Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment

Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system

Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human

BACKGROUND

Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health.

RESULTS

The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer.

CONCLUSIONS

The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics

The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R2 = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.

The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil

Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.

Difference of Microbial Community in the Stream Adjacent to the Mixed Antibiotic Effluent Source

Released antibiotics from source to stream can influence bacterial communities and potentially alter the ecosystem. This research provides a comprehensive examination of the sources, distribution, and bacterial community dynamics associated with varied antibiotic release sources adjacent to the stream. The residual of antibiotics from different sources was determined, and the bacterial community structure was examined to reveal the differences in the bacteria community in the stream. The residual of antibiotics was quantified with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the Illumina MiSeq platform was utilized to sequence bacterial 16S rRNA genes, providing comprehensive insights into the bacterial community structure in the sediment across five different sites. Results indicated that the presence and distribution of antibiotics were significantly influenced by released sources. In the case of the bacterial community, the Proteobacteria and Firmicutes were the most dominant phyla in the sediment, and especially, the Firmicutes showed higher abundance in sites mostly affected by livestock sources. Additionally, livestock gut bacteria such as Clostridium saudiense, Proteiniclasticum ruminis, and Turicibacter sanguinis were prevalent in antibiotic-contaminated sites adjacent to livestock facilities. Overall, this study provides critical insights into the effect of antibiotic contamination by verifying the relationship between the occurrence of antibiotic residuals and the alteration in the bacterial community in the stream.

An update on the prevalence of colistin and carbapenem-resistant Gram-negative bacteria in aquaculture: an emerging threat to public health

Aquaculture has been recognized as a hotspot for the emergence and spread of antimicrobial resistance genes conferring resistance to clinically important antibiotics. This review gives insights into studies investigating the prevalence of colistin and carbapenem resistance (CCR) among Gram-negative bacilli in aquaculture. Overall, a high incidence of CCR has been reported in aquatic farms in several countries, with CCR being more prevalent among opportunistic human pathogens such as Acinetobacter nosocomialis, Shewanella algae, Photobacterium damselae, Vibrio spp., Aeromonas spp., as well as members of Enterobacteriaceae family. A high proportion of isolates in these studies exhibited wide-spectrum profiles of antimicrobial resistance, highlighting their multidrug-resistance properties (MDR). Several mobile colistin resistance genes (including, mcr-1, mcr-1.1, mcr-2, mcr-2.1, mcr-3, mcr-3.1, mcr-4.1, mcr-4.3, mcr-5.1, mcr-6.1, mcr-7.1, mcr-8.1, and mcr-10.1) and carbapenemase encoding genes (including, blaOXA-48, blaOXA-55, blaNDM, blaKPC, blaIMI, blaAIM, blaVIM, and blaIMP) have been detected in aquatic farms in different countries. The majority of these were carried on MDR Incompatibility (Inc) plasmids including IncA/C, and IncX4, which have been associated with a wide host range of different sources. Thus, there is a risk for the possible spread of resistance genes between fish, their environments, and humans. These findings highlight the need to monitor and regulate the usage of antimicrobials in aquaculture. A multisectoral and transdisciplinary (One Health) approach is urgently needed to reduce the spread of resistant bacteria and/or resistance genes originating in aquaculture and avoid their global reach.

Emergence and mobilization of a novel lincosamide resistance gene lnu(I): From environmental reservoirs to pathogenic bacteria

Antimicrobial resistance remains an utmost concern in human and veterinary medicine, impacting humans, animals, and the environment while significantly influencing the principles of One Health. While Riemerella anatipestifer (R. anatipestifer) is recognized as a waterfowl pathogen with multidrug-resistant properties, the specifics of its lincosamide resistance mechanism are inadequately understood. In this study, we identified a novel lincosamide resistance gene, lnu(I), in R. anatipestifer RCAD0121, and investigated its potential origin, transfer mechanisms, and dissemination status through genomic epidemiology. This exhibited 74.80 % amino acid identity with a previously reported gene, lnu(H). PCR analysis revealed lnu(I) prevalence in at least 44 R. anatipestifer isolates collected from multiple provinces in China. Furthermore, genomic mining unveiled 56 lnu(I) sequences within publicly available databases, primarily originating from environmental sources. In addition, members of the family Flavobacteriaceae were the dominant (16/56, 28.57 %) bacteria carrying the lnu(I) gene, with Flavobacterium exhibiting a similar GC content as lnu(I). Notably, specific instances of the lnu(I) gene were linked to mobile genetic elements within human and animal pathogenic bacteria. These findings suggest that Flavobacterium species within the environment could serve as potential ancestral sources of the novel lnu(I) gene, which has undergone mobilization events toward pathogenic bacteria.

