{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T04:01:19Z","timestamp":1784865679987,"version":"3.55.0"},"reference-count":72,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Universidade Federal Do Tri\u00e2ngulo Mineiro"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Braz J Microbiol"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The\n                    <jats:italic>Rickettsia<\/jats:italic>\n                    genus comprises obligate intracellular bacteria transmitted by arthropods and responsible for clinically relevant zoonoses, rickettsioses, such as spotted fever and typhus. The difficulty of cultivating these bacteria in vitro reinforces the importance of in silico approaches, such as pangenomic and genomic plasticity analyses. This study analyzed 165 genomes from 31\n                    <jats:italic>Rickettsia<\/jats:italic>\n                    species available in the REFSEQ (NCBI) database. Tools such as Orthofinder, ANIclustermap, Gegenees, and Mauve were used to classify genes into core, shared, and singletons, assess genomic similarity, and identify structural rearrangements. The results indicate that the genus has an open pangenome (\u03b1\u2009=\u20090,842), suggesting high genetic variability and adaptive and expansion potential. Species such as\n                    <jats:italic>R. typhi<\/jats:italic>\n                    exhibited a nearly closed pangenome (\u03b1\u2009=\u20090,999), with high genomic conservation, whereas\n                    <jats:italic>R. rhipicephali<\/jats:italic>\n                    showed an open pangenome (\u03b1\u2009=\u20090,876), reflecting greater plasticity and intraspecies diversity. Functional categorization of genes revealed that the core genome is associated with vital functions, while singletons include genes related to genetic mobility, indicating possible acquisition through horizontal transfer. Synteny analysis demonstrated high gene conservation in\n                    <jats:italic>R. typhi<\/jats:italic>\n                    and extensive structural reorganization in\n                    <jats:italic>R. rhipicephali<\/jats:italic>\n                    . Statistical correlation reinforced the stability of the core genome regardless of pangenome expansion and revealed an inverse relationship between the number of singletons and the value of \u03b1. The findings demonstrate the existence of contrasting evolutionary trajectories within the\n                    <jats:italic>Rickettsia<\/jats:italic>\n                    genus, with conserved, specialized species coexisting alongside genetically dynamic species that are more adaptable to different niches. Thus, this study expands the understanding of clonality, genomic plasticity, and functional diversity within the genus, providing support for future investigations into virulence factors, vaccine targets, and bacterial evolution.\n                  <\/jats:p>","DOI":"10.1007\/s42770-026-02030-7","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:10:23Z","timestamp":1784862623000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pangenomic and genomic plasticity analyses of the genus Rickettsia"],"prefix":"10.1007","volume":"57","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-3913-0104","authenticated-orcid":false,"given":"Paula Cristina","family":"de Magalh\u00e3es","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrei Giacchetto","family":"Felice","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siomar","family":"de Castro Soares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"key":"2030_CR1","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1001\/jama.1909.25420310039002","volume":"52","author":"HT Ricketts","year":"1909","unstructured":"Ricketts HT (1909) A microorganism which apparently has a specific relationship to Rocky Mountain