Characterization of antibiotic resistance in commensal bacteria from an aquaculture ecosystem

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.

The Combination of β-Glucan and Astragalus Polysaccharide Effectively Resists Nocardia seriolae Infection in Largemouth Bass (Micropterus salmoides)

Effectively treating and preventing outbreaks is crucial for improving the economic benefits of aquaculture. Therefore, utilizing immunostimulants, either alone or in combination, is regarded as a promising strategy. In this study, β-glucan + APS (200 mg/kg + 200 mg/kg), β-glucan (200 mg/kg), APS (200 mg/kg), enrofloxacin (15 mg/kg), and sulfadiazine (15 mg/kg) were added to feed to assess the effects against Nocardia seriolae infection in largemouth bass (Micropterus salmoides) within 14 days. The survival rates did not differ between the enrofloxacin group and the β-glucan + APS group, but both were significantly higher than that of the control group. Additionally, the enrofloxacin group and the β-glucan + APS group exhibited the lowest bacterial loads and tissue damage. Importantly, the β-glucan + APS treatment significantly improved serum enzyme activities (total superoxide dismutase, lysozyme, total protein) and the expression of immune genes (IL-1β, TNF-α, IFN-γ, IgM) compared to the other treatment groups. The enrofloxacin group showed similar efficacy to the β-glucan + APS group in combating N. seriolae infection, but N. seriolae in the enrofloxacin group developed drug resistance. In summary, the combined use of β-glucan and APS is a promising strategy for treating bacterial diseases, thereby contributing to the promotion of sustainable aquaculture development.

Survey of Colistin Resistance in Commensal Bacteria from Penaeus vannamei Farms in China

Aquatic environments are important reservoirs for drug resistance. Aquatic foods may act as carriers to lead antibiotic-resistant commensal bacteria into the human gastrointestinal system, then contacting gut microbiota and spreading antibiotic resistance. Here, several shrimp farms were investigated to identify colistin resistance among commensal bacteria of aquaculture. A total of 884 (41.6%) colistin-resistant isolates were identified among 2126 strains. Electroporation demonstrated that colistin-resistant fragments were present in some commensal bacteria that could be transferred to other bacteria. Most of the resistant bacteria were Bacillus spp., with 69.3% of the Bacillus species exhibiting multiple drug resistance. Bacillus licheniformis was prevalent, with 58 strains identified that comprised six sequence types (ST) based on multilocus sequence typing. Whole-genome sequencing and comparisons with previous B. licheniformis genomes revealed a high degree of genomic similarity among isolates from different regions. Thus, this species is widely distributed, and this study provides new insights into global antibiotic-resistant characteristics of B. licheniformis. Sequence analyses further revealed some of these strains are even pathogenic and virulent, suggesting the antibiotic resistance and hazards of commensal bacteria in aquaculture should be considered. Considering the "One Health" perspective, improved monitoring of aquatic food is needed to prevent the spread of drug-resistant commensal bacteria from food-associated bacteria to humans.

Positive and negative effects of recirculating aquaculture water advanced oxidation: O3 and O3/UV treatments improved water quality but increased antibiotic resistance genes

Recirculating aquaculture systems (RASs) can be efficiently used for aquaculture, and oxidation treatment is commonly used to improve water quality. However, the effects of oxidation treatments on aquaculture water safety and fish yield in RASs are poorly understood. In this study, we tested the effects of O₃ and O₃/UV treatments on aquaculture water quality and safety during culture of crucian carp. O₃ and O₃/UV treatments reduced the dissolved organic carbon (DOC) concentration by ∼40% and destroyed the refractory organic lignin-like features. There was enrichment of ammonia oxidizing (Nitrospira, Nitrosomonas, and Nitrosospira) and denitrifying (Pelomonas, Methyloversatilis, and Sphingomonas) bacteria, and N-cycling functional genes were enriched by 23% and 48%, respectively, after O₃ and O₃/UV treatments. Treatment with O₃ and O₃/UV reduced NH₄⁺-N and NO₂^--N in RASs. O₃/UV treatment increased fish length and weight as well as probiotics in fish intestine. However, high saturated intermediates and tannin-like features induced antibiotic resistance genes (ARGs) in O₃ and O₃/UV treatments, by 52% and ∼28%, respectively, and also enhanced horizontal transfer of ARGs. Overall, the application of O₃/UV achieved better effects. However, understanding the potential biological risks posed by ARGs in RASs and determining the most efficient water treatment strategies to mitigate these risks should be goals of future work.

In Vitro Assessment of Yeasts Strains with Probiotic Attributes for Aquaculture Use

This study aimed to investigate in vitro the probiotic potential of three yeasts strains (BB06, OBT05, and MT07) isolated from agro-food natural sources. Screening was performed, including several functional, technological, and safety aspects of the yeast strains, in comparison to a reference Saccharomyces boulardii, to identify the ones with suitable probiotic attributes in aquaculture. The yeast strains were identified by 5.8S rDNA-ITS region sequencing as Metschnikowia pulcherrima OBT05, Saccharomyces cerevisiae BB06, and Torulaspora delbrueckii MT07. All yeast strains were tolerant to different temperatures, sodium chloride concentrations, and wide pH ranges. S. cerevisiae BB06 showed a strong and broad antagonistic activity. Moreover, the S. cerevisiae strain exhibited a high auto-aggregation ability (92.08 ± 1.49%) and good surface hydrophobicity to hexane as a solvent (53.43%). All of the yeast strains have excellent antioxidant properties (>55%). The high survival rate in the gastrointestinal tract (GIT) can promote yeast isolates as probiotics. All yeast strains presented a resistance pattern to the antibacterial antibiotics. Non-hemolytic activity was detected. Furthermore, freeze-drying with cryoprotective agents maintained a high survival rate of yeast strains, in the range of 74.95−97.85%. According to the results obtained, the S. cerevisiae BB06 strain was found to have valuable probiotic traits.

Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp (Litopenaeus vannamei) aquaculture system

Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m3, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.

Modulation of humoral immunological and antioxidant responses and gut bacterial community and gene expression in rainbow trout, Oncorhynchus mykiss, by dietary lactic acid supplementation

