{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T06:07:24Z","timestamp":1768716444855,"version":"3.49.0"},"reference-count":63,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2022,3,14]],"date-time":"2022-03-14T00:00:00Z","timestamp":1647216000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004576","name":"Israeli Ministry of Agriculture and Rural Development","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/501100004576","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis. Eighteen B. melitensis isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads. Short reads were assembled with INNUca with SPADes, long reads and hybrid with dragonflye. Abricate with the virulence factor database (VFDB) and in silico PCR (for the genes BetB, BPE275, BSPB, manA, mviN, omp19, perA, PrpA, VceC, and ureI) were used for identifying virulence genes, and a total of 61 virulence genes were identified in short-read, long-read, and hybrid assemblies of all 18 isolates. The phylogenetic analysis using long-read assemblies revealed several inconsistencies in cluster assignment as compared to using hybrid and short-read assemblies. Overall, hybrid assembly provided the most comprehensive data, and stand-alone short-read sequencing provided comparable data to stand-alone long-read sequencing regarding virulence genes. For genomic epidemiology studies, stand-alone ONP sequencing may require further refinement in order to be useful in endemic settings.<\/jats:p>","DOI":"10.3390\/microorganisms10030619","type":"journal-article","created":{"date-parts":[[2022,3,15]],"date-time":"2022-03-15T02:56:20Z","timestamp":1647312980000},"page":"619","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Brucella melitensis Isolates"],"prefix":"10.3390","volume":"10","author":[{"given":"Hillary A.","family":"Craddock","sequence":"first","affiliation":[{"name":"Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1289-6919","authenticated-orcid":false,"given":"Yair","family":"Motro","sequence":"additional","affiliation":[{"name":"Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bar","family":"Zilberman","sequence":"additional","affiliation":[{"name":"Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1695-6544","authenticated-orcid":false,"given":"Boris","family":"Khalfin","sequence":"additional","affiliation":[{"name":"Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Svetlana","family":"Bardenstein","sequence":"additional","affiliation":[{"name":"Israeli Ministry of Agriculture and Rural Development, Bet Dagan 50250, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacob","family":"Moran-Gilad","sequence":"additional","affiliation":[{"name":"Microbiology, Advanced Genomics and Infection Control Application Laboratory (MAGICAL) Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,3,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"363","DOI":"10.3389\/fpubh.2018.00363","article-title":"Advances in clinical sample preparation for identification and characterization of bacterial pathogens using metagenomics","volume":"6","author":"Bachmann","year":"2018","journal-title":"Front. 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