Aquatic animals promote antibiotic resistance gene dissemination in water via conjugation: Role of different regions within the zebra fish intestinal tract, and impact on fish intestinal microbiota

Gut pathobiome mediates behavioral and developmental disorders in biotoxin-exposed amphibians

Emerging evidence suggests a link between alterations in the gut microbiome and adverse health outcomes in the hosts exposed to environmental pollutants. Yet, the causal relationships and underlying mechanisms remain largely undefined. Here we show that exposure to biotoxins can affect gut pathobiome assembly in amphibians, which in turn triggers the toxicity of exogenous pollutants. We used Xenopus laevis as a model in this study. Tadpoles exposed to tropolone demonstrated notable developmental impairments and increased locomotor activity, with a reduction in total length by 4.37%-22.48% and an increase in swimming speed by 49.96%-84.83%. Fusobacterium and Cetobacterium are predominant taxa in the gut pathobiome of tropolone-exposed tadpoles. The tropolone-induced developmental and behavioral disorders in the host were mediated by assembly of the gut pathobiome, leading to transcriptome reprogramming. This study not only advances our understanding of the intricate interactions between environmental pollutants, the gut pathobiome, and host health but also emphasizes the potential of the gut pathobiome in mediating the toxicological effects of environmental contaminants.

Fish skin mucosal surface becomes a barrier of antibiotic resistance genes under apramycin exposure

Antibiotic resistance genes (ARGs) are a kind of emerging environmental contamination, and are commonly found in antibiotic application situations, attracting wide attention. Fish skin mucosal surface (SMS), as the contact interface between fish and water, is the first line of defense against external pollutant invasion. Antibiotics are widely used in aquaculture, and SMS may be exposed to antibiotics. However, what happens to SMS when antibiotics are applied, and whether ARGs are enriched in SMS are not clear. In this study, Zebrafish (Danio rerio) were exposed to antibiotic and antibiotic resistant bacteria in the laboratory to simulate the aquaculture situation, and the effects of SMS on the spread of ARGs were explored. The results showed that SMS maintained the stability of the bacterial abundance and diversity under apramycin (APR) and bacterial exposure effectively. Until 11 days after stopping APR exposure, the abundance of ARGs in SMS (mean value was 3.32 × 10-3 copies/16S rRNA copies) still did not recover to the initial stage before exposure, which means that enriched ARGs in SMS were persistently remained. Moreover, non-specific immunity played an important role in resisting infection of external contamination. Besides, among antioxidant proteins, superoxide dismutase showed the highest activity. Consequently, it showed that SMS became a barrier of antibiotic resistance genes under APR exposure, and ARGs in SMS were difficult to remove once colonized. This study provided a reference for understanding the transmission, enrichment process, and ecological impact of antibiotics and ARGs in aquatic environments.

Effects of eutrophication on the horizontal transfer of antibiotic resistance genes in microalgal-bacterial symbiotic systems

Overloading of nutrients such as nitrogen causes eutrophication of freshwater bodies. The spread of antibiotic resistance genes (ARGs) poses a threat to ecosystems. However, studies on the enrichment and spread of ARGs from increased nitrogen loading in algal-bacterial symbiotic systems are limited. In this study, the transfer of extracellular kanamycin resistance (KR) genes from large (RP4) small (pEASY-T1) plasmids into the intracellular and extracellular DNA (iDNA, eDNA) of the inter-algal environment of Chlorella pyrenoidosa was investigated, along with the community structure of free-living (FL) and particle-attached (PA) bacteria under different nitrogen source concentrations (0-2.5 g/L KNO3). The results showed that KR gene abundance in the eDNA adsorbed on solid particles (D-eDNA) increased initially and then decreased with increasing nitrogen concentration, while the opposite was true for the rest of the free eDNA (E-eDNA). Medium nitrogen concentrations promoted the transfer of extracellular KR genes into the iDNA attached to algal microorganisms (A-iDNA), eDNA attached to algae (B-eDNA), and the iDNA of free microorganisms (C-iDNA); high nitrogen contributed to the transfer of KR genes into C-iDNA. The highest percentage of KR genes was found in B-eDNA with RP4 plasmid treatment (66.2%) and in C-iDNA with pEASY-T1 plasmid treatment (86.88%). In addition, dissolved oxygen (DO) significantly affected the bacterial PA and FL community compositions. Nephelometric turbidity units (NTU) reflected the abundance of ARGs in algae. Proteobacteria, Cyanobacteria, Bacteroidota, and Actinobacteriota were the main potential hosts of ARGs. These findings provide new insights into the distribution and dispersal of ARGs in the phytoplankton inter-algal environment.

A review focusing on mechanisms and ecological risks of enrichment and propagation of antibiotic resistance genes and mobile genetic elements by microplastic biofilms

Microplastics (MPs) are emerging ubiquitous pollutants in aquatic environment and have received extensive global attention. In addition to the traditional studies related to the toxicity of MPs and their carrier effects, their unique surface-induced biofilm formation also increases the ecotoxicity potential of MPs from multiple perspectives. In this review, the ecological risks of MPs biofilms were summarized and assessed in detail from several aspects, including the formation and factors affecting the development of MPs biofilms, the selective enrichment and propagation mechanisms of current pollution status of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in MPs biofilms, the dominant bacterial communities in MPs biofilms, as well as the potential risks of ARGs and MGEs transferring from MPs biofilms to aquatic organisms. On this basis, this paper also put forward the inadequacy and prospects of the current research and revealed that the MGEs-mediated ARG propagation on MPs under actual environmental conditions and the ecological risk of the transmission of ARGs and MGEs to aquatic organisms and human beings are hot spots for future research. Relevant research from the perspective of MPs biofilm should be carried out as soon as possible to provide support for the ecological pollution prevention and control of MPs.

Antimicrobial peptides: An alternative to antibiotic for mitigating the risks of Antibiotic resistance in aquaculture

The utilization of antibiotics increases the prevalence of antibiotic resistance genes (ARGs) in various matrices and poses the potential risk of ARG transmission, garnering global attention. Antimicrobial peptides (AMPs) represent a promising novel category of antimicrobials that may address the urgent issue of antibiotic resistance. Here, a zebrafish cultivation assay in which zebrafish were fed a diet supplemented with AMP (Cecropin A) or antibiotics was conducted to determine the effects of the intervention on the microorganisms and antibiotic resistance spectrum in zebrafish gut samples. Cecropin A treatment decreased the α-diversity of the microbiota. Moreover, NMDS (nonmetric multidimensional scaling) results revealed that the β-diversity in the microbiota was more similar between the control (CK) and Cecropin A samples than between the antibiotic treatment groups. The absolute quantity of ARGs in the AMP treatment was less than that observed in the antibiotic treatment. The findings indicated that FFCH7168, Chitinibacter and Cetobacterium were the most significant biomarkers detected in the CK, Cecropin A and antibiotic treatments, respectively. Although the use of antibiotics notably enhanced the occurrence of multidrug-resistant bacteria, the application of Cecropin A did not lead to this phenomenon. The results indicated that the application of AMPs can effectively manage and control ARGs in aquaculture.