The present study was conducted to find the effects of dietary lactic acid (LA) supplementation on growth performance, hematological characteristics, humoral antioxidant and immunological factors, intestinal gene expression and bacteriological parameters in rainbow trout, Oncorhynchus mykiss. The fish (104 ± 0.90 g) were randomly distributed in twelve tanks (150 L water) as four treatments, receiving diets supplemented with 0, 5, 10, and 20 g/kg LA for 70 days. At the end of the feeding trial, no significant differences were observed in the fish growth performance and survival among the treatments. Blood/plasma red blood cell (5-20 g/kg LA), white blood cell (10 g/kg LA), hematocrit (5 and 10 g/kg LA), hemoglobin (5 and 10 g/kg LA), superoxide dismutase (10 g/kg LA), glutathione peroxidase (10 g/kg LA), total antioxidant capacity (10 g/kg LA), lysozyme (5-20 g/kg LA), and alternative complement activity (10 g/kg LA) significantly increased, as malondialdehyde (10 g/kg LA) significantly decreased in the LA-treated fish. Dietary LA supplementation induced no significant changes in the intestinal defensin gene expression, but significantly up-regulated the expression of toll-like receptor-3 (5-20 g/kg LA), Mx-9 (5-20 g/kg LA), and heat shock protein-70 (5 g/kg LA) genes; the highest expressions were observed at 5 g/kg LA supplementation. Dietary LA supplementation significantly increased total bacterial count (5 and 10 g/kg LA), Lactobacillus sp. (5-20 g/kg LA), and Bacteroides sp. (5-20 g/kg LA), but decreased Streptococcus iniae (5-20 g/kg LA) in the fish intestine; the highest Lactobacillus sp. And Bacteroides sp. Were observed in 10 and 5 g/kg LA supplementation, respectively. Overall, dietary LA supplementation, although has no significant effects on the fish growth performance, is beneficial to improve humoral antioxidant parameters, humoral and intestinal immunological parameters and intestinal microflora. According to the results, dietary 5-10 g/kg LA is recommended for the formulation of rainbow trout feed.

Alleviation of cadmium stress in rice by inoculation of Bacillus cereus

Heavy metal resistant bacteria are of great importance because they play a crucial role in bioremediation. In the present study, 11 bacterial strains isolated from industrial waste were screened under different concentrations of cadmium (Cd) (100 µM and 200 µM). Among 11 strains, the Cd tolerant Bacillus cereus (S₆D_1-105) strain was selected for in vitro and in vivo studies. B. cereus was able to solubilize potassium, and phosphate as well as produce protease and siderophores during plate essays. Moreover, we observed the response of hydroponically grown rice plants, inoculated with B. cereus which was able to promote plant growth, by increasing plant biomass, chlorophyll contents, relative water content, different antioxidant enzymatic activity such as catalase, superoxide dismutase, ascorbate peroxidase, polyphenol oxidase and phenylalanine ammonia-lyase and reducing malondialdehyde content in both roots and leaves of rice plants under Cd stress. Our results showed that the B. cereus can be used as a biofertilizer which might be beneficial for rice cultivation in Cd contaminated soils.

Multi-drug resistance, integron and transposon-mediated gene transfer in heterotrophic bacteria from Penaeus vannamei and its culture environment

Multi-drug resistance (MDR) in bacteria is regarded as an emerging pollutant in different food production avenues including aquaculture. One hundred and sixty out of 2304 bacterial isolates from shrimp farm samples (n = 192) of Andhra Pradesh, India, were MDR. Based on biochemical identification and 16S rRNA sequencing, they were grouped into 35 bacterial species with the predominance of Vibrio parahaemolyticus (12.5%). The MDR isolates showed highest resistance toward oxytetracycline (89%) with more than 0.2 MAR (multiple antibiotic resistance), demonstrates a high-risk source. The most prevalent antibiotic-resistance gene (ARG) and mobile genetic element (MGE) detected were tetA (47.5%) and int1 (46.2%), respectively. In conjugation experiments, overall transfer frequency was found to be in the range of 1.1 × 10^-9 to 1.8 × 10^-3 with the transconjugants harbouring ARGs and MGEs. This study exposed the wide distribution of MDR bacteria in shrimp and its environment, which can further aggravate the already raised concerns of antibiotic residues in the absence of proper mitigation measures.

Water as a Source of Indoor Air Contamination with Potentially Pathogenic Aeromonas hydrophila in Aquaculture

Human activities influence the presence of potentially pathogenic bacteria in indoor air. The aim of this study was to determine the effect of the experimental rearing of European grayling and European perch in a recirculating aquaculture system on the contamination of indoor air with potentially pathogenic Aeromonas hydrophila (PPAH) and the resulting health risks to humans. The PPAH counts, their resistance to seven antibiotics, and the multiple antibiotic resistance (MAR) index were determined in samples of indoor air and water from rearing tanks. The PPAH counts were highest in the laboratory bioaerosol where two fish species were reared. The calculated indoor/outdoor ratio (I/O > 1) demonstrated that tank water was the internal source of PPAH emissions. The unconstrained PCA revealed strong positive relationships (p ≤ 0.05) between the PPAH counts in the indoor air and water samples. Most of the PPAH strains isolated from laboratory air were resistant to tetracycline, cefotaxime, and erythromycin, and 26–82% of the isolates exhibited multiple drug resistance. The values of the MAR index were similar in samples of laboratory air and water (0.23–0.34 and 0.24–0.36, respectively). Agglomerative clustering revealed two clusters of strains isolated from laboratory air and tank water. The results of this study indicate that aquaculture can be a source of indoor air contamination with PPAH.

Probiotic Potentiality from Versatile Lactiplantibacillus plantarum Strains as Resource to Enhance Freshwater Fish Health

Dietary probiotic supplementation has the potential to enhance the health of fish and their disease resistance. In this study, some properties of ten Lactiplantibacillus plantarum strains have been evaluated, for their potential use as probiotics in freshwater fish diet. In particular, antimicrobial activity, antioxidant activity, the potentiality to survive the gastrointestinal transit and persist in the intestine, were evaluated in vitro. The experimental tests were carried out at 15 °C and 30 °C to determine the suitability of these lactic acid bacteria to be used as probiotics in the diet of fish grown at different temperatures. The results demonstrated that the evaluated Lp. plantarum strains, which often have significant differences among themselves, are characterized by important functional characteristics such as cell surface properties (auto-aggregation and hydrophobicity), ability to produce antioxidant substances, capacity to survive in the presence of 0.3% bile salts and acidic environment (2.5 pH), antagonistic activity against some fish opportunistic pathogens (A. salmonicida, Ps. aeruginosa, E. coli and C. freundii) and other unwanted bacteria present in fish products (S. aureus and L. innocua). The outcomes suggest that these Lp. plantarum strains may be candidates as probiotics in warm- and cold-water aquaculture.

Antimicrobial Resistance of Escherichia coli From Aquaculture Farms and Their Environment in Zhanjiang, China

