Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)

Technical specifications for a EU-wide baseline survey of antimicrobial resistance in bacteria from aquaculture animals

The European Commission requested scientific and technical assistance in the preparation of a EU-wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in Aeromonas spp. isolated from Atlantic Salmon (Salmo salar), European seabass (Dicentrarchus labrax) and trout (Salmo trutta, Salvelinus fontinalis, Oncorhynchus mykiss) intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Vibrio parahaemolyticus and Vibrio alginolyticus in blue mussel (Mytilus edulis) and Mediterranean mussel (Mytilus galloprovincialis) from production areas and at dispatch centres at the EU level. These technical specifications define the target populations, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic analysis of some of the bacteria targeted) and the data reporting requirements. The data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA reporting system.

Review of quorum-quenching probiotics: A promising non-antibiotic-based strategy for sustainable aquaculture

The emergence of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquaculture underscores the urgent need for alternative veterinary strategies to combat antimicrobial resistance (AMR). These measures are vital to reduce the likelihood of entering a post-antibiotic era. Identifying environmentally friendly biotechnological solutions to prevent and treat bacterial diseases is crucial for the sustainability of aquaculture and for minimizing the use of antimicrobials, especially antibiotics. The development of probiotics with quorum-quenching (QQ) capabilities presents a promising non-antibiotic strategy for sustainable aquaculture. Recent research has demonstrated the effectiveness of QQ probiotics (QQPs) against a range of significant fish pathogens in aquaculture. QQ disrupts microbial communication (quorum sensing, QS) by inhibiting the production, replication, and detection of signalling molecules, thereby reducing bacterial virulence factors. With their targeted anti-virulence approach, QQPs have substantial promise as a potential alternative to antibiotics. The application of QQPs in aquaculture, however, is still in its early stages and requires additional research. Key challenges include determining the optimal dosage and treatment regimens, understanding the long-term effects, and integrating QQPs with other disease control methods in diverse aquaculture systems. This review scrutinizes the current literature on antibiotic usage, AMR prevalence in aquaculture, QQ mechanisms and the application of QQPs as a sustainable alternative to antibiotics.

The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems

With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.

Tracking antimicrobial resistance indicator genes in wild flatfish from the English Channel and the North Sea area: A one health concern

Antimicrobial resistance (AMR) is a burgeoning environmental concern demanding a comprehensive One Health investigation to thwart its transmission to animals and humans, ensuring food safety. Seafood, housing bacterial AMR, poses a direct threat to consumer health, amplifying the risk of hospitalization, invasive infections, and death due to compromised antimicrobial treatments. The associated antimicrobial resistance genes (ARGs) in diverse marine species can amass and transmit through various pathways, including surface contact, respiration, and feeding within food webs. Our research, focused on the English Channel and North Sea, pivotal economic areas, specifically explores the occurrence of four proposed AMR indicator genes (tet(A), blaTEM, sul1, and intI1) in a benthic food web. Analyzing 350 flatfish samples' skin, gills, and gut, our quantitative PCR (qPCR) results disclosed an overall prevalence of 71.4% for AMR indicator genes. Notably, sul1 and intI1 genes exhibited higher detection in fish skin, reaching a prevalence of 47.5%, compared to gills and gut samples. Proximity to major European ports (Le Havre, Dunkirk, Rotterdam) correlated with increased AMR gene frequencies in fish, suggesting these ports' potential role in AMR spread in marine environments. We observed a broad dispersion of indicator genes in the English Channel and the North Sea, influenced by sea currents, maritime traffic, and flatfish movements. In conclusion, sul1 and intI1 genes emerge as robust indicators of AMR contamination in the marine environment, evident in seawater and species representing a benthic food web. Further studies are imperative to delineate marine species' role in accumulating and transmitting AMR to humans via seafood consumption. This research sheds light on the urgent need for a concerted effort in comprehending and mitigating AMR risks in marine ecosystems within the context of One Health.

