Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea

Residual heavy metals and antibiotic pollution in abandoned breeding areas along the northeast coast of Hainan Island, China

To assess the environmental status of an abandoned aquaculture and breeding area in the northeast coast of the Hainan Island, surface and well water, sediment and surface soils were sampled and analyzed for conventional physicochemical properties, heavy metals and antibiotics. Metagenome tests were also conducted to determine the composition and diversity of the microbial community in typical habitats. Affected by the discharge of wastewater from higher-place pond aquaculture, coastal freshwater rivers have undergone significant salinization, Cl- and Na+ were as high as 4.51 × 103 and 1.42 × 103 mg/L. The 3 hand-pumped wells surveyed were also suffered from varying degrees of salinization and heavy metal pollution, especially the threat of arsenic pollution. Compared with the local background values, significantly higher valves of Cu, Zn, As and Cd were observed in the surface soil and sediment, and the average concentrations for Cu, Zn, As and Cd are 5.71, 17.6, 15.4 and 0.09 mg/kg respectively. For As，the Nemerow index ranges from 7 to 16 and the geoaccumulation index is between 2 and 4, indicating moderate to severe pollution levels in surface soil. 14 antibiotics were detected in the soil and sediment samples, and the highest total amount was 73 μg/kg, with tetracycline being the dominant antibiotic. Sediment and forest soil showed different microbial community and the genetic diversity index of sediment was lower than that of the forest soils. For typical vegetation soil, the genetic diversity followed the order as P. elliottii × P. caribaea > Eucalyptus > C. equisetifolia. Among the soil and sediment samples, the highest abundances of antibiotic resistance genes (ARGs) were associated with elfamycin, peptide, rifamycin, and the most common antibiotic resistance mechanisms were antibiotic target alteration (54.5 %), antibiotic efflux (27.6 %) and antibiotic target replacement (12.1 %). The metal resistance genes (MRGs) for Cu, Fe, and Zn resistance were the main MRGs in the samples. This study identified the potential ecological environment risk factors in the abandoned coastal breeding areas, and suggested continuous monitoring and assessment of the residual pollutant abatement processes in the future.

Microplastics exacerbate the ecological risk of antibiotic resistance genes in wetland ecosystem

Wetlands are vital components of the global ecosystem, significantly influencing the retention and dissemination of microplastics (MPs) and antibiotic resistance genes (ARGs). However, the effects of different types of MPs on the environmental dynamics of ARGs within these ecosystems remain poorly understood. This study focused on the distribution and composition of ARGs associated with two primary types of MPs-polyethylene and polypropylene-within the Poyang Lake wetland, the largest freshwater lake in China, utilizing metagenomic analysis. The findings demonstrated that the bacterial communities and ARG profiles in the plastisphere were markedly distinct from those in the surrounding water. Specifically, thirteen opportunistic pathogens and forty subtypes of ARGs, primarily related to multidrug, bacitracin, and β-lactam resistance, were identified in the plastisphere. Notably, polyethylene exhibited four times more specific ARG subtypes than polypropylene. Procrustes analysis combined with network analysis indicated a lack of strong correlation between ARG abundance and bacterial populations, suggesting potential horizontal transfer of ARGs within the microbiota of the plastisphere. Additionally, three novel and functional β-lactamase genes were identified within this environment. This investigation highlights the role of MPs as reservoirs for ARGs, facilitating their exchange and posing risks to both ecological integrity and human health, thereby underscoring the need for increased attention in future research efforts.

A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli

Introduction

Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.

Methods

In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.

Results

Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread.

Discussion

This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.

Multiple antibiotic resistance and herbicide catabolic profiles of bacteria isolated from Lake Villarrica surface sediments (Chile)