Concentrations, distribution, and key influencing factors of antibiotic resistance genes and bacterial community in water and reared fish tissues in a typical tilapia farm in South China

Although previous studies have investigated the occurrence of antibiotic resistance genes (ARGs) in aquaculture, few have monitored the concentrations and propagation of ARGs in biological tissues or investigated the key factors influencing their spread in aquaculture. This study investigated the concentration, propagation, and distribution of ARGs and bacterial communities in water sources, pond water, and tilapia tissues, and their key influencing factors, in a typical tilapia farm. ErmF, sul1, and sul2 were the dominant ARGs with high concentrations. The total concentrations of ARGs (TCAs) in tilapia tissues decreased in the following order: stomach > scales > intestine > gills (P < 0.05). Redundancy analysis and multiple linear regression revealed that suspended solids (SS) and chemical oxygen demand (COD) were positively correlated with the dominant ARGs ermF sul2, and the TCAs (P < 0.05); additionally, Chloroflexi and Bacteroidetes in tilapia aquaculture water were positively correlated with the dominant ARGs ermF and sul2, as well as the TCAs (P < 0.05). This study suggests that SS and COD were the key factors driving the distribution and spread of ARGs in tilapia aquaculture water. Additionally, Chloroflexi and Bacteroidetes were the key bacterial flora affecting the propagation of ARGs in tilapia aquaculture systems.

Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement

The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.

Permeability decides the effect of antibiotics on sedimentary nitrogen removal in Jiulong River Estuary

Sedimentary denitrification takes place beneath the oxic layer at the sediment-water interface, where nitrate and antibiotics need to diffuse through the overlying water. However, the antibiotics' effect on sedimentary N removal and associated N2O production has not been adequately investigated under in situ conditions. Here, isotope pairing techniques, including slurry incubations (potential) and intact core incubations (in situ), combined with metagenomic analysis were applied to investigate the impacts of two protein-inhibiting antibiotics (oxytetracycline and thiamphenicol) on sediment nitrogen removal in a subtropical estuary. Slurry incubations showed that the two antibiotics significantly inhibited denitrification (67-98%) and anammox (49-99%), while intact core incubations presented no antibiotic effect at upstream but significant inhibition (23%-52%) at downstream. Meanwhile, N2O yields were stimulated up to 20 folds in slurry incubations yet showing insignificant response in intact cores. Such contrasting results between up- and down-stream and between slurry and intact core incubations strongly indicated that permeability, which determines diffusion of antibiotics to microbes, is the key to exert the effect of antibiotics on in situ sedimentary nitrogen removal processes regardless the existence of antibiotics resistance genes. This diffusive obstruction may mitigate the toxic effect of antibiotics on nitrogen removal related microbes in natural environments.

Exploration of the candidate beneficial bacteria for Penaeus vannamei culture by core microbiome analysis using amplicon sequencing

Globally, Penaeus vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment, and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria, and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P (<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21, and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish an aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition, and control the pathogenic agents at each stage of the culture.

Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China

Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10^-2 to 1.90 × 10^-1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil

Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.

Distribution and drivers of antibiotic resistance genes in brackish water aquaculture sediment

Brackish water aquaculture has brought numerous economic benefits, whereas anthropogenic activities in aquaculture may cause the dissemination of antibiotic resistance genes (ARGs) in brackish water sediments. The intricate relationships between environmental factors and microbial communities as well as their role in ARGs dissemination in brackish water aquaculture remain unclear. This study applied PCR and 16S sequencing to identify the variations in ARGs, class 1 integron gene (intI1) and microbial communities in brackish water aquaculture sediment. The distribution of ARGs in brackish water aquaculture sediment was similar to that in freshwater aquaculture, and the sulfonamide resistance gene sul1 was the indicator of ARGs. Proteobacteria and Firmicutes were the dominant phyla, and Paenisporosarcina (p_ Firmicutes) was the dominant genus. The results of correlation, network and redundancy analysis indicated that the microbial community in the brackish water aquaculture sediment was function-driven. The neutral model and variation partitioning analysis were used to verify the ecological processes of the bacterial community. The normalized stochasticity ratio showed that pond bacteria community was dominated by determinacy, which was affected by aquaculture activities. The total nitrogen and organic matter influenced the abundance of ARGs, while Proteobacteria and Thiobacillus (p_Proteobacteria) were the key antibiotic-resistant hosts. Our study provides insight into the prevalence of ARGs in brackish water aquaculture sediments, and indicates that brackish water aquaculture is a reservoir of ARGs.

Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO₃-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.

Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis

Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people's lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.

Rhodobacter azotoformans supplementation improves defense ability of Chinese mitten crab Eriocheir sinensis against citrobacteriosis

Rhodobacter probiotics are considered as good alternatives to antibiotics for aquaculture. Yet the beneficial effects of Rhodobacter on Chinese mitten crab Eriocheir sinensis are still unclear, and more functions of Rhodobacter supplementation need to be clarified. In this study, a 60-day feeding trial was performed to investigate the protective effects of R. azotoformans against citrobacteriosis in E. sinensis by growth performance, serum immunity, hepatopancreatic antioxidant capability, intestinal flora, and resistance to Citrobacter freundii challenge assays. The results showed that R. azotoformans supplementation significantly and dose-dependently increased weight gain and specific growth rate as well as activities of serum immune and hepatopancreatic antioxidant enzymes, leading to notable improvement in the growth performance, serum immunity and hepatopancreatic antioxidant status of E. sinensis. Besides, R. azotoformans supplementation significantly enhanced intestinal microbial abundance and diversity in E. sinensis, and conferred significant protection of the crabs against C. freundii challenge with seven-day survival rates of 70.0%-100.0%. To the best of our knowledge, this is the first study to reveal the protective effects of R. azotoformans against citrobacteriosis in E. sinensis.

