequence has been elucidated, but a definitive genome architecture remains elusive.
Collapse
Affiliation(s)
- Sivaranjani Namasivayam
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Rodrigo P Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| | - Wenyuan Xiao
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Erica M Hall
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Joseph S Doggett
- Division of Infectious Diseases, Oregon Health Sciences University, Portland, Oregon 97239, USA.,Division of Infectious Diseases, Veterans Affairs Portland Health Care System, Portland, Oregon 97239, USA
| | - Karin Troell
- Department of Microbiology, National Veterinary Institute, SE-751 89 Uppsala, Sweden
| | - Jessica C Kissinger
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
7
|
Wang X, Wang J, Liu J, Liu A, He X, Xiang Q, Li Y, Yin H, Luo J, Guan G. Insights into the phylogenetic relationships and drug targets of Babesia isolates infective to small ruminants from the mitochondrial genomes. Parasit Vectors 2020; 13:378. [PMID: 32727571 PMCID: PMC7391622 DOI: 10.1186/s13071-020-04250-8] [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: 03/12/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background Babesiosis, a tick-borne disease caused by protozoans of the genus Babesia, is widespread in subtropical and tropical countries. Mitochondria are essential organelles that are responsible for energy transduction and metabolism, calcium homeostasis and cell signaling. Mitochondrial genomes could provide new insights to help elucidate and investigate the biological features, genetic evolution and classification of the protozoans. Nevertheless, there are limited data on the mitochondrial genomes of ovine Babesia spp. in China. Methods Herein, we sequenced, assembled and annotated the mitochondrial genomes of six ovine Babesia isolates; analyzed the genome size, gene content, genome structure and cytochrome b (cytb) amino acid sequences and performed comparative mitochondrial genomics and phylogenomic analyses among apicomplexan parasites. Results The mitochondrial genomes range from 5767 to 5946 bp in length with a linear form and contain three protein-encoding genes, cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 3 (cox3) and cytb, six large subunit rRNA genes (LSU) and two terminal inverted repeats (TIR) on both ends. The cytb gene sequence analysis indicated the binding site of anti-Babesia drugs that targeted the cytochrome bc1 complex. Babesia microti and Babesia rodhaini have a dual flip-flop inversion of 184–1082 bp, whereas other Babesia spp. and Theileria spp. have one pair of TIRs, 25–1563 bp. Phylogenetic analysis indicated that the six ovine Babesia isolates were divided into two clades, Babesia sp. and Babesia motasi. Babesia motasi isolates were further separated into two small clades (B. motasi Hebei/Ningxian and B. motasi Tianzhu/Lintan). Conclusions The data provided new insights into the taxonomic relationships and drug targets of apicomplexan parasites. ![]()
Collapse
Affiliation(s)
- Xiaoxing Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Xin He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Quanjia Xiang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.
| |
Collapse
|
8
|
Virji AZ, Thekkiniath J, Ma W, Lawres L, Knight J, Swei A, Roch KL, Mamoun CB. Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes. Int J Parasitol 2019; 49:105-113. [PMID: 30176236 PMCID: PMC6395566 DOI: 10.1016/j.ijpara.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 11/22/2022]
Abstract
Babesia microti and Babesia duncani are the main causative agents of human babesiosis in the United States. While significant knowledge about B. microti has been gained over the past few years, nothing is known about B. duncani biology, pathogenesis, mode of transmission or sensitivity to currently recommended therapies. Studies in immunocompetent wild type mice and hamsters have shown that unlike B. microti, infection with B. duncani results in severe pathology and ultimately death. The parasite factors involved in B. duncani virulence remain unknown. Here we report the first known completed sequence and annotation of the apicoplast and mitochondrial genomes of B. duncani. We found that the apicoplast genome of this parasite consists of a 34 kb monocistronic circular molecule encoding functions that are important for apicoplast gene transcription as well as translation and maturation of the organelle's proteins. The mitochondrial genome of B. duncani consists of a 5.9 kb monocistronic linear molecule with two inverted repeats of 48 bp at both ends. Using the conserved cytochrome b (Cytb) and cytochrome c oxidase subunit I (coxI) proteins encoded by the mitochondrial genome, phylogenetic analysis revealed that B. duncani defines a new lineage among apicomplexan parasites distinct from B. microti, Babesia bovis, Theileria spp. and Plasmodium spp. Annotation of the apicoplast and mitochondrial genomes of B. duncani identified targets for development of effective therapies. Our studies set the stage for evaluation of the efficacy of these drugs alone or in combination against B. duncani in culture as well as in animal models.