Antibiotics and herbicides are contaminants of emerging concern in aquatic environments. Lake Villarrica is a relevant freshwater body in Chile and was recently designated a 'saturated nutrient zone'. Here, we investigated the occurrence of multiple antibiotic resistance (MAR) and herbicide catabolic profiles among bacteria present in the surface sediments of Lake Villarrica. The occurrence of antibiotic-resistant genes (ARGs; blaTEM, catA and tetM) and herbicide-catabolic genes (HCGs; phnJ and atzA) was investigated by qPCR. Subsequently, the presence of culturable bacteria with multiple resistance to amoxicillin (AMX), chloramphenicol (CHL) and oxytetracycline (OXT) was studied. Forty-six culturable MAR (AMX + CHL + OXT) strains were isolated and characterized with respect to their resistance to 11 antibiotics by using a disc diffusion assay and testing their ability to use herbicides as a nutrient source. qPCR analyses revealed that ARGs and HCGs were present in all sediment samples (101 to 103 gene copies g-1), with significant (P ≤ 0.05) higher values in sites near Villarrica city and cattle pastures. The plate method was used to recover MAR isolates from sediment (103-106 CFU g-1), and most of the 46 isolates also showed resistance to oxacillin (100%), cefotaxime (83%), erythromycin (96%) and vancomycin (93%). Additionally, 54 and 57% of the MAR isolates were able to grow on agar supplemented (50 mg L-1) with atrazine and glyphosate as nutrient sources, respectively. Most of the MAR isolates were taxonomically close to Pseudomonas (76.1%) and Pantoea (17.4%), particularly those isolated from urbanized sites (Pucón city). This study shows the presence of MAR bacteria with herbicide catabolic activity in sediments, which is valuable for conservation strategies and risk assessments of Lake Villarrica. However, major integrative studies on sediments as reservoirs or on the fate of MAR strains and traces of antibiotics and herbicides as a result of anthropic pressure are still needed.

Distribution and community structure of antibiotic resistance genes in the Three Gorges Reservoir Area

Antibiotic resistance genes (ARG) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes, and 6 resistance mechanisms were detected. The dominant ARG is the macB, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria. In this region, pH and NH4+ concentration were significantly negatively correlated with the relative abundance of most ARGs, while NO3- concentration and TN were significantly positively correlated with the relative abundance of most ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By studying the distribution of ARGs in the sediments of the Three Gorges Reservoir Area and the relationship between environmental factors and ARGs, we can more comprehensively understand the pollution status of ARGs in this area, and provide theoretical support for subsequent treatment.

Assessing Antibiotic-Resistant Genes in University Dormitory Washing Machines

University dormitories represent densely populated environments, and washing machines are potential sites for the spread of bacteria and microbes. However, the extent of antibiotic resistance gene (ARG) variation in washing machines within university dormitories and their potential health risks are largely unknown. To disclose the occurrence of ARGs and antibiotic-resistant bacteria from university dormitories, we collected samples from washing machines in 10 dormitories and used metagenomic sequencing technology to determine microbial and ARG abundance. Our results showed abundant microbial diversity, with Proteobacteria being the dominant microorganism that harbors many ARGs. The majority of the existing ARGs were associated with antibiotic target alteration and efflux, conferring multidrug resistance. We identified tnpA and IS91 as the most abundant mobile genetic elements (MGEs) in washing machines and found that Micavibrio aeruginosavorus, Aquincola tertiaricarbonis, and Mycolicibacterium iranicum had high levels of ARGs. Our study highlights the potential transmission of pathogens from washing machines to humans and the surrounding environment. Pollution in washing machines poses a severe threat to public health and demands attention. Therefore, it is crucial to explore effective methods for reducing the reproduction of multidrug resistance.

Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake

Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of ARGs over centuries to millennia remain largely unknown. In this study, we investigated the vertical change patterns of bacterial communities, ARGs and mobile genetic elements (MGEs) found in sediments of Lake Chenghai spanning the past 600 years. Within resistome preserved in sediments, 177 ARGs subtypes were found with aminoglycosides and multidrug resistance being the most abundant. The ARG abundance in the upper sediment layers (equivalent to the post-antibiotic era since the 1940s) was lower than those during the pre-antibiotic era, whereas the ARG diversity was higher during the post-antibiotic era, possibly because human-induced lake eutrophication over the recent decades facilitated the spread and proliferation of drug-resistant bacteria. Statistical analysis suggested that MGEs abundance and the bacterial community structure were significantly correlated with the abundance and diversity of ARGs, suggesting that the occurrence and distribution of ARGs may be transferred between different bacteria by MGEs. Our results provide new perspectives on the natural history of ARGs in freshwater environments and are essential for understanding the temporal dynamics and dissemination of ARGs.

