Table 5.

Stratification of environmental sources, transmission routes and risk factors of AMR ‐ aquaculture production sector

AMR Sources/risk factors aquaculture	Fresh water		Marine water			Supporting references	Comments and uncertainties
	Fish	Shrimps	Fish	Shrimps	Bivalves
Primary production
Water (fresh marine) and sediments Human faecal waste (sewage and sludge). Livestock faecal waste (manure and run‐off)	++ +	?/+ ?	+ +	?/+ ?/+	++ ++	Lupo et al. (2012), Berendonk et al. (2015), Leonard et al. (2015), Bürgmann et al. (2018), Novais et al. (2018), Antunes et al. (2018), Zago et al. (2020)	Water, and associated sediment is a major route for disseminating ARB and ARGs that can originate from sources such as human faecal waste and/or animal faecal waste. Often the pollution source is not investigated or known. Water and sediment also contain indigenous bacteria, including fish pathogens with intrinsic AMR that may pose a threat to human health.
Feed	+	+	+	+	?/–	Cabello (2006), Muziasari et al. (2017), Novais et al. (2018)	AMR has been reported as a contaminant of fish meal which is traded internationally and makes up a major component of feed in aquaculture systems.
Workers	?/+	?/+	?/+	?/+	?/+	Fernandes et al. (2018)	The mentioned literature relates to Salmonella and documents a transfer of AMR pathogens from fish products to workers not the other way around. That workers will have an impact on the aquaculture itself seems rather unlikely, especially in comparison to other sources.
Wildlife (fish, mammals, birds)	?/+	?/+	+	?/+	?/+	Radhouani et al. (2011), Di Cesare et al. (2013)
Antimicrobials	+	?/+	+	?/+	?/–	Samuelsen et al. (1991), Rico et al. (2019)	Contamination originates mostly from water (except for the antimicrobials in fish feed). Direct publications on the shrimps in Europe are not available.
Heavy metals	+	?/+	+	?/+	?/+	Costello et al. (2001), Tornero and Hanke (2016), Bannister et al. (2019)	Heavy metals are used as antifouling agents on marine aquaculture infrastructure and historically also as molluscicides.
Biocides	?/+	?/+	?/+	?/+	?/+	Costello et al. (2001), Tornero and Hanke (2016)	Biocides are used as disinfectants in many aquaculture systems.
Post‐harvest (transport and processing)
Ice	?/+	?/+	?/+	?/+	?/–	Fernandes et al. (2018), Vaiyapuri et al. (2019)	The citations do not focus on European aquaculture, here we did not find any information. Most literature only details contamination with pathogenic bacteria, which is a well‐known phenomenon.
Fresh/marine water	?/+	?/+	?/+	?/+	?/+	Fernandes et al. (2018), Vaiyapuri et al. (2019)	The citations do not focus on European aquaculture, here we did not find any information. Most literature only details contamination with pathogenic bacteria, which is a well‐known phenomenon.
Process water	?/+	?/+	?/+	?/+	?/+		Lack of data to support or dismiss process water as an AMR source during post‐harvest.
Workers	?/+	?/+	?/+	?/+	?/+		Lack of data to support or dismiss workers as an AMR source during post‐harvest.
Wildlife	?/+	?/+	?/+	?/+	?/+		Lack of data to support or dismiss wildlife as an AMR source during post‐harvest.
Equipment	?/+	?/+	?/+	?/+	?/+		Lack of data to support or dismiss equipment as an AMR source during post‐harvest.
Biocides	?/+	?/+	?/+	?/+	?/–		Lack of data to support or dismiss biocides as an AMR source during post‐harvest.

Importance of the single sources is given from – (not important) to + (represents a source/factor of AMR), ++ (important source/factor of AMR). ?: specific information is missing. ?/– No scientific evidence but presumably no source/factor, ?/+ No scientific evidence but presumably source/factor. Importance is assigned based on the presence of supporting references and expert assessment, as scientific evidence on the relative attribution of AMR to the specific environmental sources is generally lacking. Dark gold: environmental sources, red: other selective pressures/risk factors.