Antimicrobial resistance (AMR) has become a major concern worldwide. To evaluate the AMR of Escherichia coli in aquaculture farms of Zhanjiang, China, a total of 90 samples from the water, soil, and sediment of three aquaculture farms (farms I, II, and III) in Zhanjiang were collected, and 90 strains of E. coli were isolated for drug resistance analysis and AMR gene detection. The results indicated that the isolated 90 strains of E. coli have high resistance rates to penicillin, amoxicillin, ampicillin, tetracycline, compound sulfamethoxazole, sulfisoxazole, chloramphenicol, florfenicol, and rifampin (≥70%). Among these antimicrobial drugs, the resistance rate to rifampicin is as high as 100%. Among the isolated 90 strains of E. coli, all of them were resistant to more than two kinds of antimicrobial drugs, the number of strains resistant to nine kinds of drugs was the largest (19 strains), and the most resistant strain showed resistance to 16 kinds of antibacterial drugs. Regarding the AMR genes, among the three aquaculture farms, the most resistance genes were detected in farm II (28 species). The detection rate of bla_TEM, bla_CIT, bla_NDM, floR, OptrA, cmlA, aphA1, Sul2, oqxA, and qnrS in 90 isolates of E. coli was high (≥50%). The detection rate of carbapenem-resistant genes, such as bla_KPC, bla_IMP, and cfr, was relatively lower ( ≤ 30%), and the detection rate of mcr2 was the lowest (0). At least four AMR genes were detected for each strain, and 15 AMR genes were detected at most. Among them, the number of strains that carried 10 AMR genes was the largest (15 strains). Finally, a correlation analysis found that the AMR genes including bla_TEM, bla_CIT, floR, OptrA, cmlA, aac(3)-II, Sul2, ereA, ermB, oqxB, qnrA, mcr1, and mcr2 had a high correlation rate with drug resistance (≥50%). To summarize, the 90 strains of E. coli isolated from water, surrounding soil, and sediment samples showed resistance to multi-antimicrobial drugs and carried various antimicrobial resistance genes. Thus, it is essential to strengthen the rational use of antimicrobial drugs, especially the amide alcohol drugs, and control the AMR in the aquaculture industry of Zhanjiang, China.

Environmental antimicrobial resistance is associated with faecal pollution in Central Thailand's coastal aquaculture region

We assessed antimicrobial resistance (AMR) potential to seven major classes of antibiotics in Central Thailand's coastal aquaculture region using high-throughput qPCR targeting 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In parallel, we used MinION next generation sequencing (NGS) of 16S rRNA gene amplicons, qPCR of faecal pollution makers, and conventional plate count methods for the comprehensive characterization of environmental microbiomes. We tested the hypothesis that aquaculture increases environmental AMR by comparing ARGs and MGEs in water and sediment samples from five aquaculture sites and their associated canals. There was no evidence from the ARG and MGE data that aquaculture is a major driver of environmental AMR in Central Thailand. Instead, the highest relative prevalence of resistance traits was found in Hua Krabue canal water influenced by urban pollution from Bangkok at the inland edge of the coastal aquaculture region. The sum of ARGs and MGEs, relative to 16S rRNA genes used as markers for overall bacterial abundance, was between 0.495 ± 0.011 and 0.498 ± 0.013 in Hua Krabue canal water, compared with at most 0.132 ± 0.005 in all the other environmental samples. Corresponding patterns were observed for most faecal pollution markers, which were also elevated in Hua Krabue canal water.

Antibiotic resistance in shellfish and major inland pollution sources in the drainage basin of Kamak Bay, Republic of Korea

Shellfish-growing areas in marine environments are affected by pollutants that mainly originate from land, including streams, domestic wastewater, and the effluents of wastewater treatment plants (WWTPs), which may function as reservoirs of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The objective of this study was to identify the occurrence and distribution of antibiotic resistance at five oyster sampling sites and 11 major inland pollution sources in the drainage basin of Kamak Bay, Republic of Korea. Culture-based methods were used to estimate the diversity and abundance of antibiotic-resistant Escherichia coli strains isolated from oysters and major inland pollution sources. The percentages of ARB and multiple antibiotic resistance index values were significantly high in discharge water from small fishing villages without WWTPs. However, the percentages of antibiotic-resistant E. coli isolates from oysters were low, as there was no impact from major inland pollutants. Fourteen ARGs were also quantified from oysters and major inland pollution sources. Although most ARGs except for quinolones were widely distributed in domestic wastewater discharge and effluent from WWTPs, macrolide resistance genes (ermB and msrA) were detected mainly from oysters in Kamak Bay. This study will aid in tracking the sources of antibiotic contamination in shellfish to determine the correlation between shellfish and inland pollution sources.

Antimicrobial resistance in the farm-to-plate continuum: more than a food safety issue

Antimicrobial resistance (AMR) threatens to reverse the essential benefits of antibiotics, not only in humans, where decades of advancements in healthcare outcomes are endangered, but also in the food production industry. As the world moves toward Sustainable Development Goals, food safety is a critical element to improve and strengthen global health, and ensure sustainable development. Emergence of AMR in the food production industry represents a serious risk for exposed workers, their relatives and consumers. This perspective presents the challenge of AMR through the lens of food safety, by highlighting its multisectoral and multidimensional implications not only on the Sustainable Development Goals for food safety and public health but also on food security, animal health and welfare, the environment and climate, and socioeconomic development.

Antibiotic resistance related to biofilm formation in Streptococcus suis

Streptococcus suis (S. suis) is an important zoonotic agent, which seriously impacts the pig industry and human health in various countries. Biofilm formation is likely contributing to the virulence and drug resistance in S. suis. A better knowledge of biofilm formation as well as to biofilm-dependent drug resistance mechanisms in S. suis can be of great significance for the prevention and treatment of S. suis infections. This literature review updates the latest scientific data related to biofilm formation in S. suis and its impact on drug tolerance and resistance.Key points• Biofilm formation is the important reasons for drug resistance of SS infections.• The review includes the regulatory mechanism of SS biofilm formation.• The review includes the drug resistance mechanisms of SS biofilm.

Development of phage delivery by bioencapsulation of artemia nauplii with Edwardsiella tarda phage (ETP-1)

This study proposed that phage-enriched artemia could be a useful tool for transferring phage into the cultured fish (larvae or adult) as a feed, and introduce mode of phage administration and its safety in concern of tissue adaptation for efficient phage therapy in aquatic animals. First, whether Edwardsiella tarda phage (ETP-1) could attach or ingest by the artemia and optimum time period for the ETP-1 enrichment with artemia were investigated. ETP-1 dispersion, abundance and persistency, and zebrafish immune transcriptional responses and histopathology were evaluated after feeding the fish with ETP-1-enriched artemia. Hatched artemia nauplii (36 h) were enriched with 1.90 × 10¹¹ PFUmL^-1 of ETP-1, and maintained at 25 °C. The highest enrichment level was obtained after 4 h (3.00 × 10⁹ PFUmL^-1), and artemia were alive and active similar to control for 8 h. ETP-1 disseminated dose dependently to all the tissues rapidly (12 h). However, when feeding discontinued, it drastically decreased at day 3 with high abundance and persistency in the spleen (1.02 × 10³) followed by the kidney (4.00 × 10¹) and the gut (1 × 10¹ PFUmL^-1) for highest ETP-1-enriched artemia dose. In contrast, during continuous delivery of ETP-1-enriched artemia, ETP-1 detected in all the tissues (at day 10: gut; 1.90 × 10⁷, kidney; 3.33 × 10⁶, spleen; 5.52 × 10⁵, liver; 6.20 × 10⁴ PFUmL^-1mg^-1 tissues). Though the phage abundance varied, results indicated that oral fed ETP-1-enriched artemia disperse to the neighboring organs, even the absence of host as phage carrier. Non-significant differences of immune transcriptional and histopathology analysis between ETP-1-enriched artemia fed and controls suggest that no adverse apparent immune stimulation in host occurred, and use of ETP-1 at 10¹¹ PFUmL^-1 was safe. With further supportive studies, live artemia-mediated phage delivery method could be used as a promising tool during phage therapy against pathogenic bacteria to control aquatic diseases.

