{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T16:06:48Z","timestamp":1771949208074,"version":"3.50.1"},"reference-count":72,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:00:00Z","timestamp":1771891200000},"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>\n                    <jats:italic>Flavobacterium psychrophilum<\/jats:italic>\n                    is a Gram-negative bacterium that acts as a primary etiological agent of bacterial cold-water disease (BCWD) in salmonid fish. In the past 5 years, this pathogen has also been isolated from multiple freshwater fish species in China, including crucian carp (\n                    <jats:italic>Carassius auratus gibelio<\/jats:italic>\n                    ), grass carp (\n                    <jats:italic>Ctenopharyngodon idellus<\/jats:italic>\n                    ) and silver carp (\n                    <jats:italic>Hypophthalmichthys molitrix<\/jats:italic>\n                    ), and identified as the causal agent of overwintering mortality syndrome. We report the whole-genome sequencing and analysis of\n                    <jats:italic>F. psychrophilum<\/jats:italic>\n                    strain NJ01, the first isolate from crucian carp, a cyprinid host. The NJ01 genome consists of a circular chromosome of approximately 2.85 Mb with a GC content of 32.5%, encoding about 2,300 predicted proteins. Comparative genomic analysis with reference strains revealed that NJ01 retains the core genomic features of\n                    <jats:italic>F. psychrophilum<\/jats:italic>\n                    while harboring unique genetic elements that may contribute to host specificity and environmental adaptation. NJ01 also harbors genes associated with antibiotic resistance and stress response, suggesting adaptation to aquaculture conditions. Phylogenomic analysis placed NJ01 within a distinct lineage, consistent with CH46 strains isolated from rainbow trout in china. Notably, NJ01 encodes a unique combination of virulence-associated factors such as adhesion proteins, secreted enzymes, and membrane transporters, which may facilitate infection in crucian carp. This study provides novel insights into the genomic basis of\n                    <jats:italic>F. psychrophilum<\/jats:italic>\n                    pathogenicity in a cyprinid host. The distinct virulence gene repertoire of NJ01 highlights potential host-specific pathogenic strategies and broadens current understanding of\n                    <jats:italic>F. psychrophilum<\/jats:italic>\n                    evolution. These findings may support the development of targeted measures for managing emerging\n                    <jats:italic>F. psychrophilum<\/jats:italic>\n                    infections in carp aquaculture.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1751566","type":"journal-article","created":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T15:42:25Z","timestamp":1771947745000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genomics of crucian carp-isolated Flavobacterium psychrophilum: toward the foundations of overwintering mortality syndrome"],"prefix":"10.3389","volume":"17","author":[{"given":"Hucheng","family":"Jiang","sequence":"first","affiliation":[{"name":"Freshwater Fisheries Research Institute of Jiangsu Province","place":["Nanjing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhe","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Oceanography, Hohai University","place":["Nanjing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanhua","family":"Zhao","sequence":"additional","affiliation":[{"name":"Freshwater Fisheries Research Institute of Jiangsu Province","place":["Nanjing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Hao","sequence":"additional","affiliation":[{"name":"College of Oceanography, Hohai University","place":["Nanjing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Runbo","family":"Li","sequence":"additional","affiliation":[{"name":"Jiangsu Marine Fisheries Research Institute","place":["Nantong, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aijun","family":"Xia","sequence":"additional","affiliation":[{"name":"Freshwater Fisheries Research Institute of Jiangsu Province","place":["Nanjing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Xue","sequence":"additional","affiliation":[{"name":"Freshwater Fisheries Research Institute of Jiangsu