Captivity and geography influence the antibiotic resistome of non-human primates

INTRODUCTION

Antibiotic resistance poses a serious threat for animals and humans health worldwide. Yet a comprehensive exploration of the influence of captivity and geography on non-human primate (NPH) gut antibiotic resistance remains incomplete.

METHODS

In this study, 131 metagenomic sequencing datasets of five species of NHPs included different regions and lifestyles were selected to perform the antibiotic resistance analysis.

RESULTS

Nineteen related resistance antibiotics and 325 antibiotic resistance genes (ARGs) were obtained. A significantly higher abundance and diversity index of ARGs in the captive NHPs than in the wild was found but not for all of the samples. The biomarker-tracking of ARGs analysis identified key ARGs related to aminoglycoside resistance genes and tetracycline resistance genes.

DISCUSSION

These results suggest that captivity and geography changes associated with human activities can lead to marked changes in the ecology of the NHP gut flora ARGs.

Distribution and model prediction of antibiotic resistance genes in Weishan Lake based on the indication of Chironomidae larvae

The widespread contamination of antibiotic resistance genes (ARGs) in freshwater environment are becoming a serious challenge to human health and ecological safety. Rapid and efficient monitoring of ARGs pollution is of great significance to ARGs control. Water, bottom mud, and fish have all been used to indicate ARG contamination in aquatic environments. However, it is unclear whether macrobenthic invertebrates in the food chain of aquatic environments can be indicators of ARG contamination. In this study, we demonstrated that ARGs including tetA gene, sul2 gene, and km gene were distributed in Chironomidae larvae in Weishan Lake. The ARG distribution was related to animal species, body parts, sampling sites, time, urban environment, animal farming, south-to-north water diversion, food chain, antibiotics, and water storage. Mathematical model predictions of ARG contamination in Weishan Lake were constructed based on the structural equation model (SEM) and the distribution of ARG sul2 in Chironomidae larvae. Influencing factors such as water storage, metal elements, antibiotic, and temperature were found to be closely related to the prediction of ARG contamination. This study provided a new indicator for ARG contamination in freshwater environments and a method to predict ARGs contamination.

Antibiotic resistance genes and their links with bacteria and environmental factors in three predominant freshwater aquaculture modes

Rapid development of aquaculture industry and increasing demand of various inputs (especially antibiotics), are suspected to promote the occurrence and spread of ARGs in aquaculture related environments. However, the occurrences of ARGs under different freshwater aquaculture practices are rarely known. Here, we investigated the seasonal profiles of the main ARGs, intI1 and bacteria in waters from three kinds of predominant freshwater aquaculture practices around the Honghu Lake (China), as well as their co-occurrences and interrelationships with antibiotics, heavy metals and general water quality. The results indicate that quinolone resistance genes (qnrB), tetracycline resistance genes (tetB and tetX) and sulfonamide resistance genes (sul1 and sul2) were the top five predominant ARGs with seasonal variations of abundance. Fish ponds were of the highest absolute abundances of tested ARGs than the other two modes. Crayfish ponds and their adjacent ditches shared similar ARGs profile. Different subtypes of ARGs belonging to the same class of resistance were varied in abundances. Some bacteria were predicted to carry different ARGs, which indicating multi-antibiotic resistances. Moreover, the combined environmental factors (antibiotics, heavy metals and water quality) partially shaped the profiles of ARGs and bacteria composition. Overall, this study provides new comprehensive understanding on the characterization of ARGs contamination in different freshwater aquaculture practices from the perspectives of environmental chemistry, microbiology and ecology. The results would benefit the optimization of aquaculture practices toward environmental integrity and sustainability.

Metagenomic analysis of the abundances, diversity, and distribution of antibiotic resistance genes and their potential bacterial hosts in two types of shrimp-rearing farms in South China

Antibiotic resistance genes (ARGs) are attracting increasing concern worldwide. Many previous studies have investigated the occurrence and concentrations of ARGs in aquaculture. However, the sources of ARGs and the links with their potential bacterial hosts have not yet been explored. This study investigated the abundances and diversity of ARGs in two types of shrimp farms in South China through metagenomic sequencing. In total, 14 ARG types were detected. Tetracycline was the dominant ARG type. The abundances of ARGs in samples decreased in the order of duck feces > water source > sediment > shrimp gut > pond water. The samples from the duck-shrimp integrated farm contained 1.29-3.81-fold more abundant ARGs than those from the shrimp monoculture farm (p < 0.05). Several ARGs, that were most predominant in the duck feces samples, were also the most predominant in the shrimp gut samples from the duck-shrimp integrated farm. Redundancy analysis indicated that the abundances and distribution of ARGs formed three clusters: duck feces, water samples, and sediment and shrimp gut samples. The dominant genera in duck feces known as human pathogenic bacteria were potential hosts of ARGs, and were also dominant in the shrimp gut samples in the duck-shrimp integrated farm. Additionally, the abundances of dominant genera in the shrimp gut samples of the duck-shrimp integrated farm were 1.74-35.07-fold higher than those in the shrimp monoculture farm (p < 0.01). The duck-shrimp integrated farm had 3.36-fold and 4.94-fold higher abundances of ARGs and mobile genetic elements in the shrimp gut samples than those from the shrimp monoculture farm, respectively (p < 0.05). The results indicate that duck feces may be a crucial source of diverse and abundant ARGs spreading to reared shrimps in duck-shrimp integrated farms, posing a severe risk to public health.