Propagation of antibiotic resistance genes in an industrial recirculating aquaculture system located at northern China

The increasing prevalence and spread of antibiotic resistance genes (ARGs) in intensive aquaculture environments are of great concern to food safety and public health. However, the level of ARGs and their potential propagation factors in an industrial recirculating aquaculture system (RAS) have not previously been comprehensive explored. In this study, the levels of 14 different ARG markers and 2 kinds of mobile genetic elements (MGEs) were investigated in a RAS (including water, fish, feces, pellet feed meal, and biofilm samples) located northern China. qnrA, qnrB, qnrS, qepA, aac(6')-Ib, and floR were dominant ARGs, which average concentration levels were presented at 4.51-7.74 copies/L and 5.36-13.07 copies/g, respectively, suggesting that ARGs were prevalent in RAS with no recorded history of antibiotic use. Elevated level of ARGs was found in water of RAS even after the final UV treatment compared with its influent. In RAS, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Planctomycetes were the predominant phyla. Notably, elevated levels of potential opportunistic pathogens were observed along with abundant ARGs suggesting an increasing risk of capturing ARGs and MGEs for human pathogens. This study has revealed for the first time that reared fish, their feces, pellet feed meal as the introduction sources and the selection roles of treatment units co-driven the ARG profile, and the co-selection of water environmental factors and their consequently induced bacterial community shifts formed by their influence are the determining drivers for the ARG propagation in RAS.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

Unravelling the menace: detection of antimicrobial resistance in aquaculture

One of the major problems to be addressed in aquaculture is the prominence of antimicrobial resistance (AMR). The occurrence of bacterial infections in cultured fishes promotes the continuous use of antibiotics in aquaculture, which results in the selection of proliferated antibiotic-resistant bacteria and increases the possibility of transfer to the whole environment through horizontal gene transfer. Hence, the accurate cultivation-dependent and cultivation-independent detection methods are very much crucial for the immediate and proper management of this menace. Antimicrobial resistance determinants carrying mobile genetic transfer elements such as transposons, plasmids, integrons and gene cassettes need to be specifically analysed through molecular detection techniques. The susceptibility of microbes to antibiotics should be tested at regular intervals along with various biochemical assays and conjugation studies so as to determine the extent of spread of AMR. Advanced omic-based and bioinformatic tools can also be incorporated for understanding of genetic diversity. The present review focuses on different detection methods to unearth the complexity of AMR in aquaculture. This monitoring helps the authorities to curb the use of antibiotics, commencement of appropriate management measures and adequate substitute strategies in aquaculture. The long battle of AMR could be overcome by the sincere implementation of One Health approach. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of antibiotics and increased antimicrobial resistance (AMR) are of major concerns in aquaculture industry. This could result in global health risks through direct consumption of cultured fishes and dissemination of AMR to natural environment through horizontal gene transfer. Hence, timely detection of the antimicrobial-resistant pathogens and continuous monitoring programmes are inevitable. Advanced microbiological, molecular biological and omic-based tools can unravel the menace to a great extent. This will help the authorities to curb the use of antibiotics and implement appropriate management measures to overcome the threat.

Water environments: metal-tolerant and antibiotic-resistant bacteria

The potential threat of both metals and antibiotics to the environment and human health has raised significant concerns in the last decade. Metal-resistant and antibiotic-resistant bacteria are found in most environments, including water, and the risk posed to humans and animals due to the spread of antibiotic-resistant bacteria and antibiotic-resistant genes in the environment is increasing. Bacteria have developed the ability to tolerate metals even at notable concentrations. This ability tends to favor the selection of antibiotic-resistant strains, even in pristine water environments, with the potential risk of spreading this resistance to human pathogens. In this mini-review, we focus on investigations performed in marine and freshwater environments worldwide, highlighting the presence of co-resistance to metals and antibiotics.

Water environments: metal-tolerant and antibiotic-resistant bacteria

The potential threat of both metals and antibiotics to the environment and human health has raised significant concerns in the last decade. Metal-resistant and antibiotic-resistant bacteria are found in most environments, including water, and the risk posed to humans and animals due to the spread of antibiotic-resistant bacteria and antibiotic-resistant genes in the environment is increasing. Bacteria have developed the ability to tolerate metals even at notable concentrations. This ability tends to favor the selection of antibiotic-resistant strains, even in pristine water environments, with the potential risk of spreading this resistance to human pathogens. In this mini-review, we focus on investigations performed in marine and freshwater environments worldwide, highlighting the presence of co-resistance to metals and antibiotics.

Biological HRPs in wastewater

Biological high-risk pollutants (HRPs) have become a serious threat to human health worldwide, and wastewater is one of the major sources of them in a natural environment. Despite the long history of wastewater research, comprehensive understanding of the role and behavior of HRPs during wastewater treatment is still limited owing to the complexity of the community. In recent decades, the rapid development of molecular tools, especially the wide application of next generation sequencing technologies, helps to unravel the community composition, structure, and dynamic variation in wastewater. Overall, this chapter mainly focuses on biological HRPs, including bacteria, viruses, protozoa, helminth, biotoxins, antibiotic resistance genes and antibiotic resistant bacteria in wastewater. The characteristics, classification, fates, functions, and health implications of these HRPs are introduced in detail. Moreover, the biogeography of HRPs is a research hotspot in recent years, and available information is also summarized in this chapter. Finally, we also propose the future research needs of HRPs in wastewater after the comprehensive summary of the existing research reports. This chapter is wished to be helpful for beginners to quickly understand the biological HRPs in wastewater.

Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method

Fishmeal is a fundamental ingredient of feedstuffs and is used globally in aquaculture. However, there are few data on the antibiotic resistance genes (ARGs) and human pathogenic bacteria in fishmeal and little understanding of the potential risks of fishmeal application in mariculture systems. Here, we investigated the high-throughput profiles of ARGs and human potential pathogenic bacteria (HPPB) in representative fishmeals (n = 5) and the potential impact of fishmeal on mariculture sediments. ARGs were quantified with microbial DNA quantitative PCR arrays and HPPB were analyzed with Illumina sequencing of 16S rRNA genes. The impact of the fishmeal on the aquaculture sediments was assessed in a microcosm study. Twenty-four unique ARGs (3-14 per sample) and 25 HPPB species were detected in the fishmeal samples. The most prevalent ARGs were fluoroquinolone resistance genes. The overall abundance of HPPB was 5.0-25.5%, and the HPPB species were dominated by Vibrio parahaemolyticus, Clostridium novyi, and Escherichia coli. In the mariculture microcosm sediment, fishmeal significantly increased the normalized abundance of the class I integrase gene (25.4-fold), which plays an important role in the dissemination of ARGs. Dosing with fishmeal also contributed to increases in a resident sulfanilamide resistance gene (sulI gene) and the emergence of a macrolide resistance gene (ermB gene) in the sediment. These findings demonstrated that fishmeal itself is an underestimated reservoir and source of ARGs and HPPBs, and that the application of fishmeal facilitates the dissemination of ARGs in aquaculture sediments. Our results extend our knowledge of the ARGs and HPPB within fishmeal and may provide a feasible and effective approach to the detection of ARGs and HPPB in fishmeal during food safety inspection. Graphical abstract ᅟ.