spotted fever. JAMA 52:379\u2013380","journal-title":"JAMA"},{"key":"2030_CR2","doi-asserted-by":"publisher","unstructured":"Dahmani M, Zhu JC, Cook JH et al (2023) Anaphylatoxin signaling activates macrophages to control intracellular Rickettsia proliferation. Microbiology Spectrum. ;11(6). Available from: https:\/\/journals.asm.org\/doi\/https:\/\/doi.org\/10.1128\/spectrum.02538-23. Accessed 9 Jul 2025","DOI":"10.1128\/spectrum.02538-23"},{"key":"2030_CR3","doi-asserted-by":"publisher","unstructured":"Felice AG, Alves LG, Freitas ASF, Rodrigues TCV, Jaiswal AK, Tiwari S, Benevides LJ (2021) Pan-genomic analyses of 47 complete genomes of the Rickettsia genus and prediction of new vaccine targets and virulence factors of the species. Journal of Biomolecular Structure and Dynamics. ;40(16):7496\u20137510. https:\/\/doi.org\/10.1080\/07391102.2021.1898473. Available from: https:\/\/www.tandfonline.com\/doi\/ref\/10.1080\/07391102.2021.1898473. Accessed 5 Jun 2024","DOI":"10.1080\/07391102.2021.1898473"},{"key":"2030_CR4","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-026-07290-8","author":"LLN Bonif\u00e1cio","year":"2026","unstructured":"Bonif\u00e1cio LLN, Sales K, Cardoso ERN, Krawczak F, Dantas-Torres F (2026) Rickettsia tillamookensis-like strain in brown dog ticks in Brazil. Parasit Vectors. https:\/\/doi.org\/10.1186\/s13071-026-07290-8","journal-title":"Parasit Vectors"},{"issue":"12","key":"2030_CR5","doi-asserted-by":"publisher","first-page":"3781","DOI":"10.1099\/ijsem.0.003057","volume":"68","author":"A Diop","year":"2018","unstructured":"Diop A, Barker SC, Eberhard M et al (2018) Rickettsia fournieri sp. nov., a novel spotted fever group rickettsia from Argas lagenoplastis ticks in Australia. Int J Syst Evol MicroBiol 68(12):3781\u20133784. https:\/\/doi.org\/10.1099\/ijsem.0.003057","journal-title":"Int J Syst Evol MicroBiol"},{"issue":"4","key":"2030_CR6","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1099\/ijs.0.011049-0","volume":"60","author":"D Duh","year":"2010","unstructured":"Duh D, Volga Punda-Polic T, Avsic-Zupanc et al (2010) Rickettsia hoogstraalii sp. nov., isolated from hard- and soft-bodied ticks. Int J Syst Evol MicroBiol 60(4):977\u2013984. https:\/\/doi.org\/10.1099\/ijs.0.011049-0\u200c","journal-title":"Int J Syst Evol MicroBiol"},{"key":"2030_CR7","doi-asserted-by":"publisher","unstructured":"Fournier (2026) Rickettsia tamurae sp. nov., isolated from Amblyomma testudinarium ticks. International journal of systematic and evolutionary microbiology. ;56(Pt 7). https:\/\/doi.org\/10.1099\/ijs.0.64134-0","DOI":"10.1099\/ijs.0.64134-0"},{"key":"2030_CR8","doi-asserted-by":"publisher","unstructured":"Graves S, Stenos J (2026) Rickettsia honei: a spotted fever group Rickettsia on three continents. Ann N Y Acad Sci 990. https:\/\/doi.org\/10.1111\/j.1749-6632.2003.tb07338.x","DOI":"10.1111\/j.1749-6632.2003.tb07338.x"},{"issue":"8","key":"2030_CR9","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1089\/vbz.2017.2235","volume":"18","author":"M Scarpulla","year":"2018","unstructured":"Scarpulla M, Barlozzari G, Salvato L, De Liberato C, Lorenzetti R, Macr\u00ec G (2018) Rickettsia helvetica in human-parasitizing and free-living Ixodes ricinus from urban and wild green areas in the Metropolitan City of Rome, Italy. Vector Borne Zoonotic Dis 18(8):404\u2013407. https:\/\/doi.org\/10.1089\/vbz.2017.2235","journal-title":"Vector Borne Zoonotic Dis"},{"issue":"11\u201312","key":"2030_CR10","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1016\/j.micinf.2015.09.012","volume":"17","author":"S Shpynov","year":"2015","unstructured":"Shpynov S, Pozdnichenko N, Gumenuk A (2015) Approach for classification and taxonomy within family Rickettsiaceae based on the Formal Order Analysis. Microbes Infect 17(11\u201312):839\u2013844. https:\/\/doi.org\/10.1016\/j.micinf.2015.09.012","journal-title":"Microbes Infect"},{"key":"2030_CR11","doi-asserted-by":"publisher","unstructured":"Gillespie JJ, Beier MS, Rahman MS, Ammerman NC et al (2007) Plasmids and rickettsial evolution: insight from Rickettsia felis. PLoS ONE\u00a02(3):e266. https:\/\/doi.org\/10.1371\/journal.pone.0000266.