Complete genome sequence and functional analysis of a multidrug-resistant Flavobacterium bizetiae strain isolated from farmed Atlantic salmon (Salmo salar)

@article{ko2026complete,
  title = {{Complete genome sequence and functional analysis of a multidrug-resistant Flavobacterium bizetiae strain isolated from farmed Atlantic salmon (Salmo salar)}},
  author = {Sungjae Ko and Lyu Jin Jun and Suhee Hong},
  journal = {BMC Microbiology},
  year = {2026},
  month = jul,
  doi = {10.1186/s12866-026-05458-x},
  url = {https://doi.org/10.1186/s12866-026-05458-x},
  note = {CC BY-NC-ND 4.0},
}

TY  - JOUR
TI  - Complete genome sequence and functional analysis of a multidrug-resistant Flavobacterium bizetiae strain isolated from farmed Atlantic salmon (Salmo salar)
AU  - Sungjae Ko
AU  - Lyu Jin Jun
AU  - Suhee Hong
PY  - 2026
DA  - 2026/07/29
JO  - BMC Microbiology
DO  - 10.1186/s12866-026-05458-x
UR  - https://doi.org/10.1186/s12866-026-05458-x
AB  - Background: Species of the genus Flavobacterium are ubiquitous in aquatic environments and play key roles in nutrient cycling. However, their taxonomic classification is often complicated by high phenotypic similarity, and their potential as reservoirs for antimicrobial resistance (AMR) in aquaculture is a growing concern. This study aimed to resolve the taxonomic status and characterize the resistome and metabolic potential of a Flavobacterium strain isolated from a diseased Atlantic salmon (Salmo salar).  Methods: Whole-genome sequencing (WGS) was performed using the PacBio HiFi platform. Taxonomic identification was rigorously confirmed via multiple metrics, including JSpeciesWS (ANI) and the TYGS platform (dDDH and whole-genome phylogenomics). High-quality functional annotation was performed using the state-of-the-art Bakta pipeline, while antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were analyzed using CARD, ISfinder, and IntegronFinder. To validate the genomic findings, phenotypic antimicrobial susceptibility testing (AST) was conducted using disk diffusion and Minimum Inhibitory Concentration (MIC) panels, alongside conventional PCR for targeted resistance gene detection.  Results: The complete circular chromosome of 6,402,102 bp was definitively identified as Flavobacterium bizetiae AS-HAN-256023, supported by 100% phylogenomic clustering with the type strain, 95.36% ANIb, and 68.3% dDDH. Phenotypic analysis revealed an extensive multidrug-resistant (MDR) profile (e.g., ampicillin and doxycycline MICs > 128 µg/mL). The resistome comprised 21 ARGs. Crucially, MGE analysis revealed that the “last-resort” carbapenemase JOHN-1 is stably integrated, whereas multiple copies of tet(X2) are actively driven by IS1595-family transposases within an MDR island. Furthermore, the strain possesses an intact Type IX secretion system (T9SS) lacking MGE interruptions, coupled with host-barrier-degrading chitinases (GH18 and GH20), and a robust 6 mA-dominated epigenetic defense system. Notably, while targeted PCR only detected the erm(F) gene, WGS provided a much more comprehensive view of the resistome, capturing 20 additional ARGs missed by the PCR approach. The complete genome sequence of F. bizetiae AS-HAN-256023 has been deposited in GenBank under the accession number JBYJWJ000000000.  Conclusions: This study demonstrates that seemingly non-pathogenic environmental isolates like F. bizetiae act as active, functional reservoirs for high-risk, “last-resort” resistance genes in aquaculture settings. The discrepancy between PCR and WGS results underscores the limitations of targeted diagnostic methods and highlights the urgent need for non-targeted, high-resolution genomic surveillance to monitor the dissemination of AMR in the global fishing industry.
SN  - 1471-2180
ER  -