Antimicrobial resistance and associated genetic determinants of Aliivibrio colonizing the gastrointestinal tract of farmed Atlantic Salmon (Salmo salar L.)

Description

Currently there is very limited readily available data concerning antimicrobial resistance of bacteria colonizing farmed Atlantic salmon. Recent data indicates the gastrointestinal tract mucosa of adult Atlantic salmon farmed in Tasmania (Australia) is colonized con-sistently by species of Aliivibrio. Aliivibrio and other Vibrionaceae may be linked to gut dysbiosis caused by overgrowth. Antibiotic susceptibility analysis was conducted for At-lantic salmon Aliivibrio isolates and across genus Aliivibrio to link antimicrobial resistance phenotypes, presence of antibiotic resistance genes, and mobile genetic elements. Salmon Aliivibrio isolates were resistant to multiple antibiotic drug classes (penams, tetracycline, sulfonamides, macrolides, aminoglycosides), including antibiotics important for aquacul-ture prophylaxis. Susceptibility was observed for chloramphenicol, oxolinic acid, ciprof-loxacin, rifampicin, meropenem, trimethoprim, and trimethoprim-sulfamethoxazole. The resistance profile of Aliivibrio isolates can be explained by intrinsic resistance coinciding with a core set of ARGs common for genus Aliivibrio. Plasmids or integrons carrying ARGs were not found amongst the salmon isolates. Strains of several Aliivibrio species carried ARGs on integrons based on available genome data, including genes providing potential resistance to chloramphenicol (cpt, catB), tetracyclines (tetE), sulfonamides (sul2), trime-thoprim (dfrA1), and potentially aminoglycosides. From the results resistance levels be-yond estimated epidemiological cutoff values has likely not occurred in Aliivibrio in At-lantic salmon farmed in Tasmania. Predominance of the strains in the Atlantic salmon gut microbiome could be at least partly enabled by intrinsic resistance to antibiotics. The data represented here includes the following: 1) Antibiotic resistance array data showing presence absence for individual ARGs for Aliivibrio genomes. 2) Integron locational data for Aliivibrio genomes. 3) MIC data 4) 16S rRNA gene sequences (V1-V3 region) only. Data published in prior paper (https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1564052/full) 5) Supplementary data a) Genome data for Aliivibrio including results of Mob-Recon (plasmids) b) List of ARG genes found in Aliivibrio c) Integron results summary including protein coding gene content and ARG presence d) Phylogram showing alignment of CatB (chloramphenicol acetytransferase type B) and Vat (virginiamycin/streptogramin acetytransferase) proteins from Aliivibrio compared to reference proteins from KEGG orthology.

Steps to reproduce

For dataset 1: ARG detection used CARD, Mob-Recon and IntegronFinder programs. CARD database was operated online https://card.mcmaster.ca/ using Aliivibrio genome data (see dataset 5). Mob-Recon and IntegronFinder analysis used Galaxy Australia cloud server. This was followed up with BLASTP searches using proteins from the KEGG orthology which comprehensively lists antibiotic resistance genes (list is at this address - https://www.kegg.jp/brite/ko01504). The proteins in the addendum dataset in KEGG were used to survey Aliivibrio genomes For dataset 2: The annotation output from IntegronFinder - the data only includes whether the integrons were intact or CALIN, the positions including location of the integron integrase(s). For dataset 3. MIC data generated using standard dilution plating. Breakpoints (in blue or pink) were estimated from data from Vibrionaceae (no data exists for Aliivibrio). Guidelines described in CLSI VET03 and VET04 were otherwise followed. For dataset 4. 16S rRNA gene sequences (partial V1-V3 region) of Atlantic salmon isolates tested for MIC and surveyed for ARGs. This is a FASTA file. For dataset 5. Genome data was obtained from NCBI and GTDB (https://gtdb.ecogenomic.org/). ARG and integron results are refined from analyses indicated above for datasets 1 and 2. Phylogram was generated using phyogeny.fr using the one-click method with tree unmodified except labels which were made shorter. Other information is included in the manuscript "Antimicrobial resistance and associated genetic determinants of Aliivibrio colonizing the gastrointestinal tract of farmed Atlantic Salmon (Salmo salar L.)" which has been submitted for review at the journal Antibiotics (MDPI publishers).

Institutions

• University of Tasmania

  Tasmania, Hobart

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