{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T04:00:33Z","timestamp":1788840033220,"version":"build-2803163510"},"reference-count":44,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,1,22]],"date-time":"2022-01-22T00:00:00Z","timestamp":1642809600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chief Scientist Office of the Ministry of Agriculture and Rural Development, Israel.","award":["16-18-0002"],"award-info":[{"award-number":["16-18-0002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Brucellosis, a zoonosis mainly transmitted by consumption of unpasteurized dairy products, is endemic in Southern Israel, mainly among the Bedouin Arab population. However, the genomic epidemiology of B. melitensis in this region has not yet been elucidated. A cohort of brucellosis cases (n = 118) diagnosed between 2017\u20132019 was studied using whole-genome sequencing (WGS). Phylogenetic analyses utilized core genome MLST (cgMLST) for all local isolates and core genome SNPs for 347 human-associated B. melitensis genomes, including Israeli and publicly available sequences. Israeli isolates formed two main clusters, presenting a notable diversity, with no clear dominance of a specific strain. On a global scale, the Israeli genomes clustered according to their geographical location, in proximity to genomes originating from the Middle East, and formed the largest cluster in the tree, suggesting relatively high conservation. Our study unveils the genomic epidemiology of B. melitensis in Southern Israel, implicating that rather than a common source, the transmission pattern of brucellosis among Bedouin communities is complex, predominantly local, and household-based. Further, genomic surveillance of B. melitensis is expected to inform future public health and veterinary interventions and clinical care.<\/jats:p>","DOI":"10.3390\/microorganisms10020238","type":"journal-article","created":{"date-parts":[[2022,1,23]],"date-time":"2022-01-23T20:34:40Z","timestamp":1642970080000},"page":"238","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genomic Epidemiology of Clinical Brucella melitensis Isolates from Southern Israel"],"prefix":"10.3390","volume":"10","author":[{"given":"Bar","family":"Zilberman","sequence":"first","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1289-6919","authenticated-orcid":false,"given":"Yair","family":"Motro","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orli","family":"Sagi","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"},{"name":"Soroka University Medical Center, Beer Sheva 84101, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6848-2323","authenticated-orcid":false,"given":"David","family":"Kornspan","sequence":"additional","affiliation":[{"name":"Brucellosis Lab, OIE, FAO Reference Laboratory, Kimron Veterinary Institute, Bet Dagan 50250, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalom","family":"Ben-Shimol","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"},{"name":"Soroka University Medical Center, Beer Sheva 84101, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Gdalevich","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"},{"name":"Southern District Health Office, Ministry of Health, Beer Sheva 84104, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yael","family":"Yagel","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"},{"name":"Soroka University Medical Center, Beer Sheva 84101, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadav","family":"Davidovitch","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1695-6544","authenticated-orcid":false,"given":"Boris","family":"Khalfin","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Rabinowitz","sequence":"additional","affiliation":[{"name":"Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1230-0428","authenticated-orcid":false,"given":"Lior","family":"Nesher","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"},{"name":"Soroka University Medical Center, Beer Sheva 84101, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Itamar","family":"Grotto","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Svetlana","family":"Bardenstein","sequence":"additional","affiliation":[{"name":"Brucellosis Lab, OIE, FAO Reference Laboratory, Kimron Veterinary Institute, Bet Dagan 50250, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Moran-Gilad","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel"},{"name":"Soroka University Medical Center, Beer Sheva 84101, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.3325\/cmj.2010.51.289","article-title":"Brucellosis-Regionally Emerging Zoonotic Disease?","volume":"51","author":"Gwida","year":"2010","journal-title":"Croat. Med. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S1473-3099(06)70382-6","article-title":"The New Global Map of Human Brucellosis","volume":"6","author":"Pappas","year":"2006","journal-title":"Lancet Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5238","DOI":"10.1128\/IAI.71.9.5238-5244.2003","article-title":"Purification and Characterization of an Immunogenic Aminopeptidase of Brucella melitensis","volume":"71","author":"Contreras","year":"2003","journal-title":"Infect. Immun."