Evidence that microbes identified as tick-borne pathogens are nutritional endosymbionts
2021; Cell Press; Volume: 184; Issue: 9 Linguagem: Inglês
10.1016/j.cell.2021.03.053
ISSN1097-4172
Autores Tópico(s)Insect and Pesticide Research
ResumoJia et al. (Jia et al., 2020Jia N. Wang J. Shi W. Du L. Sun Y. Zhan W. Jiang J.F. Wang Q. Zhang B. Ji P. et al.Tick Genome and Microbiome Consortium (TIGMIC)Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities.Cell. 2020; 182: 1328-1340.e13Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar) reported major discoveries on genetic basis of hematophagy and vector capacities in ticks. Our re-examination of the tick metagenomic datasets shows that nutritional endosymbionts required for hematophagy were also widely present. They were misidentified as tick-borne pathogens, indicating that the risk of infection associated with ticks was lower that initially stated. Ticks do not use other food sources than blood, and as such, they ingest low levels of vitamins: they need a vitamin supplementation through associations with nutritional bacterial partners, usually Coxiella-like endosymbionts (Coxiella-LE hereafter) or Francisella-like endosymbionts (Francisella-LE) (Duron and Gottlieb, 2020Duron O. Gottlieb Y. Convergence of nutritional symbioses in obligate blood feeders.Trends Parasitol. 2020; 36: 816-825Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar). The sequencing of Coxiella-LE and Francisella-LE genomes indicated that they produce the same three B vitamin types: biotin (vitamin B7), riboflavin (B2), and folate (B9) (Duron and Gottlieb, 2020Duron O. Gottlieb Y. Convergence of nutritional symbioses in obligate blood feeders.Trends Parasitol. 2020; 36: 816-825Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar). Further experiments confirmed that this B vitamin supplementation is critical for growth, reproduction, and survival of ticks (Zhong et al., 2007Zhong J. Jasinskas A. Barbour A.G. Antibiotic treatment of the tick vector Amblyomma americanum reduced reproductive fitness.PLoS ONE. 2007; 2: e405Crossref PubMed Scopus (148) Google Scholar; Ben-Yosef et al., 2020Ben-Yosef M. Rot A. Mahagna M. Kapri E. Behar A. Gottlieb Y. Coxiella-Like endosymbiont of Rhipicephalus sanguineus is required for physiological processes during ontogeny.Front. Microbiol. 2020; 11: 493Crossref PubMed Scopus (32) Google Scholar; Duron et al., 2018Duron O. Morel O. Noël V. Buysse M. Binetruy F. Lancelot R. Loire E. Ménard C. Bouchez O. Vavre F. Vial L. Tick-bacteria mutualism depends on B vitamin synthesis pathways.Curr. Biol. 2018; 28: 1896-1902.e5Abstract Full Text Full Text PDF PubMed Scopus (92) Google Scholar; Guizzo et al., 2017Guizzo M.G. Parizi L.F. Nunes R.D. Schama R. Albano R.M. Tirloni L. Oldiges D.P. Vieira R.P. Oliveira W.H.C. Leite M.S. et al.A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus.Sci. Rep. 2017; 7: 17554Crossref PubMed Scopus (59) Google Scholar; Li et al., 2018Li L.H. Zhang Y. Zhu D. Effects of antibiotic treatment on the fecundity of Rhipicephalus haemaphysaloides ticks.Parasit. Vectors. 2018; 11: 242Crossref PubMed Scopus (19) Google Scholar). Coxiella-LE and Francisella-LE belong to bacterial genera dominated by virulent pathogens, including the agent of Q fever, Coxiella burnetii, and the agent of tularemia, Francisella tularensis, respectively. High abundance of C. burnetii and F. tularensis, but no nutritional endosymbiont (except once in the cattle tick Rhipicephalus microplus), were primarily reported from tick metagenomes (Jia et al., 2020Jia N. Wang J. Shi W. Du L. Sun Y. Zhan W. Jiang J.F. Wang Q. Zhang B. Ji P. et al.Tick Genome and Microbiome Consortium (TIGMIC)Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities.Cell. 2020; 182: 1328-1340.e13Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar). However, our re-analyses of metagenomic datasets (supplemental information) is indicative of misidentifications since we rarely detected the presence of C. burnetii and never that of F. tularensis (Tables S1 and S2). We rather showed that Coxiella-LE and Francisella-LE are widely present in samples of five of the six tick species