Spatiotemporal variation in nitrogen and phosphorus levels and microbial community in the upstream water transport channel to the Douhe Reservoir

The Douhe Reservoir is an important diversion water source and drinking water resource for Tianjin and the Tangshan cities. Panjiakou, Daheiting, Qiuzhuang, and the Douhe Reservoirs located from top to bottom in the LuanHe River region forming a group of cascade reservoirs. After over 30 years of aquaculture, the concentration of nitrogen (N) and phosphorus (P) have exceeded Class III of Environmental Quality Standard for Surface Water in China. We selected the Douhe Reservoir as the study site and choose sampling points in several upstream reservoirs and main reservoir area, and we collected a total of 18 water samples. Moreover, the distribution characteristics of N and P levels in flood season and dry season were studied in the Douhe Reservoir and upstream water channel, respectively. The results indicated that there were significant spatial differences between N and P distribution in the Douhe Reservoir and the upstream sites. We observed that the distribution of N and P had seasonal characteristics, and the contents of nitrate(NO3^--N), nitrogen(TN), total phosphorus(TP), and total dissolved phosphorus(TDP) in flood periods were higher than those in dry periods. The microbial community structure illustrated that the dominant phylum displayed seasonal differences between the upstream channel and the reservoir area. Among them, the abundance of some genera changed with the location of the channel, the microbial community structure, and the levels of N and P, especially in flood season. Particularly, NO₃^--N and TN had the most significant correlation. Hence, this study presented an important theoretical foundation for the risk prevention and the control of nutrient elements in the LuanHe River basin in the future, which would enhance the drinking water safety of Tianjin and Tangshan residents.

Metagenomic analysis of microbial community structure and distribution of resistance genes in Daihai Lake, China

The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9-94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03-91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.

Bacteriophage therapy in aquaculture: current status and future challenges

The escalation of antibiotic resistance has revitalized bacteriophage (phage) therapy. Recently, phage therapy has been gradually applied in medicine, agriculture, food, and environmental fields due to its distinctive features of high efficiency, specificity, and environmental friendliness compared to antibiotics. Likewise, phage therapy also holds great promise in controlling pathogenic bacteria in aquaculture. The application of phage therapy instead of antibiotics to eliminate pathogenic bacteria such as Vibrio, Pseudomonas, Aeromonas, and Flavobacterium and to reduce fish mortality in aquaculture has been frequently reported. In this context, the present review summarizes and analyzes the current status of phage therapy in aquaculture, focusing on the key parameters of phage application, such as phage isolation, selection, dosage, and administration modes, and introducing the strategies and methods to boost efficacy and restrain the emergence of resistance. In addition, we discussed the human safety, environmental friendliness, and techno-economic practicability of phage therapy in aquaculture. Finally, this review outlines the current challenges of phage therapy application in aquaculture from the perspectives of phage resistance, phage-mediated resistance gene transfer, and effects on the host immune system.

Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system

To meet the rapidly growing global demand for aquaculture products, large amounts of antibiotics were used in aquaculture, which might accelerate the evolution of antibiotic-resistant bacteria (ARB) and the propagation of antibiotic genes (ARGs). In our research, we revealed the ARGs profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis. The residual antibiotic seems to increase the propagation of ARGs in the crab pond, but there was no clear relationship between a given antibiotic type and the corresponding resistance genes. The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities, but increased the relative abundance of sulfonamide resistance gene. A higher abundance of MGEs, especially plasmid, increased the potential ARGs dissemination risk in crab and purification ponds. Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs. The horizontal gene transfer was likely to occur among a variety of microorganisms, and various ARGs hosts including Pseudomonas, Acinetobacter, Escherichia, and Klebsiella were identified. Bacterial community influenced the composition of ARG hosts, and Proteobacteria was the predominant hosts. Overall, our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals

Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.

Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment

The increasing pollution of urban drinking water sources by antibiotic resistance genes (ARGs) threatens human health worldwide. However, the distribution and influencing factors of ARGs, especially how to reveal the risks of ARGs in this environment remains unclear. Hence, Chaohu Lake was selected as an example to investigate the characteristics of ARGs and explore the interactions among physicochemical factors, microorganisms, and ARGs by metagenomic approach. In this work, 75 ARG subtypes with an average of 30.4 × /Gb (ranging from 15.2 ×/Gb to 57.9 ×/Gb) were identified, and multidrug and bacA were most frequent in Chaohu Lake. Non-random co-occurrence patterns and potential host bacteria of ARGs were revealed through co-occurrence networks. Microbial community and mobile genetic elements (MGEs) were the major direct factors in ARG profiles. The dissemination of ARGs was mainly driven by plasmids. Considering the interactions among MGEs, human bacterial pathogens, and ARGs, antibiotic resistome risk index (ARRI) was proposed to manifest the risks of ARGs. Overall, our work systemically investigated the composition and associated factors of ARGs and built ARRI to estimate the potential risks of ARGs in a typical urban drinking water source, providing an intuitive indicator for managing similar lakes.

