{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:17:53Z","timestamp":1760059073518,"version":"build-2065373602"},"reference-count":31,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T00:00:00Z","timestamp":1747958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"AMED project","doi-asserted-by":"publisher","award":["JP20wm0125007","GP24-03"],"award-info":[{"award-number":["JP20wm0125007","GP24-03"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"JSPS Bilateral Program Joint Research Projects","award":["JP20wm0125007","GP24-03"],"award-info":[{"award-number":["JP20wm0125007","GP24-03"]}]},{"name":"Kajima Foundation\u2019s Support Program for International Joint Research Activities","award":["JP20wm0125007","GP24-03"],"award-info":[{"award-number":["JP20wm0125007","GP24-03"]}]},{"name":"BIKEN Taniguchi Scholarship","award":["JP20wm0125007","GP24-03"],"award-info":[{"award-number":["JP20wm0125007","GP24-03"]}]},{"name":"Juntendo University Center for Diversity and Inclusion","award":["JP20wm0125007","GP24-03"],"award-info":[{"award-number":["JP20wm0125007","GP24-03"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Brucella intermedia, a gram-negative, non-lactose-fermenting, aerobic, rod-shaped bacterium, is found in environmental sources (e.g., soil and water). In 2020, Ochrobactrum was reclassified as Brucella. We conducted a genomic analysis of B. intermedia from hospital wastewater samples in western Ghana. A hybrid genome assembly was constructed integrating short-read data from DNA Nanoball sequencing with long-read sequences generated by Oxford Nanopore MinION technology. Identification and antimicrobial susceptibility profiles were determined using MicroScan autoSCAN-4 based on Clinical and Laboratory Standard Institute documents. ResFinder and CARD Resistance Gene Identifier (RGI) were used to identify antimicrobial resistance (AMR) genes, and BLAST and VFDB datasets were used to identify virulence factor genes. The complete genome had two chromosomes, no plasmid, and a high average nucleotide identity value (98.05%) with B. intermedia. Resistance to trimethoprim-sulfamethoxazole was revealed, the first report in this species. CARD RGI revealed the presence of AMR genes, including ANT(9)-Ic and adeF. Local BLAST analysis revealed Cgs, a B. melitensis virulence factor. B. intermedia is an opportunistic human pathogen clinically isolated several times, suggesting the importance of accurately identifying multidrug resistance. B. intermedia may possess virulence factors similar to those of B. melitensis. Further study is needed to fully elucidate its pathogenesis.<\/jats:p>","DOI":"10.3390\/pathogens14060522","type":"journal-article","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T06:35:09Z","timestamp":1747982109000},"page":"522","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic and Virulence Characteristics of Brucella intermedia Isolated from Hospital Wastewater in Ghana"],"prefix":"10.3390","volume":"14","author":[{"given":"Runa","family":"Furuya","sequence":"first","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5519-7408","authenticated-orcid":false,"given":"Satomi","family":"Takei","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3734-0346","authenticated-orcid":false,"given":"Yoko","family":"Tabe","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Ablordey","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon P. O. Box LG 25, Ghana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3398-8572","authenticated-orcid":false,"given":"Ryoichi","family":"Saito","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"H\u00f6rdt, A., L\u00f3pez, M.G., Meier-Kolthoff, J.P., Schleuning, M., Weinhold, L.-M., Tindall, B.J., Gronow, S., Kyrpides, N.C., Woyke, T., and G\u00f6ker, M. (2020). Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00468"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Yagel, Y., Sestito, S., Motro, Y., Shnaiderman-Torban, A., Khalfin, B., Sagi, O., Navon-Venezia, S., Steinman, A., and Moran-Gilad, J. (2020). Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum. Antibiotics, 9.","DOI":"10.3390\/antibiotics9040177"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3003","DOI":"10.1016\/j.ygeno.2020.04.030","article-title":"Pan-Genomics of Ochrobactrum Species from Clinical and Environmental Origins Reveals Distinct Populations and Possible Links","volume":"112","author":"Gohil","year":"2020","journal-title":"Genomics"},{"key":"ref_4","unstructured":"She, R., Anglewicz, C., Jerke, K., Relich, R., Glazier, M., Filkins, L., and Schuetz, A. (2023). Brucella and Ochrobactrum Taxonomic Updates for Laboratories, American Society for Microbiology."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Ryan, M.P., and Pembroke, J.T. (2020). The Genus Ochrobactrum as Major Opportunistic Pathogens. Microorganisms, 8.","DOI":"10.3390\/microorganisms8111797"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"107171","DOI":"10.1016\/j.envint.2022.107171","article-title":"Systematic Review of Wastewater Surveillance of Antimicrobial Resistance in Human Populations","volume":"162","author":"Chau","year":"2022","journal-title":"Environ. Int."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3011","DOI":"10.2147\/IDR.S468000","article-title":"Colistin Resistance Mediated by Mcr-3-Related Phosphoethanolamine Transferase Genes in Aeromonas Species Isolated from Aquatic Environments in Avaga and Pakro Communities in the Eastern Region of Ghana","volume":"17","author":"Mahazu","year":"2024","journal-title":"IDR"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving Bacterial Genome Assemblies from Short and Long Sequencing Reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_9","unstructured":"CLSI (2014). Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fourth Informational Supplement, Clinical and Laboratory Standards Institute. CLSI Guideline M100-S24."},{"key":"ref_10","unstructured":"CLSI (2022). Performance Standards for Antimicrobial Susceptibility Testing CLSI Guideline M100-Ed32, Clinical and Laboratory Standards Institute."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Hall, B.G., and Nisbet, J. (2023). Building Phylogenetic Trees from Genome Sequences With kSNP4. Mol. Biol. Evol., 40.","DOI":"10.1093\/molbev\/msad235"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"173","DOI":"10.12938\/bmfh.16-003","article-title":"DFAST and DAGA: Web-Based Integrated Genome Annotation Tools and Resources","volume":"35","author":"Tanizawa","year":"2016","journal-title":"Biosci. Microbiota Food Health"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for Predictions of Phenotypes from Genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e02744-23","DOI":"10.1128\/spectrum.02744-23","article-title":"A Standardized Nomenclature for Resistance-Modifying Agents in the Comprehensive Antibiotic Resistance Database","volume":"11","author":"Smith","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic Local Alignment Search Tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"D871","DOI":"10.1093\/nar\/gkae968","article-title":"VFDB 2025: An Integrated Resource for Exploring Anti-Virulence Compounds","volume":"53","author":"Zhou","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate Structure Prediction of Biomolecular Interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e4792","DOI":"10.1002\/pro.4792","article-title":"UCSF ChimeraX: Tools for Structure Building and Analysis","volume":"32","author":"Meng","year":"2023","journal-title":"Protein Sci."},{"key":"ref_20","first-page":"129","article-title":"A Case of Bacteremia Caused by Ochrobactrum intermedium","volume":"90","author":"Hirai","year":"2017","journal-title":"J. Jpn. Assoc. Infect. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/S0255-0857(21)02105-8","article-title":"Review of Clinical and Laboratory Features of Human Brucellosis","volume":"25","author":"Mantur","year":"2007","journal-title":"Indian J. Med. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1093\/glycob\/cwj113","article-title":"Identification of Active Site Residues of the Inverting Glycosyltransferase Cgs Required for the Synthesis of Cyclic \u03b2-1,2-Glucan, a Brucella abortus Virulence Factor","volume":"16","author":"Ciocchini","year":"2006","journal-title":"Glycobiology"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Leclercq, S.O., Cloeckaert, A., and Zygmunt, M.S. (2020). Taxonomic Organization of the Family Brucellaceae Based on a Phylogenomic Approach. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.03083"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1086\/320532","article-title":"Resistance to Trimethoprim-Sulfamethoxazole","volume":"32","author":"Huovinen","year":"2001","journal-title":"Clin. Infect. Dis."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Lin, N., Xu, W., Huang, D., Liu, C., Lu, J., Zhu, M., Bao, Q., and Pan, W. (2025). Aac(6\u2019)-Iaq, a Novel Aminoglycoside Acetyltransferase Gene Identified from an Animal Isolate Brucella Intermedia DW0551. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1551240"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1038\/s41594-022-00868-7","article-title":"Mechanism of Cyclic \u03b2-Glucan Export by ABC Transporter Cgt of Brucella","volume":"29","author":"Sedzicki","year":"2022","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Moreno, E., Blasco, J.M., Letesson, J.J., Gorvel, J.P., and Moriy\u00f3n, I. (2022). Pathogenicity and Its Implications in Taxonomy: The Brucella and Ochrobactrum Case. Pathogens, 11.","DOI":"10.3390\/pathogens11030377"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Yang, Z., Chai, Z., Wang, X., Zhang, Z., Zhang, F., Kang, F., Liu, W., Ren, H., Jin, Y., and Yue, J. (2024). Comparative Genomic Analysis Provides Insights into the Genetic Diversity and Pathogenicity of the Genus Brucella. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1389859"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Zhang, S., Huang, J., Zhao, Z., Cao, Y., and Li, B. (2020). Hospital Wastewater as a Reservoir for Antibiotic Resistance Genes: A Meta-Analysis. Front. Public Health, 8.","DOI":"10.3389\/fpubh.2020.574968"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"136916","DOI":"10.1016\/j.scitotenv.2020.136916","article-title":"Sulfamethoxazole\/Trimethoprim Ratio as a New Marker in Raw Wastewaters: A Critical Review","volume":"715","author":"Thiebault","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s13756-017-0208-x","article-title":"The Threat of Antimicrobial Resistance in Developing Countries: Causes and Control Strategies","volume":"6","author":"Ayukekbong","year":"2017","journal-title":"Antimicrob. Resist. Infect. Control"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/6\/522\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:39:02Z","timestamp":1760031542000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/6\/522"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,23]]},"references-count":31,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["pathogens14060522"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14060522","relation":{},"ISSN":["2076-0817"],"issn-type":[{"type":"electronic","value":"2076-0817"}],"subject":[],"published":{"date-parts":[[2025,5,23]]}}}