\u00a0Accessed 2 Mar 2025","DOI":"10.1371\/journal.pone.0000266"},{"key":"2030_CR12","doi-asserted-by":"publisher","unstructured":"Perlman SJ, Hunter MS, Zchori-Fein E (2006) The emerging diversity of Rickettsia. Proceedings of the Royal Society B: Biological Sciences. ;273(1598):2097\u20132106. Available from: https:\/\/doi.org\/10.1098\/rspb.2006.3541. Accessed 20 May 2024","DOI":"10.1098\/rspb.2006.3541"},{"key":"2030_CR13","doi-asserted-by":"crossref","unstructured":"Sokani S\u00e1nchez-Montes, Colunga-Salas P, Lozano-Sardaneta YN et al (2021) The genus Rickettsia in Mexico: current knowledge and perspectives. Ticks and Tick-borne Diseases. ;12(2):101633. Available from: https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1877959X20305033?casa_token=x2rRoxUk_S8AAAAA:SxuZBYM1LAeOTxBKRJ_bc9sVDvvM2_NlnKtUfyqrLJp8qhmNTlEJ9AKxrduNcuhX8x8IQRJHYg#bib0465. Accessed 24 Nov 2024","DOI":"10.1016\/j.ttbdis.2020.101633"},{"key":"2030_CR14","doi-asserted-by":"crossref","unstructured":"Ara\u00fajo RP, Navarro MBMA, Cardoso TAO (2015) Febre maculosa no Brasil: estudo da mortalidade para a vigil\u00e2ncia epidemiol\u00f3gica. Cadernos Sa\u00fade Coletiva. ;23(4):354\u2013361. Available from: https:\/\/www.scielo.br\/j\/cadsc\/a\/6VwNXXV6pjJwGd984LZqpBk\/?lang=pt. Accessed 13 Feb 2025","DOI":"10.1590\/1414-462X201500040094"},{"key":"2030_CR15","doi-asserted-by":"crossref","unstructured":"Carvalho R, Fernandes J, Gon\u00e7alves-Oliveira J et al (2022) Out of the shadows, into the spotlight: Invisible zoonotic diseases in Brazil. The Lancet Regional Health \u2013 Americas. ;8:100202. Available from: https:\/\/www.thelancet.com\/journals\/lanam\/article\/PIIS2667-193X(22)00019-9\/fulltext. Accessed 13 Feb 2025","DOI":"10.1016\/j.lana.2022.100202"},{"key":"2030_CR16","doi-asserted-by":"crossref","unstructured":"Abdad MY, Abou Abdallah R, Fournier P et al (2018) A concise review of the epidemiology and diagnostics of rickettsioses: Rickettsia and Orientia spp. J Clin Microbiol 56(8)","DOI":"10.1128\/JCM.01728-17"},{"key":"2030_CR17","doi-asserted-by":"crossref","unstructured":"Medini D, Donati C, Rappuoli R et al (2020) The Pangenome: A data-driven discovery in biology. NIH Bookshelf. Available from: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK558829\/. Accessed 6 Mar 2025","DOI":"10.1007\/978-3-030-38281-0_1"},{"key":"2030_CR18","doi-asserted-by":"crossref","unstructured":"Tettelin H, Masignani V, Cieslewicz MJ et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial pan-genome. Proceedings of the National Academy of Sciences. ;102(39):13950\u201313955. Available from: https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC1216834\/. Accessed 14 Feb 2025","DOI":"10.1073\/pnas.0506758102"},{"key":"2030_CR19","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens13080661","author":"A Rymaszewska","year":"2024","unstructured":"Rymaszewska A, Piotrowski M (2024) Rickettsia species: genetic variability, vectors, and rickettsiosis\u2014a review. Pathogens. https:\/\/doi.org\/10.3390\/pathogens13080661","journal-title":"Pathogens"},{"key":"2030_CR20","doi-asserted-by":"publisher","unstructured":"Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology. ;16(1). Available from: https:\/\/genomebiology.biomedcentral.com\/articles\/https:\/\/doi.org\/10.1186\/s13059-015-0721-2. Accessed 12 Dec 2024","DOI":"10.1186\/s13059-015-0721-2"},{"key":"2030_CR21","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink B, Reuter K, Drost HG (2021) Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 