examined (Tables S1 and S2). Indeed, Hyalomma asiaticum tick specimens (n = 19) were early reported as infected by C. burnetii or F. tularensis (Jia et al., 2020Jia N. Wang J. Shi W. Du L. Sun Y. Zhan W. Jiang J.F. Wang Q. Zhang B. Ji P. et al.Tick Genome and Microbiome Consortium (TIGMIC)Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities.Cell. 2020; 182: 1328-1340.e13Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar). However, phylogenetic analyses of the Francisella multilocus typing system (MLST) genes (supplemental information) showed that Francisella-LE, and not F. tularensis or other pathogenic Francisella species, are present in these 19 specimens of Hy. asiaticum (Figure S1A). We further reconstructed these Francisella-LE genomes (Table S2) and confirmed that they are divergent from F. tularensis (Figure S1B). The Francisella-LE genomes (1.55 Mb) of Hy. asiaticum are similar in size and organization to other Francisella-LE genomes with a substantial level of genome reduction and rearrangement compared to F. tularensis (2 Mb) (Figure S1B). Most of the Francisella virulence genes, including the Francisella Pathogenicity Island (FPI), have been pseudogenized or are completely absent (Figure S1C). In contrast, complete pathways for biotin, riboflavin, and folate synthesis are conserved, as observed in other Francisella-LE (Figure S1D). This suggests that the Francisella of Hy. asiaticum are not pathogens but nutritional endosymbionts. Further examination confirmed the presence of C. burnetii in 5 of the 19 Hy. Asiaticum specimens. Phylogenetic analyses of Coxiella genomes found in Hy. Asiaticum (Table S2; Figure S1E) and their genomes' size and organization (Figure S1F) revealed that they belong to the C. burnetii species. They also harbor the Dot/Icm (defect in organelle trafficking/intracellular multiplication) system, which is used by C. burnetii to secrete a range of virulence factors into vertebrate cells (Figure S1G). However, we did not observe C. burnetii in the five other tick species, while it was early reported in each of them (Jia et al., 2020Jia N. Wang J. Shi W. Du L. Sun Y. Zhan W. Jiang J.F. Wang Q. Zhang B. Ji P. et al.Tick Genome and Microbiome Consortium (TIGMIC)Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities.Cell. 2020; 182: 1328-1340.e13Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar). We have re-examined randomly sampled metagenomes of the ticks Ixodes persulcatus (n = 5), Haemaphysalis longicornis (n = 5), Dermacentor silvarum (n = 4), R. sanguineus (n = 3), and R. microplus (n = 3), and we systematically obtained large Coxiella-LE contigs (and never C. burnetii) from each examined metagenomes (but not in I. persulcatus; Table S2). These Coxiella-LE are well divergent from C. burnetii (Figure S1E). In tick species for which we obtained complete genomes (R. sanguineus and R. microplus), Coxiella-LE show a large-scale genome streamlining compared to C. burnetii: their genomes range from 0.81 to 1.55 Mb, as observed in other Coxiella-LE, while the C. burnetii genome size is typically 2 Mb (Figure S1F). In all Coxiella-LE genomes, the virulence genes encoding the Dot/Icm secretion system have been pseudogenized or are completely absent (Figure S1G). In the (complete) Coxiella-LE genomes of R. sanguineus and R. microplus, the genes of biotin, riboflavin, and folate synthesis have been found all intact (Figure S1F). In the (partial) Coxiella-LE genomes of Hae. longicornis and D. silvarum, most of these B vitamin synthesis genes are also present and intact, but we only detected partial sequences for a few of them (Figure S1F). These partial gene sequences never contain internal codon stop disrupting their coding sequences but are always located at the end of unassembled contigs, suggesting that incomplete gene sequences are due to low sequencing quality. Overall, this indicates that the Coxiella of Hae. longicornis, D silvarum, R. sanguineus, and R. microplus are also nutritional endosymbionts. In I. persulcatus, Coxiella and Francisella are absent (Table S1), but we detected the presence of Lariskella (Rickettsiales: Midichloriaceae) that are uncommon bacterial endosymbionts of arthropods (Duron et al., 2017Duron O. Binetruy F. Noël V. Cremaschi J. McCoy K.D. Arnathau C. Plantard O. Goolsby J. Pérez de León A.A. Heylen D.J.A. et al.Evolutionary changes in symbiont community structure in ticks.Mol. Ecol. 2017; 26: 2905-2921Crossref PubMed Scopus (115) Google Scholar; Matsuura et al., 2012Matsuura Y. Kikuchi Y. Meng X.Y. Koga R. Fukatsu T. Novel clade of alphaproteobacterial endosymbionts associated with stinkbugs and other arthropods.Appl. Environ. Microbiol. 