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Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21–15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21–15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of blaMOX-9 and blaOXA-427 β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes.

Additional file 1: Figure S1. Stereo view of the unmodeled electron density at the catalytic center. The σA-weighted 2mFo-Fc electron density around the histidine brace is contoured at 1.0 σ; the phased anomalous difference density map contoured at 4.0 σ shows a large peak, modeled as a copper ion. The figure includes a large peak in the σA-weighted Fo-Fc map contoured at 3.0 σ, visible between the histidine brace and the putative catalytic base (Glu206) and left unmodeled. Table S1. Data collection and refinement statistics

Additional file 4. Differentially abundant ASVs between the yeast and control diets (ileum, caecum). A ileum, d 7 PW, B ileum, d 14 PW, C ileum, d 14 PW (family level), D caecum, d 7 PW (phylum level), E caecum, d 14 PW (phylum level). All taxonomic entities appeared as differentially abundant at FDR = 0.05.

Additional file 2. Relative abundance of bacterial genera in the sequenced mock community standards along with their expected abundance.

The request from NFSA and NEA: Antimicrobial agents and microorganisms are introduced to sewage systems by different human activities, from private homes, institutions such as schools and hospitals, office buildings, industrial and commercial activities, i.e., from everywhere where people work and live. The Norwegian Food Safety Authority (NFSA) and Norwegian Environment Agency (NEA) asked the Norwegian Scientific Committee for Food and Environment (Vitenskapskomiteen for mat og miljø, VKM) for an extension of the 2009 VKM report “Risk assessment of contaminants in sewage sludge applied on Norwegian soils” regarding the impact of wastewater (WW)- and sewage sludge treatment methods used in Norway, on the fate and survival of antimicrobial resistant bacteria, fate of antimicrobial resistance genes, and main drivers for resistance (e.g. antibiotics, antifungal agents, heavy metals, disinfectants). The request addressed by VKM: VKM appointed a working group, consisting of three members of the Panel on Microbial Ecology, four external members and VKM staff to prepare a draft Opinion document. The Panel on Microbial Ecology has reviewed and revised the draft prepared by the working group and approved the Opinion document “Assessment of the impact of wastewater and sewage sludge treatment methods on antimicrobial resistance”. The antimicrobial resistance cycle: Exposure to antimicrobial agents is regarded as the most important driver for development and dissemination of AMR in microorganisms. Consequently, an important location for the development of AMR is the gut of humans or animals receiving antimicrobial drug therapy. As ARB, ARG, resistance genes and antimicrobial agents will end up in the WW system, this system could be regarded as a potential hot spot for interactions between different microorganisms, between different antimicrobial agents, and between microorganisms and antimicrobial agents. Hospitals and pharmaceutical companies are regarded as being an important source for antimicrobial drug residues released in WW. At the wastewater treatment plant (WWTP), bacteria and genes end up either in the effluent wastewater fraction or in the sludge fraction. When ARB and ARG are distributed with the WW sludge, they may reach arable land when the sludge is used as soil improver and fertilising product, and thus be recycled into the food-production chain. When following the effluent WW fraction, ARB and ARB will be released into WW recipients, such as lakes, rivers or fjords, and may, from these environments, also be recycled into food production. In each step of these cycles, ARB and ARG will be introduced into new environmental compartments to which they must adapt, and to microbial communities with which they must compete for survival and growth. Depending on the bacterial species, these new environmental compartments will be more or less hostile, but they will also provide opportunities for microbial interactions, like dissemination of ARG due to horizontal gene transfer (HGT) within and between bacterial species. Findings: It is challenging to deliver a general assessment of the nature of as well as the probability for direct discharge of ARB and ARG into effluent WW and applied sludge. This is due to the combined complexity of resistance carriers, traits, various sources of variation, and the WW systems. Moreover, there is currently a lack of harmonized methods and protocols to compare studies from different systems. However, there are no strong indications that there is a significant enrichment of ARB in WWTP operated under European conditions, which, on a general level, also applies to the Norwegian situation. Although some studies indicate a slight increase in the fraction of ARB, the absolute reduction in bacterial load during WW treatment (WWT) is significant; removal of between 99 % to 99.9 % of faecal indicator bacteria is generally achieved by secondary treatment, including biological and physico chemical treatment steps. Effluent WW is often released into water recipients, and there are many mechanisms (physical, mechanical, and chemical) that will limit the extent that ARB of faecal origin are transferred to the food-production chain. However, there are different views on the significance of this release for the development of AMR. Results from single studies indicate that WWTP effluents contribute little to the total AMR exposure of micro – and macro organisms in aquatic and marine environments. On the other hand, freshwater environments in general are regarded as an important reservoir of novel antibiotic resistance determinants, and in some areas, relative abundance of resistance determinants in effluents has been observed to be considerably higher than in pristine natural water sources. Some imprint of AMR in recipient waters, compared to pristine waters, is unavoidable. During WWT, bacteria largely adhere to particles that are aggregated and precipitated to form a solid sludge. The mandatory hygienisation of sludge kills a large proportion of these bacteria, notably all thermosensitive faecal bacteria. However, the resulting hygienised sludge is still rich in bacteria, some of which are carriers of ARGs. The current Norwegian regulations on use of sludge on soil contribute to prevent contamination of food with antimicrobial resistant bacteria and antimicrobial resistance genes from sludge. Yet, soils do contain a pool of both natural and sludge-derived antimicrobial resistance. The contribution of sludge to this antimicrobial resistance pool is probably temporally limited to a period after soil amendment with sludge. A recent, comprehensive study from Sweden showed that long-term application of sewage sludge on farmland only resulted in minor changes of soil bacterial community composition. No evidence could be found for enrichment of antimicrobial resistant bacteria or antimicrobial resistance genes in soil amended with digested and stored sewage. Hospital WW contains more ARB, ARG, and antibiotic residues than municipal sewage, but the difference is not large for ARB and the impact may be minimal in large WW systems. In smaller WW infrastructures, a hospital or similar institution may have a higher impact on the effluent water from the WWTP, and this might suggest that local treatment of the WW at the hospital could be advantageous. A recent Norwegian study monitored bacterial diversity in different WW in the Oslo area, and found the highest concentration of AMR (ARB and/or ARG) in hospital WW. But surprisingly, high concentrations were also found in the studied community wastewater. The relative contribution of hospital effluents seemed low in terms of dissemination of antimicrobial resistant bacteria to the wastewater treatment plant. All measures that can be taken at source to avoid dissemination of antimicrobial agents, ARB, and ARG should be evaluated for their contribution towards combatting AMR emergence. Concentrations of antimicrobial agents, ARB, and ARG are highest in the sewage system and at the inlet to WWTPs. Separation of the different fractions of antimicrobials, ARB, and ARG for individual treatment may therefore reduce the total load reaching the WWTPs. Due to the high concentrations of ARB and ARG in the sewage system, risks from sewage pipe leakages are of concern. Intrusion of contaminated water into the drinking water distribution system should also raise concern. Rehabilitation of the sewage and drinking water networks will considerably mitigate risks. The level of sewage treatment in Norway is rather low, and upgrading will decrease the concentration of bacteria discharged. However, WWTPs are generally not designed for removal of AMR. Membrane processes seem to be the most promising option for increasing such removal rates. Future perspectives: The opinion discusses how the “concept of sensitive recipients” for requirements of the level of WWT could be revisited. This concept is currently based on controlling nutrient loads to the environment, rather than on trace contaminants or contaminants such as ARB and ARG that develop in the stressed environment. In the future, it might be of value to define requirements for WWT based on the relative increase caused by the discharge to the pollution level. Using such a paradigm, a small load with contaminants to a rather unpolluted environment would be rated as being highly critical and the discharge would require further treatment. In addition to the amount of ARB, the type of resistance and their level of horizontal mobility are also important in this aspect. This opinion also proposes the establishment of a new monitoring programme, parallel to the existing NORM and NORM-VET monitoring programmes; “NORM-ECO”. There is relatively little knowledge on AMR in non-clinical compartments, compared with hospital and other clinical settings, and parameters that would trigger immediate responses from NFAS or NEA are not yet identified. However, establishment of a “NORM-ECO”-system requires clarification of that needs further definition.