18:366\u2013368. https:\/\/doi.org\/10.1038\/s41592-021-01101-x","journal-title":"Nat Methods"},{"key":"2030_CR22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0053818","volume":"8","author":"SC Soares","year":"2013","unstructured":"Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Ali A, Santos AR, Pinto AC, Diniz C et al (2013) The pangenome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains. PLoS One 8:e53818","journal-title":"PLoS One"},{"key":"2030_CR23","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","volume":"11","author":"H Tettelin","year":"2008","unstructured":"Tettelin H, Riley D, Cattuto C, Medini D (2008) Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11:472\u2013477","journal-title":"Curr Opin Microbiol"},{"key":"2030_CR24","doi-asserted-by":"crossref","unstructured":"Galperin MY, Makarova KS, Wolf YI et al (2014) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Research. ;43(D1):D261\u2013D269. Available from: https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC4383993\/. Accessed 16 Dec 2024","DOI":"10.1093\/nar\/gku1223"},{"key":"2030_CR25","doi-asserted-by":"crossref","unstructured":"\u00c5gren J, Sundstr\u00f6m A, H\u00e5fstr\u00f6m T et al (2012) Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE. ;7(6):e39107. Available from: https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0039107. Accessed 16 Dec 2024","DOI":"10.1371\/journal.pone.0039107"},{"issue":"1","key":"2030_CR26","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1039\/C5AY02550H","volume":"8","author":"L Pritchard","year":"2015","unstructured":"Pritchard L, Glover RH, Humphris S et al (2015) Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8(1):12\u201324. https:\/\/doi.org\/10.1039\/C5AY02550H","journal-title":"Anal Methods"},{"key":"2030_CR27","doi-asserted-by":"crossref","unstructured":"Gillespie JJ, Salje J (2023) Orientia and Rickettsia: different flowers from the same garden. Current Opinion in Microbiology. ;74:102318. Available from: https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1369527423000553?via%3Dihub. Accessed 9 Jun 2025","DOI":"10.1016\/j.mib.2023.102318"},{"key":"2030_CR28","doi-asserted-by":"crossref","unstructured":"Darling ACE, Mau B, Blattner FR et al (2004) Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Research. ;14(7):1394\u20131403. Available from: https:\/\/pubmed.ncbi.nlm.nih.gov\/15231754\/. Accessed 9 Jul 2025","DOI":"10.1101\/gr.2289704"},{"issue":"3","key":"2030_CR29","doi-asserted-by":"publisher","first-page":"216","DOI":"10.4046\/trd.2017.0091","volume":"81","author":"S Ryoo","year":"2018","unstructured":"Ryoo S, Lee J, Oh JY et al (2018) Comparing two Mycobacterium tuberculosis genomes from Chinese immigrants with native genomes using Mauve alignments. Tuberc Respir Dis 81(3):216","journal-title":"Tuberc Respir Dis"},{"issue":"14","key":"2030_CR30","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059\u20133066. https:\/\/doi.org\/10.1093\/nar\/gkf436","journal-title":"Nucleic Acids Res"},{"key":"2030_CR31","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2019","unstructured":"Minh BQ, Schmidt H, Chernomor O, Schrempf D, Woodhams M, Von Haeseler A, Lanfear R (2019) IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol 37:1530\u20131534. https:\/\/doi.org\/10.1093\/molbev\/msaa015","journal-title":"Mol Biol Evol"},{"key":"2030_CR32","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic I, Bork P (2024) Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 52:W78\u2013W82. https:\/\/doi.org\/10.1093\/nar\/gkae268","journal-title":"Nucleic Acids Res"},{"key":"2030_CR33","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0","author":"M Feldgarden","year":"2021","unstructured":"Feldgarden M, Brover V, Gonzalez-Escalona N et al (2021) AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. https:\/\/doi.org\/10.1038\/s41598-021-91456-0","journal-title":"Sci