Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam

A comparative genomics study of the microbiome and freshwater resistome in Southern Pantanal

This study explores the resistome and bacterial diversity of two small lakes in the Southern Pantanal, one in Aquidauana sub-region, close to a farm, and one in Abobral sub-region, an environmentally preserved area. Shotgun metagenomic sequencing data from water column samples collected near and far from the floating macrophyte Eichhornia crassipes were used. The Abobral small lake exhibited the highest diversity and abundance of antibiotic resistance genes (ARGs), antibiotic resistance classes (ARGCs), phylum, and genus. RPOB2 and its resistance class, multidrug resistance, were the most abundant ARG and ARGC, respectively. Pseudomonadota was the dominant phylum across all sites, and Streptomyces was the most abundant genus considering all sites.

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.

Detection of clinically relevant antibiotic-resistant bacteria in shared fomites, waste water and municipal solid wastes disposed near residential areas of a Nigerian city

Studies investigating environmental hotspots of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in Nigeria are limited. This study was designed to assess various environmental sources and commonly touched surfaces as potential carriers of ARB and ARGs with implications for public health. A total of 392 samples, including sewage (36), sludge (36), diapers (20), plastics (20), water sachet polythene bags (20), food wastes (20), soil beneath dump sites (20), and frequently touched surfaces such as restroom floors (80), corridors (24), door handles (56), and room floors and walls (60), were collected and screened for the presence of resistant bacteria carrying genes such as bla KPC, bla NDM-1, bla CMY-2, bla IMP, bla OXA66 and MecA. Additionally, we employed standard techniques to detect methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii . We also evaluated the effectiveness of routine disinfection procedures in eliminating ARB from restroom floors. Our findings revealed that sewage, sludge, diapers, food wastes and restroom floors are frequently contaminated with highly and moderately resistant strains of E. coli, K. pneumoniae, P. aeruginosa and MRSA. Notably, we identified two variants of the bla OXA51-like gene (bla OXA-66 and bla OXA-180) in A. baumannii isolated from these environmental sources. Furthermore, we detected seven ESBL- K. pneumoniae , five ESBL- A. baumannii , two ESBL- E. coli and one ESBL- P. aeruginosa , all carrying one or more ARGs (bla KPC, bla NDM-1, bla CMY-2), in isolates recovered from sewage, sludge, restroom floors and plastics. It is of note that ARB persisted on restroom floors even after disinfection procedures. In conclusion, this study highlights that environmental wastes indiscriminately discarded in residential areas and shared surfaces among individuals are heavily colonized by ARB carrying ARGs of significant public health importance.

What samples are suitable for monitoring antimicrobial-resistant genes? Using NGS technology, a comparison between eDNA and mrDNA analysis from environmental water

Introduction

The rise in antimicrobial resistance (AMR) that is affecting humans, animals, and the environment, compromises the human immune system and represents a significant threat to public health. Regarding the impact on water sanitation, the risk that antimicrobial-resistant genes (ARGs) and antimicrobial-resistant bacteria in surface water in cities pose to human health remains unclear. To determine the prevalence of AMR in environmental surface water in Japan, we used DNA sequencing techniques on environmental water DNA (eDNA) and the DNA of multidrug-resistant bacteria (mrDNA).

Methods

The eDNA was extracted from four surface water samples obtained from the Tokyo area and subjected to high- throughput next-generation DNA sequencing using Illumina-derived shotgun metagenome analysis. The sequence data were analyzed using the AmrPlusPlus pipeline and the MEGARes database. Multidrug-resistant bacteria were isolated using a culture-based method from water samples and were screened by antimicrobial susceptibility testing (for tetracycline, ampicillin-sulbactam, amikacin, levofloxacin, imipenem, and clarithromycin). Of the 284 isolates, 22 were identified as multidrug-resistant bacteria. The mrDNA was sequenced using the Oxford nanopore MinION system and analyzed by NanoARG, a web service for detecting and contextualizing ARGs.

Results and discussion

The results from eDNA and mrDNA revealed that ARGs encoding beta-lactams and multidrug resistance, including multidrug efflux pump genes, were frequently detected in surface water samples. However, mrDNA also revealed many sequence reads from multidrug-resistant bacteria, as well as nonspecific ARGs, whereas eDNA revealed specific ARGs such as pathogenic OXA-type and New Delhi metallo (NDM)-beta-lactamase ARGs.

Conclusion

To estimate potential AMR pollution, our findings suggested that eDNA is preferable for detecting pathogen ARGs.