Collapse
Affiliation(s)
- Azan Z Virji
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jose Thekkiniath
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Wenxiu Ma
- Department of Statistics, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Lauren Lawres
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - James Knight
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Andrea Swei
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA
| | - Karine Le Roch
- Department of Cell Biology & Neuroscience, 900 University Avenue, University of California, Riverside, CA 92521, USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
9
|
van de Vossenberg BTLH, Brankovics B, Nguyen HDT, van Gent-Pelzer MPE, Smith D, Dadej K, Przetakiewicz J, Kreuze JF, Boerma M, van Leeuwen GCM, André Lévesque C, van der Lee TAJ. The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen. BMC Evol Biol 2018; 18:136. [PMID: 30200892 PMCID: PMC6131824 DOI: 10.1186/s12862-018-1246-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen. RESULTS We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence. CONCLUSIONS Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.
Collapse
Affiliation(s)
- Bart T. L. H. van de Vossenberg
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Balázs Brankovics
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 Utrecht, CT Netherlands
| | - Hai D. T. Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P. E. van Gent-Pelzer
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
| | - Donna Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - Kasia Dadej
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Jarosław Przetakiewicz
- Plant Breeding and Acclimatization Institute, National Research Institute, 05-870 Blonie, Radzikow, Warsaw, Poland
| | - Jan F. Kreuze
- International Potato Centre, Avenida La Molina, 1895 Lima, Peru
| | - Margriet Boerma
- Hilbrands Laboratorium BV, Kampsweg 27, 9418 PD Wijster, Wijster, The Netherlands
| | - Gerard C. M. van Leeuwen
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - C. André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A. J. van der Lee
- Wageningen UR, Droevendaalsesteeg 1, Biointeractions and Plant Health & Plant Breeding, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
10
|
Bogema DR, Micallef ML, Liu M, Padula MP, Djordjevic SP, Darling AE, Jenkins C. Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes. BMC Genomics 2018; 19:298. [PMID: 29703152 PMCID: PMC5921998 DOI: 10.1186/s12864-018-4701-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T. orientalis sourced from Australian herds. RESULTS Using de novo assembled sequences and a single nucleotide variant (SNV) analysis pipeline, we found extensive genetic divergence between the T. orientalis genotypes. A genome-wide phylogeny reconstructed to address continued confusion over nomenclature of this species displayed concordance with prior phylogenetic studies based on the major piroplasm surface protein (MPSP) gene. However, average nucleotide identity (ANI) values revealed that the divergence between isolates is comparable to that observed between other theilerias which represent distinct species. Analysis of SNVs revealed putative recombination between the Chitose and Buffeli genotypes and also between Australian and Japanese Ikeda isolates. Finally, to inform future vaccine studies, dN/dS ratios and surface location predictions were analysed. Six predicted surface protein targets were confirmed to be expressed during the piroplasm phase of the parasite by mass spectrometry. CONCLUSIONS We used whole genome sequencing to demonstrate that the T. orientalis Ikeda, Chitose and Buffeli variants show substantial genetic divergence. Our data indicates that future researchers could potentially consider disease-associated Ikeda and closely related genotypes as a separate species from non-pathogenic Chitose and Buffeli.