Source Attribution of Antibiotic Resistance Genes in Estuarine Aquaculture: A Machine Learning Approach

Aquaculture located in urban river estuaries, where other anthropogenic activities may occur, has an impact on and may be affected by the environment where they are inserted, namely by the exchange of antimicrobial resistance genes. The latter may ultimately, through the food chain, represent a source of resistance genes to the human resistome. In an exploratory study of the presence of resistance genes in aquaculture sediments located in urban river estuaries, two machine learning models were applied to predict the source of 34 resistome observations in the aquaculture sediments of oysters and gilt-head sea bream, located in the estuaries of the Sado and Lima Rivers and in the Aveiro Lagoon, as well as in the sediments of the Tejo River estuary, where Japanese clams and mussels are collected. The first model included all 34 resistomes, amounting to 53 different antimicrobial resistance genes used as source predictors. The most important antimicrobial genes for source attribution were tetracycline resistance genes tet(51) and tet(L); aminoglycoside resistance gene aadA6; beta-lactam resistance gene blaBRO-2; and amphenicol resistance gene cmx_1. The second model included only oyster sediment resistomes, amounting to 30 antimicrobial resistance genes as predictors. The most important antimicrobial genes for source attribution were the aminoglycoside resistance gene aadA6, followed by the tetracycline genes tet(L) and tet(33). This exploratory study provides the first information about antimicrobial resistance genes in intensive and semi-intensive aquaculture in Portugal, helping to recognize the importance of environmental control to maintain the integrity and the sustainability of aquaculture farms.

Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics

Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.

Antibiotic Resistance Profiles and ARG Detection from Isolated Bacteria in a Culture-Dependent Study at the Codfish Industry Level

The antibiotic resistance phenomenon horizontally involves numerous bacteria cultured from fresh or processed seafood matrix microbiomes. In this study, the identified bacteria from food-producing processes and industrial environments were screened for phenotypic and genotypic resistance determinants. A total of 684 bacterial strains [537 from processed codfish (Gadus morhua and Gadus macrocephalus) products as salted and seasoned and soaked and 147 from environmental samples] were isolated. Antibiotic susceptibility tests showed resistance against tetracycline, oxacillin, and clindamycin in the Staphylococcus genus (both from food and environmental samples) and against beta-lactams (cefotaxime, carbapenems, etc.) and nitrofurans (nitrofurantoin) from E. coli and Salmonella enterica serovar. Enteritidis isolates. One-thousand and ten genetic determinants-tetracycline tetC (25.17%), tetK (21.06%), tetL (11.70%), clindamycin ermC (17.23%), ermB (7.60%), linezolid cfr (8.22%), optrA (3.62%), poxtA (2.05%), and oxacillin mecA (17.37%)-were amplified from Gram-positive resistant and phenotypically susceptible bacteria. Concerning Gram-negative bacteria, the beta-lactam-resistant genes (bla_TEM, bla_CIT, bla_CTX-M, bla_IMP, bla_KPC, bla_OXA-48-like) represented 57.30% of the amplified ARGs. This study found high antibiotic resistance genes in circulation in the fish food industry chain from the macro- to microenvironment. The obtained data confirmed the diffusion of the "antibiotic resistance phenomenon" and its repercussions on the One-health and food-producing systems.

Misunderstandings and misinterpretations: Antimicrobial use and resistance in salmon aquaculture

The exponential growth of aquaculture over the past 30 years has been accompanied by a parallel increase in the use of antimicrobials. This widespread use has had negative effects on animal, human and environmental health and affected the biodiversity of the environments where aquaculture takes place. Results showing these harmful effects have been resisted and made light of by the aquaculture industry and their scientific supporters through introduction of misunderstandings and misinterpretations of concepts developed in the evolution, genetics, and molecular epidemiology of antimicrobial resistance. We focus on a few of the most obvious scientific shortcomings and biases of two recent attempts to minimise the negative impacts of excessive antimicrobial use in Chilean salmon aquaculture on human and piscine health and on the environment. Such open debate is critical to timely implementation of effective regulation of antimicrobial usage in salmon aquaculture in Chile, if the negative local and worldwide impacts of this usage are to be avoided.