The potential contribution of aquatic wildlife to antibiotic resistance dissemination in freshwater ecosystems: A review

Antibiotic resistance (AR) is one of the major health threats of our time. The presence of antibiotics in the environment and their continuous release from sewage treatment plants, chemical manufacturing plants and animal husbandry, agriculture and aquaculture, result in constant selection pressure on microbial organisms. This presence leads to the emergence, mobilization, horizontal gene transfer and a selection of antibiotic resistance genes, resistant bacteria and mobile genetic elements. Under these circumstances, aquatic wildlife is impacted in all compartments, including freshwater organisms with partially impermeable microbiota. In this narrative review, recent advancements in terms of occurrence of antibiotics and antibiotic resistance genes in sewage treatment plant effluents source compared to freshwater have been examined, occurrence of antibiotic resistance in wildlife, as well as experiments on antibiotic exposure. Based on this current state of knowledge, we propose the hypothesis that freshwater aquatic wildlife may play a crucial role in the dissemination of antibiotic resistance within the environment. Specifically, we suggest that organisms with high bacterial density tissues, which are partially isolated from the external environment, such as fishes and amphibians, could potentially be reservoirs and amplifiers of antibiotic resistance in the environment, potentially favoring the increase of the abundance of antibiotic resistance genes and resistant bacteria. Potential avenues for further research (trophic transfer, innovative exposure experiment) and action (biodiversity eco-engineering) are finally proposed.

Occurrence of Antimicrobial-Resistant Bacteria in Intestinal Contents of Wild Marine Fish in Chile

Antimicrobial-resistant bacteria (ARB) from the intestinal contents of wild fish may have a relevant ecological significance and could be used as indicators of antimicrobial-resistance dissemination in natural bacterial populations in water bodies impacted by urban contamination. Thus, the occurrence of ARB in the intestinal contents of pelagic and demersal wild fishes captured in anthropogenic-impacted Coquimbo Bay in Chile was studied. Culturable counts of total and antimicrobial-resistant bacteria were determined by a spread plate method using Trypticase soy agar and R2A media, both alone and supplemented with the antimicrobials amoxicillin, streptomycin, florfenicol, oxytetracycline and ciprofloxacin, respectively. Heterotrophic plate counts of pelagic and demersal fishes ranged from 1.72 × 106 CFU g-1 to 3.62 × 109 CFU g-1, showing variable proportions of antimicrobial resistance. Representative antimicrobial-resistant isolates were identified by 16S rRNA gene sequencing, and isolates (74) from pelagic fishes mainly belonged to Pseudomonas (50.0%) and Shewanella (17.6%) genera, whereas isolates (68) from demersal fishes mainly belonged to Vibrio (33.8%) and Pseudomonas (26.5%) genera. Antimicrobial-resistant isolates were tested for susceptibility to 12 antimicrobials by an agar disk diffusion method, showing highest resistance to streptomycin (85.2%) and amoxicillin (64.8%), and lowest resistance to oxytetracycline (23.2%) and ciprofloxacin (0.7%). Only furazolidone and trimethoprim/sulfamethoxazole were statistically different (p < 0.05) in comparisons between isolates from pelagic and demersal wild fishes. Furthermore, an important number of these isolates carried plasmids (53.5%) and produced Extended-Spectrum-β-lactamases (ESBL) (16.9%), whereas the detection of Metallo-β-Lactamases and class 1-integron was rare. This study provides evidence that wild fish are important reservoirs and spreading-vehicles of ARB, carrying plasmids and producing ESBLs in Chilean marine environments.

Molecular characteristic of mcr-1 gene in Escherichia coli from aquatic products in Guangdong, China

OBJECTIVES

Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study aimed to determine the prevalence of colistin-resistant mcr-like genes in Enterobacteriales in aquatic products, which may be contribute to the transfer of ARGs in water environments.

METHODS

The mcr-1-positive Escherichia coli were recovered from 123 freshwater fish and 34 cultured crocodile cecum samples from 10 farmers' markets in Guangdong, China. Minimum inhibitory concentration (MIC) was determined using the agar dilution method. Genotyping was performed using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Conjugation assay was carried out to investigate the transferability of mcr-1. Genomic information was obtained by whole genome sequencing (WGS) and bioinformatic analysis.

RESULTS

Forty-four mcr-1 positive isolates showed co-resistance to tetracycline, trimethoprim/sulfamethoxazole, and gentamicin, while they were all sensitive to tigecycline, meropenem, and amikacin. They were typed into sixteen PFGE clusters. ST10 and ST117 were the most popular sequence types, followed by ST1114. S1-PFGE verified the presence of the mcr-1 gene on plasmids in sizes of ∼60 kb (n = 1) and ∼240 kb (n = 3). Whole genome sequencing-based analysis identified mcr-1 integrated in IncHI2 plasmid (n = 3), IncI2 plasmid (n = 2), and bacterial chromosome in two copies (n = 1). In addition to mcr-1, they carried several other antibiotic resistance genes, such as blaCTX-M-14, fosA3, and aac(6')-Ib-cr.

CONCLUSION

These data suggest that aquatic products are an important antibiotic resistance reservoir and highlight possible risks regarding food safety.

Antibiotic resistance gene-free probiont administration to tilapia for growth performance and Streptococcus agalactiae resistance

Background and Aim

The rapid development of aquaculture as a major food sector is accompanied by challenges, including diseases that affect tilapia farming worldwide. One such infectious disease caused by Streptococcus agalactiae poses a serious threat to tilapia populations. Probiotics have emerged as a potentially safe preventive measure against S. agalactiae infection. However, antimicrobial resistance from antibiotic-resistant bacteria remains a concern because it can lead to the spread of resistant bacteria and serve as a reservoir of antibiotic-resistant genes in fishes and the surrounding environment. This study aimed to identify candidate probiotic bacteria capable of promoting tilapia growth, providing resistance to S. agalactiae infection, devoid of potential pathogenicity, and free from antibiotic resistance genes. Subsequently, the performance of these probiotic candidates in tilapia was evaluated.

Materials and Methods

Lactococcus garvieae, Priestia megaterium, Bacterium spp., Bacillus megaterium, Bacillus subtilis, and Bacillus pumilus were examined to assess their antibacterial properties, hemolytic patterns, and antibiotic resistance genes. We used the specific primers tetA, tetB, tetD, tetE, tetO, tetQ, ermB, and qnrS that were used for antibiotic resistance gene detection. In vivo probiotic efficacy was evaluated by administering probiotic candidates in tilapia feed at a concentration of 1 × 106 colonies/mL/50 g of feed over a 60-day maintenance period. Resistance to S. agalactiae infection was observed for 14 days after the challenge test.