Collapse
Affiliation(s)
- Daniel R Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Melinda L Micallef
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Michael Liu
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Matthew P Padula
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.
| |
Collapse
|
11
|
Qurollo BA, Archer NR, Schreeg ME, Marr HS, Birkenheuer AJ, Haney KN, Thomas BS, Breitschwerdt EB. Improved molecular detection of Babesia infections in animals using a novel quantitative real-time PCR diagnostic assay targeting mitochondrial DNA. Parasit Vectors 2017; 10:128. [PMID: 28264705 PMCID: PMC5339974 DOI: 10.1186/s13071-017-2064-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Babesiosis is a protozoal, tick transmitted disease found worldwide in humans, wildlife and domesticated animals. Commonly used approaches to diagnose babesiosis include microscopic examination of peripheral blood smears, detection of circulating antibodies and PCR. To screen and differentiate canine Babesia infections many PCR assays amplify the 18S rRNA gene. These sequences contain hypervariable regions flanked by highly conserved regions allowing for amplification of a broad-range of Babesia spp. However, differences in the 18S rRNA gene sequence of distantly related clades can make it difficult to design assays that will amplify all Babesia species while excluding the amplification of other eukaryotes. By targeting Babesia mitochondrial genome (mtDNA), we designed a novel three primer qPCR with greater sensitivity and broader screening capabilities to diagnose and differentiate Babesia spp. METHODS Using 13 Babesia mtDNA sequences, a region spanning two large subunit rRNA gene fragments (lsu5-lsu4) was aligned to design three primers for use in a qPCR assay (LSU qPCR) capable of amplifying a wide range of Babesia spp. Plasmid clones were generated and used as standards to determine efficiency, linear dynamic range and analytical sensitivity. Animals naturally infected with vector-borne pathogens were tested retrospectively and prospectively to determine relative clinical sensitivity and specificity by comparing the LSU qPCR to an established 18S rDNA qPCR. RESULTS The LSU qPCR efficiencies ranged between 92 and 100% with the limit of detection at five copies/reaction. The assay did not amplify mammalian host or other vector-borne pathogen gDNA except Cytauxzoon felis (a feline protozoal pathogen). The LSU qPCR assay amplified 12 different Babesia. sp. and C. felis from 31/31 (100%) archived samples, whereas the 18S qPCR amplified only 26/31 (83.9%). By prospective analysis, 19/394 diagnostic accessions (4.8%) were LSU qPCR positive, compared to 11/394 (2.8%) 18S rDNA qPCR positive. CONCLUSIONS We have developed a more sensitive qPCR assay with a more expansive range of Babesia spp. detection by targeting a highly conserved region of mtDNA, when compared to an established 18S qPCR.
Collapse
Affiliation(s)
- Barbara A Qurollo
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
| | - Nikole R Archer
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Megan E Schreeg
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Henry S Marr
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Adam J Birkenheuer
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Kaitlin N Haney
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Brittany S Thomas
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Edward B Breitschwerdt
- Vector-borne Disease Diagnostic Laboratory, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
12
|
Wang T, Guan G, Korhonen PK, Koehler AV, Young ND, Hall RS, Yin H, Gasser RB. Mitochondrial genomes of two Babesia taxa from sheep in China as a foundation for population genetic and epidemiological investigations. INFECTION GENETICS AND EVOLUTION 2016; 47:51-55. [PMID: 27845269 DOI: 10.1016/j.meegid.2016.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/03/2016] [Indexed: 11/19/2022]
Abstract
Here, we sequenced, assembled and annotated the mitochondrial (mt) genomes of two operational taxonomic units of Babesia from sheep from China using a deep sequencing-coupled approach. Then, we defined and compared the gene order of these mt genomes (~5.8 to 6.2kb in size), assessed sequence differences in mt genes among Babesia taxa and evaluated genetic relationships among these taxa and related apicomplexans (Theileria) for which mt genomic data sets were available. We also identified mt genetic regions that might be useful as markers for future population genetic and molecular epidemiological studies of Babesia from small ruminants. We propose that the sequencing-bioinformatic approach used here should be applicable to a wide range of protists of veterinary importance.