Additional file 5. Differentially abundant ASVs between the yeast and control diets (caecum). A, caecum, d 7 PW, B caecum, d 14 PW, C caecum, d 7 PW (family level), D caecum, d 14 PW (family level). All taxonomic entities appeared as differentially abundant at FDR = 0.05.

Additional file 6. Differentially abundant ASVs between the yeast and control diets (colon). A colon, d 7 PW, B colon, d 14 PW, C colon, d 7 PW (family level), D colon, d 14 PW (family level). All taxonomic entities appeared as differentially abundant at FDR = 0.05.

Additional file 3. Alpha bacterial diversity as measured by a) Observed species and b) Shannon diversity index. The average values between the control and yeast group are represented as mean values with standard deviation (SD) along with medians with inter-quartile ranges (IQR). Comparison pairs that correspond to p-values less than 0.05 (MWW test) are given in bold.

Additional file 8. Association of liver index with individual bacterial groups, and colonic butyrate concentration. Panel A: Principal component analysis performed on the relative abundance of Spirochaetaceae, Faecalibacterium and the liver index of pigs measured at days 7 and 14 PW (n = 32 but 2 dots are not shown). The dots are coloured by the diet (control pink; yeast dark cyan). The vectors represent the degree of correlation between the bacterial groups data and the liver index data. Panel B: Correlation plot of colonic butyrate concentration (measured in μM per gram of intestinal contents) against liver index measured in the control group pigs at days 7 and 14 PW (n = 16). The dots are coloured by the diet (control pink). Pearson’s rho is reported above the regression line. Panel C: Correlation plot of colonic butyrate concentration (μM/gram of intestinal contents) against liver index measured in the yeast group pigs at days 7 and 14 PW (n = 16). The dots are coloured by the diet (yeast dark cyan). Pearson’s rho is reported above the regression line.

Additional file 7. Association of colonic butyrate concentration with individual bacterial groups. Panel A: Correlation plot of colonic butyrate concentration (measured in μM per gram of intestinal contents) against F. prausnitzii relative abundance measured at days 7 and 14 PW (n = 32). The dots are coloured by the diet (control pink; yeast dark cyan). Pearson’s rho is reported above the regression line. Panel B: Principal component analysis performed on the relative abundance of Spirochaetaceae, Faecalibacterium, Dialister and molarities of butyrate in the colon of pigs measured at days 7 and 14 PW (n = 32 but 3 dots are not shown). The dots are coloured by the diet (control pink; yeast dark cyan). The vectors represent the degree of correlation between the bacterial groups data and the butyrate concentration data.

Additional file 1. Comparison of bacterial CFUs on the selective agar plates. The values are the group medians (IQR) of logCFUs per gram of lumen contents. The bold font indicates statistically significant level (p