Contaminants of Emerging Concern in the Lower Volta River, Ghana, West Africa: The Agriculture, Aquaculture, and Urban Development Nexus

Contaminants of emerging concern (CECs) are ubiquitous in aquatic environments across all continents and are relatively well known in the developed world. However, few studies have investigated their presence and biological effects in low- and middle-income countries. We provide a survey of CEC presence in the Volta River, Ghana, and examine the microbial consequences of anthropogenic activities along this economically and ecologically important African river. Water and sediment samples were taken by boat or from shore at 14 sites spanning 118 km of river course from the Volta estuary to the Akosombo dam. Sample extracts were prepared for targeted analysis of antimicrobial CECs, N,N-diethyl-meta-toluamide, and per- and polyfluoroalkyl substances (PFAS; water only). Concurrent samples were extracted to characterize the microbial community and antibiotic-resistant genes (ARGs). Antibiotics and PFAS (PFAS, 2-20 ng/L) were found in all water samples; however, their concentrations were usually in the low nanograms per liter range and lower than reported for other African, European, and North American studies. N,N-Diethyl-meta-toluamide was present in all samples. The number of different genes detected (between one and 10) and total ARG concentrations varied in both water (9.1 × 10^-6 to 8.2 × 10^-3 ) and sediment (2.2 × 10^-4 to 5.3 × 10^-2 ), with increases in gene variety at sites linked to urban development, sand mining, agriculture, and shellfish processing. Total ARG concentration spikes in sediment samples were associated with agriculture. No correlations between water quality parameters, CEC presence, and/or ARGs were noted. The presence of CECs in the lower Volta River highlights their global reach. The overall low concentrations of CECs detected is encouraging and, coupled with mitigation measures, can stymie future CEC pollution in the Volta River. Environ Toxicol Chem 2022;41:369-381. © 2021 SETAC.

Is rice-crayfish co-culture a better aquaculture model: From the perspective of antibiotic resistome profiles

Aquaculture ecosystem is a hot-spot for antibiotic resistance genes (ARGs). Rice-crayfish co-culture was considered an eco-friendly aquaculture model and has been widely adopted in China. However, it is unclear whether rice-crayfish co-culture is one of the most eco-friendly models from the perspective of antibiotic resistance profiles. In this study, we evaluated the eco-friendliness of rice-crayfish co-culture, and compared this model with other aquaculture models, from the perspectives of antibiotics and ARG patterns, based on multi-omics and antibiotic profiles. Results showed that the nutrient levels, antibiotic concentrations, dominant microbial genera and ARG patterns in the rice-crayfish co-culture model were profoundly different from the other three aquaculture models (crab only aquaculture model, crayfish only aquaculture model, and crab-crayfish co-culture models). Specifically, the rice-crayfish co-culture model has significantly lower diversity of ARGs and lower potential risks of ARGs when compared to the other aquaculture models. Nutrient and antibiotic concentrations were the important environmental factors for shaping ARG patterns, but compared with environmental factors, the effects of mobile genes and bacteria community on the proliferation and transmission of ARGs were stronger. This study has deepened our understanding of ARGs in freshwater aquaculture ecosystem, and suggested that rice-crayfish co-culture model is a relatively eco-friendly aquaculture model when compared with the other aquaculture models.

Responses of microbial function, biomass and heterotrophic respiration, and organic carbon in fir plantation soil to successive nitrogen and phosphorus fertilization

Carbon dioxide (CO₂) emissions from forest ecosystems originate largely from soil respiration, and microbial heterotrophic respiration plays a critical role in determining organic carbon (C) stock. This study investigated the impacts of successive nitrogen (N) and phosphorus (P) fertilization after 9 years on soil organic C stock; CO₂ emission; and microbial biomass, community, and function in a Chinese fir plantation. The annual fertilization rates were (1) CK, control without N or P fertilization; (2) N50, 50 kg N ha^-1; (3) N100, 100 kg N ha^-1; (4) P50, 50 kg P ha^-1; (5) N50P50, 50 kg N ha^-1 + 50 kg P ha^-1; and (6) N100P50, 100 kg N ha^-1 + 50 kg P ha^-1. The N100P50 treatment had the highest cumulative soil CO₂ emissions, but the CK treatment had the lowest cumulative soil CO₂ emissions among all treatments. The declines of soil organic C (SOC) after successive 9-year fertilization were in the order of 100 kg N ha^-1 year^-1 > 50 kg N ha^-1 year^-1 > CK. Compared to the CK treatment, successive N fertilization significantly changed soil microbial communities at different application rates and increased the relative gene abundances of glycoside hydrolases, glycosyl transferases, carbohydrate-binding modules, and polysaccharide lyases at 100 kg N ha^-1 year^-1. Relative to P fertilization alone (50 kg P ha^-1 year^-1), combined N and P fertilization significantly altered the soil microbial community structure and favored more active soil microbial metabolism. Microbial community and metabolism changes caused by N fertilization could have enhanced CO₂ emission from heterotrophic respiration and eventually led to the decrease in organic C stock in the forest plantation soil. KEY POINTS: • N fertilization, alone or with P, favored more active microbial metabolism genes. • 100 kg N ha^-1 fertilization significantly changed microbial community and function. • N fertilization led to a "domino effect" on the decrease of soil C stock.

