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Lehman SS, Verhoeve VI, Driscoll TP, Beckmann JF, Gillespie JJ. Metagenome diversity illuminates the origins of pathogen effectors. mBio 2024; 15:e0075923. [PMID: 38564675 PMCID: PMC11077975 DOI: 10.1128/mbio.00759-23] [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: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024] Open
Abstract
Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.
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Affiliation(s)
- Stephanie S. Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria I. Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Timothy P. Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - John F. Beckmann
- Department of Microbiology and Immunology, University of South Alabama, Mobile, Alabama, USA
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Polsomboon Nelson S, Ergunay K, Bourke BP, Reinbold-Wasson DD, Caicedo-Quiroga L, Kirkitadze G, Chunashvili T, Tucker CL, Linton YM. Nanopore-based metagenomics reveal a new Rickettsia in Europe. Ticks Tick Borne Dis 2024; 15:102305. [PMID: 38150911 DOI: 10.1016/j.ttbdis.2023.102305] [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: 04/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
Accurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing (NS) and commonly used PCR assays amplifying Rickettsia genes in field-collected ticks. The study included a total of 310 ticks, originating from Poland (44.2 %) and Bulgaria (55.8 %). Samples comprised 7 species, the majority of which were Ixodes ricinus (62.9 %), followed by Dermacentor reticulatus (21.2 %). Screening was carried out in 55 pools, using total nucleic acid extractions from individual ticks. NS and ompA/gltA PCRs identified Rickettsia species in 47.3 % and 54.5 % of the pools, respectively. The most frequently detected species were Rickettsia asiatica (27.2 %) and Rickettsia raoultii (21.8 %), followed by Rickettsia monacensis (3.6 %), Rickettsia helvetica (1.8 %), Rickettsia massiliae (1.8 %) and Rickettsia tillamookensis (1.8 %). Phylogeny construction on mutS, uvrD, argS and virB4 sequences and a follow-up deep sequencing further supported R. asiatica identification, documented in Europe for the first time. NS further enabled detection of Anaplasma phagocytophilum (9.1 %), Coxiella burnetii (5.4 %) and Neoehrlichia mikurensis (1.8 %), as well as various endosymbionts of Rickettsia and Coxiella. Co-detection of multiple rickettsial and non-rickettsial bacteria were observed in 16.4 % of the pools with chromosome and plasmid-based contigs. In conclusion, non-targeted metagenomic sequencing was documented as a robust strategy capable of providing a broader view of the tick-borne bacterial pathogen spectrum.
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Affiliation(s)
- Suppaluck Polsomboon Nelson
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
| | - Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA; Hacettepe University, Faculty of Medicine, Ankara, Turkey.
| | - Brian P Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
| | | | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
| | - Giorgi Kirkitadze
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
| | - Cynthia L Tucker
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA
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3
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Paludo RLDR, Paula WVDF, Neves LC, de Paula LGF, de Lima NJ, da Silva BBF, Pereira BG, Pádua GT, Dantas-Torres F, Labruna MB, Martins TF, Sponchiado J, de Sousa-Paula LC, Hannibal W, Krawczak FDS. Rickettsial Infection in Ticks from a National Park in the Cerrado Biome, Midwestern Brazil. Pathogens 2023; 13:13. [PMID: 38251322 PMCID: PMC10818336 DOI: 10.3390/pathogens13010013] [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: 11/05/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
This study was carried out from February 2020 to September 2021 in Parque Nacional das Emas (PNE), a national park located in the Cerrado biome, midwestern Brazil, as well as in surrounding rural properties. Serum and tick samples were collected from dogs, terrestrial small mammals, and humans. Ticks were also collected from the environment. Dogs were infested with Rhipicephalus linnaei adults, whereas small mammals were infested by immature stages of Amblyomma spp., Amblyomma triste, Amblyomma dubitatum, and Amblyomma coelebs. Ticks collected from vegetation belonged to several species of the genus Amblyomma, including A. coelebs, A. dubitatum, Amblyomma naponense, Amblyomma sculptum, and A. triste. Two Rickettsia species were molecularly detected in ticks: Rickettsia parkeri in A. triste from the vegetation and a Rickettsia sp. (designated Rickettsia sp. strain PNE) in A. sculptum and A. triste collected from lowland tapirs (Tapirus terrestris). Based on short gltA gene fragments, this rickettsial organism showed 99.7-100% to Rickettsia tillamookensis. Seroreactivity to Rickettsia antigens was detected in 21.9% of dogs, 15.4% of small mammals, and 23.5% of humans. The present study reveals the richness of ticks and demonstrates the circulation of rickettsial agents in one of the largest conservation units in the Cerrado biome in Brazil. To our knowledge, this is the first report of a rickettsial phylogenetically related to R. tillamookensis in Brazil.
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Affiliation(s)
- Raquel Loren dos Reis Paludo
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
- Centro Universitário de Mineiros—UNIFIMES, Mineiros 75833-130, Brazil
| | - Warley Vieira de Freitas Paula
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Lucianne Cardoso Neves
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Luiza Gabriella Ferreira de Paula
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Nicolas Jalowitzki de Lima
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Bianca Barbara Fonseca da Silva
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Brenda Gomes Pereira
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Gracielle Teles Pádua
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
| | - Filipe Dantas-Torres
- Departamento de Imunologia, Instituto Ageu Magalhães—IAM, Fundação Oswaldo Cruz (Fiocruz), Recife 50740-465, Brazil;
| | - Marcelo B. Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo—USP, São Paulo 05508-270, Brazil; (M.B.L.); (T.F.M.)
| | - Thiago Fernandes Martins
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo—USP, São Paulo 05508-270, Brazil; (M.B.L.); (T.F.M.)