Collapse
Affiliation(s)
- Tao Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China; Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China
| | - Pasi K Korhonen
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anson V Koehler
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Ross S Hall
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Gansu, PR China.
| | - Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria, Australia; State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| |
Collapse
|
13
|
Schreeg ME, Marr HS, Tarigo JL, Cohn LA, Bird DM, Scholl EH, Levy MG, Wiegmann BM, Birkenheuer AJ. Mitochondrial Genome Sequences and Structures Aid in the Resolution of Piroplasmida phylogeny. PLoS One 2016; 11:e0165702. [PMID: 27832128 PMCID: PMC5104439 DOI: 10.1371/journal.pone.0165702] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 10/17/2016] [Indexed: 12/02/2022] Open
Abstract
The taxonomy of the order Piroplasmida, which includes a number of clinically and economically relevant organisms, is a hotly debated topic amongst parasitologists. Three genera (Babesia, Theileria, and Cytauxzoon) are recognized based on parasite life cycle characteristics, but molecular phylogenetic analyses of 18S sequences have suggested the presence of five or more distinct Piroplasmida lineages. Despite these important advancements, a few studies have been unable to define the taxonomic relationships of some organisms (e.g. C. felis and T. equi) with respect to other Piroplasmida. Additional evidence from mitochondrial genome sequences and synteny should aid in the inference of Piroplasmida phylogeny and resolution of taxonomic uncertainties. In this study, we have amplified, sequenced, and annotated seven previously uncharacterized mitochondrial genomes (Babesia canis, Babesia vogeli, Babesia rossi, Babesia sp. Coco, Babesia conradae, Babesia microti-like sp., and Cytauxzoon felis) and identified additional ribosomal fragments in ten previously characterized mitochondrial genomes. Phylogenetic analysis of concatenated mitochondrial and 18S sequences as well as cox1 amino acid sequence identified five distinct Piroplasmida groups, each of which possesses a unique mitochondrial genome structure. Specifically, our results confirm the existence of four previously identified clades (B. microti group, Babesia sensu stricto, Theileria equi, and a Babesia sensu latu group that includes B. conradae) while supporting the integration of Theileria and Cytauxzoon species into a single fifth taxon. Although known biological characteristics of Piroplasmida corroborate the proposed phylogeny, more investigation into parasite life cycles is warranted to further understand the evolution of the Piroplasmida. Our results provide an evolutionary framework for comparative biology of these important animal and human pathogens and help focus renewed efforts toward understanding the phylogenetic relationships within the group.
Collapse
Affiliation(s)
- Megan E. Schreeg
- North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Henry S. Marr
- North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Jaime L. Tarigo
- North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
- University of Georgia, College of Veterinary Medicine, Athens, Georgia, United States of America
| | - Leah A. Cohn
- University of Missouri, College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - David M. Bird
- North Carolina State University, College of Agriculture and Life Sciences, Raleigh, North Carolina, United States of America
| | - Elizabeth H. Scholl
- North Carolina State University, College of Agriculture and Life Sciences, Raleigh, North Carolina, United States of America
| | - Michael G. Levy
- North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Brian M. Wiegmann
- North Carolina State University, College of Agriculture and Life Sciences, Raleigh, North Carolina, United States of America
| | - Adam J. Birkenheuer
- North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| |
Collapse
|
14
|
Schreeg ME, Marr HS, Griffith EH, Tarigo JL, Bird DM, Reichard MV, Cohn LA, Levy MG, Birkenheuer AJ. PCR amplification of a multi-copy mitochondrial gene (cox3) improves detection of Cytauxzoon felis infection as compared to a ribosomal gene (18S). Vet Parasitol 2016; 225:123-30. [PMID: 27369587 DOI: 10.1016/j.vetpar.2016.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 06/02/2016] [Accepted: 06/08/2016] [Indexed: 11/19/2022]
Abstract
Cytauxzoon felis is a tick-transmitted protozoan parasite that infects felids. Clinical disease caused by acute C. felis infection rapidly progresses in domestic cats, leading to high morbidity and mortality. Accurately diagnosing cytauxzoonosis as soon as possible during acute infection would allow for earlier initiation of antiprotozoal therapy which could lead to higher survival rates. Molecular detection of parasite rRNA genes (18S) by PCR has previously been shown to be a sensitive method of diagnosing C. felis infections. Based on evidence from related apicomplexan species, we hypothesized that C. felis mitochondrial genes would exist at higher copy numbers than 18S and would be a more sensitive diagnostic target. In this study we have designed a PCR assay targeting the C. felis mitochondrial gene cytochrome c oxidase subunit III (cox3). Herein we demonstrate that (1) the cox3 PCR can detect as low as 1 copy of DNA target and can detect C. felis in samples with known mitochondrial sequence heterogeneity, (2) cox3 copy number is increased relative to 18S in blood and tissue samples from acutely infected cats, and (3) the cox3 PCR is more sensitive than 18S PCR for detection of C. felis during early infections.