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on (i) the risk assessment in surface waters, (ii) selective pressures contributing to its transfer and propagation and (iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.

Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes

Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.

Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants

This work monitored the effect of a municipal and a village wastewater treatment plant (WWTP) technology on the fate of beta-lactam resistance genes in bacterial populations in different phases of the wastewater treatment process. In case of the municipal WWTP1, the bacteria possessing a high ampicillin resistance (minimal inhibitory concentration (MIC) values of 20 mg/mL) accumulated in the sedimentation tank, which was accompanied with a higher concentration of ampicillin in the wastewater samples (28.09 ng/L) and an increase in the relative abundance of the blaTEM gene in the bacterial population. However, an opposite trend was revealed with the blaNDM-1 gene, making the sedimentation processes of WWTP1 crucial only for the accumulation of the blaTEM gene. Similarly, the comparison with the WWTP2 showed that the accumulation of the ampicillin resistance in bacterial population probably depended on the WWTP technology and wastewater composition. Out of the four tested resistance genes (blaTEM, blaKPC, blaNDM-1, and blaOXA-48), blaTEM and blaNDM-1 genes were the only two detected in this study. According to NGS analysis of bacterial 16 S rRNA gene, Gammaproteobacteria dominated the ampicillin-resistant bacteria of the WWTP sedimentation tanks. Their relative abundance in the bacterial population also increased during the sedimentation processes in WWTP1. It could indicate the role of the bacterial taxon in ampicillin resistance accumulation in this WWTP and show that only 9.29% of the original bacterial population from the nitrification tank is involved in the documented shifts in beta-lactam resistance of the bacterial population.

Distribution and Influence on the Microbial Ecological Relationship of Antibiotic Resistance Genes in Soil at a Watershed Scale

Antibiotic resistance genes (ARGs) are ubiquitous in the environment, with previous studies mainly focusing on the terrestrial ecosystem, which is prone to higher antibiotic application. However, the characteristics, distribution pattern, and driving factors of soil ARGs at the macro scale are still unclear. In this study, the soil ARGs, antibiotics, mobile genetic elements (MGEs), soil properties, toxic metals, polycyclic aromatic hydrocarbons (PAHs), and bacterial community in the Taipu River Basin were analyzed to investigate the distribution and dissemination of ARGs at a watershed scale. The results revealed that ARGs were widespread in the soils along the Taipu River, and that ARG profiles varied greatly with different types of land use, but showed regional similarities. The characteristics were mainly determined by antibiotic input and the ARG transmission mediated by MGEs. The order of the contribution of environmental factors to ARG distribution was toxic metals > PAHs > soil properties. Toxic metal pollution was coupled with ARGs through MGE mediation, while PAHs and soil properties were most likely to affect the ARG distribution by shifting the bacterial community. The microbial–ecological relationship changed significantly with the enrichment of ARGs, and its impact may extend to the watershed scale. Transposon IS1247 can be used as an indicator of the ARGs impact on the microbial ecological relationship in the soils of the Taipu River Basin.

Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures

The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.

Modification of DNA regions with metagenomic DNA fragments (MDRMDF): A convenient strategy for efficient protein engineering

In this study, we have established a convenient and efficient approach named Modification of DNA Regions with Metagenomic DNA Fragments (MDRMDF) for protein engineering. Degenerate primers were designed corresponding to conserved regions of the gene of interest which were used for amplification of fragments with template of the metagenomic DNA. The resulting PCR products were used to replace the corresponding regions of the gene of interest to introduce modified gene for function-based screening. Therefore, this method can make full use of the metagenomic DNA sequences with unknown metagenomic gene information for efficient protein engineering. The β-xylosidase BH3683 was used to construct a MDRMDF library which was screened with a newly designed p-NPX-M9 medium-based strategy. As a result, a mutant protein Xyl-M56 showing high activity, improved pH stability and higher tolerance to organic solvents was obtained which may have potential for industrial application. The MDRMDF method may find wide application in enzyme engineering, metabolic engineering and other fields, especially offering a new methodological option for the directed evolution of proteins.

Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area

Aquaculture is the productive activity that will play a crucial role in the challenges of the millennium, such as the need for proteins that support humans and the respect for the environment. Aquaculture is an important economic activity in the Mediterranean basin. A great impact is presented, however, by aquaculture practices as they involve the use of antibiotics for treatment and prophylaxis. As a consequence of the use of antibiotics in aquaculture, antibiotic resistance is induced in the surrounding bacteria in the column water, sediment, and fish-associated bacterial strains. Through horizontal gene transfer, bacteria can diffuse antibiotic-resistance genes and mobile resistance genes further spreading genetic determinants. Once triggered, antibiotic resistance easily spreads among aquatic microbial communities and, from there, can reach human pathogenic bacteria, making vain the use of antibiotics for human health. Climate change claims a significant role in this context, as rising temperatures can affect cell physiology in bacteria in the same way as antibiotics, causing antibiotic resistance to begin with. The Mediterranean Sea represents a 'hot spot' in terms of climate change and aspects of antibiotic resistance in aquaculture in this area can be significantly amplified, thus increasing threats to human health. Practices must be adopted to counteract negative impacts on human health, with a reduction in the use of antibiotics as a pivotal point. In the meantime, it is necessary to act against climate change by reducing anthropogenic impacts, for example by reducing CO2 emissions into the atmosphere. The One Health type approach, which involves the intervention of different skills, such as veterinary, ecology, and medicine in compliance with the principles of sustainability, is necessary and strongly recommended to face these important challenges for human and animal health, and for environmental safety in the Mediterranean area.

Phylogenetic characterization and multidrug resistance of bacteria isolated from seafood cocktails

The continual increase in resistance to antibacterial drugs has become a major public health problem, and their indiscriminate use in agriculture, aquaculture, and the treatment of human and animal diseases has severely contributed to the occurrence and spread of multidrug resistance genes. This study phylogenetically characterized multidrug-resistant bacteria isolated from seafood cocktails. Seafood cocktail dishes from 20 establishments on public roads were sampled. Samples were grown on TCBS agar and blood agar. Forty colonies with different macro- and microscopic characteristics were isolated. The 16S rRNA gene V4 and V6 hypervariable regions were amplified, sequenced and phylogenetically analyzed. Antibacterial drug resistance was determined by disk diffusion assay. Isolated bacteria were identical to species of the genera Enterococcus, Proteus, Vibrio, Staphylococcus, Lactococcus, Vagococcus, Micrococcus, Acinetobacter, Enterobacter, and Brevibacterium, with 75-100% presenting resistance or intermediate resistance to dicloxacillin, ampicillin, and penicillin; 50-70% to cephalosporins; 30-67.5% to amikacin, netilmicin and gentamicin; 40% to nitrofurantoin and other antibacterial drugs; 25% to chloramphenicol; and 2.5% to trimethoprim with sulfamethoxazole. In general, 80% of the bacteria showed resistance to multiple antibiotics. The high degree of bacterial resistance to antibacterial drugs indicates that their use in producing raw material for marine foods requires established guidelines and the implementation of good practices.

Ciprofloxacin increased abundance of antibiotic resistance genes and shaped microbial community in epiphytic biofilm on Vallisneria spiralis in mesocosmic wetland

This study investigated the fate of ciprofloxacin (CIP) in wetlands dominated by Vallisneria spiralis. About 99% of CIP was degraded from overlaying water within 4 days of treatment but significantly inhibited the nutrient removal capacity (TN, TP, and COD) by causing a drastic reduction in microbial aggregation in epiphytic biofilm and bacterial biodiversity. CIP triggered resistance mechanisms among dominant bacteria phyla such as Proteobacteria, Actinobacteria, and Planctomycetes causing their increased relative abundance. Additionally, the relative abundances of eukaryotic microorganisms (including; Chloroplastida, Metazoa, and Rhizaria) and 13 ARGs subtypes (including; Efflux pump, Tetracycline, Multi-drug, Rifampin, Beta-lactam, Peptide, Trimethoprim) were significantly increased. While dominant metabolic pathways such as Carbohydrate, amino acid, energy and nucleotide metabolism were inhibited. This study revealed that V. spiralis has great sorption capacity for CIP than sediment and though CIP was effectively removed from the overlying water, it caused a prolonged effect on the epiphytic biofilm microbial communities.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus)

Simple Summary

The gut microbiota (all microbes in the intestine) of fishes is known to play an essential role in diverse aspects of their life. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. This study characterised the microbial composition in gut samples of Nile Tilapia collected from Lake Tana and the Bahir Dar aquaculture facility centre applying modern molecular techniques. The results show clear differences in the gut microbiota in fish from the Lake Tana and the ones from aquaculture. Further, also significant differences were observed on the composition of the gut microbiota across sampling months. Samples from the aquaculture centre displayed a higher diversity than the wild catch Nile tilapia from Lake Tana even though there is also an overlapping of the detected microbial groups. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work will help to precisely explain the causes of these changes and their influence of the health and growth of Nile tilapia in Ethiopian lakes as well as under aquaculture conditions.

Abstract

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., "reporting the water bacterial community composition", "resistance to antibiotics", and "antibiotic resistance genes (ARG)", were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.