Province","place":["Nanjing, China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,2,24]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e126","DOI":"10.1093\/nar\/gks406","article-title":"PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies","volume":"40","author":"Akhter","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids"},{"key":"B3","doi-asserted-by":"publisher","first-page":"giz119","DOI":"10.1093\/gigascience\/giz119","article-title":"PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria","volume":"8","author":"Bayliss","year":"2019","journal-title":"Gigascience"},{"key":"B4","doi-asserted-by":"publisher","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","article-title":"MISA-web: a web server for microsatellite prediction","volume":"33","author":"Beier","year":"2017","journal-title":"Bioinformatics"},{"key":"B5","doi-asserted-by":"publisher","first-page":"W30","DOI":"10.1093\/nar\/gkx343","article-title":"IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets","volume":"45","author":"Bertelli","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1577\/1548-8667(1994)006<0224:EDOPFS>2.3.CO;2","article-title":"Electrophoretic detection of proteases from selected strains of Flexibacter psychrophilus and assessment of their variability","volume":"6","author":"Bertolini","year":"1994","journal-title":"J. Aquat. Anim. Health"},{"key":"B7","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3390\/microorganisms4010014","article-title":"Bacterial multidrug efflux pumps: much more than antibiotic resistance determinants","volume":"4","author":"Blanco","year":"2016","journal-title":"Microorganisms"},{"key":"B8","doi-asserted-by":"publisher","first-page":"W32","DOI":"10.1093\/nar\/gkaf334","article-title":"antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation","volume":"53","author":"Blin","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1128\/CMR.00019-11","article-title":"Stenotrophomonas maltophilia: an emerging global opportunistic pathogen","volume":"25","author":"Brooke","year":"2012","journal-title":"Clin. Microbiol. Rev."},{"key":"B10","doi-asserted-by":"publisher","first-page":"D233","DOI":"10.1093\/nar\/gkn663","article-title":"The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics","volume":"37","author":"Cantarel","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B11","doi-asserted-by":"publisher","first-page":"e0152515","DOI":"10.1371\/journal.pone.0152515","article-title":"Comparative genome analysis provides insights into the pathogenicity of Flavobacterium psychrophilum","volume":"11","author":"Castillo","year":"2016","journal-title":"PLoS ONE"},{"key":"B12","doi-asserted-by":"publisher","first-page":"929","DOI":"10.11964\/jfc.20200512260","article-title":"Isolation, identification and pathogenicity of Flavobacterium psychrophilum from Oncorhynchus mykiss","volume":"45","author":"Chai","year":"2021","journal-title":"J. Fish. China"},{"key":"B13","doi-asserted-by":"publisher","first-page":"1606","DOI":"10.1038\/s41467-021-21748-6","article-title":"Biofilm formation in the lung contributes to virulence and drug tolerance of Mycobacterium tuberculosis","volume":"12","author":"Chakraborty","year":"2021","journal-title":"Nat. Commun."},{"key":"B14","doi-asserted-by":"publisher","first-page":"594","DOI":"10.11964\/jfc.20200912406","volume":"46","author":"Chen","year":"2022","journal-title":"Oncorhynchus mykiss. J. Fish. China"},{"key":"B15","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"004736","DOI":"10.1099\/ijsem.0.004736","article-title":"Flavobacterium baculatum sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field","volume":"71","author":"Chhetri","year":"2021","journal-title":"Int. J. Syst. Evol. Microbiol"},{"key":"B17","author":"Cialini","year":"2025"},{"key":"B18","doi-asserted-by":"publisher","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The Gene Ontology (GO) database and informatics resource","volume":"32","author":"Consortium","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"B19","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1038\/s41579-019-0195-4","article-title":"Type IV pili: dynamics, biophysics and functional consequences","volume":"17","author":"Craig","year":"2019","journal-title":"Nat. Rev. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1111\/raq.12030","article-title":"Virulence mechanisms of bacterial aquaculture pathogens and antivirulence therapy for aquaculture","volume":"6","author":"Defoirdt","year":"2014","journal-title":"Rev. Aqualcult"},{"key":"B22","doi-asserted-by":"publisher","first-page":"W185","DOI":"10.1093\/nar\/gkab341","article-title":"EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure","volume":"49","author":"Dieckmann","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B23","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1016\/S1369-5274(00)00250-2","article-title":"Whole genome plasticity in pathogenic bacteria","volume":"4","author":"Dobrindt","year":"2001","journal-title":"Curr. Opin. Microbiol"},{"key":"B24","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1038\/nrmicro884","article-title":"Genomic islands in pathogenic and environmental microorganisms","volume":"2","author":"Dobrindt","year":"2004","journal-title":"Nat. Rev. Microbiol"},{"key":"B25","doi-asserted-by":"publisher","first-page":"628309","DOI":"10.3389\/fmicb.2021.628309","article-title":"Phage-Mediated control of flavobacterium psychrophilum in aquaculture: in vivo experiments to compare delivery methods","volume":"12","author":"Donati","year":"2021","journal-title":"Front Microbiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1038\/nbt1313","article-title":"Complete genome sequence of the fish pathogen Flavobacterium psychrophilum","volume":"25","author":"Duchaud","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"138","DOI":"10.3389\/fmicb.2018.00138","article-title":"Genomic diversity and evolution of the fish pathogen Flavobacterium psychrophilum","volume":"9","author":"Duchaud","year":"2018","journal-title":"Front. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1111\/j.1365-2761.2006.00756.x","article-title":"Isolation of Flavobacterium psychrophilum from sea lamprey, Petromyzon marinus L., with skin lesions in Lake Ontario","volume":"29","author":"Elsayed","year":"2006","journal-title":"J. Fish Dis."},{"key":"B29","year":"2020","journal-title":"The State of World Fisheries and Aquaculture 2020: Sustainability in Action"},{"key":"B30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1590\/1808-1657000362019","article-title":"Antimicrobials and resistant bacteria in global fish farming and the possible risk for public health","volume":"87","author":"Gazal","year":"2020","journal-title":"Arq. Inst. Biol"},{"key":"B31","doi-asserted-by":"publisher","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","article-title":"Circlize implements and enhances circular visualization in R","volume":"30","author":"Gu","year":"2014","journal-title":"Bioinformatics"},{"key":"B32","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s40793-015-0032-y","article-title":"High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes","volume":"10","author":"Hahnke","year":"2015","journal-title":"Stand Genomic Sci."},{"key":"B33","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/j.micpath.2010.08.002","article-title":"Hemolytic activity in Flavobacterium psychrophilum is a contact-dependent, two-step mechanism and differently expressed in smooth and rough phenotypes","volume":"49","author":"H\u00f6gfors-R\u00f6nnholm","year":"2010","journal-title":"Microb. Pathog"},{"key":"B34","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/s12864-022-08353-7","article-title":"A positive correlation between GC content and growth temperature in prokaryotes","volume":"23","author":"Hu","year":"2022","journal-title":"BMC Genom"},{"key":"B35","unstructured":"Kirby-Bauer disk diffusion susceptibility test protocol\n          \n          123\n          \n            \n              Hudzicki\n              J.\n            \n          \n          Am. Soc. Microbiol.\n          15\n          2009"},{"key":"B36","doi-asserted-by":"publisher","first-page":"059410","DOI":"10.11964\/jfc.20230914162","article-title":"Isolation, identification, and histopathological observation of Flavobacterium psychrophilum from diseased Carassius auratus gibelio","volume":"48","author":"Jiang","year":"2024","journal-title":"J. Fish. China"},{"key":"B37","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"B38","doi-asserted-by":"publisher","first-page":"7676","DOI":"10.1073\/pnas.90.16.7676","article-title":"Cleavage of interleukin 1 beta (IL-1 beta) precursor to produce active IL-1 beta by a conserved extracellular cysteine protease from Streptococcus