Rep"},{"issue":"D1","key":"2030_CR34","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2022","unstructured":"Alcock BP, Huynh W, Chalil R et al (2022) CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 51(D1):D690\u2013D699. https:\/\/doi.org\/10.1093\/nar\/gkac920","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2030_CR35","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1128\/aac.01310-13","volume":"58","author":"SK Gupta","year":"2014","unstructured":"Gupta SK, Padmanabhan BR, Diene SM et al (2014) ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes. Antimicrob Agents Chemother 58(1):212\u2013220. https:\/\/doi.org\/10.1128\/aac.01310-13","journal-title":"Antimicrob Agents Chemother"},{"issue":"12","key":"2030_CR36","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RS, Ruppe E et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491\u20133500. https:\/\/doi.org\/10.1093\/jac\/dkaa345","journal-title":"J Antimicrob Chemother"},{"key":"2030_CR37","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000064","author":"DJ Ingle","year":"2016","unstructured":"Ingle DJ, Valcanis M, Kuzevski A et al (2016) In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microb Genom. https:\/\/doi.org\/10.1099\/mgen.0.000064","journal-title":"Microb Genom"},{"issue":"D1","key":"2030_CR38","doi-asserted-by":"publisher","first-page":"D744","DOI":"10.1093\/nar\/gkac1047","volume":"51","author":"N Bonin","year":"2022","unstructured":"Bonin N, Doster E, Worley H et al (2022) MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. Nucleic Acids Res 51(D1):D744\u2013D752. https:\/\/doi.org\/10.1093\/nar\/gkac1047","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2030_CR39","doi-asserted-by":"publisher","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","volume":"44","author":"L Chen","year":"2015","unstructured":"Chen L, Zheng D, Liu B, Yang J, Jin Q (2015) VFDB 2016: hierarchical and refined dataset for big data analysis\u201410 years on. Nucleic Acids Res 44(D1):D694\u2013D697. https:\/\/doi.org\/10.1093\/nar\/gkv1239","journal-title":"Nucleic Acids Res"},{"key":"2030_CR40","doi-asserted-by":"publisher","unstructured":"Vieira AA, Piccoli BC, Castro TRY, Casarin BC, Tessele LF, Martins R, Schwarzbold A, Trindade PA (2023) Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae. Sci Rep 13. https:\/\/doi.org\/10.1038\/s41598-023-42154-6","DOI":"10.1038\/s41598-023-42154-6"},{"issue":"7","key":"2030_CR41","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/aac.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli A, Zankari E, Garc\u00eda-Fern\u00e1ndez A et al (2014) In silico detection and typing of plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing. Antimicrob Agents Chemother 58(7):3895\u20133903. https:\/\/doi.org\/10.1128\/aac.02412-14","journal-title":"Antimicrob Agents Chemother"},{"key":"2030_CR42","doi-asserted-by":"publisher","unstructured":"Goris J, Konstantinidis KT, Klappenbach JA et al (2007) DNA\u2013DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology. ;57(1):81\u201391. Available from: https:\/\/www.microbiologyresearch.org\/content\/journal\/ijsem\/https:\/\/doi.org\/10.1099\/ijs.0.64483-0. Accessed 9 Jul 2025","DOI":"10.1099\/ijs.0.64483-0"},{"issue":"16","key":"2030_CR43","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics14161800","volume":"14","author":"N Versmessen","year":"2024","unstructured":"Versmessen N, Mispelaere M, Vandekerckhove M et al (2024) Average Nucleotide Identity and Digital DNA-DNA Hybridization Analysis Following PromethION Nanopore-Based Whole Genome Sequencing Allows for Accurate Prokaryotic Typing. Diagnostics (Basel) 14(16):1800. https:\/\/doi.org\/10.3390\/diagnostics14161800","journal-title":"Diagnostics (Basel)"},{"key":"2030_CR44","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1225207","author":"RL Lindsey","year":"2023","unstructured":"Lindsey RL, Gladney LM, Huang AD et al (2023) Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics. Front Microbiol. https:\/\/doi.org\/10.3389\/fmicb.2023.1225207","journal-title":"Front Microbiol"},{"key":"2030_CR45","doi-asserted-by":"crossref","unstructured":"Richter M, Rossell\u00f3-M\u00f3ra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences. ;106(45):19126\u201319131. Available from: https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC2776425\/. Accessed 3 Jul 2025","DOI":"10.1073\/pnas.0906412106"},{"key":"2030_CR46","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0168-6445(00)00040-1","volume":"25","author":"R Rossell\u00f3-M\u00f3ra","year":"2001","unstructured":"Rossell\u00f3-M\u00f3ra R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39\u201367. https:\/\/doi.org\/10.1016\/S0168-6445(00)00040-1","journal-title":"FEMS Microbiol Rev"},{"key":"2030_CR47","doi-asserted-by":"crossref","unstructured":"Wersebe MJ, Sherman RE, Jeyasingh PD et al (2022) The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex. Molecular Ecology. ;32(6):1478\u20131496. Available from: https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mec.16383. Accessed 3 Jul 2025","DOI":"10.1111\/mec.16383"},{"key":"2030_CR48","doi-asserted-by":"crossref","unstructured":"Merhej V, Raoult D (2010) Rickettsial evolution in the light of comparative genomics. Biological Reviews. ;86(2):379\u2013405. Available from: https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1469-185X.2010.00151.x. Accessed 3 Jul 2025","DOI":"10.1111\/j.1469-185X.2010.00151.x"},{"issue":"4","key":"2030_CR49","doi-asserted-by":"publisher","first-page":"245","DOI":"10.2174\/1389202916666150423002311","volume":"16","author":"LC Guimar\u00e3es","year":"2015","unstructured":"Guimar\u00e3es LC, Florczak-Wyspia\u0144ska J, de Jesus LB, Viana MV, Silva A, Ramos RT, Soares S (2015) Inside the pan-genome \u2013 Methods and software overview. Curr Genom 16(4):245\u2013252. https:\/\/doi.org\/10.2174\/1389202916666150423002311","journal-title":"Curr Genom"},{"key":"2030_CR50","doi-asserted-by":"publisher","unstructured":"Weinert LA, Werren JH, Aebi A et al (2009) Evolution and diversity of Rickettsia bacteria. BMC Biology. ;7(1). Available from: https:\/\/bmcbiol.biomedcentral.com\/articles\/https:\/\/doi.org\/10.1186\/1741-7007-7-6. Accessed 8 Feb 2025","DOI":"10.1186\/1741-7007-7-6"},{"key":"2030_CR51","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002018","author":"JJ Gillespie","year":"2008","unstructured":"Gillespie JJ, Williams KT, Shukla M, Snyder E, Nordberg E, Ceraul S, Dharmanolla C, Rainey D, Soneja J, Shallom J, Vishnubhat ND, Wattam R, Purkayastha A, Czar M, Crasta O, Setubal J, Azad A, Sobral B (2008) Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One. https:\/\/doi.org\/10.1371\/journal.pone.0002018","journal-title":"PLoS One"},{"key":"2030_CR52","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s13059-024-03443-z","volume":"26","author":"H Passarelli-Araujo","year":"2025","unstructured":"Passarelli-Araujo H, Venancio TM, Hanage WP (2025) Relating ecological diversity to genetic discontinuity across bacterial species. Genome Biol 26:8. https:\/\/doi.org\/10.1186\/s13059-024-03443-z","journal-title":"Genome Biol"},{"key":"2030_CR53","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s12864-019-6430-6","volume":"21","author":"AK Jaiswal","year":"2020","unstructured":"Jaiswal AK, Tiwari S, Jamal SB et al (2020) The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis. BMC Genomics 21:33. https:\/\/doi.org\/10.1186\/s12864-019-6430-6","journal-title":"BMC Genomics"},{"key":"2030_CR54","doi-asserted-by":"crossref","unstructured":"Kato CY, Chung IH, Robinson LK et al (2022) Genetic typing of