Variation in microbial populations and antibiotic resistance genes in mariculture sediments in the present of the seaweed Ulva fasciata and under selective pressure of oxytetracycline

The widely distributed seaweed Ulva fasciata has nutrient absorption abilities and can be used in the bioremediation of polluted maricultural environments. This study explored microbial community and antibiotic resistance gene (ARG) variation in mariculture sediments in response to different trace levels (10, 100, and 500 μg L^-1) of oxytetracycline (OTC) and the presence of Ulva fasciata. The increase in OTC level promoted nutrient (NO₃_-N and PO₄^3--P) removal mainly due to Ulva fasciata adsorption. The abundances of the Euryarchaeota and Planctomycetes phyla in sediments were positively related to the increase in OTC stress, while a negative correlation occurred for the Proteobacteria phylum via metagenomic analysis. Compared with the control system, the increase rates of total ARGs were 3.90%, 7.36% and 13.42% at the OTC levels of 10, 100 and 500 μg L^-1, respectively. OTC stress mainly favoured the collateral enrichment of non-corresponding polypeptide and MLS ARGs, mainly due to the enrichment of the phyla Planctomycetes and Euryarchaeota by the synergistic effect of OTC and nutrients. The results of quantitative PCR with tetracycline resistance genes (TRGs) (tetO, tetT, tetPB, tetW and otrA) and a horizontal transfer gene (intl1) demonstrated that all of genes had much higher gene numbers in sediments after 3 months of OTC stress than in those without OTC stress, which was strongly related to the variation in the phyla Bacteroidetes, Gemmatimonadetes and Acidobacteria. The significant correlation between intl1 and the target TRGs is indicative of the important role of the horizontal transfer of integron-resistant genes in the spread of TRGs.

Metagenomic analysis reveals antibiotic resistance genes in the bovine rumen

Metagenomics and network analysis were used to profile antibiotic resistance genes (ARGs) and their cooccurrence patterns in bovine rumen microbes. A total of 4941 ruminal microbial genomes and 20 metagenome samples were used in this study. In general, 103 ARG subtypes belonging to 20 ARG types in 79 candidate genomes were identified, showing the broad-spectrum profiles of ARGs in the bovine rumen environment. A wide distribution of genes encoding bacitracin resistance was found among the candidate genomes, suggesting the possibility that bovines might be one of the sources of bacitracin resistance genes. Cooccurrence patterns were found within or between the ARG types, and a positive correlation was found between some ARGs and bacteria, which revealed potential dominant hosts of ARGs. The investigation showed that bovine rumen systems are important ARG reservoirs, and our research might provide a theoretical basis for the evaluation of the harmfulness of ARGs and antibiotic-resistant bacteria (ARB) to food safety and human health.

Metagenomic Profiles of Antibiotic Resistance Genes in Activated Sludge, Dewatered Sludge and Bioaerosols

Wastewater treatment plants (WWTPs) have been considered hotspots for the development and dissemination of antibiotic resistance in the environment. Although researchers have reported a significant increase in bioaerosols in WWTPs, the associated bacterial taxa, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) remain relatively unknown. In this study, we have investigated the abundance and occurrences of ARGs and MGEs, as well as the bacterial community compositions in activated sludge (AS), dewatered sludge (DS) and bioaerosols (BA) in a WWTP. In total, 153 ARG subtypes belonging to 19 ARG types were identified by the broad scanning of metagenomic profiles obtained using Illumina HiSeq. The results indicated that the total occurrences and abundances of ARGs in AS and DS samples were significantly higher than those in BA samples (p < 0.05). However, some specific ARG types related to sulfonamide, tetracycline, macrolide resistance were present in relatively high abundance in BA samples. Similar to many other full-scale WWTPs, the Proteobacteria (58%) and Bacteroidetes (18%) phyla were dominant in the AS and DS samples, while the Firmicutes (25%) and Actinobacteria (20%) phyla were the most dominant in the BA samples. Although the abundance of genes related to plasmids and integrons in bioaerosols were two to five times less than those in AS and DS samples, different types of MGEs were observed in BA samples. These results suggest that comprehensive analyses of resistomes in BA are required to better understand the emergence of both ARGs and MGEs in the wastewater treatment process due to the significant increase of scientific attention toward bioaerosols effects.

Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons

Bacterial communities play an important role in diffuse sediment pollution in aquaculture farms. Previous studies have revealed the short-term influence of wastewater drainage on the bacterial communities but the seasonal response of the sediment bacterial communities to wastewater drainage from aquaculture farms remains unclear. This study used the 16S rRNA approach to explore the profiles of bacterial communities over four seasons in a typical crab aquaculture farm that included a pond and an outlet ditch. Nineteen sediment samples and an equal number of water samples were collected and analysed during spring, summer, autumn, and winter during 2018-19. Our results showed that Proteobacteria, Chloroflexi, and Bacteroides were the predominant phyla in aquaculture pond sediment with the relative abundance of 28.95%, 17.32%, and 15.31%, respectively. The relative abundance of Proteobacteria and Bacteroides was higher in autumn and winter, and the relative abundance of Chloroflexi was highest in spring. The Shannon diversity index value ranged from 6.17 to 9.30 and showed significant positive correlation (P < 0.01) with the concentrations of TN, NH₄⁺-N, and TP in the water. The variation in the bacterial community and relative abundance in outlet ditch sediment were consistent with those in the pond sediment. Our results show that determinisation of the bacterial community composition in the outlet ditch sediment provides a novel tool to monitor watersheds sensitive to the influence of aquacultures.