},{"key":"ref_4","first-page":"10","article-title":"Reemergence of Human Brucellosis in Israel","volume":"21","author":"Eljay","year":"2019","journal-title":"IMAJ"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"31","DOI":"10.4269\/ajtmh.16-0116","article-title":"Brucellosis Outbreak in Children and Adults in Two Areas in Israel","volume":"95","author":"Megged","year":"2016","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e469","DOI":"10.1016\/j.ijid.2009.06.031","article-title":"Clinical Manifestations and Complications in 1028 Cases of Brucellosis: A Retrospective Evaluation and Review of the Literature","volume":"14","author":"Buzgan","year":"2010","journal-title":"Int. J. Infect. Dis."},{"key":"ref_7","first-page":"836","article-title":"Brucellosis: Clinical Presentation, Diagnosis, Complications and Therapeutic Options","volume":"145","author":"Sakran","year":"2006","journal-title":"Harefuah"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"34","DOI":"10.2174\/1574891X11308010007","article-title":"Clinical Presentations and Diagnosis of Brucellosis","volume":"8","author":"Metan","year":"2013","journal-title":"Recent Pat. Anti-Infect. Drug Discov."},{"key":"ref_9","first-page":"1","article-title":"Laboratory Techniques in Brucellosis. Monograph series","volume":"55","author":"Alton","year":"1967","journal-title":"World Health Organ."},{"key":"ref_10","first-page":"653","article-title":"Isolation and Biotyping of Brucella melitensis from Upper Egypt","volume":"7","author":"Affi","year":"2011","journal-title":"J. Am. Sci."},{"key":"ref_11","first-page":"383","article-title":"Typing of Brucella Field Strains Isolated from Livestock Populations in Italy between 2001 and 2006","volume":"44","author":"Ancora","year":"2010","journal-title":"Vet. Ital."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.mimet.2012.11.007","article-title":"MLVA-16 Loci Panel on Brucella Spp. Using Multiplex PCR and Multicolor Capillary Electrophoresis","volume":"92","author":"Garofolo","year":"2013","journal-title":"J. Microbiol. Methods"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"le Fl\u00e8che, P., Jacques, I., Grayon, M., al Dahouk, S., Bouchon, P., Denoeud, F., N\u00f6ckler, K., Neubauer, H., Guilloteau, L.A., and Vergnaud, G. (2006). Evaluation and Selection of Tandem Repeat Loci for a Brucella MLVA Typing Assay. BMC Microbiol., 6.","DOI":"10.1186\/1471-2180-6-9"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Maquart, M., le Fl\u00e8che, P., Foster, G., Tryland, M., Ramisse, F., Dj\u00f8nne, B., al Dahouk, S., Jacques, I., Neubauer, H., and Walravens, K. (2009). MLVA-16 Typing of 295 Marine Mammal Brucella Isolates from Different Animal and Geographic Origins Identifies 7 Major Groups within Brucella Ceti and Brucella Pinnipedialis. BMC Microbiol., 9.","DOI":"10.1186\/1471-2180-9-145"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.mimet.2006.12.015","article-title":"Evaluation of Brucella MLVA Typing for Human Brucellosis","volume":"69","author":"Jacques","year":"2007","journal-title":"J. Microbiol. Methods"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13620-016-0062-9","article-title":"Use of Serology and Real Time PCR to Control an Outbreak of Bovine Brucellosis at a Dairy Cattle Farm in the Nile Delta Region, Egypt","volume":"69","author":"Gwida","year":"2015","journal-title":"Ir. Vet. J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.3389\/fmicb.2016.02049","article-title":"Extended Multilocus Sequence Analysis to Describe the Global Population Structure of the Genus Brucella: Phylogeography and Relationship to Biovars","volume":"7","author":"Whatmore","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Pelerito, A., Nunes, A., N\u00fancio, M.S., and Gomes, J.P. (2020). Genome-Scale Approach to Study the Genetic Relatedness among Brucella melitensis Strains. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0229863"},{"key":"ref_19","first-page":"30547","article-title":"Whole Genome Sequencing (WGS) for Food-Borne Pathogen Surveillance and Control-Taking the Pulse","volume":"22","year":"2017","journal-title":"Eurosurveillance"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.cmi.2017.10.013","article-title":"Next-Generation Sequencing Technologies and Their Application to the Study and Control of Bacterial Infections","volume":"24","author":"Besser","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.3389\/fmicb.2019.01107","article-title":"Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges","volume":"10","author":"Collineau","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_22","first-page":"20382","article-title":"Bioinformatics in Bacterial Molecular Epidemiology and Public Health: Databases, Tools and the next-Generation Sequencing Revolution","volume":"18","author":"Sabat","year":"2013","journal-title":"Eurosurveillance"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.3201\/eid2706.204902","article-title":"Brucellosis Outbreak Traced to Commercially Sold Camel Milk through Whole-Genome Sequencing, Israel","volume":"27","author":"Bardenstein","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"698","DOI":"10.3390\/microbiolres12030050","article-title":"Whole Genome Sequence Analysis of Brucella melitensis Phylogeny and Virulence Factors","volume":"12","author":"Rabinowitz","year":"2021","journal-title":"Microbiol. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved Metagenomic Analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref_26","first-page":"e000446","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":"ref_27","doi-asserted-by":"crossref","first-page":"e00517-18","DOI":"10.1128\/JCM.00517-18","article-title":"Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections","volume":"56","author":"Janowicz","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., and Young, S.K. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"i142","DOI":"10.1093\/bioinformatics\/bty266","article-title":"Versatile Genome Assembly Evaluation with QUAST-LG","volume":"34","author":"Mikheenko","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Jolley, K.A., and Maiden, M.C. (2010). BIGSdb: Scalable Analysis of Bacterial Genome Variation at the Population Level. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-595"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-Access Bacterial Population Genomics: BIGSdb Software, the PubMLST.Org Website and Their Applications","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref_34","first-page":"e000166","article-title":"ChewBBACA: A Complete Suite for Gene-by-Gene Schema Creation and Strain Identification","volume":"4","author":"Silva","year":"2018","journal-title":"Microb. Genom."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Hyatt, D., Chen, G.-L., LoCascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010). Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification. BMC Bioinform., 11.","DOI":"10.1186\/1471-2105-11-119"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: Visualization of Core Genomic Relationships among 100,000 Bacterial Pathogens","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1900519","DOI":"10.2807\/1560-7917.ES.2020.25.20.1900519","article-title":"Multilevel Genome Typing: Genomics-Guided Scalable Resolution Typing of Microbial Pathogens","volume":"25","author":"Payne","year":"2020","journal-title":"Eurosurveillance"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s13073-014-0090-6","article-title":"SRST2: Rapid Genomic Surveillance for Public Health and Hospital Microbiology Labs","volume":"6","author":"Inouye","year":"2014","journal-title":"Genome Med."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: A Fast Phage Search Tool","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e15","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":"ref_41","doi-asserted-by":"crossref","unstructured":"Tan, K.-K., Tan, Y.-C., Chang, L.-Y., Lee, K.W., Nore, S.S., Yee, W.-Y., Mat Isa, M.N., Jafar, F.L., Hoh, C.-C., and AbuBakar, S. (2015). Full Genome SNP-Based Phylogenetic Analysis Reveals the Origin and Global Spread of Brucella melitensis. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1294-x"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Georgi, E., Walter, M.C., Pfalzgraf, M.-T., Northoff, B.H., Holdt, L.M., Scholz, H.C., Zoeller, L., Zange, S., and Antwerpen, M.H. (2017). Whole Genome Sequencing of Brucella melitensis Isolated from 57 Patients in Germany Reveals High Diversity in Strains from Middle East. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0175425"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Pisarenko, S.V., Kovalev, D.A., Volynkina, A.S., Ponomarenko, D.G., Rusanova, D.V., Zharinova, N.V., Khachaturova, A.A., Tokareva, L.E., Khvoynova, I.G., and Kulichenko, A.N. (2018). Global Evolution and Phylogeography of Brucella melitensis Strains. BMC Genom., 19.","DOI":"10.1186\/s12864-018-4762-2"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Sacchini, L., Wahab, T., Di Giannatale, E., Zilli, K., Abass, A., Garofolo, G., and Janowicz, A. (2019). Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden. Microorganisms, 7.","DOI":"10.3390\/microorganisms7100398"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/2\/238\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:05:48Z","timestamp":1760133948000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/2\/238"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,22]]},"references-count":44,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["microorganisms10020238"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10020238","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,22]]}}}