{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T15:17:36Z","timestamp":1789053456223,"version":"build-2803163510"},"reference-count":60,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T00:00:00Z","timestamp":1629417600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p><jats:italic>Brucella melitensis<\/jats:italic> causes small ruminant brucellosis and a zoonotic pathogen prevalent worldwide. Whole genome phylogeny of all available <jats:italic>B. melitensis<\/jats:italic> genomes (<jats:italic>n<\/jats:italic> = 355) revealed that all Indian isolates (<jats:italic>n<\/jats:italic> = 16) clustered in the East Mediterranean lineage except the ADMAS-GI strain. Pangenome analysis indicated the presence of limited accessory genomes with few clades showing specific gene presence\/absence pattern. A total of 43 virulence genes were predicted in all the Indian strains of <jats:italic>B. melitensis<\/jats:italic> except 2007BM-1 (<jats:italic>ricA<\/jats:italic> and <jats:italic>wbkA<\/jats:italic> are absent). Multilocus sequence typing (MLST) analysis indicated all except one Indian strain (ADMAS-GI) falling into sequence type (ST 8). In comparison with MLST, core genome phylogeny indicated two major clusters (&amp;gt;70% bootstrap support values) among Indian strains. Clusters with &amp;lt;70% bootstrap support values represent strains with diverse evolutionary origins present among animal and human hosts. Genetic relatedness among animal (sheep and goats) and human strains with 100% bootstrap values shows its zoonotic transfer potentiality. SNP-based analysis indicated similar clustering to that of core genome phylogeny. Among the Indian strains, the highest number of unique SNPs (112 SNPs) were shared by a node that involved three strains from Tamil Nadu. The node SNPs involved several peptidase genes like U32, M16 inactive domain protein, clp protease family protein, and M23 family protein and mostly represented non-synonymous (NS) substitutions. Vaccination has been followed in several parts of the world to prevent small ruminant brucellosis but not in India. Comparison of Indian strains with vaccine strains showed that M5 is genetically closer to most of the Indian strains than Rev.1 strain. The presence of most of the virulence genes among all Indian strains and conserved core genome compositions suggest the use of any circulating strain\/genotypes for the development of a vaccine candidate for small ruminant brucellosis in India.<\/jats:p>","DOI":"10.3389\/fmicb.2021.698069","type":"journal-article","created":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T08:37:37Z","timestamp":1629448657000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":14,"title":["Genome Sequencing and Comparative Genomics of Indian Isolates of Brucella melitensis"],"prefix":"10.3389","volume":"12","author":[{"given":"Kumaragurubaran","family":"Karthik","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subbaiyan","family":"Anbazhagan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prasad","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Murugesan","family":"Ananda Chitra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tuticorin Maragatham Alagesan","family":"Senthilkumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramaswamy","family":"Sridhar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gopal","family":"Dhinakar Raj","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,8,20]]},"reference":[{"key":"B1","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B2","first-page":"383","article-title":"Brucella melitensis","author":"Alton","year":"1990","journal-title":"\u201cAnimal brucellosis"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1968","DOI":"10.1093\/bioinformatics\/btp347","article-title":"ABACAS: algorithm-based automatic contiguation of assembled sequences.","volume":"25","author":"Assefa","year":"2009","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1155\/2016\/3034756","article-title":"Genetic characterization and comparative genome analysis of Brucella melitensis isolates from India.","volume":"2016","author":"Azam","year":"2016","journal-title":"Int. J. Genomics"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology.","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1475","DOI":"10.1128\/jcm.40.2.1475-1480.2002","article-title":"Identification of the Brucella melitensis vaccine strain Rev.1 in animals and humans in Israel by PCR analysis of the PstI site polymorphism of its omp2 gene.","volume":"40","author":"Bardenstein","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"1741","DOI":"10.1016\/j.vaccine.2009.01.025","article-title":"Rough mutants defective in core and O-polysaccharide synthesis and export induce antibodies reacting in an indirect ELISA with smooth lipopolysaccharide and are less effective than Rev 1 vaccine against Brucella melitensis infection of sheep.","volume":"27","author":"Barrio","year":"2009","journal-title":"Vaccine"},{"key":"B8","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cvfa.2010.10.003","article-title":"Control and eradication of Brucella melitensis infection in sheep and goats.","volume":"27","author":"Blasco","year":"2011","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"B9","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1093\/molbev\/mss279","article-title":"The adaptation of temperate bacteriophages to their host genomes.","volume":"30","author":"Bobay","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/s1045-1056(05)80025-9","article-title":"Brucella melitensis Rev. 1 living attenuated vaccine: stability of markers, residual virulence and immunogenicity in mice.","volume":"19","author":"Bosseray","year":"1991","journal-title":"Biologicals"},{"key":"B11","doi-asserted-by":"publisher","first-page":"2660","DOI":"10.1128\/JCM.32.11.2660-2666.1994","article-title":"Differentiation of Brucella abortus bv. 1, 2, and 4, Brucella melitensis, Brucella ovis, and Brucella suis bv. 1 by PCR.","volume":"32","author":"Bricker","year":"1994","journal-title":"J. Clin. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1111\/j.1462-5822.2011.01601.x","article-title":"Identification of a Brucella spp. secreted effector specifically interacting with human small GTPase Rab2.","volume":"13","author":"de Barsy","year":"2011","journal-title":"Cell Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"27","DOI":"10.2174\/1574891x11308010006","article-title":"Brucella as a potential agent of bioterrorism.","volume":"8","author":"Doganay","year":"2013","journal-title":"Recent Pat. Antiinfect. Drug Discov"},{"key":"B15","doi-asserted-by":"publisher","first-page":"D40","DOI":"10.1016\/j.vaccine.2009.08.058","article-title":"Brucellosis: the case for live, attenuated vaccines.","volume":"27","author":"Ficht","year":"2009","journal-title":"Vaccine"},{"key":"B16","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1093\/bioinformatics\/btv271","article-title":"kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.","volume":"31","author":"Gardner","year":"2015","journal-title":"Bioinformatics"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00024","article-title":"Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata.","volume":"7","author":"Hammerl","year":"2016","journal-title":"Front. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000446","article-title":"Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy.","volume":"6","author":"Janowicz","year":"2020","journal-title":"Microb. Genom."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0070852","article-title":"Comparative genomic analysis of Brucella melitensis vaccine strain M5 provides insights into virulence attenuation.","volume":"8","author":"Jiang","year":"2013","journal-title":"PLoS One"},{"key":"B20","first-page":"205","article-title":"Responses of ewes to B. melitensis Rev1 vaccine administered by subcutaneous or conjunctival routes at different stages of pregnancy.","volume":"20","author":"Jim\u00e9nez de Bagu\u00e9s","year":"1989","journal-title":"Ann. Rech. Vet."},{"key":"B21","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.vetmic.2014.10.015","article-title":"Brucellosis outbreak in a Swedish kennel in 2013: determination of genetic markers for source tracing.","volume":"174","author":"Kaden","year":"2014","journal-title":"Vet. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10060759","article-title":"Whole-Genome Sequencing for Tracing the Genetic Diversity of Brucella abortus and Brucella melitensis Isolated from Livestock in Egypt.","volume":"10","author":"Khan","year":"2021","journal-title":"Pathogens"},{"key":"B23","doi-asserted-by":"publisher","first-page":"e00079","DOI":"10.1128\/genomeA.00079-18","article-title":"Whole-Genome Sequence of Brucella melitensis CIIMS-BH-2, a Biovar 2 Strain Isolated from Human Blood.","volume":"6","author":"Kishnani","year":"2018","journal-title":"Genome Announc"},{"key":"B24","doi-asserted-by":"publisher","first-page":"7053","DOI":"10.1128\/iai.71.12.7053-7060.2003","article-title":"Attenuated signature- tagged mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice.","volume":"71","author":"Lestrate","year":"2003","journal-title":"Infect. Immun."},{"key":"B25","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/j.molimm.2015.04.004","article-title":"A Brucella melitensis M5-90 wboA deletion strain is attenuated and enhances vaccine efficacy.","volume":"66","author":"Li","year":"2015","journal-title":"Mol. Immunol."},{"key":"B27","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: a comparative pathogenomic platform with an interactive web interface.","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1860","DOI":"10.1128\/JB.06561-11","article-title":"Spontaneous excision of the O-polysaccharide wbkA glycosyltranferase gene is a cause of dissociation of smooth to rough Brucella colonies.","volume":"194","author":"Mancilla","year":"2012","journal-title":"J. Bacteriol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1007\/s12038-008-0072-1","article-title":"Brucellosis in India \u2013 a review.","volume":"33","author":"Mantur","year":"2008","journal-title":"J. Biosci"},{"key":"B30","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1586\/erv.11.172","article-title":"Acellular vaccines for ovine brucellosis: a safer alternative against a worldwide disease.","volume":"11","author":"Martins Rda","year":"2012","journal-title":"Expert Rev. Vaccines"},{"key":"B31","doi-asserted-by":"publisher","first-page":"e2919","DOI":"10.1128\/AEM.02919-19","article-title":"Comparative whole-genome phylogeny of animal, environmental, and human strains confirms the genogroup organization and diversity of the Stenotrophomonas maltophilia complex.","volume":"86","author":"Mercier-Darty","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"B32","year":"2018","journal-title":"Brucellosis (Brucella abortus, B. melitensis and B. suis) (Infection with B. abortus, B. melitensis and B. suis)."},{"key":"B33","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1006\/cimm.1996.0241","article-title":"Recombinant Brucella abortus proteins that induce proliferation and gamma-interferon secretion by CD4+ T cells from Brucella-vaccinated mice and delayed-type hypersensitivity in sensitized guinea pigs.","volume":"172","author":"Oliveira","year":"1996","journal-title":"Cell. Immunol."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4762-2","article-title":"Global evolution and phylogeography of Brucella melitensis strains.","volume":"19","author":"Pisarenko","year":"2018","journal-title":"BMC Genomics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1007\/s00239-001-0034-9","article-title":"The effect of recombination on the accuracy of phylogeny estimation.","volume":"54","author":"Posada","year":"2002","journal-title":"J. Mol. Evol."