Metagenomic insights into the antibiotic resistome in freshwater and seawater from an Antarctic ice-free area

Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems

The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.

Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics

The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources. Pseudomonas were the most abundant genus, followed by Flavobacterium, Acinetobacter, Acidovorax, and Limnohabitans. However, their relative abundance varied significantly both across the sampling sites and habitats i.e. SW and PS (p < 0.05). Additionally, various ARGs were detected in SW and PS, with PS (372) having significantly more potential ARGs than SW (293). The results further showed significant variations in the relative abundance of potential pathogenic bacteria across the sampling sites and habitats (p < 0.05). Further moreover, significant differences were observed in antibiotic resistome risk scores, ARGs and MGEs across different habitats. Over all, this study suggests that pollution source and water quality parameters had a significant impact on microbiome composition and antibiotic resistome in SW and PS.

Bacterial community and antibiotic resistance genes assembly processes were shaped by different mechanisms in the deep-sea basins of the Western Pacific Ocean

As the intrinsic property of microorganisms, antibiotic resistance genes (ARGs) are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, human activities often obscure the natural distribution of ARGs through deterministic selective pressures. The deep-sea basin of the western Pacific Ocean is one of the least disturbed areas globally by human activities, providing a natural laboratory to investigate the intrinsic mechanisms governing ARGs in natural environments. In this study, we analyzed bacterial community and ARG diversity in 15 surface sediment samples from three deep-sea basins in the western Pacific Ocean. The relative abundance of ARGs in the surface sediments ranged from 3.10 × 10-3 to 5.37 × 10-2 copies/16S rRNA copies, with multidrug and β-lactam resistance genes dominated in all samples (49.06%-100%). The bacteria were mainly dominated by the Proteobacteria. The principal coordinate analysis (PCoA) showed significant spatial heterogeneity of ARGs and bacteria among the three basins. Null model, neutral community models (NCM), and normalized stochasticity ratio (NST) indicated that bacterial community was dominated by stochastic assembly, driven by geographic barriers leading to independent evolution. Conversely, the NST revealed that the ARGs profile was mainly shaped by deterministic processes. Environmental factors are more crucial than geographical factors and bacterial community for ARG occurrence among the selected factors. Meanwhile, we found that the spread of ARGs was mainly through vertical gene transfer in the pre-antibiotic era. The disparity between the assembly processes of bacterial community and ARGs may be attributed to the fact that ARG hosts were not the dominant bacteria in the community. This study first reported the distribution and assembly processes of ARGs and bacterial community in surface sediments of the western Pacific.

Metagenomics reveals the potential transmission risk of resistomes from urban park environment to human

Urban parks play a significant role in urban ecosystems and are strongly associated with human health. Nevertheless, the biological contamination of urban parks - opportunistic pathogens and antibiotic resistance genes (ARGs) - has been poorly reported. Here, metagenomic and 16 S rRNA sequencing methods were used to study the distribution and assembly of opportunistic pathogens and ARGs in soil and water from nine parks in Lanzhou city, and further compared them with local human gut microbiomes to investigate the potential transmission risk. Our results revealed that the most important type of drug resistance in urban parks was multidrug resistance, with various resistance mechanisms. Approximately half of ARGs were shared between human gut and park environment, and it was noteworthy that cross-species transmission might exist among some high-risk ARGs, such as mepA and mdtE, with a significant enrichment in human gut. Metagenomic binning uncovered several bacterial genomes carrying adjacent ARGs, MGEs, and virulence genes, indicating a possibility that these genes may jointly transfer among different environments, particularly from park environment to human. Our results provided a reference point for the management of environmental pollutants in urban parks.

Tracking the impact of perfluoroalkyl acid emissions on antibiotic resistance gene profiles in receiving water by metagenomic analysis

The ecological risks posed by perfluoroalkyl acids (PFAAs) to the aquatic environment have recently been of great concern. However, little information was available on the impact of PFAAs on antibiotic resistance genes (ARGs) profiles. In this study, the receiving river of the largest fluoropolymer production facility in China was selected to investigate the effects of PFAAs on ARGs profiles. The highest PFAAs concentration for water samples near the industrial effluent discharge point was 310.9 μg/L, which was thousands times of higher than the average concentration collected at upstream sites. Perfluorooctanoic acid accounted for more than 67.2 % of ∑PFAAs concentration in water samples collected at the downstream sites, followed by perfluorohexanoic acid (3.6 %-15.9 %). 145 ARG subtypes including high-risk ARGs were detected by metagenomic technology. The results indicated that the discharge of PFAA-containing effluents had a significant impact on the abundance and diversity of ARGs in receiving waters, and PFAAs and water quality parameters (e.g., pH, NH3N, CODMn, TP) could largely affect ARG profiles. Specifically, short-chain PFAAs had similar impacts on ARG profiles compared to the restricted long-chain PFAAs. This study confirmed the potential effects of PFAAs on ARGs in aquatic environment and provided more insights into the ecological risk raised by PFAAs.

Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut

Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.

Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica

Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.

Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning

Ship ballast water promoting the long-range migration of antibiotic resistance genes (ARGs) has raised a great concern. This study attempted to reveal ARGs profile in ballast water and decipher their hosts and potential risk using metagenomic approaches. In total, 710 subtypes across 26 ARG types were identified among the ballast water samples from 13 ships of 11 countries and regions, and multidrug resistance genes were the most dominant ARGs. The composition of ARGs were obviously different across samples, and only 5% of the ARG subtypes were shared by all samples. Procrustes analysis showed the bacterial community contributed more than the mobile genetic elements (MGEs) in shaping the antibiotic resistome. Further, 79 metagenome-assembled genomes (46 genera belong to four phyla) were identified as ARG hosts, with predominantly affiliated with the Proteobacteria. Notably, potential human pathogens (Alcaligenes, Mycolicibacterium, Rhodococcus and Pseudomonas) were also recognized as the ARG hosts. Above 30% of the ARGs hosts contained the MGEs simultaneously, supporting a pronounced horizontal gene transfer capability. A total of 43 subtypes (six percent of overall ARGs) of ARGs were assessed with high-risk, of which 23 subtypes belonged to risk Rank I (including rsmA, ugd, etc.) and 20 subtypes to the risk Rank II (including aac(6)-I, sul1, etc.). In addition, antibiotic resistance risk index indicated the risk of ARGs in ballast water from choke points of maritime trade routes was significantly higher than that from other regions. Overall, this study offers insights for risk evaluation and management of antibiotic resistance in ballast water.

NO3- as an electron acceptor elevates antibiotic resistance gene and human bacterial pathogen risks in managed aquifer recharge (MAR): A comparison with O2

Managed aquifer recharge (MAR) stands out as a promising strategy for ensuring water resource sustainability. This study delves into the comparative impact of nitrate (NO3-) and oxygen (O2) as electron acceptors in MAR on water quality and safety. Notably, NO3-, acting as an electron acceptor, has the potential to enrich denitrifying bacteria, serving as hosts for antibiotic resistance genes (ARGs) and enriching human bacterial pathogens (HBPs) compared to O2. However, a direct comparison between NO3- and O2 remains unexplored. This study assessed risks in MAR effluent induced by NO3- and O2, alongside the presence of the typical refractory antibiotic sulfamethoxazole. Key findings reveal that NO3- as an electron acceptor resulted in a 2 times reduction in dissolved organic carbon content compared to O2, primarily due to a decrease in soluble microbial product production. Furthermore, NO3- significantly enriched denitrifying bacteria, the primary hosts of major ARGs, by 747%, resulting in a 66% increase in the overall abundance of ARGs in the effluent of NO3- MAR compared to O2. This escalation was predominantly attributed to horizontal gene transfer mechanisms, as evidenced by a notable 78% increase in the relative abundance of mobile ARGs, alongside a minor 27% rise in chromosomal ARGs. Additionally, the numerous denitrifying bacteria enriched under NO3- influence also belong to the HBP category, resulting in a significant 114% increase in the abundance of all HBPs. The co-occurrence of ARGs and HBPs was also observed to intensify under NO3- influence. Thus, NO3- as an electron acceptor in MAR elevates ARG and HBP risks compared to O2, potentially compromising groundwater quality and safety.

Unraveling the mystery of antibiotic resistance genes in green and red Antarctic snow

Antarctic snow is a thriving habitat for a diverse array of complex microorganisms, and can present in different colors due to algae blooms. However, the potential role of Antarctic snow as reservoirs for antibiotic resistance genes (ARGs) has not been studied. Using metagenomic sequencing, we studied ARGs in green-snow and red-snow on the Fildes Peninsula, Antarctica. Alpha and beta diversities of ARGs, as well as co-occurrence between ARGs and bacteria were assessed. The results showed that a total of 525 ARGs conferring resistance to 30 antibiotic classes were detected across the samples, with half of the ARGs presented in all samples. Green-snow exhibited a higher number of ARGs compared to red-snow. The most abundant ARGs conferring resistance to commonly used antibiotics, including disinfecting agents and antiseptics, peptide, isoniazid, MLS, fluoroquinolone, aminocoumarin, etc. Multidrug resistance genes stood out as the most diverse and abundant, with antibiotic efflux emerging as the dominant resistance mechanism. Interestingly, the composition of ARGs in green-snow markedly differed from that in red-snow, highlighting distinct ARG profiles. Beta-diversity partitioning showed a higher contribution of nestedness for ARG's variation in green-snow, while higher contribution of turnover in red-snow. Furthermore, the co-occurrence analysis between ARGs and bacteria unveiled intricate relationships, indicating that certain ARGs may have multiple potential hosts. The observed differences in co-occurrence networks between green-snow and red-snow suggested distinct host relationships between ARGs and bacteria in these colored snows. Given the increasing appearance of the colored snow around the world due to the climate change, the results shed light on the mystery and potential implication of ARGs in green and red Antarctic snow.

Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China

Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.

Large-Scale Biogeographical Shifts of Abundance of Antibiotic Resistance Genes and Marine Bacterial Communities as Their Carriers along a Trophic Gradient

The role of marine environments in the global spread of antibiotic resistance still remains poorly understood, leaving gaps in the One Health-based research framework. Antibiotic resistance genes (ARGs) encoding resistance to five major antibiotic classes, including sulfonamides (sul1, sul2), tetracyclines (tetA, tetB), β-lactams (blaCTX-M, blaTEMblaVIM), macrolides (ermB, mphA), aminoglycosides (aac3-2), and integrase gene (intl1) were quantified by RT-qPCR, and their distribution was investigated in relation to environmental parameters and the total bacterial community in bottom layer and surface waters of the central Adriatic (Mediterranean), over a 68 km line from the wastewater-impacted estuary to coastal and pristine open sea. Seasonal changes (higher in winter) were observed for antibiotic resistance frequency and the relative abundances of ARGs, which were generally higher in eutrophic coastal areas. In particular, intl1, followed by blaTEM and blaVIM, were strongly associated with anthropogenic influence and Gammaproteobacteria as their predominant carriers. Water column stratification and geographic location had a significant influence on ARGs distribution in the oligotrophic zone, where the bacterial community exhibited a seasonal shift from Gammaproteobacteria in winter to Marine group II in summer.

Subplenones A-J: Dimeric Xanthones with Antibacterial Activity from the Endophytic Fungus Subplenodomus sp. CPCC 401465

Subplenones A-J (1-10), 10 new xanthone dimers, have been isolated and characterized from the endophytic fungus Subplenodomus sp. CPCC 401465, which resides within the Chinese medicinal plant Gentiana straminea. The isolation process was guided by antibacterial assays and molecular-networking-based analyses. The chemical structures of these compounds were elucidated through the interpretation of nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectrometry (HRESIMS) data. Furthermore, the relative configuration of the compounds was determined using NMR and single-crystal X-ray diffraction analyses, and the absolute configuration was established using electronic circular dichroism calculations. All of the isolated compounds exhibited significant inhibitory activity against Gram-positive bacteria. Notably, compounds 1, 5, and 7 displayed remarkable inhibitory activity against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 700698, with a minimum inhibitory concentration (MIC) of 0.25 μg/mL, and against vancomycin-resistant Enterococcus faecium (VRE) ATCC 700221, with MIC values ranging from 0.5 to 1.0 μg/mL.

Marine resistome of a temperate zone: Distribution, diversity, and driving factors across the trophic gradient

Marine and ocean environments are the most widespread habitats in the world but are still the least studied from the aspect of antibiotic resistance. The indigenous and tetracycline (TET)- and sulfamethoxazole (SXT)-resistant planktonic bacterial communities were simultaneously investigated for the first time along a trophic gradient of a temperate zone, regarding their taxonomic and functional structures as well as biotic and abiotic factors affecting their dynamics as vehicles of antibiotic resistance genes (ARGs), thus impacting the ARGs distribution at seasonal and spatial scales. A total of 80 microbiomes, recovered seasonally from bottom layer and surface waters along a 68-km transect from wastewater-impacted estuary to coastal and pristine open sea in the central Adriatic (Mediterranean Sea), were analysed using 16S rRNA amplicon sequencing, PICRUSt2 bioinformatics and extensive biostatistics. Eighty-one bacterial phyla were identified, with majority (n = 49) in summer when communities were found to be more species enriched across the gradient. Microbial diversity was more site-specific and pronounced in surface microbiomes in winter. Nevertheless, both richness and community diversity decreased with distance from the coast. Although the microbiomes from human-influenced sites significantly differed from those in oligotrophic offshore area, Proteobacteria were still the most abundant phylum during both seasons at the surface and seabed along the gradient, and the major contributors to the marine resistome regarding native and TET- and SXT-resistant microbial communities. Resistome structure was more diverse in winter, whereas peptide, vancomycin and multidrug resistance modules predominated regardless of season, trophic status, or antibiotic. However, multidrug, beta-lactam resistance modules as well as macrolide, phenicol, aminoglycoside, and particularly imipenem resistance genes were much more frequent in winter, suggesting that the diversity of indigenous resistomes is highly dependent on seasonal variations of the water column, driven by thermohaline stratification and nutrients. Moreover, several pathogenic genera stood out as important carriers of multiple resistance traits in TET- and SXT-related resistomes in both seasons, particularly Acinetobacter, Vibrio, Bacillus and Pseudomonas, beside which Proteus, Serratia and Bacteroides prevailed in native resistomes. This study evidenced seasonal and spatial variations of the marine microbiome and resistome and their driving forces along the trophic gradient, providing a comprehensive insight into the diversity and distribution of antibiotic resistance in the marine ecosystem of a temperate zone.