2012; 78: 4149-4156Crossref PubMed Scopus (55) Google Scholar). Lariskella contigs were largely incomplete, and we have not found B vitamin biosynthesis pathways. However, partial 16S rRNA gene sequences showed that Lariskella are related to an intra-mitochondrial bacterium, Midichloria mitochondrii (Figure S1I), which is known to encode complete synthesis pathways for biotin, riboflavin, and folate (Sassera et al., 2011Sassera D. Lo N. Epis S. D'Auria G. Montagna M. Comandatore F. Horner D. Peretó J. Luciano A.M. Franciosi F. et al.Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor.Mol. Biol. Evol. 2011; 28: 3285-3296Crossref PubMed Scopus (86) Google Scholar). If these pathways have been conserved intact in Lariskella, it may suggest that they are nutritional endosymbionts of I. persulcatus. The absence of functional virulence genes indicates their non-pathogenic nature, while the presence of B vitamin synthesis pathways confirms their pivotal nutritional role in ticks. These observations highlight that mutualism with microbes is one of the keys to the origins of hematophagy in ticks (Duron and Gottlieb, 2020Duron O. Gottlieb Y. Convergence of nutritional symbioses in obligate blood feeders.Trends Parasitol. 2020; 36: 816-825Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar). Another important conclusion is that ticks only occasionally carry C. burnetti and F. tularensis. This paradigm needs to be changed. Further studies should take into account the fact that tick microbial communities are largely dominated by non-pathogenic microorganisms. The inclusion of this neglected microbial diversity is now necessary to change our understanding of ticks, tick-borne microbes, and hematophagy (Duron and Gottlieb, 2020Duron O. Gottlieb Y. Convergence of nutritional symbioses in obligate blood feeders.Trends Parasitol. 2020; 36: 816-825Abstract Full Text Full Text PDF PubMed Scopus (22) Google Scholar). The bacterial genomes obtained in this study have been deposited in Dryad (10.5061/dryad.t76 hdr80p) and in GenBank (https://www.ncbi.nlm.nih.gov/genbank/) with accession numbers GenBank: MW648737–MW648739. This work was supported by 'Investissements d'Avenir' managed by the Agence Nationale de la Recherche (ANR, France, Laboratoire d'Excellence CEBA, ref. ANR-10-LABX-25-01 ). M.B. and O.D. conceived and designed the study; M.B. performed the bioinformatics analyses; M.B. and O.D. wrote the manuscript. Download .pdf (4.38 MB) Help with pdf files Document S1. Supplemental information, Figure S1, and Tables S1–S3 Reply to Evidence that microbes identified as tick-borne pathogens are nutritional endosymbiontsJia et al.CellApril 29, 2021In BriefWe are delighted that Buysse and Duron provide deep insights into the endosymbionts of ticks using our released metagenomic datasets to analyze the virulence genes encoding Francisella Pathogenicity Islands and the Dot/Icm system of Coxiella burnetii for differentiating pathogens from endosymbionts. Our original article focused on tick genomics and vector capacities of ticks to provide a large-scale dataset as a resource for research and control of ticks and tick-borne diseases (Jia et al., 2020). Full-Text PDF Open ArchiveLarge-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector CapacitiesJia et al.CellAugust 18, 2020In BriefThe high-quality genomes of six ixodid tick species and resequencing of 678 tick specimens are a resource to understand the genetic diversity, population structure, and pathogen distribution of ticks with implications for control of ticks and tick-borne diseases. Full-Text PDF Open Archive
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