isolates of Rickettsia typhi. PLoS Neglected Tropical Diseases. ;16(5):e0010354. Available from: https:\/\/journals.plos.org\/plosntds\/article?id=10.1371\/journal.pntd.0010354. Accessed 2 Jul 2025","DOI":"10.1371\/journal.pntd.0010354"},{"key":"2030_CR55","doi-asserted-by":"publisher","unstructured":"Zering\u00f3ta V, Maturano R, Luz HR, et al (2017) Molecular detection of Rickettsia rhipicephali and other spotted fever group Rickettsia species in Amblyomma ticks infesting wild birds in the state of Minas Gerais, Brazil. Ticks and Tick-borne Diseases 8(1):81\u201389. https:\/\/doi.org\/10.1016\/j.ttbdis.2016.10.001","DOI":"10.1016\/j.ttbdis.2016.10.001"},{"issue":"1","key":"2030_CR56","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/nar\/28.1.33","volume":"28","author":"RL Tatusov","year":"2000","unstructured":"Tatusov RL (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33\u201336. https:\/\/doi.org\/10.1093\/nar\/28.1.33","journal-title":"Nucleic Acids Res"},{"key":"2030_CR57","doi-asserted-by":"publisher","unstructured":"Nishino S, Tominaga K, Omae K, Deguchi T, Hamasaki K, Yoshizawa S, Nishimura Y (2025) Functional Unknomics of the SAR11 clade using bioinformatics approaches.\u00a0bioRxiv.\u00a0https:\/\/doi.org\/10.64898\/2025.12.11.693642","DOI":"10.64898\/2025.12.11.693642"},{"key":"2030_CR58","doi-asserted-by":"publisher","first-page":"R611","DOI":"10.1016\/j.cub.2022.04.083","volume":"32","author":"D Shore","year":"2022","unstructured":"Shore D, Albert B (2022) Ribosome biogenesis and the cellular energy economy. Curr Biol 32:R611\u2013R617. https:\/\/doi.org\/10.1016\/j.cub.2022.04.083","journal-title":"Curr Biol"},{"key":"2030_CR59","doi-asserted-by":"publisher","unstructured":"Jespersen MG, Hayes AJ, Tong SYC et al (2024) Pangenome evaluation of gene essentiality in Streptococcus pyogenes. Microbiology Spectrum. ;12(8). Available from: https:\/\/journals.asm.org\/doi\/https:\/\/doi.org\/10.1128\/spectrum.03240-23. Accessed 3 Jul 2025","DOI":"10.1128\/spectrum.03240-23"},{"key":"2030_CR60","doi-asserted-by":"publisher","first-page":"12320","DOI":"10.1093\/nar\/gkab1143","volume":"49","author":"MS Vincent","year":"2021","unstructured":"Vincent MS, Uphoff S (2021) Cellular heterogeneity in DNA alkylation repair increases population genetic plasticity. Nucleic Acids Res 49:12320\u201312331. https:\/\/doi.org\/10.1093\/nar\/gkab1143","journal-title":"Nucleic Acids Res"},{"key":"2030_CR61","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.14408","author":"M Tokuda","year":"2024","unstructured":"Tokuda M, Shintani M (2024) Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol. https:\/\/doi.org\/10.1111\/1751-7915.14408","journal-title":"Microb Biotechnol"},{"issue":"2","key":"2030_CR62","doi-asserted-by":"publisher","first-page":"747","DOI":"10.22207\/jpam.18.2.55","volume":"18","author":"NH Harun","year":"2024","unstructured":"Harun NH, Yuhana MY, Chua A, Wang SM (2024) Role of Rickettsial outer membrane protein A in the pathogenesis of Rickettsial diseases. J Pure Appl Microbiol 18(2):747\u2013761. https:\/\/doi.org\/10.22207\/jpam.18.2.55","journal-title":"J Pure Appl Microbiol"},{"issue":"5","key":"2030_CR63","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/j.eimc.2012.08.001","volume":"31","author":"S Santib\u00e1\u00f1ez","year":"2013","unstructured":"Santib\u00e1\u00f1ez S, Portillo A, Santib\u00e1\u00f1ez P, Palomar AM, Oteo JA (2013) Usefulness of rickettsial PCR assays for the molecular diagnosis of human rickettsioses. Enferm Infecc Microbiol Clin 31(5):283\u2013288. https:\/\/doi.org\/10.1016\/j.eimc.2012.08.001","journal-title":"Enferm Infecc Microbiol Clin"},{"key":"2030_CR64","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature02318","volume":"427","author":"E Gouin","year":"2004","unstructured":"Gouin E, Egile C, Dehoux P, Villiers V, Adams