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2020.104635","article-title":"Genomic insights into Brucella.","volume":"87","author":"Rajendhran","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"B37","first-page":"65","article-title":"Study on the Brucella melitensis strain M5-90 vaccine.","volume":"6","year":"1991","journal-title":"Chin. J. Control Endemic Dis."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1436","DOI":"10.1080\/21505594.2018.1511677","article-title":"Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation.","volume":"9","author":"Salmon-Divon","year":"2018","journal-title":"Virulence"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2021.635547","article-title":"Tracking the Origin of Austrian Human Brucellosis Cases Using Whole Genome Sequencing.","volume":"8","author":"Schaeffer","year":"2021","journal-title":"Front. Med"},{"key":"B40","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B41","doi-asserted-by":"publisher","first-page":"19","DOI":"10.14737\/journal.aavs\/2014\/2.3s.19.22","article-title":"Detection of Brucella melitensis Rev\u20131 vaccinal antibodies in sheep in India.","volume":"2","author":"Shome","year":"2014","journal-title":"Adv. Anim. Vet. Sci."},{"key":"B42","doi-asserted-by":"publisher","first-page":"2199","DOI":"10.1111\/tbed.13871","article-title":"Spatial sero-prevalence of brucellosis in small ruminants of India: nationwide cross-sectional study for the year 2017-2018.","volume":"68","author":"Shome","year":"2020","journal-title":"Transbound. Emerg. Dis."},{"key":"B43","doi-asserted-by":"publisher","first-page":"237","DOI":"10.3855\/jidc.6617","article-title":"Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.","volume":"10","author":"Shome","year":"2016","journal-title":"J. Infect. Dev. Ctries."},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-85441-w","article-title":"Brucellosis in wildlife in Africa: a systematic review and meta-analysis.","volume":"11","author":"Simpson","year":"2021","journal-title":"Sci. Rep."},{"key":"B45","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1016\/j.jgar.2018.04.008","article-title":"Draft genome sequence of field isolate Brucella melitensis strain 2007BM\/1 from India.","volume":"13","author":"Singh","year":"2018","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"B46","doi-asserted-by":"crossref","first-page":"W74","DOI":"10.1093\/nar\/gkz380","article-title":"Prophage Hunter: an integrative hunting tool for active prophages.","volume":"47","author":"Song","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21207749","article-title":"Brucella Genomics: macro and Micro Evolution.","volume":"21","author":"Su\u00e1rez-Esquivel","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fvets.2017.00215","article-title":"Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China.","volume":"4","author":"Sun","year":"2017","journal-title":"Front. Vet. Sci."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1294-x","article-title":"Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis.","volume":"16","author":"Tan","year":"2015","journal-title":"BMC Genomics"},{"key":"B50","doi-asserted-by":"publisher","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline.","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline.","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol."},{"key":"B52","doi-asserted-by":"crossref","first-page":"2434","DOI":"10.1128\/JB.01349-07","article-title":"Staphylococcus aureus pathogenicity island DNA is packaged in particles composed of phage proteins.","volume":"190","author":"Tormo","year":"2008","journal-title":"J. Bacteriol."},{"key":"B53","doi-asserted-by":"crossref","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.","volume":"44","author":"Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-04707-4","article-title":"Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny.","volume":"7","author":"Tsang","year":"2017","journal-title":"Sci. Rep."},{"key":"B55","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1007\/s12088-015-0545-5","article-title":"Identification of Recombination and Positively Selected Genes in Brucella.","volume":"55","author":"Vishnu","year":"2015","journal-title":"Indian J. Microbiol"},{"key":"B56","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.drup.2016.06.001","article-title":"Cryptic prophages as targets for drug development.","volume":"27","author":"Wang","year":"2016","journal-title":"Drug Resist. Updat."},{"key":"B57","doi-asserted-by":"crossref","first-page":"3569","DOI":"10.1128\/JB.01767-08","article-title":"Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.","volume":"191","author":"Wattam","year":"2009","journal-title":"J. Bacteriol."},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-7-34","article-title":"Characterisation of the genetic diversity of Brucella by multilocus sequencing.","volume":"7","author":"Whatmore","year":"2007","journal-title":"BMC Microbiol"},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads.","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"B60","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.micpath.2017.09.016","article-title":"The Brucella melitensis M5-90\u0394manB live vaccine candidate is safer than M5-90 and confers protection against wild-type challenge in BALB\/c mice.","volume":"112","author":"Zhang","year":"2017","journal-title":"Microb. Pathog."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.698069\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T08:37:50Z","timestamp":1629448670000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.698069\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,20]]},"references-count":60,"alternative-id":["10.3389\/fmicb.2021.698069"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2021.698069","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,20]]},"article-number":"698069"}}