Use of probiotics in aquaculture of China-a review of the past decade

China is the largest aquaculture producer in the world. Antibiotics were extensively used to ensure the development of the intensive aquaculture; however, the use of antibiotics causes safety- and environment-associated problems. As an alternative strategy to antibiotics, aquatic probiotics have attracted attention. The microbial organisms used as probiotics or tested as potential probiotics in Chinese aquaculture belong to various taxonomic divisions, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and yeast. Moreover, the mixture of probiotic strains and synbiotics are also widely used. Studies on the mode of action of aquatic probiotics have extended our understanding of the probiotic effects, and novel mechanisms have been discovered, such as interference of quorum sensing. However, use of probiotics in Chinese aquaculture is still at an initial stage, and there are potential risks for some probiotic applications in aquaculture. Further regulation and management are required to normalize the production and usage of aquatic probiotics. In this review, we discuss species, effects, and mode of actions of probiotics in Chinese aquaculture since 2008. Challenges and future directions for research are also discussed.

Monitoring Antimicrobial Resistance Dissemination in Aquatic Systems

This special issue on Antimicrobial Resistance in Environmental Waters features 11 articles on monitoring and surveillance of antimicrobial resistance (AMR) in natural aquatic systems (reservoirs, rivers), and effluent discharge from water treatment plants to assess the effectiveness of AMR removal and resulting loads in treated waters. The occurrence and distribution of antimicrobials, antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was determined by utilizing a variety of techniques including liquid chromatography—mass spectrometry in tandem (LC-MS/MS), traditional culturing, antibiotic susceptibility testing (AST), molecular and OMIC approaches. Some of the key elements of AMR studies presented in this special issue highlight the underlying drivers of AMR contamination in the environment and evaluation of the hazard imposed on aquatic organisms in receiving environments through ecological risk assessments. As described in this issue, screening antimicrobial peptide (AMP) libraries for biofilm disruption and antimicrobial candidates are promising avenues for the development of new treatment options to eradicate resistance. This editorial puts into perspective the current AMR problem in the environment and potential new methods which could be applied to surveillance and monitoring efforts.

The effects of marine farm-scale sequentially integrated multi-trophic aquaculture systems on microbial community composition, prevalence of sulfonamide-resistant bacteria and sulfonamide resistance gene sul1

Aquaculture, one of the most important food production practices worldwide, faces serious challenges of mitigating the detrimental impacts of intensive farming on the environment and increased prevalence of antibiotic resistance. To develop an environment-friendly aquaculture system, a land-based and farm-scale sequentially integrated multi-trophic aquaculture (IMTA) system was established for farming Chanos chanos in southwestern Taiwan. In this system, fishes are cultured in combination with organic extractive shellfish and inorganic extractive seaweed. This study aimed to evaluate the prevalence of sulfonamide-resistant bacteria, microbial community structure, and occurrence of sulfonamide resistance genes in the IMTA and traditional aquaculture systems. Water and sediment samples were collected before raising and after harvesting C. chanos. Our results showed that the occurrence of sulfonamide-resistant phenotypes in the IMTA system was comparable with that in influent seawater, while the traditional system exhibited a high sulfonamide resistance rate. Additionally, the traditional system resulted in a deviation of the bacterial community structure from that of seawater. In the water samples from the IMTA system and influent seawater, Proteobacteria and Bacteroidetes were the two dominant phyla, representing approximately 75% and 15% of the community, respectively. In the traditional system, Actinobacteria, constituting 39% of the community, was the dominant bacterial phylum. Thirty-one sulfonamide-resistant bacterial species were isolated. In conclusion, a sequentially IMTA system showed superior ability to maintain the prevalence of antibiotic resistance and the integrity of the bacterial community structure compared to the traditional farming system, representing a potentially valuable aquaculture system for preserving the sustainability of the marine environment.

Analysis of adult damselfly fecal material aids in the estimation of antibiotic-resistant Enterobacterales contamination of the local environment

Because damselflies are ubiquitously but focally present in natural environments and play a critical role as predators of other insect species, the fecal matter of damselflies may be useful for investigating antibiotic-resistant bacterial populations, including human pathogens, in local environments. We therefore examined the prevalence of antibiotic-resistant bacteria, including Enterobacterales, in fecal material from 383 damselflies (adults and larvae) collected from seven locations around Sapporo City, Japan, in 2016 and 2017. Fecal samples were plated on soybean casein digest (SCD) agar plates with and without antibiotics (SCD-A and SCD-w/o, respectively) to identify environmental bacteria and gut bacteria, respectively, and on MacConkey agar plates with antibiotics (MacConkey-A) to select for Gram-negative bacteria, including human pathogenic Enterobacterales species. The prevalence of colonies on each of the plates was compared, and representative colonies on MacConkey-A plates were identified to the species level using an API 20E kit and the MALDI Biotyper system. Overall, SCD-w/o plates showed a gut bacterial load of approximately 10⁸ colony-forming units per adult damselfly or larva. There was a significant difference between the prevalence of colonies on the SCD-A and MacConkey-A plates, and a significantly increased prevalence of antibiotic-resistant bacteria on MacConkey-A plates was observed in samples collected from Shinoroshinkawa. Cluster analysis based on minimum inhibitory concentration values of 59 representative isolates from MacConkey-A agar plates revealed that samples from Shinoroshinkawa contained a higher prevalence of Enterobacterales than those from other sampling locations. Thus, fecal materials discharged by adult damselflies could be used in future studies as a simple tool for estimating antibiotic-resistant bacteria, including Enterobacterales species, in the local environment.

Use of a filtering process to remove solid waste and antibiotic resistance genes from effluent of a flow-through fish farm

The objective of this study was to investigate reduction in antibiotic resistance genes (ARGs) via targeting solid waste in effluent from a flow-through aquaculture in South Korea. The level of suspended solids in the filtrates was approximately 12.5±2.3mg/L, corresponding to a removal efficiency of 68.8±5.7% irrespective of variations in the size of the filter pores. The total number of particles in the effluent was reduced to the lowest numbers of particles using a filter pore size of 25μm, corresponding to a removal efficiency of 40.3%. Among the 23 ARGs conferring resistance to tetracyclines, beta-lactam antibiotics, sulfonamides, quinolones, macrolides, florfenicol and multidrug, tetracycline resistance genes were the most prevalent with a relative abundance of 67.5%. Of eleven tetracycline resistance genes (tetA, tetB, tetD, tetE, tetG, tetH, tetM, tetQ, tetX, tetZ, tetB/P) analyzed, the relative abundance of tetG was the highest in the effluent. The removal efficiency of the total number of particles showed similar patterns to the removal efficiency of ARGs depending on the size of the filter pores. Levels of ARGs in the filtrates were reduced to approximately 60.5% of those of the ARGs in the effluents. With a filter pore size of 25μm, a maximum removal efficiency of 66.0% was achieved. In particular, the relative abundance of detected tetracycline resistance genes decreased only after passing through the filters, perhaps reflecting the presence of high quantities of tetracycline resistance genes in particles from the fish farm. Using Illumina sequencing based on a 16S rRNA gene, the dominant phyla were found to be Bacteroidetes, Proteobacteria, Planctomycetes and Verrucomicrobia in the effluent. Although the overall composition of the bacterial communities was not significantly changed via filtering tests, only the relative abundance of Bacteroidetes and Proteobacteria was changed. These results demonstrate that a filtering process in aquaculture facilities can be used to reduce solid waste as well as ARGs from aquaculture farms.