Tetracycline Resistance Genes in the Traditional Swedish Sour Herring surströmming as Revealed Using qPCR

Antibiotic resistance (AR) represents a global concern for human health. To the best of the authors' knowledge, no study addressing AR in surströmming, a traditional Swedish fermented herring, has been performed to date. The aim of the present research was to study the prevalence of tet(O), tet(S), tet(W), tet(K), and tet(M) genes encoding for resistance to tetracycline using quantitative PCR (qPCR) applied to ready-to-eat surströmming samples collected from three producers located in Sweden. The tet(M) gene was found in all the analyzed samples, and it was also the most abundant among the tested tet genes; moreover, tet(O) was the least frequently detected gene. As a general trend, all the analyzed samples showed a high occurrence of the target genes, with slight variations among the producers. A principal component analysis did not reveal any separation among the samples or producers. All the collected data allowed for a drawing of a first picture of the occurrence of tetracycline resistance genes in ready-to-eat surströmming samples. Since no differences among the samples manufactured by the different producers were observed, it is likely that the detected genes were homogeneously spread among the microbial species shared by the herrings used as raw materials. Moreover, it can be hypothesized that the presence of the detected genes was also the result of a selective pressure of the natural marine environment on the herrings' gut microbiota and, hence, on the pro-technological microorganisms responsible for the fermentation of surströmming. However, the contribution of the manufacturers to the contamination of the processed herrings cannot be excluded.

Characterization of Antibiotic Resistant Coliform Bacteria and Resistance Genes Isolated from Samples of Smoothie Drinks and Raw Milk

Raw foodstuffs have been marked as a healthier alternative in the context of nutrient content and are becoming more popular with consumers. Thermally untreated foods may represent a microbiological risk connected with the possible presence of antimicrobial resistance. The aim of this study was to prove that popular raw food beverages such as smoothies and raw milk may be a source of antibiotic-resistant coliform bacteria and resistant genes. The majority of antibiotic-resistant isolates (110) were identified as Enterobacter spp., Escherichia coli, and species of Klebsiella spp., predominantly β-lactam and chloramphenicol resistant. Multidrug resistance has been registered in one-third of resistants. Overproduction of efflux pumps was clarified in 8 different bacteria. The majority of resistant isolates were strong biofilm producers. Antibiotic resistance gene blaOXA was detected in 25% of isolates, especially in E. coli. Resistance genes blaTEM and blaSHV were detected in 19% and 14%, respectively. This is the first study to point out that popular raw drinks such as smoothies or raw milk, besides their nutrient benefits, could represent a reservoir of antibiotic-resistant bacteria as well as antibiotic resistance genes. According to this, raw drinks could contribute to the dissemination of antibiotic resistance in the human gastrointestinal tract and environment.

Antibiotic standards stored as a mixture in water: methanol are unstable at various temperatures irrespective of pH and glass container silanization

It is well-established that antibiotics stored individually at their optimal pH and in appropriate solvents are stable over time. However, limited information exists on the stability of antibiotics from multiple classes when prepared and stored as a mixture prior to multiresidue analysis by mass spectrometry. This study tested the stability of antibiotic standard mixtures from eight classes [amphenicols, tetracyclines, sulfonamides, quinolones, macrolides, β-lactams, lincosamides and miscellaneous (i.e., trimethoprim)] in relation to the water:methanol ratio, presence of sodium hydroxide base (to solubilise quinolones), storage temperature, and container type including plain and silanized glass vials. Antibiotics were analysed by ultra-high-performance liquid chromatography coupled to tandem mass spectrometry. Several antibiotics, mainly quinolones, tetracyclines and macrolides, were unstable when stored as mixtures for one week regardless of the water:methanol ratio, storage temperature (4, -20 or -80 °C) and presence/absence of sodium hydroxide. Silanization of glassware improved the storage stability of quinolones and macrolides but reduced the stability of tetracyclines and other antibiotics including florfenicol amine, penicillin G, erythromycin and sulfadiazine. Our results show that several antibiotics in water:methanol are unstable when stored as a mixture and suggest a limited advantage of using base or silanized glass vials for the preparation and storage of antibiotic standards mixed together. Freshly prepared antibiotic standard mixtures are recommended for multi-residue quantitation of antibiotics.Abbreviations AMOX: amoxicillin; AMP: ampicillin; AZ: azithromycin; CAP: chloramphenicol; CE: collision energy; CTC: chlortetracycline; CIP: ciprofloxacin; DOX: doxycycline; ENO: enoxacin; ENRO: enrofloxacin; ERYTH: erythromycin; FF: florfenicol; FFA: florfenicol amine; FLU: flumequine; HDPE: high-density polyethylene; LC-MS/MS: liquid chromatography-tandem mass spectrometry; LIN: lincomycin; MRM: multiple reaction monitoring; NOR: norfloxacin; OFL-D3: ofloxacin-D3; OXO: oxolinic acid; OTC: oxytetracycline; PEN-G: penicillin G; PEN-V: penicillin V; ROX: roxithromycin; SDM: sulfadimethoxine; SDZ: sulfadiazine; SMX: sulfamethoxazole; SMZ-D4: sulfamethazine-D4; SSZ: sulfasalazine; TC: tetracycline; TAP: thiamphenicol; TILM: tilmicosin; TRIM: trimethoprim; TL: tolerance limit; VIRG: virginiamycin; UPLC-MS/MS: ultra-high pressure liquid chromatography-tandem mass spectrometry.