Occurrence and source identification of antibiotics and antibiotic resistance genes in groundwater surrounding urban hospitals

Urban groundwater, serving as a critical reservoir for potable water, faces susceptibility to contamination from discrete sources such as hospital wastewater. This study investigates the distribution and plausible origins of antibiotics and antibiotic resistance genes (ARGs) in urban groundwater, drawing comparisons between areas proximal to hospitals and non-hospital areas. Ofloxacin and oxytetracycline emerged as the prevalent antibiotics across all samples, with a discernibly richer array of antibiotic types observed in groundwater sourced from hospital-adjacent regions. Employing a suite of multi-indicator tracers encompassing indicator drugs, Enterococci, ammonia, and Cl/Br mass ratio, discernible pollution from hospital or domestic sewage leakage was identified in specific wells, correlating with an escalating trajectory in antibiotic contamination. Redundancy analysis underscored temperature and dissolved organic carbon as principal environmental factors influencing antibiotics distribution in groundwater. Network analysis elucidated the facilitating role of mobile genetic elements, such as int1 and tnpA-02 in propagating ARGs. Furthermore, ARGs abundance exhibited positive correlations with temperature, pH and metallic constituents (e.g., Cu, Pb, Mn and Fe) (p < 0.05). Notably, no conspicuous correlation manifested between antibiotics and ARGs. These findings accentuate the imperative of recognizing the peril posed by antibiotic contamination in groundwater proximal to hospitals and advocate for the formulation of robust prevention and control strategies to mitigate the dissemination of antibiotics and ARGs.

Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary

To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.

Investigation of antibiotic resistance genotypic and phenotypic characteristics of marine aquaculture fish carried in the Dalian area of China

Due to the long-term and irrational use of antibiotics for the prevention and control of bacterial diseases in aquaculture, antibiotic resistance genes have become a new source of pollution in aquatic products. Factors such as the spread of drug-resistant strains and the horizontal transfer of drug-resistant genes have led to multi-drug resistance in fish-infecting bacteria, which seriously affects the quality and safety of aquatic products. In this study, 50 samples of horse mackerel and puffer fish sold in Dalian aquatic products market and seafood supermarket were collected, and the phenotypic characteristics of the bacteria carried by the fish for drugs such as sulfonamides, amide alcohols, quinolones, aminoglycosides and tetracyclines were tested and analyzed, and the resistance genes carried by fish samples were detected by SYBG qPCR. Our statistical analyses demonstrated that the drug resistance phenotypes and genotypes of bacteria carried by mariculture horse mackerel and puffer fish in the Dalian area of China were complex, and the multi-drug resistance rate reached 80%. Among the examined antibiotics, the resistance rates to cotrimoxazole, tetracycline, chloramphenicol, ciprofloxacin, norfloxacin, levofloxacin, kanamycin, and florfenicol exceeded 50%, whereas the resistance rates to gentamicin and tobramycin were 26 and 16%, respectively. The detection rate of the drug resistance genes tetA, sul1, sul2, qnrA, qnrS, and floR exceeded 70% and all samples carried more than three drug resistance genes. The correlation analysis of drug resistance genes and drug resistance phenotypes showed that the detection of the drug resistance genes sul1, sul2, floR, and qnrD was correlated with the detection of drug resistance phenotypes (p < 0.01). However, the correlation between the resistance genes cmlA, cfr, tetA, qnrA, qnrS, and aac(6')-Ib-cr and the corresponding resistance phenotype was not significant (p > 0.05). In general, our findings indicated that the multi-drug resistance of bacteria carried by marine horse mackerel and puffer fish in the Dalian area was serious. From the perspective of drug resistance rate and drug resistance gene detection rate, the aminoglycosides gentamicin and tobramycin are still considered effective in controlling bacterial infection in marine fish in the study area. Collectively, our findings provide a scientific basis for the management of drug use in mariculture, which can prevent the transmission of drug resistance through the food chain and minimize the associated human health risks.

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds

Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.

Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment

Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.

Metagenomic analysis reveals the diversity and distribution of antibiotic resistance genes in thermokarst lakes of the Yellow River Source Area

Thermokarst lakes form as the results of ice-rich permafrost thawing and act as important water resources in cold regions. However, the distributions of antibiotic resistance genes (ARGs) in thermokarst lakes are far less studied. Using metagenomic sequencing approach, we provided the first study to document ARGs in thermokarst lakes of the Yellow River Source Area on the Qinghai-Tibet Plateau (QTP). The results revealed that both sediment and water of the thermokarst lakes harbor diverse ARGs. Multidrug resistance genes were the most diverse, while rifamycin resistance genes were the most abundant with rpoB2 and rpoB genes having the highest proportion. Sediment samples contained more ARGs than water samples, but their composition differed between the two types of samples. However, the composition variations of sediment and water ARGs were closely correlated. The Sorensen dissimilarities of ARGs were controlled by strong turnover processes in sediment samples, and by turnover and nestedness in water samples. High contributions of nestedness were found between sediment and water samples. Moreover, ARGs in water had more significant relationships with environmental variables than that in sediment. Given the role of thermokarst lakes as important water resources in permafrost landscape, as well as intensifying influences of climate change and anthropogenetic activities, thermokarst lakes could bring potential ARG risks, warranting further investigation and evaluation.