Efficacy of cell free supernatant from Bacillus licheniformis in protecting Artemia salina against Vibrio alginolyticus and Pseudomonas gessardii

Bacterial diseases are widespread in aquaculture farms and causative agents often adapt to biofilm mode of growth. These biofilms are detrimental to aquaculture species as they resist antibiotics and other agents that are used to control them. Two bacterial pathogens isolated from infected prawn samples were identified as Vibrio alginolyticus and Pseudomonas gessardii on the basis of morphological features, biochemical characteristics, 16S r RNA gene sequencing and phylogenetic analysis. Their pathogenic nature was confirmed by performing in vivo challenge experiments using Artemia salina as a model system. Seven days post infection, the mortality observed with V. alginolyticus and P. gessardii was 97 ± 4.08% and 77.5 ± 5.24%, respectively. The isolates formed extensive biofilms on polystyrene and glass surfaces. These infections could be controlled in an effective manner by using the cell free supernatant (CFS) of a tropical marine epizoic strain of Bacillus licheniformis D1 that is earlier reported to contain an antimicrobial protein (BLDZ1). The CFS inhibited biofilms in an efficient manner (82.35 ± 1.69 and 82.52 ± 1.11% for V. alginolyticus and P. gessardii, respectively) on co-incubation. In addition, pre-formed biofilms of V. alginolyticus and P. gessardii were also removed (84.53 ± 1.26 and 67.08 ± 1.43%, respectively). Fluorescence and scanning electron microscopic studies confirmed the antibiofilm potential of this protein on glass surfaces. The antibiofilm nature was due to the anti-adhesion and antimicrobial properties exhibited by the CFS. Treatment of A. salina with CFS (6 h prior to infections) was effective in protecting larvae against infections by field isolates. This study highlights the significance of marine natural products in providing alternative biofilm controlling agents to tackle infections and decreasing the usage of antibiotics in aquaculture settings.

Polyvalent protective immunogens identified from outer membrane proteins of Vibrio parahaemolyticus and their induced innate immune response

Vaccines are the most economic, efficient and environment-friendly agents in protecting host against bacterial infection. In aquaculture, polyvalent vaccines targeting more than one bacterial specie are highly demanded due to the presence of various types of bacterial pathogens in farming environment. Here eighteen genes encoding outer membrane proteins of Vibrio parahaemolyticus were cloned and expressed. The expressed recombinant proteins were used for antiserum preparation. Passive and active immune protection of the antiserum and recombinant proteins was investigated in the zebrafish model. Two recombinant proteins, VP1667 and VP2369, showed effective immune protection against at least two genera of bacteria, Vibrio (V. parahaemolyticus and V. alginolyticus), Pseudomonas (P. fluorescens) or/and Aeromonas (A. hydrophila), and thereby are potential polyvalent vaccine candidates to defend against bacterial infection in fish farming. Furthermore, the mechanisms for the two polyvalent vaccines in triggering immune response were explored. Antiserum to VP1667 or VP2369 was not cross-reacted with P. fluorescens and A. hydrophila, whereas both recombinant proteins induced significant innate immune response. Comparatively, VP1667 stimulates stronger lymphokine and monokine, and VP2369 induces stronger humoral immune response, while both produce similar NF-κB, COX-2, TLR-1 and TLR-3 expression. Our results identify two polyvalent vaccines and demonstrate characteristics features of their cross-protection at the content of the innate immune response.

EPSP of L. casei BL23 Protected against the Infection Caused by Aeromonas veronii via Enhancement of Immune Response in Zebrafish

Aquaculture is the fastest-growing food production sector in the world, and it supplies nearly 50% of the global food fish supply. However, disease outbreaks have become a major problem in the fish farming industry. The beneficial contribution of probiotic bacteria to aquatic animals' health has been widely described, and they have been widely used in aquaculture for disease control and growth promotion. However, the action of probiotic bacterial components and mechanisms underlying protection against pathogens afforded by probiotic bacteria remain poorly understood. In the present study, we pre-colonized zebrafish larvae (before hatching) with 17 potential probiotic bacterial strains and screened for those possessing anti-infective effects against Aeromonas veronii. We found that Lactobacillus casei BL23 significantly increased the survival of zebrafish larvae upon A. veronii infection. Using a germ-free (GF) zebrafish model and gut microbiota transplant experiment, we showed that L. casei BL23 per se has anti-infective effects in zebrafish larvae, which does not involve microbiota. Furthermore, we identified an exopolysaccharide-protein complex (EPSP) extracted from L. casei BL23 cells, which consisted of a 40-45 KD size protein and an exopolysaccharide composed of α-Rha, α-Glc, β-GlcNAc, and β-GalNAc. EPSP significantly increased the survival rate of GF zebrafish at a dose of 10-20 μg/ml after A. veronii infection (P < 0.01). In addition, the EPSP induced a higher expression of TLR1 and TLR2, and modulated the expression profile of pro-inflammatory and anti-inflammatory cytokines in zebrafish liver (ZFL) cells. Our data indicated that the anti-infective effect of EPSP from L. casei BL23 was mediated by enhancement of immune responses in zebrafish, which might involve the TLR1/TLR2 signal pathway.