No evidence for a relationship between farm or transformation process locations and antibiotic resistance patterns of Pseudomonas population associated with rainbow trout (Oncorhynchus mykiss)

AIMS

Study the relationship between antibiotic resistance patterns of Pseudomonas isolated from farmed rainbow trout fillets and farm or transformation process locations.

METHODS AND RESULTS

Pseudomonas strains were isolated from rainbow trout sampled in two differently located farms and filleted in laboratory or in a processing factory. One hundred and twenty-five isolates were confirmed as belonging to Pseudomonas using CFC selective media, Gram staining, oxidase test and quantitative polymerase chain reaction methods. Fifty-one isolates from separate fish fillets were further identified using MALDI-TOF mass spectrometry, and the minimal inhibitory concentrations (MIC) of 11 antibiotics were also determined by microdilution method. Most of the isolates belonged to the Pseudomonas fluorescens group (94.1%), and no relationship was established between antibiotic resistance patterns and sampling locations (farms or filleting areas). Multiple resistance isolates with high MIC values (from 64 µg ml^-1 to more than 1024 µg ml^-1 ) were identified.

CONCLUSIONS

Antibiotic resistance patterns found in Pseudomonas isolates were not influenced by farms or transformation process locations. Seven isolates were found highly resistant to four different antibiotic classes.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study does not provide evidence of a relationship between farm or transformation process locations on antibiotic resistance patterns of Pseudomonas population.

Antimicrobial Susceptibility Profiles and Resistance Genes in Genus Aeromonas spp. Isolated from the Environment and Rainbow Trout of Two Fish Farms in France

This study presents the occurrence and abundance of Aeromonas antibiotic-resistant bacteria (ARB) and genes (ARGs) isolated from water, biofilm and fish in two commercial trout farms before and one week after flumequine treatment. Wild (WT) and non-wild (NWT) strains were determined for quinolones (flumequine, oxolinic acid and enrofloxacin), oxytetracycline (OXY), florfenicol (FFN), trimethoprim-sulfamethoxazole (TMP) and colistin (COL), and pMAR (presumptive multi-resistant) strains were classified. Forty-four ARGs for the mentioned antibiotics, β-lactams and multi-resistance were quantified for 211 isolates. BlaSHV-01, mexF and tetE were the dominant ARGs. A greater occurrence and abundance of tetA2, sul3, floR1, blaSHV-01 and mexF were observed for NWT compared to WT. The occurrence of pMAR and NWT Aeromonas for quinolones, OXY, FFN, TMP, COL and ARGs depended on the Aeromonas origin, antibiotic use and the presence of upstream activities. Our results revealed the impact of a flumequine treatment on Aeromonas present on a fish farm through an increase in NWT and pMAR strains. The link between fish and their environment was shown by the detection of identical ARB and ARGs in the two types of samples. There appears to be a high risk of resistance genes developing and spreading in aquatic environments.