Results

Lactococcus garvieae, P. megaterium, and Bacterium spp. were identified as promising probiotic candidates among the bacterial isolates. On the other hand, B. megaterium, B. subtilis, and B. pumilus carried resistance genes and exhibited a β hemolytic pattern, rendering them unsuitable as probiotic candidates. The selected probiotic candidates (L. garvieae, P. megaterium, and Bacterium spp.) demonstrated the potential to enhance tilapia growth, exhibited no pathogenic tendencies, and were free from antibiotic resistance genes. Supplementation with L. garvieae and Bacterium spp. enhanced tilapia resistance to S. agalactiae infection, whereas P. megaterium supplementation showed an insignificant survival rate compared with controls after the challenge test period.

Conclusion

Probiotics, particularly L. garvieae, P. megaterium, and Bacterium spp., enhance growth and resistance against S. agalactiae infection, without harboring antibiotic resistance genes. Selecting probiotic candidates based on antibiotic resistance genes is essential to ensure the safety of fish, the environment, and human health.

Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer

Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.

Dietary exposure to sulfamethazine alters fish intestinal homeostasis and promotes resistance gene transfer

The present study was undertaken to explore the effects of sulfamethazine (SMZ) dietary exposure on the enrichment of the intestine microbial structure, and antibiotic resistance gene (ARGs) transmission in marine medaka, with respect to antibiotic dose, duration, and sex. In male fish, a dietary exposure of 10 μg/L SMZ led to a heightened SMZ enrichment in the intestine, whereas metabolite (N-SMZ) levels were elevated at a higher exposure concentration (100 μg/L). Conversely, female fish exhibited stable levels of accumulation and metabolic rates across the exposure period. The composition of intestinal microorganisms revealed that exposure duration exerted a greater impact on the abundance and diversity of gut microbes, and microbial responses to SMZ varied across exposure time points. The expansion of Bacteroidetes and Ruegeria likely stimulated SMZ metabolism and contributed to the more balanced level of SMZ and N-SMZ observed in females. In males, short-term SMZ stress resulted in a disruption of intestinal homeostasis, while the rise in the abundance of the Fusobacteria and Propionigeniuma suggested a potential enhancement in intestinal anti-inflammatory capacity over time. Overall, female medaka exhibited greater adaptability to SMZ, and males appear to experience prolonged effects due to SMZ. A total of 11 ARGs and 5 mobile genetic elements (MGEs) were identified. Ruegeria is the main carrier of two types of MGEs (IS1247, ISSm2-Xanthob), and may serve as an indicator of ARG transmission. Therefore, it is rational to consider some fish breeding areas in natural waters as potential "reservoirs" of antibiotic resistance. This research will provide a valuable reference for the transmission of drug resistance along the food chain.

Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors

The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.

Effects of Aeromonas hydrophila infection on the intestinal microbiota, transcriptome, and metabolomic of common carp (Cyprinus carpio)

Aeromonas hydrophila frequently has harmful effects on aquatic organisms. The intestine is an important defense against stress. In this study, we investigated the intestinal microbiota and transcriptomic and metabolomic responses of Cyprinus carpio subjected to A. hydrophila infection. The results showed that obvious variation in the intestinal microbiota was observed after infection, with increased levels of Firmicutes and Bacteroidetes and decreased levels of Proteobacteria. Several genera of putatively beneficial microbiota (Cetobacterium, Bacteroides, and Lactobacillus) were abundant, while Demequina, Roseomonas, Rhodobacter, Pseudoxanthomonas, and Cellvibrio were decreased; pathogenic bacteria of the genus Vibrio were increased after microbiota infection. The intestinal transcriptome revealed several immune-related differentially expressed genes associated with the cytokines and oxidative stress. The metabolomic analysis showed that microbiota infection disturbed the metabolic processes of the carp, particularly amino acid metabolism. This study provides insight into the underlying mechanisms associated with the intestinal microbiota, immunity, and metabolism of carp response to A. hydrophila infection; eleven stress-related metabolite markers were identified, including N-acetylglutamic acid, capsidiol, sedoheptulose 7-phosphate, prostaglandin B1, 8,9-DiHETrE, 12,13-DHOME, ADP, cellobiose, 1H-Indole-3-carboxaldehyde, sinapic acid and 5,7-dihydroxyflavone.

Stimulants and donors promote megaplasmid pND6-2 horizontal gene transfer in activated sludge

The activated sludge process is characterized by high microbial density and diversity, both of which facilitate antibiotic resistance gene transfer. Many studies have suggested that antibiotic and non-antibiotic drugs at sub-inhibitory concentrations are major inducers of conjugative gene transfer. The self-transmissible plasmid pND6-2 is one of the endogenous plasmids harbored in Pseudomonas putida ND6, which can trigger the transfer of another co-occurring naphthalene-degrading plasmid pND6-1. Therefore, to illustrate the potential influence of stimulants on conjugative transfer of pND6-2, we evaluated the effects of four antibiotics (ampicillin, gentamycin, kanamycin, and tetracycline) and naphthalene, on the conjugal transfer efficiency of pND6-2 by filter-mating experiment. Our findings demonstrated that all stimulants within an optimal dose promoted conjugative transfer of pND6-2 from Pseudomonas putida GKND6 to P. putida KT2440, with tetracycline being the most effective (100 µg/L and 10 µg/L), as it enhanced pND6-2-mediated intra-genera transfer by approximately one hundred-fold. Subsequently, seven AS reactors were constructed with the addition of donors and different stimulants to further elucidate the conjugative behavior of pND6-2 in natural environment. The stimulants positively affected the conjugal process of pND6-2, while donors reshaped the host abundance in the sludge. This was likely because stimulant addition enhanced the expression levels of conjugation transfer-related genes. Furthermore, Blastocatella and Chitinimonas were identified as the potential receptors of plasmid pND6-2, which was not affected by donor types. These findings demonstrate the positive role of sub-inhibitory stimulant treatment on pND6-2 conjugal transfer and the function of donors in re-shaping the host spectrum of pND6-2.

Spatially and Temporally Confined Response of Gastrointestinal Antibiotic Resistance Gene Levels to Sulfadiazine and Extracellular Antibiotic Resistance Gene Exposure in Mice

This work aims to investigate the impact of antibiotics and extracellular antibiotic resistance genes (eARGs) on the dynamics of gastrointestinal antimicrobial resistance (AMR). The antibiotic resistance gene (ARG) levels of different segments of the gastrointestinal tract of mouse models were analyzed and compared after exposure to clinical concentrations of sulfadiazine and environmental levels of eARGs carried by the conjugative plasmid pR55. Exposure to sulfadiazine and eARGs led to significant changes in ARG levels by as many as four log-folds. Further analysis showed that the response of ARG levels appeared from 12-16 days after exposure and diminished 20 days after exposure. The responses in ARG levels were also restricted to different gastrointestinal segments for sulfadiazine and eARGs. Combined exposure of sulfadiazine and eARGs was unable to further increase ARG levels. From these findings, we concluded that the short-term consumption of environmental levels of eARGs and uptake of clinical levels of antibiotics lead to a spatially and temporally confined response in gastrointestinal AMR. These findings further clarify the detrimental impacts of antibiotic and eARG uptake, and the complexity of AMR development and dissemination dynamics in the gastrointestinal tract.

