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Background <p>Species of the genus <i>Flavobacterium</i> 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 <i>Flavobacterium</i> strain isolated from a diseased Atlantic salmon (<i>Salmo salar</i>).</p> Methods <p>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.</p> Results <p>The complete circular chromosome of 6,402,102&#xa0;bp was definitively identified as <i>Flavobacterium bizetiae</i> 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 &gt; 128&#xa0;µg/mL). The resistome comprised 21 ARGs. Crucially, MGE analysis revealed that the “last-resort” carbapenemase <i>JOHN-1</i> is stably integrated, whereas multiple copies of <i>tet(</i>X2<i>)</i> are actively driven by <i>IS1595</i>-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&#xa0;mA-dominated epigenetic defense system. Notably, while targeted PCR only detected the <i>erm(</i>F<i>)</i> 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 <i>F. bizetiae</i> AS-HAN-256023 has been deposited in GenBank under the accession number JBYJWJ000000000.</p> Conclusions <p>This study demonstrates that seemingly non-pathogenic environmental isolates like <i>F. bizetiae</i> 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.</p>

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

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  • 发表日期：

    2026年7月29日

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  • Sungjae Ko,
  • Lyu Jin Jun,
  • Suhee Hong

摘要

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.