Collapse
Affiliation(s)
- Megan E Schreeg
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Dr., Raleigh, NC 27607, United States
| | - Henry S Marr
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Dr., Raleigh, NC 27607, United States
| | - Emily H Griffith
- North Carolina State University, College of Sciences, Campus Box 8201/4216, Broughton Hall, Raleigh, NC 27695, United States
| | - Jaime L Tarigo
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Dr., Raleigh, NC 27607, United States
| | - David M Bird
- North Carolina State University, College of Agriculture and Life Sciences, 317A Ricks Hall 1, Lampe Dr., Raleigh, NC 27695, United States
| | - Mason V Reichard
- Oklahoma State University, Center for Veterinary Health Sciences, 205 McElroy Hall, Stillwater, OK 74078, United States
| | - Leah A Cohn
- University of Missouri, College of Veterinary Medicine, 900 E. Campus Dr., Columbia, MO, 65211, United States
| | - Michael G Levy
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Dr., Raleigh, NC 27607, United States
| | - Adam J Birkenheuer
- North Carolina State University, College of Veterinary Medicine, 1060 William Moore Dr., Raleigh, NC 27607, United States.
| |
Collapse
|
15
|
The PCR detection and phylogenetic characterization of Babesia microti in questing ticks in Mongolia. Parasitol Int 2015. [DOI: 10.1016/j.parint.2015.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
16
|
Shoguchi E, Shinzato C, Hisata K, Satoh N, Mungpakdee S. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans. Genome Biol Evol 2015. [PMID: 26199191 PMCID: PMC4558855 DOI: 10.1093/gbe/evv137] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures.
Collapse
Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Sutada Mungpakdee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| |
Collapse
|
17
|
Ogedengbe ME, Qvarnstrom Y, da Silva AJ, Arrowood MJ, Barta JR. A linear mitochondrial genome of Cyclospora cayetanensis (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) suggests the ancestral start position within mitochondrial genomes of eimeriid coccidia. Int J Parasitol 2015; 45:361-5. [PMID: 25812835 DOI: 10.1016/j.ijpara.2015.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/17/2022]
Abstract
The near complete mitochondrial genome for Cyclospora cayetanensis is 6184 bp in length with three protein-coding genes (Cox1, Cox3, CytB) and numerous lsrDNA and ssrDNA fragments. Gene arrangements were conserved with other coccidia in the Eimeriidae, but the C. cayetanensis mitochondrial genome is not circular-mapping. Terminal transferase tailing and nested PCR completed the 5'-terminus of the genome starting with a 21 bp A/T-only region that forms a potential stem-loop. Regions homologous to the C. cayetanensis mitochondrial genome 5'-terminus are found in all eimeriid mitochondrial genomes available and suggest this may be the ancestral start of eimeriid mitochondrial genomes.