Evaluation of FEAST for metagenomics-based source tracking of antibiotic resistance genes

A metagenomics-based technological framework has been proposed for evaluating the potential and utility of FEAST as an ARG profile-based source apportionment tool. To this end, a large panel of metagenomic data sets was analyzed, associating with eight source types of ARGs in environments. Totally, 1089 different ARGs were found in the 604 source metagenomes, and 396 ARG indicators were identified as the source-specific fingerprints to characterize each of the source types. With the source fingerprints, predictive performance of FEAST was checked using "leave-one-out" cross-validation strategy. Furthermore, artificial sink communities were simulated to evaluate the FEAST for source apportionment of ARGs. The prediction of FEAST showed high accuracy values (0.933 ± 0.046) and specificity values (0.959 ± 0.041), confirming its suitability to discriminate samples from different source types. The apportionment results reflected well the expected output of artificial communities which were generated with different ratios of source types to simulate various contamination levels. Finally, the validated FEAST was applied to track the sources of ARGs in river sediments. Results showed STP effluents were the main contributor of ARGs, with an average contribution of 76 %, followed by sludge (10 %) and aquaculture effluent (2.7 %), which were basically consistent with the actual environment in the area.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Metagenomic evidence for increasing antibiotic resistance in progeny upon parental antibiotic exposure as the cost of hormesis

Antibiotics are widely consumed in the intensive mariculture industry. A better understanding of the effect of antibiotics on intergenerational antibiotic resistance in organisms is urgent since intergenerational transmission is crucial for the spread of antibiotic resistance genes (ARGs) in the environment. Herein, marine medaka (Oryzias melastigma) chronically exposed to low doses of sulfamethazine (SMZ) hormetically affected the progeny, characterized by increased richness and diversity of fecal microbiota and intestinal barrier-related gene up-regulation. Progeny immunity was modulated and caused by genetic factors due to the absence of significant SMZ accumulation in F1 embryos. In addition, some of the top genera in the progeny were positively correlated with immune diseases, while the expression of some immune-related genes, such as TNFα, IL1R2, and TLR3 changed significantly. This further indicated that the host selection caused by changes in progeny immunity was probably the primary determinant of progeny intestinal microbial colonization. Metagenomic analysis revealed that Proteobacteria represented the primary carriers of ARGs, while parental SMZ exposure facilitated the distribution and enrichment of multiple ARGs involved in the antibiotic inactivation in the progeny by promoting the diversity of Gammaproteobacteria and Bacteroidetes, further illustrating that antibiotic selection pressure persisted even if the offspring were not exposed. Therefore, SMZ induced hormesis in the progeny at the expense of increasing antibiotic resistance. Collectively, these findings provide a comprehensive overview of the intergenerational effect of antibiotics and serve as a reminder that the ARG transmission induced by the intergenerational impact of antibiotics on organisms should not be ignored.

Legacy metal contamination is reflected in the fish gut microbiome in an urbanised estuary

Estuaries are critical habitats subject to a range of stressors requiring effective management. Microbes are gaining recognition as effective environmental indicators, however, the response of host associated communities to stressors remains poorly understood. We examined microbial communities from seawater, sediments and the estuarine fish Pelates sexlineatus, in Australia's largest urbanised estuary, and hypothesised that anthropogenic contamination would be reflected in the microbiology of these sample types. The human faecal markers Lachno3 and HF183 were not detected, indicating negligible influence of sewage, but a gradient in copy numbers of the class 1 integron (intI-1), which is often used as a marker for anthropogenic contamination, was observed in sediments and positively correlated with metal concentrations. While seawater communities were not strongly driven by metal contamination, shifts in the diversity and composition of the fish gut microbiome were observed, with statistical links to levels of metal contamination (F_{2, 21} = 1.536, p < 0.01). Within the fish gut microbiome, we further report increased relative abundance of amplicon sequence variants (ASVs; single inferred DNA sequences obtained in sequencing) identified as metal resistant and potentially pathogenic genera, as well as those that may have roles in inflammation. These results demonstrate that microbial communities from distinct habitats within estuarine systems have unique response to stressors, and alterations of the fish gut microbiome may have implications for the adaptation of estuarine fish to legacy metal contamination.

Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient

The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.

Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies

This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.

Modulatory effect of Gracilaria gracilis on European seabass gut microbiota community and its functionality

Seaweeds are an important source of nutrients and bioactive compounds and have a high potential as health boosters in aquaculture. This study evaluated the effect of dietary inclusion of Gracilaria gracilis biomass or its extract on the European seabass (Dicentrarchus labrax) gut microbial community. Juvenile fish were fed a commercial-like diet with 2.5% or 5% seaweed biomass or 0.35% seaweed extract for 47 days. The gut microbiome was assessed by 16S rRNA amplicon sequencing, and its diversity was not altered by the seaweed supplementation. However, a reduction in Proteobacteria abundance was observed. Random forest analysis highlighted the genera Photobacterium, Staphylococcus, Acinetobacter, Micrococcus and Sphingomonas, and their abundances were reduced when fish were fed diets with algae. SparCC correlation network analysis suggested several mutualistic and other antagonistic relationships that could be related to the predicted altered functions. These pathways were mainly related to the metabolism and biosynthesis of protective compounds such as ectoine and were upregulated in fish fed diets supplemented with algae. This study shows the beneficial potential of Gracilaria as a functional ingredient through the modulation of the complex microbial network towards fish health improvement.

Environmentally relevant concentrations of triclosan exposure promote the horizontal transfer of antibiotic resistance genes mediated by Edwardsiella piscicida

Aquaculture pathogen and antibiotic resistance genes (ARGs) co-occur in the aquatic environment. Accumulated evidence suggests that aquaculture pathogens can facilitate the horizontal transfer of plasmid-mediated ARGs. However, the role of Edwardsiella piscicida (E. piscicida) in ARG dissemination is still not fully understood. In addition, the potential impact of triclosan (TCS) on the spread of ARGs mediated by E. piscicida is still unknown, so a mating model system was established to investigate the transfer process of ARGs. The results showed that E. piscicida disseminated ARGs on RP4 by horizontal gene transfer (HGT). Furthermore, TCS exposure promoted this process. The conjugative transfer frequencies were enhanced approximately 1.2-1.4-fold by TCS at concentrations from 2 to 20 μg/L, when compared with the control. TCS promoted the HGT of ARGs by stimulating reactive oxygen species (ROS) production, increasing cell membrane permeability, and altering expressions of conjugative transfer-associated genes. Together, the results suggested that aquaculture pathogens spread ARGs and that the emerging contaminant TCS enhanced the transfer of ARGs between bacteria.