Wastewater-based epidemiology for tracking bacterial diversity and antibiotic resistance in COVID-19 isolation hospitals in Qatar

BACKGROUND

Hospitals are hotspots for antimicrobial resistance genes (ARGs), and play a significant role in their emergence and spread. Large numbers of ARGs will be ejected from hospitals via wastewater systems. Wastewater-based epidemiology has been consolidated as a tool to provide real-time information, and represents a promising approach to understanding the prevalence of bacteria and ARGs at community level.

AIMS

To determine bacterial diversity and identify ARG profiles in hospital wastewater pathogens obtained from coronavirus disease 2019 (COVID-19) isolation hospitals compared with non-COVID-19 facilities during the pandemic.

METHODS

Wastewater samples were obtained from four hospitals: three assigned to patients with COVID-19 patients and one assigned to non-COVID-19 patients. A microbial DNA quantitative polymerase chain reaction was used to determine bacterial diversity and ARGs.

FINDINGS

The assay recorded 27 different bacterial species in the samples, belonging to the following phyla: Firmicutes (44.4%), Proteobacteria (33.3%), Actinobacteria (11%), Bacteroidetes (7.4%) and Verrucomicrobiota (3.7%). In addition, 61 ARGs were detected in total. The highest number of ARGs was observed for the Hazem Mebaireek General Hospital (HMGH) COVID-19 patient site (88.5%), and the lowest number of ARGs was found for the HMGH non-patient site (24.1%).

CONCLUSION

The emergence of contaminants in sewage water, such as ARGs and high pathogen levels, poses a potential risk to public health and the aquatic ecosystem.

Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions

Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.

Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework

The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.

Role of Biofilms in Waste Water Treatment

Biofilm cells have a different physiology than planktonic cells, which has been the focus of most research. Biofilms are complex biostructures that form on any surface that comes into contact with water on a regular basis. They are dynamic, structurally complex systems having characteristics of multicellular animals and multiple ecosystems. The three themes covered in this review are biofilm ecology, biofilm reactor technology and design, and biofilm modeling. Membrane-supported biofilm reactors, moving bed biofilm reactors, granular sludge, and integrated fixed-film activated sludge processes are all examples of biofilm reactors used for water treatment. Biofilm control and/or beneficial application in membrane processes are improving. Biofilm models have become critical tools for biofilm foundational research as well as biofilm reactor architecture and design. At the same time, the differences between biofilm modeling and biofilm reactor modeling methods are acknowledged.

Degradation of Sulfonamides by UV/Electrochemical Oxidation and the Effects of Treated Effluents on the Bacterial Community in Surface Water

This study evaluated the effects of ultraviolet (UV) photolysis combined with electrochemical oxidation on sulfonamides (SAs) as well as its treated effluent on the bacterial community in surface water. In terms of degradation rate, the best anode material for electrochemical oxidation was Ti/RuO2-IrO2, which had the highest degradation kinetic constant compared to Ti/Ta2O5-IrO2 and Ti/Pt. Experiments showed the highest degradation rate of SAs at 8.3 pH. Similarly, increasing the current leads to stronger degradation due to the promotion of free chlorine production, and its energy consumption rate decreases slightly from 73 to 67 W h/mmol. Compared with tap water, the kinetic constants decreased by 20-62% for SAs in three different surface water samples, which was related to the decrease in free chlorine. When extending the reaction time to 24 h, the concentrations of chemical oxygen demand and total organic carbon decreased by approximately 30-40%, indicating that the SAs and their products could be mineralized. The diversity analysis showed that the effluents influenced the richness and diversity of the bacterial community, particularly in the 4 h sample. Additionally, there were 86 operational taxonomic units common to all samples, excluding the 4 h sample; significant differences were derived from changes in the Actinobacteriota and Bacteroidota phyla. The toxicity of the products might explain these changes, and these products could be mineralized, as observed in the 24 h sample. Therefore, the extension of treatment time would greatly reduce the ecological harm of treated effluent and ensure that the UV/electrochemical process is a feasible treatment option. Overall, this study provides valuable insight into the optimization and feasibility of UV/electrochemical processes as a sustainable treatment option for sulfonamide-contaminated water sources, emphasizing the importance of considering ecological impacts and the need for extended treatment times that address environmental concerns and ensuring improved water quality.