Non-corresponding contaminants in marine surface sediments as a factor of ARGs spread in the Sea of Azov

The present study aims to analyze the level and total toxicity of the most common pollutants in surface sediments and assess their impact on the occurrence of antibiotic resistance genes (ARGs) in the Sea of Azov. Biotesting using the whole-cell bacterial lux-biosensors showed high integral toxicity of surface sediments and the presence of genotoxicants and substances that cause oxidative stress and protein damage. Using cluster analysis, it was shown that the distribution of pollutants in the Sea of Azov depends on the type of surface sediments. The relative abundance and distribution of 14 ARGs in surface sediments were shown. Principle component analyses results suggest that non-corresponding contaminants do not exert direct influence on the ARGs abundance in the surface sediments of the Sea of Azov. Thus, the need to investigate the significance of non-corresponding pollutants in the selection and distribution of ARGs in the aquatic environment remains a pressing problem.

Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms

The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.

Impact of the surrounding environment on antibiotic resistance genes carried by microplastics in mangroves

The pollution of antibiotic resistance genes (ARGs) carried by microplastics (MPs) is a growing concern. Mangroves are located at the intersection of land and sea and are seriously affected by MP pollution. However, few studies have systematic research evaluating the transmission risk of ARGs carried by MPs in mangroves. We conducted in situ experiments by burying five different MPs (polypropylene, high-density polyethylene, polystyrene, polyethylene glycol terephthalate, and polycaprolactone particles) in mangroves with different surrounding environments. A total of 10 genes in the MPs of mangroves were detected using quantitative real-time polymerase chain reactions, including eight ARGs and two mobile genetic elements (MGEs). The abundance of ARGs in Guanhai park mangroves in living areas (GH) was higher than that of Gaoqiao mangroves in protected areas (GQ) and Beiyue dike mangroves in aquaculture pond areas (BY). Pathogenic bacteria, such as Acinetobacter, Bacillus, and Vibrio were found on the MP surfaces of the mangroves. The number of ARGs carried by multiple drug-resistant bacteria in the GH mangroves was greater than that in the GQ and BY mangroves. Moreover, the ARGs carried by MPs in GH mangroves had the highest potential transmission risk by horizontal gene transfer. Sociometric and environmental factors were the main drivers shaping the distribution characteristics of ARGs and MGEs. Polypropylene and high-density polyethylene particles are preferred substrates for obtaining diffuse ARGs. This study investigated the drivers of ARGs in the MPs of mangroves and provided essential guidance on the use and handling of plastics.

Microplastics accumulation in mangroves increasing the resistance of its colonization Vibrio and Shewanella

The enrichment of various pollutants in mangrove has attracted widespread attention. Especially, microplastics accumulation in mangrove may provide a more challenging ecological colonization site by enriching pollutants, thus affecting the change of microplastics antibiotic resistance and increasing the risk of antibiotic failure. Herein, the antibiotic-resistant of microplastics and sediment from mangrove were investigated. The results show that isolates are mainly colonized by Vibrio parahemolyticus (V. parahemolyticus), Vibrio alginolyticus (V. alginolyticus), and Shewanella. 100% mangrove microplastics isolates are resistant to chloramphenicol, cefazolin, and tetracycline, especially amoxicillin clavulanate and ampicillin. Meanwhile, the multiple antibiotics resistance (MAR) indexes of V. parahaemolyticus, Shewanella, and V. alginolyticus in mangrove microplastics are 0.72, 0.77, and 0.77, respectively, which are far higher than the MAR index standard (0.2) and that of mangrove sediment isolates. Furthermore, compared with V. parahaemolyticus isolated from the same mangrove microplastics, Shewanella and V. alginolyticus show stronger drug resistance. It should be noted that there is a closely related relationship between the type of microplastics and the antibiotics resistance of isolated bacteria. For the antibiotics sensitivity test of norfloxacin, streptomycin, amoxicillin, and chloramphenicol, V. parahaemolyticus have the lower antibiotics resistance than that of V. alginolyticus isolated from the same mangrove microplastics. However, Vibrio isolated from PE has stronger antibiotics resistance. Results reveal that mangrove may be one of the potential risks for emergence and spread of bacterial antibiotics-resistant and multidrug-resistant, and microplastic biofilms may act as promoters of bacterial antibiotic resistance.