pyogenes","volume":"90","author":"Kapur","year":"1993","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B39","doi-asserted-by":"publisher","first-page":"4016","DOI":"10.1093\/nar\/gki714","article-title":"Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures","volume":"33","author":"Khachane","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B40","doi-asserted-by":"publisher","first-page":"2110","DOI":"10.1128\/AEM.02800-06","article-title":"Selective phylogenetic analysis targeting 16S rRNA genes of hyperthermophilic archaea in the deep-subsurface hot biosphere","volume":"73","author":"Kimura","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"31","DOI":"10.3147\/jsfp.45.31","article-title":"Mode of the intra-ovum infection of Flavobacterium psychrophilum in salmonid eggs","volume":"45","author":"Kumagai","year":"2010","journal-title":"Fish Pathol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"104053","DOI":"10.1016\/j.micpath.2020.104053","article-title":"Genomic diversity in flavobacterial pathogens of aquatic origin","volume":"142","author":"Kumru","year":"2020","journal-title":"Microb. Pathog."},{"key":"B43","doi-asserted-by":"publisher","first-page":"217","DOI":"10.3354\/dao010217","article-title":"First isolation of Cytophaga psychrophila from a systemic disease in eel and cyprinids","volume":"10","author":"Lehmann","year":"1991","journal-title":"Dis. Aquat. Org"},{"key":"B44","doi-asserted-by":"publisher","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: visualization of intersecting sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans. Vis Comput. Graph."},{"key":"B45","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.1111\/1462-2920.14957","article-title":"Phenotypic divergence of thermotolerance: molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier-inhabiting Cryobacterium strains","volume":"22","author":"Liu","year":"2020","journal-title":"Environ. Microbiol"},{"key":"B46","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/nrmicro3565","article-title":"Twenty years of bacterial genome sequencing","volume":"13","author":"Loman","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"197","DOI":"10.3354\/dao031197","article-title":"Characterization of isolates of Flavobacterium psychrophilum associated with coldwater disease or rainbow trout fry syndrome I: phenotypic and genomic studies","volume":"31","author":"Lorenzen","year":"1997","journal-title":"Dis. Aquat. Org"},{"key":"B48","doi-asserted-by":"publisher","first-page":"e85","DOI":"10.1038\/emi.2016.82","article-title":"flrA, flrB and flrC regulate adhesion by controlling the expression of critical virulence genes in Vibrio alginolyticus","volume":"5","author":"Luo","year":"2016","journal-title":"Emerg. Microb. Infect"},{"key":"B49","doi-asserted-by":"publisher","first-page":"27","DOI":"10.3354\/dao043027","article-title":"Flavobacterium psychrophilum, invasion into and shedding by rainbow trout Oncorhynchus mykiss","volume":"43","author":"Madetoja","year":"2000","journal-title":"Dis. Aquat. Org"},{"key":"B50","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1007\/s00239-020-09974-w","article-title":"Revisiting the relationships between genomic G + C content, RNA secondary structures, and optimal growth temperature","volume":"89","author":"Meyer","year":"2021","journal-title":"J. Mol. Evol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"e01541","DOI":"10.1128\/mBio.01541-16","article-title":"Antibiotic resistance and regulation of the gram-negative bacterial outer membrane barrier by host innate immune molecules","volume":"7","author":"Miller","year":"2016","journal-title":"mBio"},{"key":"B52","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1016\/j.str.2023.11.014","article-title":"PAS domain of flagellar histidine kinase FlrB has a unique architecture and binds heme as a sensory ligand in an unconventional fashion","volume":"32","author":"Mukherjee","year":"2024","journal-title":"Structure"},{"key":"B53","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1046\/j.1365-2761.2003.00488.x","article-title":"Flavobacterium psychrophilum infections in salmonid fish","volume":"26","author":"Nematollahi","year":"2003","journal-title":"J. Fish Dis."},{"key":"B54","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1111\/jfd.12730","article-title":"Antimicrobial susceptibility of Flavobacterium psychrophilum isolates from the United Kingdom","volume":"41","author":"Ngo","year":"2018","journal-title":"J. Fish Dis."