Detection and various environmental factors of antibiotic resistance gene horizontal transfer

Bacterial antibiotic resistance in water environments is becoming increasingly severe, and new antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have also attracted the attention of researchers. The horizontal transfer of ARGs in water environments is considered one of the main sources of bacterial resistance in the natural environment. Horizontal gene transfer (HGT) mainly includes conjugation, natural transformation, and transduction, and conjugation has been investigated most. Several studies have shown that there are a large number of environmental factors that might affect the horizontal transfer of ARGs in water environments, such as nanomaterials, various oxidants, and light; however, there is still a lack of systematic and comprehensive reviews on the detection and the effects of the influence factors of on ARG horizontal transfer. Therefore, this study introduced three HGT modes, analysed the advantages and disadvantages of current methods for monitoring HGT, and then summarized the influence and mechanism of various factors on ARG horizontal transfer, and the possible reasons for the different effects caused by similar factors were mainly critically discussed. Finally, existing research deficiencies and future research directions of ARG horizontal transfer in water environments were discussed.

The Spread of Antibiotic Resistance Genes In Vivo Model

Infections caused by antibiotic-resistant bacteria are a major public health threat. The emergence and spread of antibiotic resistance genes (ARGs) in the environment or clinical setting pose a serious threat to human and animal health worldwide. Horizontal gene transfer (HGT) of ARGs is one of the main reasons for the dissemination of antibiotic resistance in vitro and in vivo environments. There is a consensus on the role of mobile genetic elements (MGEs) in the spread of bacterial resistance. Most drug resistance genes are located on plasmids, and the spread of drug resistance genes among microorganisms through plasmid-mediated conjugation transfer is the most common and effective way for the spread of multidrug resistance. Experimental studies of the processes driving the spread of antibiotic resistance have focused on simple in vitro model systems, but the current in vitro protocols might not correctly reflect the HGT of antibiotic resistance genes in realistic conditions. This calls for better models of how resistance genes transfer and disseminate in vivo. The in vivo model can better mimic the situation that occurs in patients, helping study the situation in more detail. This is crucial to develop innovative strategies to curtail the spread of antibiotic resistance genes in the future. This review aims to give an overview of the mechanisms of the spread of antibiotic resistance genes and then demonstrate the spread of antibiotic resistance genes in the in vivo model. Finally, we discuss the challenges in controlling the spread of antibiotic resistance genes and their potential solutions.

Occurrence of multidrug resistant Gram-negative bacteria and resistance genes in semi-aquatic wildlife - Trachemys scripta, Neovison vison and Lutra lutra - as sentinels of environmental health

Emergence of antimicrobial resistance (AMR) in bacterial pathogens has been recognized as a major public health concern worldwide. In the present study, antimicrobial resistant Gram-negative bacteria (AMRGNB) and AMR genes were assessed in semi-aquatic wild animals from a highly populated and intensive farming region of Spain, Catalonia. Cloacal/rectal swab samples were collected from 241 animals coming from invasive species Trachemys scripta (n = 91) and Neovison vison (n = 131), and endangered-protected species Lutra lutra (n = 19). Accordingly, 133 (55.2%) isolates were identified as AMRGNB. Escherichia coli and Pseudomonas fluorescens were among the bacteria most frequently isolated in all animal species, but other nosocomial agents such as Klebsiella pneumoniae, Salmonella spp. or Citrobacter freundii, were also prevalent. The phenotypic susceptibility testing showed the highest resistance to β-lactams (91%). Molecular analysis showed 25.3% of turtles (15.4% ESBL/Ampc genes), 21% of Eurasian otters (10.5% ESBL/Ampc genes) and 14.5% of American minks (8.4% ESBL/Ampc genes) were positive to AMR genes. The genotyping frequency was tetM (20.6%), blaCMY-2 (13%), ermB (6.1%), blaCMY-1 (4.6%), blaCTX-M-15 (3.1%) and mcr-4 (0.8%). Turtles had a larger prevalence of AMRGNB and AMR genes than mustelids, but American mink carried mcr-4 colistin-resistance gene. Moreover, cluster analysis of AMR gene distribution revealed that an ESBL/AmpC cluster in a highly populated area comprising big metropolitan regions, and another tetM/emrB cluster in an expended area with highly intensive livestock production. Although the mcr-4 positive case was not included in those clusters, that case was found in a county with a high pig farm density. In conclusion, semi-aquatic wild animals are a good sentinel for environmental contamination with AMRGNB and AMR genes. Therefore, One Health Approach is urgently needed in highly populated regions, and with intensive livestock production like Catalonia.

Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China

Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and blaTEM-1 genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.

Transmission routes of antibiotic resistant bacteria: a systematic review

Background

Quantification of acquisition routes of antibiotic resistant bacteria (ARB) is pivotal for understanding transmission dynamics and designing cost-effective interventions. Different methods have been used to quantify the importance of transmission routes, such as relative risks, odds ratios (OR), genomic comparisons and basic reproduction numbers. We systematically reviewed reported estimates on acquisition routes’ contributions of ARB in humans, animals, water and the environment and assessed the methods used to quantify the importance of transmission routes.

Methods

PubMed and EMBASE were searched, resulting in 6054 articles published up until January 1st, 2019. Full text screening was performed on 525 articles and 277 are included.

Results

We extracted 718 estimates with S. aureus (n = 273), E. coli (n = 157) and Enterobacteriaceae (n = 99) being studied most frequently. Most estimates were derived from statistical methods (n = 560), mainly expressed as risks (n = 246) and ORs (n = 239), followed by genetic comparisons (n = 85), modelling (n = 62) and dosage of ARB ingested (n = 17). Transmission routes analysed most frequently were occupational exposure (n = 157), travelling (n = 110) and contacts with carriers (n = 83). Studies were mostly performed in the United States (n = 142), the Netherlands (n = 87) and Germany (n = 60). Comparison of methods was not possible as studies using different methods to estimate the same route were lacking. Due to study heterogeneity not all estimates by the same method could be pooled.

Conclusion

Despite an abundance of published data the relative importance of transmission routes of ARB has not been accurately quantified. Links between exposure and acquisition are often present, but the frequency of exposure is missing, which disables estimation of transmission routes’ importance. To create effective policies reducing ARB, estimates of transmission should be weighed by the frequency of exposure occurrence.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07360-z.

How to evaluate the potential toxicity of therapeutic carbon nanomaterials? A comprehensive study of carbonized nanogels with multiple animal toxicity test models

Carbon-based nanomaterials have great potential in medical applications, especially in the treatment of infectious diseases and even tumors. However, to safely execute the application of carbon nanomaterials in human treatments, conducting safety assessments and establishing suitable evaluation criteria are necessary. In this study, lysine-carbonized nanogels (Lys-CNGs) that display antibacterial and antiviral abilities were employed in a comprehensive evaluation of their toxicity profiles through assessments in different animal models and growth stages. It was observed that zebrafish at the embryo and eleutheroembryo stages experienced significant toxic effects at a concentration of 15-fold the recommended dosage (0.5 ppm), whereas adult zebrafish following long-term consumption of fodder containing Lys-CNGs presented no adverse effects. Further microbiota analysis indicated that Lys-CNGs did not cause significant changes in the composition of the intestinal bacteria. In contrast, in the toxicity assessments with mammalian animal models, the Lys-CNGs showed no adverse effects, such as weight loss, dermal irritation, and skin sensitization responses in rabbits and guinea pigs, even at a high dose of 2000 mg/kg body weight. Our study revealed that Lys-CNGs have different toxic effects on different growth stages of zebrafish. Researchers in this field should carefully consider the implications of these toxicity profiles during the development of therapeutic carbon-based nanomaterials and for comparison of studies.

