Study of the Microbial Ecology, and its Resistome, in Wild Caught and Commercialised Atlantic Mackerel (Scomber scombrus L.)

Abstract

Atlantic mackerel is a commercial fish species that is caught and consumed in many countries. As a potential vector for hazardous bacteria to enter our food chain, it is important to investigate when these bacteria are more likely to originate, and to what extent this is affected by current health issues, such as the rise of antimicrobial resistance. To this purpose, we explored the taxonomy and metabolic functions from the commensal microbial communities (skin and intestinal mucosa) of mackerel caught from the Solent strait (Portsmouth, U.K), as well as allochthonous and environmental microbiomes (digesta, water and sediment). By further exploring the microbiota of commercially available specimens, we investigated whether potential hazardous bacteria, such as carriers of antimicrobial resistance genes, were more likely to originate in nature and/or during the handling process. Emphasis was placed on monitoring the presence of extended-spectrum β-lactamase producing Enterobacteriaceae and vancomycin-resistant Enterococcus. A polyphasic approach, using culture-based techniques as well as metataxonomic and whole-genome shotgun sequencing, was used. The different methodologies provided different viewpoints of the microbial community present, however, the metataxonomic analysis was the most reliable indicator of diversity in this study. The results revealed that the water influenced the skin microbiome of wild caught specimens more than that of mucosa and digesta samples. However, the skin microbiome remained significantly distinct, mostly because of the high relative abundance of members of the bacterial genera Vibrio, Photobacterium, Aliivibrio, Shewanella and Mycoplasma. The composition of the microbiome of the intestinal mucosa was similar to that of the digesta, but members of the bacterial genera Desulfovibrio, Mycoplasma and
Brevinema were more abundant and appeared to be commensal. In the commercial samples, the skin was dominated by the genera Photobacterium, Pseudomonas, Shewanella, Psychrobacter and Pseudoalteromonas, but other spoilage bacteria such as Brochothrix, Carnobacterium and Flavobacterium were also significantly more abundant than in other samples. In the intestinal mucosa of commercial specimens, the genus Photobacterium was the most abundant, representing over 94% of the relative abundance. Although some species within these genera could represent a health threat to consumers, none of the isoi
lates recovered from the previous samples were identified as hazardous. Mapping sequencing reads against the Comprehensive Antibiotic Resistance Database, revealed that most relative abundant antimicrobial resistance genes potentially found across samples – sul1, acrB, mdtE, mexK, mdtK, mexW, emrR and CTX-M – could potentially confer sulfonamide, β-lactam and multidrug resistance. Thus, clinically important antimicrobial resistance genes accumulated to detectable levels in all samples. To date, this is the most in-depth study exploring the microbiota of wild caught and commercially available Atlantic mackerel and the
potential risk they represent to human health.

Date of Award	3 Apr 2023
Original language	English
Awarding Institution	University of Portsmouth
Supervisor	Joy Watts (Supervisor) & Michelle Hale (Supervisor)