A hybrid DNA sequencing approach is needed to properly link genotype to phenotype in multi-drug resistant bacteria

Antibiotic resistance genes (ARGs) are now viewed as emerging contaminants posing a potential worldwide human health risk. The degree to which ARGs are transferred to other bacteria via mobile genetic elements (MGEs), including insertion sequences (ISs), plasmids, and phages, has a strong association with their likelihood to function as resistance transfer determinants. Consequently, understanding the structure and function of MGEs is paramount to assessing future health risks associated with ARGs in an environment subjected to strong antibiotic pressure. In this study we used whole genome sequencing, done using MinION and HiSeq platforms, to examine antibiotic resistance determinants among four multidrug resistant bacteria isolated from fish farm effluent in Jeju, South Korea. The combined data was used to ascertain the association between ARGs and MGEs. Hybrid assembly using HiSeq and MinION reads revealed the presence of IncFIB(K) and pVPH2 plasmids, whose sizes were verified using pulsed field gel electrophoresis. Twenty four ARGs and 95 MGEs were identified among the 955 coding sequences annotated on these plasmids. More importantly, 22 of 24 ARGs conferring resistance to various antibiotics were found to be located near MGEs, whereas about a half of the ARGs (11 out of 21) were so in chromosomes. Our results also suggest that the total phenotypic resistance exhibited by the isolates was mainly contributed by these putatively mobilizable ARGs. The study gives genomic insights into the origins of putatively mobilizable ARGs in bacteria subjected to selection pressure.

Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities

Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.

Antibiotics, Multidrug-Resistant Bacteria, and Antibiotic Resistance Genes: Indicators of Contamination in Mangroves?

Multidrug-resistant bacteria and antibiotic resistance genes can be monitored as indicators of contamination in several environments. Mangroves are among the most productive ecosystems, and although they can be resilient to the action of climate phenomena, their equilibrium can be affected by anthropogenic activities. Regarding the presence and persistence of multidrug-resistant bacteria in mangroves, it is common to think that this ecosystem can function as a reservoir, which can disperse the antibiotic resistance capacity to human pathogens, or serve as a filter to eliminate drug-resistant genes. The possible impact of anthropogenic activities carried out near mangroves is reviewed, including wastewater treatment, food production systems, leisure, and tourism. Adverse effects of antibiotic resistance genes or multidrug-resistant bacteria, considered as emerging contaminants, have not been reported yet in mangroves. On the contrary, mangrove ecosystems can be a natural way to eliminate antibiotics, antibiotic-resistant bacteria, and even antibiotic-resistant genes from the environment. Although mangroves’ role in decreasing antibiotics and antibiotic resistance genes from the environment is being proposed, the mechanisms by which these plants reduce these emerging contaminants have not been elucidated and need further studies. Additionally, further evaluation is needed on the effects of antibiotics and antibiotic-resistant bacteria in mangroves to generate an analysis of the human contribution to the degradation of this specific ecosystem as well as to define if these contaminants can be used as indicators of contamination in mangrove ecosystems.

A systematic review of antibiotics and antibiotic resistance genes in estuarine and coastal environments

Antibiotics and antibiotic resistance genes (ARGs) are prevalent in estuarine and coastal environments due to substantial terrestrial input, aquaculture effluent, and sewage discharge. In this article, based on peer-reviewed papers, the sources, spatial patterns, driving factors, and environmental implications of antibiotics and ARGs in global estuarine and coastal environments are discussed. Riverine runoff, WWTPs, sewage discharge, and aquaculture, are responsible for the prevalence of antibiotics and ARGs. Geographically, pollution due to antibiotics in low- and middle-income countries is higher than that in high-income countries, and ARGs show remarkable latitudinal variations. The distribution of antibiotics is driven by antibiotic usage and environmental variables (heavy metals, nutrients, organic pollutants, etc.), while ARGs are affected by antibiotics residues, environmental variables, microbial communities, and mobile genetic elements (MGEs). Antibiotics and ARGs alter microbial communities and biogeochemical cycles, as well as pose threats to marine organisms and human health. Our results provide comprehensive insights into the transport and environmental behaviors of antibiotics and ARGs in global estuarine and coastal environments.

Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities - A study in Hainan Island, China

Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 10⁷-6.88 × 10⁸ copies per g sediment (1.27 × 10^-2-3.39 × 10^-2 copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.

Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment

Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.

Emerging pollutants-Part II: Treatment

Emerging pollutants (EPs) refer to a class of pollutants, which are emerging in the environment or recently attracted attention. EPs mainly include pharmaceutical and personal care products (PPCPs), endocrine-disrupting chemicals (EDCs), and antibiotic resistance genes (ARGs). EPs have potential threats to human health and ecological environment. In recent years, the continuous detections of EPs in surface and ground water have brought huge challenges to water treatment and also made the treatment of EPs become an international research hotspot. This paper summarizes some research results on EPs treatment published in 2019. This paper may be helpful to understand the current situations and development trends of EP treatment technologies.

Antimicrobial resistance: A multifaceted problem with multipronged solutions

Infectious diseases still stand as a major cause of morbidity and mortality, and this problem can be worsened with the current antimicrobial resistance crisis. To tackle this crisis more studies analyzing the causes, routes, and reservoirs where antimicrobial resistance can emerge and expand, together with new antimicrobials and strategies for fighting antimicrobial resistance are needed. In the current special issue of MicrobiologyOpen, a set of articles dealing with the multiple faces of antimicrobial resistance are presented. These articles provide new information for understanding and addressing this problem.

Insights into Antagonistic Interactions of Multidrug Resistant Bacteria in Mangrove Sediments from the South Indian State of Kerala

Antibiotic resistance is a global issue which is magnified by interspecies horizontal gene transfer. Understanding antibiotic resistance in bacteria in a natural setting is crucial to check whether they are multidrug resistant (MDR) and possibly avoid outbreaks. In this study, we have isolated several antibiotic-resistant bacteria (ARB) (n = 128) from the mangroves in Kerala, India. ARBs were distributed based on antibiotics (p = 1.6 × 10^-5). The 16S rRNA gene characterization revealed dominance by Bacillaceae (45%), Planococcaceae (22.5%), and Enterobacteriaceae (17.5%). A high proportion of the isolates were MDR (75%) with maximum resistance to methicillin (70%). Four isolates affiliated to plant-growth promoters, probiotics, food, and human pathogens were resistant to all antibiotics indicating the seriousness and prevalence of MDR. A significant correlation (R = 0.66; p = 2.5 × 10^-6) was observed between MDR and biofilm formation. Antagonist activity was observed in 62.5% isolates. Gram-positive isolates were more susceptible to antagonism (75.86%) than gram-negative (36.36%) isolates. Antagonism interactions against gram-negative isolates were lower (9.42%) when compared to gram-positive isolates (89.85%). Such strong antagonist activity can be harnessed for inspection of novel antimicrobial mechanisms and drugs. Our study shows that MDR with strong biofilm formation is prevalent in natural habitat and if acquired by deadly pathogens may create havoc in public health.

Prevalence and proliferation of antibiotic resistance genes in the subtropical mangrove wetland ecosystem of South China Sea

The emerging pollutants antibiotic resistance genes (ARGs) are prevalent in aquatic environments such as estuary. Coastal mangrove ecosystems always serve as natural wetlands for receiving sewage which always carry ARGs. Currently, the research considering ARG distribution in mangrove ecosystems gains more interest. In this work, we investigated the diversity of ARGs in an urban estuary containing mangrove and nonmangrove areas of the South China Sea. A total of 163 ARGs that classified into 22 resistance types and six resistance mechanisms were found. ARG abundance of the samples in the estuary is between 0.144 and 0.203. This is within the general range of Chinese estuaries. The difference analysis showed that abundances of total ARGs, six most abundant ARGs (mtrA, rpoB, rpoC, rpsL, ef‐Tu, and parY), the most abundant resistance types (elfamycin, multidrug, and peptide), and the most abundant resistance mechanism (target alteration) were significantly lower in mangrove sediment than that in nonmangrove sediment (p < 0.05). Network and partial redundancy analysis showed that sediment properties and mobile genetic elements were the most influential factors impacting ARG distribution rather than microbial community. The two factors collectively explain 51.22% of the differences of ARG distribution. Our study indicated that mangrove sediments have the capacity to remove ARGs. This work provides a research paradigm for analysis of ARG prevalence and proliferation in the subtropical marine coastal mangrove ecosystem.