Distribution and Transfer of Antibiotic Resistance Genes in Coastal Aquatic Ecosystems of Bohai Bay

Antibiotic resistance genes (ARGs) are abundant in diverse ecosystems and the resistome may constitute a health threat for humans and animals. It is necessary to uncover ARGs and the accumulation mechanisms from different environmental sources. Various habitats, such as soil, seawater and fish intestines, could overflow a considerable amount of ARGs and the horizontal transfer of ARGs may occur in these environments. Thus, we assessed the composition and abundance of ARGs in seawater, soil and intestinal tracts of Cynoglossus semilaevis collected from different sites in Bohai Bay (China), including a natural area and three fish farms, through a high-throughput qPCR array. In total, 243 ARGs were uncovered, governing the resistance to aminoglycoside, multidrug, beta-lactamase, macrolide lincosamide streptomycin B (MLSB), chloramphenicol, sulfonamide, tetracycline, vancomycin and other antibiotics. The action mechanisms of these ARGs were mainly antibiotic deactivation, efflux pump and cellular protection. Importantly, similar ARGs were detected in different samples but show dissimilar enrichment levels. ARGs were highly enriched in the fish farms compared to the natural sea area, with more genes detected, while some ARGs were detected only in the natural sea area samples, such as bacA-02, tetL-01 and ampC-06. Regarding sample types, water samples from all locations shared more ARGs in common and held the highest average level of ARGs detected than in the soil and fish samples. Mobile genetic elements (MGEs) were also detected in three sample types, in the same trend as ARGs. This is the first study comparing the resistome of different samples of seawater, soil and intestines of C. semilaevis. This study contributes to a better understanding of ARG dissemination in water sources and could facilitate the effective control of ARG contamination in the aquatic environment.

Antibiotics and resistant genes in the gut of Chinese nine kinds of freshwater or marine fish

Antibiotic resistance genes (ARGs) may lead to bacterial resistance and using antibiotics will promote ARGs spread. Large amounts of antibiotics were used in aquaculture, but little attention was paid to the antibiotic resistant in fish gut. In this study, nine kinds of Chinese freshwater and marine fish were acquired in a city of northern China to test the amount of antibiotics and ARGs residues in their intestinal contents. The results showed that 4 kinds of antibiotics were detected from the intestinal contents, including Doxycycline (DOX), Tetracycline (TC), Sulfamethoxazole (SMX) and Roxithromycin (ROX), and the antibiotics with the largest detected amount was ROX in Sardinops sagax (2.83 μg kg^-1). Ten kinds of ARGs were detected from the intestinal contents, including strA, strB, ermB, bla_TEM, oxa-30, qnrB, qnrD, sul1, sul2 and tetB, as well as one type of integron intI1. The most abundant ARGs were bla_TEM. Correlation analysis showed huge difference between freshwater fish and marine fish. The results can improve our understanding of the antibiotics and ARGs residues in edible fish.

High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota

Diet can not only provide nutrition for intestinal microbiota, it can also remodel them. However, is unclear whether and how diet affects the spread of antibiotic resistance genes (ARGs) in the intestinal microbiota. Therefore, we employed selected high-sugar, high-fat, high-protein, and normal diets to explore the effect. The results showed that high-sugar, high-fat, and high-protein diets promoted the amplification and transfer of exogenous ARGs among intestinal microbiota, and up-regulated the expression of trfAp and trbBp while significantly altered the intestinal microbiota and its metabolites. Inflammation-related products were strongly correlated with the spread of ARGs, suggesting the intestinal microenvironment after diet remodeling might be conducive to the spreading of ARGs. This may be attributed to changes in bacterial membrane permeability, the SOS response, and bacterial composition and diversity caused by diet-induced inflammation. In addition, acceptor bacteria (zygotes) screened by flow cytometry were mostly Proteobacteria, Firmicutes and Actinobacteria, and most were derived from dominant intestinal bacteria remodeled by diet, indicating that the transfer of ARGs was closely linked to diet, and had some selectivity. Metagenomic results showed that the gut resistance genome could be affected not only by diet, but by exogenous antibiotic resistant bacteria (ARB). Many ARG markers coincided with bacterial markers in diet groups. Therefore, dominant bacteria in different diets are important hosts of ARGs in specific dietary environments, but the many pathogenic bacteria present may cause serious harm to human health.

Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome

Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.

A systematic review of advances in intestinal microflora of fish

Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.

Chironomidae larvae: A neglected enricher of antibiotic resistance genes in the food chain of freshwater environments

Infection caused by pathogenic bacteria carrying antibiotic resistance genes (ARGs) is a serious challenge to human health. Water environment, including water and surface sediments, is an important repository of ARGs, and the activity of aquatic animal can affect the development of ARG pollution in the water environment. Macrobenthic invertebrates are an important component of aquatic ecosystems, and their effects on ARG development in aquatic environments remain unreported. The distribution of ARGs, including tetA gene, sul2 gene, and kan gene, in Chironomidae larvae is demonstrated in this study for the first time. The ARG distribution was related to sampling points, metal elements, and seasons. Animal models demonstrated that Chironomidae larvae enriched ARGs from water and passed them on to downstream predators in the food chain. Conjugative transfer mediated by resistant plasmids was crucial in the spread of ARG in Chironomidae larvae, and upregulated expression of trfAp gene and trbBp gene was the molecular mechanism. Escherichia in Proteobacteria and Flavobacterium in Bacteroidetes, which are gram-negative bacteria in Chironomidae larvae, are the primary host bacteria of ARGs confirmed via resistance screening and DNA sequencing of V4 region of 16S rRNA gene. Feeding experiments further confirmed that ARGs from Chironomidae larvae can be enriched in the fish gut. Research gaps in food chain between sediments and fish are addressed in this study, and Chironomidae larvae is an important enricher of ARGs in the freshwater environment.