Resistance to Antibiotics, Biocides, Preservatives and Metals in Bacteria Isolated from Seafoods: Co-Selection of Strains Resistant or Tolerant to Different Classes of Compounds

Multi-drug resistant bacteria (particularly those producing extended-spectrum β-lactamases) have become a major health concern. The continued exposure to antibiotics, biocides, chemical preservatives, and metals in different settings such as the food chain or in the environment may result in development of multiple resistance or co-resistance. The aim of the present study was to determine multiple resistances (biocides, antibiotics, chemical preservatives, phenolic compounds, and metals) in bacterial isolates from seafoods. A 75.86% of the 87 isolates studied were resistant to at least one antibiotic or one biocide, and 6.90% were multiply resistant to at least three biocides and at least three antibiotics. Significant (P < 0.05) moderate or strong positive correlations were detected between tolerances to biocides, between antibiotics, and between antibiotics with biocides and other antimicrobials. A sub-set of 30 isolates selected according to antimicrobial resistance profile and food type were identified by 16S rDNA sequencing and tested for copper and zinc tolerance. Then, the genetic determinants for biocide and metal tolerance and antibiotic resistance were investigated. The selected isolates were identified as Pseudomonas (63.33%), Acinetobacter (13.33%), Aeromonas (13.33%), Shewanella, Proteus and Listeria (one isolate each). Antibiotic resistance determinants detected included sul1 (43.33% of tested isolates), sul2 (6.66%), blaTEM (16.66%), blaCTX-M (16.66%), blaPSE (10.00%), blaIMP (3.33%), blaNDM-1 (3.33%), floR (16.66%), aadA1 (20.0%), and aac(6')-Ib (16.66%). The only biocide resistance determinant detected among the selected isolates was qacEΔ1 (10.00%). A 23.30 of the selected isolates were able to grow on media containing 32 mM copper sulfate, and 46.60% on 8 mM zinc chloride. The metal resistance genes pcoA/copA, pcoR, and chrB were detected in 36.66, 6.66, and 13.33% of selected isolates, respectively. Twelve isolates tested positive for both metal and antibiotic resistance genes, including one isolate positive for the carbapenemase gene blaNDM-1 and for pcoA/copA. These results suggest that exposure to metals could co-select for antibiotic resistance and also highlight the potential of bacteria on seafoods to be involved in the transmission of antimicrobial resistance genes.

Selenium nanoparticle-enriched biomass of Yarrowia lipolytica enhances growth and survival of Artemia salina

Controlling disease outbreaks is a major challenge in aquaculture farms and conventional methods are often ineffective. Nutritional supplementation and probiotic preparations help in reducing severity of such infections. The generally regarded as safe yeast (Yarrowia lipolytica) was used in the current study. A marine strain of Y. lipolytica exhibited tolerance towards sodium selenite and formed cell associated selenium nanoparticles (SeNPs). The synthesized nanoparticles were characterized by UV-vis spectroscopy, X-ray diffraction (XRD) and Field Emission Scanning Electron Microscope (FE-SEM) observations. Fourier transform infra-red (FTIR) spectroscopy indicated the role of carboxylic and amine groups in the synthesis of nanoparticles. This SeNP-enriched biomass was used as feed for the model aquaculture system, Artemia salina and compared with normal feed, baker's yeast (Saccharomyces cerevisiae). A. salina fed with SeNP-enriched biomass, showed increased survival rates (96.66%) as compared to those fed with S. cerevisiae (60.0%). The size of the larvae fed with SeNP-enriched biomass of Y. lipolytica was also found to be larger. Additionally, larval groups fed with SeNP-enriched biomass were better protected (70.0% survival) against V. harveyi infection when compared with groups fed with S. cerevisiae (24.44%). This combination of selenium in the nanoparticle form associated with the biomass of Y. lipolytica has potential application in improving health of aquaculture species in farms.

Tetracycline does not directly inhibit the function of bacterial elongation factor Tu

Understanding the molecular mechanism of antibiotics that are currently in use is important for the development of new antimicrobials. The tetracyclines, discovered in the 1940s, are a well-established class of antibiotics that still have a role in treating microbial infections in humans. It is generally accepted that the main target of their action is the ribosome. The estimated affinity for tetracycline binding to the ribosome is relatively low compared to the actual potency of the drug in vivo. Therefore, additional inhibitory effects of tetracycline on the translation machinery have been discussed. Structural evidence suggests that tetracycline inhibits the function of the essential bacterial GTPase Elongation Factor (EF)-Tu through interaction with the bound nucleotide. Based on this, tetracycline has been predicted to impede the nucleotide-binding properties of EF-Tu. However, detailed kinetic studies addressing the effect of tetracycline on nucleotide binding have been prevented by the fluorescence properties of the antibiotic. Here, we report a fluorescence-based kinetic assay that minimizes the effect of tetracycline autofluorescence, enabling the detailed kinetic analysis of the nucleotide-binding properties of Escherichia coli EF-Tu. Furthermore, using physiologically relevant conditions, we demonstrate that tetracycline does not affect EF-Tu’s intrinsic or ribosome-stimulated GTPase activity, nor the stability of the EF-Tu•GTP•Phe-tRNA^Phe complex. We therefore provide clear evidence that tetracycline does not directly impede the function of EF-Tu.

Prevalence, Virulence Genes, Antimicrobial Susceptibility, and Genetic Diversity of Staphylococcus aureus from Retail Aquatic Products in China

Staphylococcus aureus is an important food-borne opportunistic pathogen that frequently causes severe blood and tissue infections or even fatal illnesses. Although S. aureus has been extensively studied in livestock and poultry foods in China, limited information has been reported in aquatic products. Accordingly, in this study, we aimed to characterize S. aureus in aquatic products purchased from retail markets in China. In total, 320 aquatic food samples were collected from 32 provincial capitals in China. The results showed that 119 samples (37.2%, 119/320) were positive for S. aureus by both qualitative and quantitative analyses. The contamination levels of 78.2% of samples ranged from 0.3 to 10 MPN/g, and six samples exceeded 110 MPN/g. A total of 119 S. aureus isolates from positive samples were selected to evaluate virulence factors, antibiotic resistance, and molecular characteristics. All S. aureus isolates were evaluated for the presence of 11 virulence genes by multiplex polymerase chain reaction, and α-hemolysin (hlα, 84.9%), fibronectin-binding protein A (fnbA, 79.0%), S. aureus enterotoxin E (see, 53.8%), and Panton-Valentine leucocidin (pvl, 50.4%) were identified as the major genes. These genes formed 56 different profiles, with the major profile identified as pvl-hlα-fnbA (28.6%). The antimicrobial susceptibility of all isolates was analyzed through the disk diffusion method, and the results showed high resistance to β-lactams, macrolides and tetracyclines, but susceptibility to linezolid and vancomycin. In addition, 26 sequence types (STs) were obtained via multilocus sequence typing, including seven novel STs, among which ST1 (20.2%), ST15 (18.5%), and ST188 (13.4%) were the most common STs. All the isolates were mecC negative, but nine isolates carrying mecA were evaluated by staphylococcal cassette chromosome mec (SCCmec) typing, all of which were SCCmecIII or SCCmecIV types. Isolates of SCCmecIII showed a high prevalence and were multidrug resistant. Our results showed that aquatic products could be a vehicle for transmission of virulence genes and multidrug-resistant S. aureus, representing a potential public health risk. The STs identified in this study indicated the genetic diversity of S. aureus, thereby providing important basic data for the dissemination of S. aureus in aquatic products.

Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture

With the rapid development of aquaculture, the large amounts of pollutants were discharged into the aquatic environment, where the detected antibiotic resistance genes (ARGs) have drawn increasing attention due to their potential threats to ecological environment and human health. Thus, the impact of mariculture on ARGs was assessed and the underlying mechanism of their propagation was explained. Sediments from eight sampling sites were collected along a mariculture drainage ditch, and the sediment in Yellow River Delta National Park was used as a non-mariculture control. Microbial ARGs qPCR array and illumina sequencing of 16S rRNA gene were applied to examine the changing patterns of ARGs and bacterial communities. Results showed that 18 ARGs (3 fluoroquinolone, 1 aminoglycoside, 3 macrolide-lincosamide-streptogramin B, 2 tetracycline, and 9 beta-lactam resistance genes) were influenced by mariculture, and ARGs abundance and diversity were significantly increased in mariculture sediments (p < 0.05). A remarkable shift in bacterial community structure and composition was also observed. The abundance of most of ARGs were significantly decreased in the estuary samples, implying that seawater had a significant dilution effect on the ARGs emission from the mariculture sites. Partial redundancy analysis showed that nutrients, heavy metals, and bacteria communities might directly and indirectly contribute to ARGs propagation, suggesting that the profile and dissemination of ARGs were driven by the combined effects of multiple factors in mariculture-impacted sites.

Evidence of Increased Antibiotic Resistance in Phylogenetically-Diverse Aeromonas Isolates from Semi-Intensive Fish Ponds Treated with Antibiotics

The genus Aeromonas is ubiquitous in aquatic environments encompassing a broad range of fish and human pathogens. Aeromonas strains are known for their enhanced capacity to acquire and exchange antibiotic resistance genes and therefore, are frequently targeted as indicator bacteria for monitoring antimicrobial resistance in aquatic environments. This study evaluated temporal trends in Aeromonas diversity and antibiotic resistance in two adjacent semi-intensive aquaculture facilities to ascertain the effects of antibiotic treatment on antimicrobial resistance. In the first facility, sulfadiazine-trimethoprim was added prophylactically to fingerling stocks and water column-associated Aeromonas were monitored periodically over an 11-month fish fattening cycle to assess temporal dynamics in taxonomy and antibiotic resistance. In the second facility, Aeromonas were isolated from fish skin ulcers sampled over a 3-year period and from pond water samples to assess associations between pathogenic strains to those in the water column. A total of 1200 Aeromonas isolates were initially screened for sulfadiazine resistance and further screened against five additional antimicrobials. In both facilities, strong correlations were observed between sulfadiazine resistance and trimethoprim and tetracycline resistances, whereas correlations between sulfadiazine resistance and ceftriaxone, gentamicin, and chloramphenicol resistances were low. Multidrug resistant strains as well as sul1, tetA, and intI1 gene-harboring strains were significantly higher in profiles sampled during the fish cycle than those isolated prior to stocking and these genes were extremely abundant in the pathogenic strains. Five phylogenetically distinct Aeromonas clusters were identified using partial rpoD gene sequence analysis. Interestingly, prior to fingerling stocking the diversity of water column strains was high, and representatives from all five clusters were identified, including an A. salmonicida cluster that harbored all characterized fish skin ulcer samples. Subsequent to stocking, diversity was much lower and most water column isolates in both facilities segregated into an A. veronii-associated cluster. This study demonstrated a strong correlation between aquaculture, Aeromonas diversity and antibiotic resistance. It provides strong evidence for linkage between prophylactic and systemic use of antibiotics in aquaculture and the propagation of antibiotic resistance.

Prevalence, Molecular Characterization, and Antibiotic Susceptibility of Vibrio parahaemolyticus from Ready-to-Eat Foods in China

Vibrio parahaemolyticus is the leading cause of foodborne outbreaks, particularly outbreaks associated with consumption of fish and shellfish, and represents a major threat to human health worldwide. This bacterium harbors two main virulence factors: the thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH). Additionally, various serotypes have been identified. The extensive use of antibiotics is a contributing factor to the increasing incidence of antimicrobial-resistant V. parahaemolyticus. In the current study, we aimed to determine the incidence and features of V. parahaemolyticus in ready-to-eat (RTE) foods in China. We found 39 V. parahaemolyticus strains on Chinese RTE foods through investigation of 511 RTE foods samples from 24 cities in China. All isolates were analyzed for the presence of tdh and trh gene by PCR, serotyping was performed using multiplex PCR, antibiotic susceptibility analysis was carried out using the disk diffusion method, and molecular typing was performed using enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) typing and multilocus sequence typing (MLST). The results showed that none of the isolates were positive for tdh and trh. Most of the isolates (33.3%) were serotype O2. Antimicrobial susceptibility results indicated that most strains were resistant to streptomycin (89.7%), cefazolin (51.3%), and ampicillin (51.3%). The isolates were grouped into five clusters by ERIC-PCR and four clusters by MLST. We updated 10 novel loci and 33 sequence types (STs) in the MLST database. Thus, our findings demonstrated the presence of V. parahaemolyticus in Chinese RTE foods, provided insights into the dissemination of antibiotic-resistant strains, and improved our knowledge of methods of microbiological risk assessment in RTE foods.

Pharmacokinetics, efficacy prediction indexes, and residue depletion of ribavirin in Atlantic salmon's (Salmo salar) muscle after oral administration in feed

Ribavirin is an antiviral used in human medicine, but it has not been authorized for use in veterinary medicine although it is effective against infectious salmon anemia (ISA) virus, between others. In this study, we present a pharmacokinetic profile of ribavirin in Atlantic salmon (Salmo salar), efficacy prediction indexes, and the measure of its withdrawal time. To determine the pharmacokinetic profile, fishes were orally administered with a single ribavirin dose of 1.6 mg/kg bw, and then, plasma concentrations were measured at different times. From the time-vs.-concentration curve, Cmax = 413.57 ng/mL, Tmax  = 6.96 h, AUC = 21394.01 μg·h/mL, t1/2  = 81.61 h, and K10  = 0.0421/h were obtained. Ribavirin reached adequate concentrations during the pharmacokinetic study, with prediction indexes of Cmax /IC50  = 20.7, AUC/IC50  = 1069.7, and T>IC50  = 71 h, where IC is the inhibitory concentration 50%. For ribavirin depletion study, fishes were orally administered with a dairy dose of 1.6 mg/kg bw during 10 days. Concentrations were measured on edible tissue on different days post-treatment. A linear regression of the time vs. concentration was conducted, obtaining a withdrawal time of 1966 °C days. Results obtained reveal that the dose of 1.6 mg/kg bw orally administered is effective for ISA virus, originating a reasonable withdrawal period within the productive schedules of Atlantic salmon.

Streptomyces Bacteria as Potential Probiotics in Aquaculture

In response to the increased seafood demand from the ever-going human population, aquaculture has become the fastest growing animal food-producing sector. However, the indiscriminate use of antibiotics as a biological control agents for fish pathogens has led to the emergence of antibiotic resistance bacteria. Probiotics are defined as living microbial supplement that exert beneficial effects on hosts as well as improvement of environmental parameters. Probiotics have been proven to be effective in improving the growth, survival and health status of the aquatic livestock. This review aims to highlight the genus Streptomyces can be a good candidate for probiotics in aquaculture. Studies showed that the feed supplemented with Streptomyces could protect fish and shrimp from pathogens as well as increase the growth of the aquatic organisms. Furthermore, the limitations of Streptomyces as probiotics in aquaculture is also highlighted and solutions are discussed to these limitations.