Marine aquaculture practices and their influence on the circulation of antibiotic microbial resistances and pathogens in floating farm socio-ecosystems

Most research on Infectious Diseases (IDs) and antimicrobial resistances (AMRs) has focused on inland systems with comparatively little efforts directed towards marine habitats. However, marine and particularly coastal environments can function as transmission foci for potentially pathogenic bacteria (PPB) and/or AMRs because they gather concentrated aggregations of environmental, human and animal related bacteria from different sources, both marine and terrestrial. Health risk is exacerbated in developing regions where treatment of hospital and household sewages, an important source of pathogens, antimicrobial resistance genes (ARGs) and antibiotics released into the coastal environment, is limited (if not inexistent) and where intensive aquaculture has expanded over the last three decades. Here we present the results from an interdisciplinary project that investigates the relation between aquaculture farming practices and their potential contribution to AMR and PPB development and spread in Vietnamese floating fish farms. Our study focuses on the case of farms located in the Nha Trang bay area. Our dataset combines 55 qualitative interviews conducted with farmers, as well as with other stakeholders of the fish/crustaceans supply chain (including juvelines providers, pharmacists, civil officers in charge of the enforcement of animal health regulations etc.) with environmental and biological data: 384 water and sediments samples, 249 animal samples and 65 human samples (skin and fecal swabs). 

Our results show that despite existing regulations regarding their use, antibiotics are part of a risk management strategy in a context of uncertainty, where farmers have no insurance and little control and information about water quality, feed prices and market demand. This uncertainty, along with the wide availability of antibiotics, explains the wide use of several drugs including antibiotics belonging to the critical list from the WHO. Metabarcoding and metagenomic analyses reveal a strong imprint of aquaculture activities on the coastal pathobiome and resistome with a high prevalence of resistance (80%) to rifampicin in marine bacteria. Other phenotypic resistances are also revealed, particularly to carbapenems, although at a lower extent, but multidrug resistance is relatively frequent, which is a concern. In addition, our cultural approach shows that 10 potential human pathogenic bacteria (including E. coli and K. pneumoniae) are shared between all compartments (livestock, humans and the environment) suggesting a strong connectivity with an active circulation of potential pathogenic bacteria and resistome between compartments. Overall our work will shed light on the embededness of livestock health management and human health risk; it will thus discuss the « one health » risk related to aquaculture production in marine environments.