Collapse
Affiliation(s)
- Mosun E Ogedengbe
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Yvonne Qvarnstrom
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alexandre J da Silva
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA; United States Food and Drug Administration, Laurel, MD, USA
| | - Michael J Arrowood
- United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barta
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
| |
Collapse
|
18
|
Garg A, Stein A, Zhao W, Dwivedi A, Frutos R, Cornillot E, Mamoun CB. Sequence and annotation of the apicoplast genome of the human pathogen Babesia microti. PLoS One 2014; 9:e107939. [PMID: 25280009 PMCID: PMC4184790 DOI: 10.1371/journal.pone.0107939] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/18/2014] [Indexed: 12/25/2022] Open
Abstract
The apicomplexan intraerythrocytic parasite Babesia microti is an emerging human pathogen and the primary cause of human babesiosis, a malaria-like illness endemic in the United States. The pathogen is transmitted to humans by the tick vector, Ixodes scapularis, and by transfusion of blood from asymptomatic B. microti-infected donors. Whereas the nuclear and mitochondrial genomes of this parasite have been sequenced, assembled and annotated, its apicoplast genome remained incomplete, mainly due to its low representation and high A+T content. Here we report the complete sequence and annotation of the apicoplast genome of the B. microti R1 isolate. The genome consists of a 28.7 kb circular molecule encoding primarily functions important for maintenance of the apicoplast DNA, transcription, translation and maturation of organellar proteins. Genome analysis and annotation revealed a unique gene structure and organization of the B. microti apicoplast genome and suggest that all metabolic and non-housekeeping functions in this organelle are nuclear-encoded. B. microti apicoplast functions are significantly different from those of the host, suggesting that they might be useful as targets for development of potent and safe therapies for the treatment of human babesiosis.
Collapse
Affiliation(s)
- Aprajita Garg
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anna Stein
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - William Zhao
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Ankit Dwivedi
- Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé - UMR 5236, Institut de Biologie Computationnelle, Montpellier, France
| | - Roger Frutos
- Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé - UMR 5236, Institut de Biologie Computationnelle, Montpellier, France
- CIRAD, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, Montpellier, France
| | - Emmanuel Cornillot
- Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé - UMR 5236, Institut de Biologie Computationnelle, Montpellier, France
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
19
|
Shinzato C, Mungpakdee S, Satoh N, Shoguchi E. A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum. Front Microbiol 2014; 5:336. [PMID: 25071748 PMCID: PMC4083563 DOI: 10.3389/fmicb.2014.00336] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022] Open
Abstract
Far more intimate knowledge of scleractinian coral biology is essential in order to understand how diverse coral-symbiont endosymbioses have been established. In particular, molecular and cellular mechanisms enabling the establishment and maintenance of obligate endosymbiosis with photosynthetic dinoflagellates require further clarification. By extension, such understanding may also shed light upon environmental conditions that promote the collapse of this mutualism. Genomic data undergird studies of all symbiotic processes. Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. We discuss Acropora genes involved in calcification, embryonic development, innate immunity, apoptosis, autophagy, UV resistance, fluorescence, photoreceptors, circadian clocks, etc. We also detail gene loss in amino acid metabolism that may explain at least part of the Acropora stress-response. Characteristic features of the Symbiodinium genome are also reviewed, focusing on the expansion of certain gene families, the molecular basis for permanently condensed chromatin, unique spliceosomal splicing, and unusual gene arrangement. Salient features of the Symbiodinium plastid and mitochondrial genomes are also illuminated. Although many questions regarding these interdependent genomes remain, we summarize information necessary for future studies of coral-dinoflagellate endosymbiosis.