Conjugation Inhibitors Effectively Prevent Plasmid Transmission in Natural Environments

Plasmid conjugation is a major route for the spread of antibiotic resistance genes. Inhibiting conjugation has been proposed as a feasible strategy to stop or delay the propagation of antibiotic resistance genes. Several compounds have been shown to be conjugation inhibitors in vitro, specifically targeting the plasmid horizontal transfer machinery. However, the in vivo efficiency and the applicability of these compounds to clinical and environmental settings remained untested. Here we show that the synthetic fatty acid 2-hexadecynoic acid (2-HDA), when used as a fish food supplement, lowers the conjugation frequency of model plasmids up to 10-fold in controlled water microcosms. When added to the food for mice, 2-HDA diminished the conjugation efficiency 50-fold in controlled plasmid transfer assays carried out in the mouse gut. These results demonstrate the in vivo efficiency of conjugation inhibitors, paving the way for their potential application in clinical and environmental settings. IMPORTANCE The spread of antibiotic resistance is considered one of the major threats for global health in the immediate future. A key reason for the speed at which antibiotic resistance spread is the ability of bacteria to share genes with each other. Antibiotic resistance genes harbored in plasmids can be easily transferred to commensal and pathogenic bacteria through a process known as bacterial conjugation. Blocking conjugation is thus a potentially useful strategy to curtail the propagation of antibiotic resistance. Conjugation inhibitors (COINS) are a series of compounds that block conjugation in vitro. Here we show that COINS efficiently block plasmid transmission in two controlled natural environments, water microcosms and the mouse gut. These observations indicate that COIN therapy can be used to prevent the spread of antibiotic resistance.

Fish farm effluents as a source of antibiotic resistance gene dissemination on Jeju Island, South Korea

The abuse or misuse of antibiotics is directly linked to the emergence of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs) in the environment. Most fish farms located on Jeju Island operate a flow-through system that pumps in seawater for fish farming and discharges it back to the ocean. To investigate the amount of ARGs that these fish farm effluents discharge into the marine environment, we conducted a metagenomic-based resistome analysis. We observed higher levels of ARGs in fish farm effluents than in seawater at beach and residential areas. A greater proportion of ARGs was found on plasmid rather than on chromosomal DNA, especially for sulfonamide and phenicol classes. The distribution of ARGs did not differ between summer and winter, but the microbial community did. In addition, fish farm samples contained significantly more opportunistic pathogens (i.e., Vibrio, Photobacterium, Aliivibrio, and Tenacibaculum) and virulence factors than non-fish farm samples. Vibrio was the most frequently identified host of ARGs and virulence factors. The presence of Vibrio in the coastal area has been increasing owing to the recent rise in the temperature of seawater. This study suggests the need for actions to treat or monitor ARGs in the coastal areas where fish farms operating a flow-through system are located.

Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut

By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as the donor of the plasmid pB10::gfp When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciens P. shigelloides was unable to donate the plasmid, and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut, but only to Achromobacter, a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.IMPORTANCE To understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others are dead ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.

Fate and removal of bacteria and antibiotic resistance genes in horizontal subsurface constructed wetlands: Effect of mixed vegetation and substrate type

This study aimed to investigate the influence of cropping method and substrate type on the fate and the removal of bacterial and antibiotic resistance genes (ARGs) indicators from primary wastewater by constructed wetlands (CWs) during startup and maturation stages. Four small-scale CWs differing in their plantation pattern (monoculture vs. polyculture) and substrate type were constructed and operated under field conditions. While for bacteria, the greatest impact of the cropping method and substrate type on removal was during the startup stage rather than the maturation stage, for ARGs, such impact was significant at both stages. During startup, the removal efficiencies of heterotrophic bacteria, fecal coliforms, E. coli, 16S rRNA genes and lacZ increased with the operation time. At maturation, the removal efficiencies were constant and were within the range of 89.2-99.4%, 93.7-98.9%, 89-98.8%, 94.1-99.6% and 92.9-98.7%, respectively. The removal efficiencies of intl1, tetM, intl1, sul1, ermB and total ARGs were also increased with the operation time. However, they were ARG type and configuration-dependent; at maturation they ranged between 50.7%-89.4%, 85.9%-97%, 49.6%-92.9%, 58.2%-96.7% and 79.9-94.3%, respectively. The tuff-filled serially planted CW was also the only one capable of removing these genes at similar high efficiency. Metagenomic analysis showed that none of the ARGs was among the most common ARGs in water and biofilm samples; rather most ARGs belonged to bacterial efflux transporter superfamilies. Although ARGs were removed, they were still detected in substrate biofilm and their relative concentrations were increased in the effluents. While the removal of both bacteria and ARGs was higher during summer compared to winter, the season had no effect on the removal pattern of ARGs. Hence, combination of the serial plantation with substrate having high surface area is a potential strategy that can be used to improve the performance of CWs.

River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus)

Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10^-1/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.

Critical insight into the fate of antibiotic resistance genes during biological treatment of typical biowastes

Antibiotic resistance genes (ARGs) in biowaste, such as livestock manure and excess activated sludge, pose potential threat to human and ecological health when applied to agricultural fields. Biological treatment approaches, such as thermophilic composting/vermicomposting and anaerobic digestion, widely adopted to stabilize biowaste have demonstrated significant effects on the fate of ARGs. However, the influence of these biological treatments on ARGs is not known. This review summarizes the occurrence of ARGs in biowaste and the impact of thermophilic composting, vermicomposting, and anaerobic digestion on the fate of ARGs with discussion on factors, including substrate properties, pretreatments, additives, and operational parameters, associated with ARGs during biological treatment of biowaste. Finally, this review explores the research implications and proposes new avenues in the field of biological treatment of organic waste.

The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage

Food wastes are significant reservoir of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) available for exchange with clinical pathogens. However, food wastes-related changes of antibiotic resistance in long-period decomposition have been overlooked. Here, we evaluated the comprehensive ARG profile and its association with microbial communities, explained how this might vary with household garbage decomposition. Average of 128, 150 and 91 ARGs were detected in meat, vegetable and fruit wastes, respectively, with multidrug and tetracycline as the predominant ARG types. ARG abundance significantly increased at initial stage of waste fermentation and then decreased. High abundance of Eubacterium-coprostanoligenes, Sporanaerobacter, Peptoniphilus, Peptostreptococcus might be explained for the high relative abundance of ARGs in meat, while high abundance of Advenella, Prevotella, Solobacterium was attributed to the high diversity of ARGs in vegetables. Significant correlations were observed among volatile organic compounds, mobile genetic elements and ARGs, implying that they might contribute to transfer and transport of ARGs. Network analysis revealed that aph(2')-Id-01, acrA-05, tetO-1 were potential ARG indicators, while Hathewaya, Paraclostridium and Prevotellaceae were possible hosts of ARGs. Our work might unveil underlining mechanism of the effects of food wastes decomposition on development and spread of ARGs in environment and also clues to ARG mitigation.

