Supporting shrimp producers to improve antimicrobial stewardship
A successful SAAFE pilot project has confirmed the feasibility of combining targeted and broad-spectrum approaches for identifying AMR determinants in shrimps and farming environments.
A reliable and reproducible method for identifying antimicrobial resistance (AMR) determinants in farmed shrimp and farming environments has been developed by SAAFE partners. Early findings show that the method can accurately detect AMR genes while also offering insights into potential environmental pathways at a landscape level. The approach provides a starting point for shrimp producers to adopt practical, science-based strategies for improving antibiotic stewardship in collaboration with other key stakeholders.
Having reliable data on AMR will allow seafood producers and regulators to assess risks and develop effective safeguards.
The AMR Keystone Project was led by SAAFE partners SeaBOS (Seafood Business for Ocean Stewardship) and the University of South Australia. SeaBOS is a unique international coalition bringing academic researchers together with some of the world’s largest seafood companies.
“We hope that the project will help SeaBOS member companies to become stewards of responsible use of antibiotics and to inspire others in the global seafood industry to follow,” said Dr Max Troell, a senior researcher at the Stockholm Resilience Centre and the Beijer Institute in Sweden and a lead member of the SeaBOS task force on AMR.
The SAAFE project team started by developing sampling protocols, methodology and analyses using shrimp samples from Thailand, one of the world’s major shrimp producers.
“Our goal was to develop sampling protocols, methodologies and analytical approaches for farm-gate samples from shrimp farms in Thailand to screen for antimicrobial resistance determinants and to support local certified laboratories in building their analytical capacity,” said project lead Associate Professor Barbara Drigo from the University of South Australia.
The first step was to screen for known AMR genes. Dr Oskar Nyberg from the Stockholm Resilience Centre obtained shrimp samples from different farms and worked with researchers at Chulalongkorn University in Bangkok to optimise approaches for whole-genome sequencing and DNA extraction.
The samples were then sent to the University of South Australia for metagenomics analysis, which profiles the composition and functional properties of all microbial communities present in the shrimp, beyond those targeted by whole-genome sequencing.
“Metagenomics allows us to see whatever is in the sample,” said A/Prof. Drigo, “including any evidence of emerging resistance to antimicrobials or disinfection products.”
The sample analyses enabled the team to detect genes conferring resistance to antimicrobial agents and disinfectants in the hepatopancreas of shrimp. The results may indicate potential sources of AMR determinants from upstream agricultural, industrial or urban activities, as well as to guide improvements in farming practices that enhance the yield, quality and overall productivity of the shrimp farms.
The project team also compared shrimp samples from two different farming systems: a conventional grow-out system, where ponds are open to the environment, and an advanced recirculating aquaculture system, where shrimp are held in ultra-pure conditions.
“We found advantages and disadvantages in both systems in terms of mitigating AMR risks,” explained A/Prof. Drigo.
SeaBOS will share these findings with major seafood producers to help them refine their operations and address AMR more effectively.
“The information from this project will help seafood producers better understand the links between their management practices and the determinants of AMR,” said SeaBOS task force member Dr Patrik Henriksson from Leiden University, the Stockholm Resilience Centre and the Beijer Institute. “Moreover, it will provide the scientific basis for decision making to underpin any risk management or trade protocols if required.”
After confirming the feasibility of their approach using additional samples, the project team hopes to expand it, not only to other shrimp-producing countries, including Ecuador, Cambodia, Vietnam and Guatemala, but also for other species, such as tuna in Japan. One of their goals is to build local laboratory capacity, enabling producers in low- and middle-income countries to access this testing capability.