Collapse
Affiliation(s)
- Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Sutada Mungpakdee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan
| |
Collapse
|
20
|
He L, Zhang Y, Zhang QL, Zhang WJ, Feng HH, Khan MK, Hu M, Zhou YQ, Zhao JL. Mitochondrial genome of Babesia orientalis, apicomplexan parasite of water buffalo (Bubalus babalis, Linnaeus, 1758) endemic in China. Parasit Vectors 2014; 7:82. [PMID: 24580772 PMCID: PMC3941609 DOI: 10.1186/1756-3305-7-82] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Apicomplexan parasites of the genus Babesia, Theileria and Plasmodium are very closely related organisms. Interestingly, their mitochondrial (mt) genomes are highly divergent. Among Babesia, Babesia orientalis is a new species recently identified and specifically epidemic to the southern part of China, causing severe disease to water buffalo. However, no information on the mt genome of B. orientalis was available. METHODS Four pairs of primers were designed based on the full genome sequence of B. orientalis (unpublished data) and by aligning reported mt genomes of B. bovis, B. bigemina, and T. parva. The entire mt genome was amplified by four sets of PCR. The obtained mt genome was annotated by aligning with published apicomplexan mt genomes and Artemis software v11. Phylogenetic analysis was performed by using cox1 and cob amino acid sequences. RESULTS The complete mt genome of B. orientalis (Wuhan strain) was sequenced and characterized. The entire mt genome is 5996 bp in length with a linear form, containing three protein-coding genes including cytochrome c oxidase I (cox1), cytochrome b (cob) and cytochrome c oxidase III (cox3) and six rRNA large subunit gene fragments. The gene arrangement in B. orientalis mt genome is similar to those of B. bovis, B. gibsoni and Theileria parva, but different from those of T. orientalis, T. equi and Plasmodium falciparum. Comparative analysis indicated that cox1 and cob genes were more conserved than cox3. Phylogenetic analysis based on amino acid sequences of cox1, cob and cox1 + cob, respectively, revealed that B. orientalis fell into Babesia clade with the closest relationship to B. bovis. CONCLUSIONS The availability of the entire mt genome sequences of B. orientalis provides valuable information for future phylogenetic, population genetics and molecular epidemiological studies of apicomplexan parasites.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Jun-Long Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| |
Collapse
|
21
|
Whole genome mapping and re-organization of the nuclear and mitochondrial genomes of Babesia microti isolates. PLoS One 2013; 8:e72657. [PMID: 24023759 PMCID: PMC3762879 DOI: 10.1371/journal.pone.0072657] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/12/2013] [Indexed: 11/19/2022] Open
Abstract
Babesia microti is the primary causative agent of human babesiosis, an emerging pathogen that causes a malaria-like illness with possible fatal outcome in immunocompromised patients. The genome sequence of the B. microti R1 strain was reported in 2012 and revealed a distinct evolutionary path for this pathogen relative to that of other apicomplexa. Lacking from the first genome assembly and initial molecular analyses was information about the terminal ends of each chromosome, and both the exact number of chromosomes in the nuclear genome and the organization of the mitochondrial genome remained ambiguous. We have now performed various molecular analyses to characterize the nuclear and mitochondrial genomes of the B. microti R1 and Gray strains and generated high-resolution Whole Genome maps. These analyses show that the genome of B. microti consists of four nuclear chromosomes and a linear mitochondrial genome present in four different structural types. Furthermore, Whole Genome mapping allowed resolution of the chromosomal ends, identification of areas of misassembly in the R1 genome, and genomic differences between the R1 and Gray strains, which occur primarily in the telomeric regions. These studies set the stage for a better understanding of the evolution and diversity of this important human pathogen.
Collapse
|
22
|
Hikosaka K, Kita K, Tanabe K. Diversity of mitochondrial genome structure in the phylum Apicomplexa. Mol Biochem Parasitol 2013; 188:26-33. [PMID: 23466751 DOI: 10.1016/j.molbiopara.2013.02.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
Mitochondria are ubiquitous organelles in all eukaryotes that are essential for a range of cellular processes and cellular signaling. Nearly all mitochondria have their own DNA or mitochondrial (mt) genome, which varies considerably in size, structure and organization. The phylum Apicomplexa includes a variety of unicellular eukaryotes, some of which are parasites of clinical or economic importance. Recent studies have demonstrated that apicomplexan mt genomes, which include the smallest 6 kb genome of the malaria parasites, exhibit remarkably diverse structures. Apicomplexan parasites are interesting model organisms in order to understand the evolution of mt genomes. This review summarizes the structure of apicomplexan mt genomes and highlights the unique features and the evolution of the mt genome.
Collapse
Affiliation(s)
- Kenji Hikosaka
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | | | | |
Collapse
|