Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.

Aims: To survey the presence of indigenous and nonindigenous foodborne bacterial pathogens in displayed prepacked portions of fresh marine fish. Methods and Results: A survey of 50 different samples of fresh marine fish (conger, swordfish, sole, grouper and whiting) was conducted over a period of 5 months. Trays of fillets and steaks were obtained at retail level and tested for foodborne bacterial pathogens. Vibrio cholerae and Salmonella were not detected. Two samples (4%) yielded Vibrio strains carrying a DNA fragment specific for Vibrio parahaemolyticus, but resulted negative to PCR amplification of the virulence‐related tdh gene. Levels of motile Aeromonas ranging from 2·29 to 7·20 log CFU g⁻¹ were found in 31 (62%) samples. All fish portions were positive for the Aeromonas hlyA gene and 38 for both aerA and hlyA genes, which may contribute to diarrhoea‐related virulence. The incidence of Listeria monocytogenes was 10%. Levels of Staphylococcus aureus lower than 2 log CFU g⁻¹ were found in 15 (30%) samples. Numbers of presumptive Clostridium perfringens ranging from 1·82 ± 0·22 to 4·26 ± 1·25 log CFU g⁻¹ were detected in 42 (84%) samples. Edwardsiella tarda was detected in two samples of grouper fillets. Conclusions: Displayed portions of raw fish carried bacteria that can cause foodborne disease. The risk posed by fresh fish when properly cooked is low, but high when destined to be consumed raw, undercooked or very lightly processed. Significance and Impact of the Study: This study revealed that raw fish sold in Spain could be a source of foodborne bacterial pathogens. Improvements in handling and processing are needed to minimize the prevalence of pathogenic bacteria.