},{"key":"B55","doi-asserted-by":"publisher","first-page":"02928","DOI":"10.3389\/fmicb.2018.02928","article-title":"Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers environmental b.acteria and clinical pathogens","volume":"9","author":"Peterson","year":"2018","journal-title":"Front Microbiol"},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.594921","author":"Pritchard","year":"2019","journal-title":"pyani v0.2.8: Average Nucleotide Identity (ANI) and Related Measures for Whole Genome Comparisons"},{"key":"B57","doi-asserted-by":"publisher","first-page":"e02535","DOI":"10.1128\/AEM.02535-18","volume":"85","author":"Rochat","year":"2019","journal-title":"Flavobacterium psychrophilum. Appl. Environ. Microbiol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1128\/AAC.49.2.781-782.2005","article-title":"The biocide triclosan selects Stenotrophomonas maltophilia mutants that overproduce the SmeDEF multidrug efflux pump","volume":"49","author":"Sanchez","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"B59","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1007\/s10482-018-1144-3","article-title":"Temperature-dependent expression of different guanine-plus-cytosine content 16S rRNA genes in Haloarcula strains of the class Halobacteria","volume":"112","author":"Sato","year":"2019","journal-title":"Antonie Van Leeuwenhoek"},{"key":"B60","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":"B61","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1186\/s40168-021-01084-z","article-title":"Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution","volume":"9","author":"Shen","year":"2021","journal-title":"Microbiome"},{"key":"B62","doi-asserted-by":"publisher","first-page":"e00643","DOI":"10.1128\/msystems.00643-23","article-title":"Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon","volume":"8","author":"Silva","year":"2023","journal-title":"mSystems"},{"key":"B63","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1128\/9781555817534.ch13","author":"S\u00f8rum","year":"2005"},{"key":"B64","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"B65","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1016\/j.mib.2008.09.006","article-title":"Comparative genomics: the bacterial pan-genome","volume":"11","author":"Tettelin","year":"2008","journal-title":"Curr. Opin. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1089\/mdr.2016.0103","article-title":"Antimicrobial Susceptibilities of Flavobacterium psychrophilum Isolates from the Great Lakes Basin, Michigan","volume":"23","author":"Van Vliet","year":"2017","journal-title":"Microb. Drug Resist."},{"key":"B67","doi-asserted-by":"publisher","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PloS ONE"},{"key":"B68","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1093\/jac\/dkg050","article-title":"The importance of efflux pumps in bacterial antibiotic resistance","volume":"51","author":"Webber","year":"2003","journal-title":"J. Antimicrob. Chemother."},{"key":"B69","doi-asserted-by":"publisher","first-page":"6668","DOI":"10.1128\/IAI.73.10.6668-6673.2005","article-title":"Expression of the Rickettsia prowazekii pld or tlyC gene in Salmonella enterica serovar Typhimurium mediates phagosomal escape","volume":"73","author":"Whitworth","year":"2005","journal-title":"Infect. Immun."},{"key":"B70","doi-asserted-by":"publisher","first-page":"e1005595","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":"B71","doi-asserted-by":"publisher","first-page":"W6","DOI":"10.1093\/nar\/gkl164","article-title":"BLAST: improvements for better sequence analysis","volume":"34","author":"Ye","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"B72","doi-asserted-by":"publisher","first-page":"D871","DOI":"10.1093\/nar\/gkae968","article-title":"VFDB: an integrated resource for exploring anti-virulence compounds","volume":"53","author":"Zhou","year":"2025","journal-title":"Nucleic Acids Res"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1751566\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T15:42:33Z","timestamp":1771947753000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1751566\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,24]]},"references-count":72,"alternative-id":["10.3389\/fmicb.2026.1751566"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1751566","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,24]]},"article-number":"1751566"}}