J, Gertler F, Li R, Cossart P (2004) The RickA protein of Rickettsia conorii activates the Arp2\/3 complex. Nature 427:457\u2013461","journal-title":"Nature"},{"key":"2030_CR65","doi-asserted-by":"publisher","unstructured":"Karkouri EK, Ghigo E, Raoult D, Fournier P (2022) Genomic evolution and adaptation of arthropod-associated Rickettsia. Sci Rep 12. https:\/\/doi.org\/10.1038\/s41598-022-07725-","DOI":"10.1038\/s41598-022-07725-"},{"key":"2030_CR66","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-2-r42","volume":"9","author":"H-H Fuxelius","year":"2008","unstructured":"Fuxelius H-H, Darby A, Cho N-H, Andersson S (2008) Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol 9:R42 - R42. https:\/\/doi.org\/10.1186\/gb-2008-9-2-r42","journal-title":"Genome Biol"},{"key":"2030_CR67","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0030014","author":"G Blanc","year":"2007","unstructured":"Blanc G, Ogata H, Robert C, Audic S, Suhre K, Vestris G, Claverie J, Raoult D (2007) Reductive genome evolution from the mother of Rickettsia. PLoS Genet. https:\/\/doi.org\/10.1371\/journal.pgen.0030014","journal-title":"PLoS Genet"},{"issue":"6","key":"2030_CR68","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/s41579-021-00661-1","volume":"20","author":"D Jur\u0117nas","year":"2022","unstructured":"Jur\u0117nas D, Fraikin N, Goormaghtigh F, Van Melderen L (2022) Biology and evolution of bacterial toxin\u2013antitoxin systems. Nat Rev Microbiol 20(6):335\u2013350. https:\/\/doi.org\/10.1038\/s41579-021-00661-1","journal-title":"Nat Rev Microbiol"},{"key":"2030_CR69","doi-asserted-by":"publisher","unstructured":"Lima-Mendez G, Alvarenga DO, Ross K, Hallet B, Van Melderen L, Varani A, Chandler M (2019) Toxin-antitoxin gene pairs found in Tn3 family transposons appear to be an integral part of the transposition module. mBio, p 11. https:\/\/doi.org\/10.1128\/mbio.00452-20)","DOI":"10.1128\/mbio.00452-20)"},{"key":"2030_CR70","doi-asserted-by":"publisher","unstructured":"Akter A, Ooka T, Gotoh Y et al (2017) Extremely low genomic diversity of Rickettsia japonica distributed in Japan. Genome Biol Evol. https:\/\/doi.org\/10.1093\/gbe\/evw304","DOI":"10.1093\/gbe\/evw304"},{"issue":"5537","key":"2030_CR71","doi-asserted-by":"publisher","first-page":"2093","DOI":"10.1126\/science.1061471","volume":"293","author":"H Ogata","year":"2001","unstructured":"Ogata H (2001) Mechanisms of Evolution in Rickettsia conorii and R. prowazekii. Science 293(5537):2093\u20132098. https:\/\/doi.org\/10.1126\/science.1061471\u200c","journal-title":"Science"},{"key":"2030_CR72","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/978-3-030-38281-0_4","volume-title":"The Pangenome","author":"G Vernikos","year":"2020","unstructured":"Vernikos G (2020) A review of pangenome tools and recent studies. The Pangenome. pp 89\u2013112"}],"container-title":["Brazilian Journal of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s42770-026-02030-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s42770-026-02030-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s42770-026-02030-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:10:38Z","timestamp":1784862638000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s42770-026-02030-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,24]]},"references-count":72,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["2030"],"URL":"https:\/\/doi.org\/10.1007\/s42770-026-02030-7","relation":{},"ISSN":["1517-8382","1678-4405"],"issn-type":[{"value":"1517-8382","type":"print"},{"value":"1678-4405","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,24]]},"assertion":[{"value":"18 December 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All authors declare that they have no competing interests with this manuscript.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"217"}}