Effects of free antibiotic resistance genes in the environment on intestinal microecology of mice

The rapid spread of antibiotic resistance genes (ARGs) is a great challenge to the ecological safety and human health. The intestine of humans and animals is an important site for the increase and spread of ARGs due to the great diversity and abundance of microorganisms in the intestinal microecology. ARGs, including the intracellular (iARGs) and the extracellular (eARGs) ARGs, are usually introduced into the intestinal tract through the diet, and the iARGs are colonized and spread in the intestinal microbiota with the help of the host bacteria. However, whether the eARGs can enter the intestinal microorganisms in the absence of host bacteria is not known. Here, we show the transformation and the diffusion of the ampramycin resistance gene (Ap) carried by the free plasmid RK2 in the intestinal microbiota of mice. After two days of consecutive gavage with free RK2, the intracellular Ap gene increases from days 0-8 in the feces of mice, and has remained constant. Bacterial transformation happens in the small intestine, including proximal and distal jejuna and proximal and distal ilea, at the early stage (first two days), and the intracellular RK2 is diffused into the intestinal microbiota of mice by conjugation on days 2-8 day, which is based on the distribution of eARG and iARG and the mRNA expression levels of trbBp, trfAp, korA, korB, and trbA. The characteristics of ARGs susceptible microbiota for transformation are analyzed using 16s rRNA gene sequencing, transmission electron microscopy, and flow cytometric. The ingestion of RK2 affects the composition of intestinal microbiota especially for Proteobacteria, and the antibiotic residue promotes the increase in Escherichia coli. These findings are important to assess the risk of ARGs, especially the eARGs in the intestinal microecology.

Spread of resistance genes from duck manure to fish intestine in simulated fish-duck pond and the promotion of cefotaxime and As

Integrated culture is a widespread culture mode in South China, in which resistance genes (RGs) also spread in the circulation system with nutrients. Accordingly, the aim of the present study was to investigate the spread of RGs in a fish-duck pond and the RGs and bacterial community of fish intestines. Five fish tanks, including a control tank and four experimental tanks (duck manure, duck manure + cefotaxime, duck manure + As, and duck manure + cefotaxime + As), were tested for 100 days. The results showed that duck manure increased both the diversity and relative abundance of RGs in fish intestines, and the addition of stress factors (cefotaxime, As) increased the relative abundance of RGs by one to two orders of magnitude. The stress-inducing effect of cefotaxime was greater than that of As. Tetracycline resistance genes were more sensitive to stress factors and were the predominant RGs in fish intestines. RGs in duck manure preferentially spread from the water to biofilm and then to fish intestines, whereas co-stress of cefotaxime and As obviously promoted the spread of RGs to fish intestines. In comparison to the control tank, duck manure and stress factors significantly changed the bacterial community of fish intestines. Correlation analysis also revealed that arsB, MOX, tetA and sul1 were significantly correlated with intI1 (P < 0.01), which hinted a potentially dissemination risk of RGs in fish intestines. These findings provide a theoretical basis for further investigating the dissemination of RGs in integrated culture systems and for evaluating the ecological risk of antibiotic and As use in aquaculture.

Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health

Background

Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome.

Results

The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens.

Conclusions

Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.

The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health

The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture‐animal‐manure‐soil‐water‐plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic‐resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro‐ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro‐ecosystem; and possible ways to curtail the menace of antimicrobial resistance.

High variability of plasmid uptake rates in Escherichia coli isolated from sewage and river sediments

The horizontal transfer of plasmids is a key mechanism behind the spread of antibiotic resistance in bacteria. So far, transfer rate constants were measured for a variety of plasmids, donors and recipients. The employed strains typically had a long history in laboratories. Existing data are, therefore, not necessarily representative for real-world environments. Moreover, information on the inter-strain variability of plasmid transfer rates is scarce. Using a high-throughput approach, we studied the uptake of RP4 by various Escherichia coli recipients using Serratia marcescens as the donor. The recipient strains were isolated from human-borne sewage and river sediments. The rate constants of plasmid transfer generally followed a log-normal distribution with considerable variance. The rate constants for good and poor recipients (95 and 5% quantile) differed by more than three orders of magnitude. Specifically, the inter-strain variability of the rate constant was large in comparison to alterations induced by low-level antibiotic exposure. We did not find evidence for diverging efficiencies of plasmid uptake between E. coli recipients of different origin. On average, strains isolated from river bottom sediments were equally efficient in the acquisition of RP4 as isolates extracted from sewage. We conclude that E. coli strains persisting in the aquatic environment and those of direct human origin share a similar intrinsic potential for the conjugative uptake of certain plasmids. In view of the large inter-strain variability, we propose to work towards probabilistic modeling of the environmental spread of antibiotic resistance.

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure

An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.

Characterization of tetracycline effects on microbial community, antibiotic resistance genes and antibiotic resistance of Aeromonas spp. in gut of goldfish Carassius auratus Linnaeus

The gut of aquatic animals was a significant niche for dissemination of antibiotic resistance genes (ARGs) and direct response of living conditions. In this study, the gut microbiota of goldfish Carassius auratus Linnaeus was sampled at 7 days and 21 days after treatment with tetracycline at 0.285 and 2.85 μg L^-1 to investigate the influences on the microbial structure and antibiotic resistance. The proportion of tetracycline resistance bacteria was 1.02% in the control group, while increased to 23.00%, 38.43%, 62.05% in groups of high concentration for 7 days (H7), low concentration for 21 days (L21) and high concentration for 21 days (H21), respectively. Compared to the control group, the diversity of isolated Aeromonas spp. was decreased in the treatment groups and the minimal inhibitory concentration (MIC) of resistant isolates was enhanced from 32 to 256 μg mL^-1 with the treatment of tetracycline in time- and dose-dependent manners. Furthermore, the abundance of most genes was increased in treatment groups and efflux genes mainly responded to the stress of tetracycline with an average level of 1.0 × 10^-2. After treatment with tetracycline, the predominant species were changed both at phylum and genus levels. The present study explored the impact of tetracycline on gut microbiota of goldfish at environmentally realistic concentrations for the first time and our findings will provide a reference for characterizing the microbiome of fish in the natural environment.

Effects of traditional Chinese medicines on immunity and culturable gut microflora to Oncorhynchus masou

The present study was conducted to evaluate the effect of dietary traditional Chinese medicines on the growth, immunity, and composition of culturable gut microflora in Oncorhynchus masou. Diets were formulated to contain no medicine (control), antitoxic decoction (A), general antiphlogistic decoction (B), or Herbae Artemisiae Capillariae decoction (C). Fish were manually fed twice daily till apparent satiation for 30 days. Compared with that in the control group, supplementation with the three kinds of Chinese herbal medicine enhanced fish growth significantly (P < 0.05). The activities of liver superoxide dismutase and glutathione peroxidase in the treatment groups were significantly higher compared with those in the control group (P < 0.05). The quantity of intestinal microflora was higher in the treatment groups compared with that in the control group. Moreover, there were some effects of dietary Chinese herbal medicine on the composition of intestinal microflora. Microflora of Pseudomonas sp., Psychrobacter sp., Microbacterium sp., Macrococcus sp., Burkholderia sp., and Arthrobacter sp. were found in the treatment groups, whereas there were none in the control group. There was a significant increase in their amounts in the treatment groups (P < 0.05). The three kinds of traditional Chinese medicines can improve the growth and immunity of Oncorhynchus masou and affect the quantity and composition of intestinal microflora.