- Instituto Pasteur, Área Técnica de Doenças Vinculadas a Vetores e Hospedeiros Intermediários, Secretaria de Estado da Saúde de São Paulo, São Paulo 01027-000, Brazil
| | - Jonas Sponchiado
- Instituto Federal de Educação, Ciência e Tecnologia Farroupilha, Campus Alegrete, Alegrete 97541-000, Brazil;
| | - Lucas Christian de Sousa-Paula
- Tick-Pathogen Transmission Unit, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA;
| | - Wellington Hannibal
- Laboratório de Ecologia e Biogeografia de Mamíferos, Universidade Estadual de Goiás—UEG, Quirinópolis 75860-000, Brazil;
| | - Felipe da Silva Krawczak
- Setor de Medicina Veterinária Preventiva, Departamento de Medicina Veterinária, Escola de Veterinária e Zootecnia, Universidade Federal de Goiás—UFG, Goiânia 74690-900, Brazil; (R.L.d.R.P.); (W.V.d.F.P.); (L.C.N.); (L.G.F.d.P.); (N.J.d.L.); (B.B.F.d.S.); (B.G.P.); (G.T.P.)
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Cull B, Burkhardt NY, Wang XR, Thorpe CJ, Oliver JD, Kurtti TJ, Munderloh UG. The Ixodes scapularis Symbiont Rickettsia buchneri Inhibits Growth of Pathogenic Rickettsiaceae in Tick Cells: Implications for Vector Competence. Front Vet Sci 2022; 8:748427. [PMID: 35071375 PMCID: PMC8770908 DOI: 10.3389/fvets.2021.748427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
Ixodes scapularis is the primary vector of tick-borne pathogens in North America but notably does not transmit pathogenic Rickettsia species. This tick harbors the transovarially transmitted endosymbiont Rickettsia buchneri, which is widespread in I. scapularis populations, suggesting that it confers a selective advantage for tick survival such as providing essential nutrients. The R. buchneri genome includes genes with similarity to those involved in antibiotic synthesis. There are two gene clusters not found in other Rickettsiaceae, raising the possibility that these may be involved in excluding pathogenic bacteria from the tick. This study explored whether the R. buchneri antibiotic genes might exert antibiotic effects on pathogens associated with I. scapularis. Markedly reduced infectivity and replication of the tick-borne pathogens Anaplasma phagocytophilum, R. monacensis, and R. parkeri were observed in IRE11 tick cells hosting R. buchneri. Using a fluorescent plate reader assay to follow infection dynamics revealed that the presence of R. buchneri in tick cells, even at low infection rates, inhibited the growth of R. parkeri by 86-100% relative to R. buchneri-free cells. In contrast, presence of the low-pathogenic species R. amblyommatis or the endosymbiont R. peacockii only partially reduced the infection and replication of R. parkeri. Addition of host-cell free R. buchneri, cell lysate of R. buchneri-infected IRE11, or supernatant from R. buchneri-infected IRE11 cultures had no effect on R. parkeri infection and replication in IRE11, nor did these treatments show any antibiotic effect against non-obligate intracellular bacteria E. coli and S. aureus. However, lysate from R. buchneri-infected IRE11 challenged with R. parkeri showed some inhibitory effect on R. parkeri infection of treated IRE11, suggesting that challenge by pathogenic rickettsiae may induce the antibiotic effect of R. buchneri. This research suggests a potential role of the endosymbiont in preventing other rickettsiae from colonizing I. scapularis and/or being transmitted transovarially. The confirmation that the observed inhibition is linked to R. buchneri's antibiotic clusters requires further investigation but could have important implications for our understanding of rickettsial competition and vector competence of I. scapularis for rickettsiae.
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Affiliation(s)
- Benjamin Cull
- Department of Entomology, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Nicole Y. Burkhardt
- Department of Entomology, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Xin-Ru Wang
- Department of Entomology, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Cody J. Thorpe
- Department of Entomology, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Jonathan D. Oliver
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Timothy J. Kurtti
- Department of Entomology, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Ulrike G. Munderloh
- Department of Entomology, College of Food, Agricultural, and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, United States
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Karpathy SE, Paddock CD, Grizzard SL, Batra D, Rowe LA, Gauthier DT. Complete Genome Sequence of Rickettsia parkeri Strain Black Gap. Microbiol Resour Announc 2021; 10:e0062321. [PMID: 34734759 PMCID: PMC8567792 DOI: 10.1128/mra.00623-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/03/2021] [Indexed: 11/20/2022] Open
Abstract
A unique genotype of Rickettsia parkeri, designated R. parkeri strain Black Gap, has thus far been associated exclusively with the North American tick, Dermacentor parumapertus. The compete genome consists of a single circular chromosome with 1,329,522 bp and a G+C content of 32.5%.
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Affiliation(s)
- Sandor E. Karpathy
- Rickettsial Zoonoses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher D. Paddock
- Rickettsial Zoonoses Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A. Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David T. Gauthier
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
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