Antibiotic Resistance in the Finfish Aquaculture Industry: A Review

Significant challenges to worldwide sustainable food production continue to arise from environmental change and consistent population growth. In order to meet increasing demand, fish production industries are encouraged to maintain high growth densities and to rely on antibiotic intervention throughout all stages of development. The inappropriate administering of antibiotics over time introduces selective pressure, allowing the survival of resistant bacterial strains through adaptive pathways involving transferable nucleotide sequences (i.e., plasmids). This is one of the essential mechanisms of antibiotic resistance development in food production systems. This review article focuses on the main international regulations and governing the administering of antibiotics in finfish husbandry and summarizes recent data regarding the distribution of bacterial resistance in the finfish aquaculture food production chain. The second part of this review examines promising alternative approaches to finfish production, sustainable farming techniques, and vaccination that circumvents excessive antibiotic use, including new animal welfare measures. Then, we reflect on recent adaptations to increasingly interdisciplinary perspectives in the field and their greater alignment with the One Health initiative.

Frequent contamination of edible freshwater fish with colistin-resistant Escherichia coli harbouring the plasmid-mediated mcr-1 gene

The threat of antimicrobial resistance is increasing. Microbial food contamination poses a serious public health risk; however, there are only a few studies on the prevalence of colistin-resistant Escherichia coli (COL-E) contamination in freshwater fish. This study aimed to characterise the antibiotic resistance genes and antibiotic susceptibility profiles of COL-E in freshwater fish in Vietnam. In total, 103 fish were collected and 63 COL-E were isolated. COL-E was investigated by genotyping mcr and AmpC/extended-spectrum β-lactamase (ESBL)-related genes. The results show that COL-E and AmpC/ESBL-producing COL-E were confirmed in 24.3 % and 14.6 % of the fish, respectively. Multiplex PCR for mcr-1-9 showed that all 63 COL-E harboured mcr-1, while mcr-3 was detected in 7.9 % of COL-E. The minimum inhibitory concentration of colistin ranged from 2 to 256 μg/mL. Meanwhile, antibiotic susceptibility results show that all COL-E were resistant to ampicillin, streptomycin, and chloramphenicol.

Co-driving factors of tidal effect on the abundance and distribution of antibiotic resistance genes in the Yongjiang Estuary, China

The unreasonable use of antibiotics and the transmission of antibiotic resistance genes (ARGs) induced by antibiotics have led to a large number of ARGs entered the water environment, which seriously threatened human health and environmental safety. The estuarine aquatic environment connects with inland rivers and sea and is frequently influenced by human activities. This study aims to reveal the occurrences and abundances of ARGs and bacterial community composition by high-throughput quantitative PCR including 296 primers and high-throughput sequencing in the tide rising and ebbing of surface water in the Yongjiang Estuary, China. The results showed that there were a large number of ARGs and mobile genetic elements (MGEs) detected in the rising tide and ebb tide water bodies. The numbers of detected ARGs in each sample at rising and ebb tide ranged from 16 to 77 and 61 to 88, respectively, and the absolute abundance ranges were 1.69 × 10⁴-1.69 × 10⁹ copies/L and 3.18 × 10³-2.57 × 10⁹ copies/L, respectively. Obvious tidal distribution characteristics of ARGs were showed. Most of ARGs conferred resistance to multidrug, aminoglycosides and sulfanilamides. Proteobacteria, Actinobacteria and Bacteroidetes were the dominantly bacterial phylum in the Yongjiang Estuary. Network analysis results indicated that multi-genera were identified as possible ARGs hosts, and they carried more than two types of ARGs genes. Partial least squares path modeling further revealed that MGEs and bacterial community composition were the most important driving factors. The results of the study can provide the corresponding scientific basis for the diffusion and control of ARGs in estuaries.

Removal of Sulfonamide Resistance Genes in Fishery Reclamation Mining Subsidence Area by Zeolite

A majority of subsidence lakes were reclaimed as fish ponds, but the widespread use of antibiotics has caused the pollution of antibiotic resistance genes (ARGs). This paper uses zeolite as a filter material to construct a horizontal submersible wastewater treatment device and explores its effect on the removal of conventional pollutants and sulfonamide ARGs in wastewater. The results showed that the removal of total nitrogen and ammonia nitrogen by the zeolite filter media were 59.0% and 63.8%, respectively, which were higher than the removal of total phosphorus and COD. The absolute abundances of sul1 and sul2 in wastewater were 2.81 × 10⁴ copies·L⁻¹ and 2.42 × 10³ copies·L⁻¹. On average, 60.62% of sul1 and 75.84% of sul2 can be removed, and more than 90% of sul1 and sul2 can be removed. Experiments showed that the residence time of wastewater in the treatment device had a significant impact on removal. The microbial community structure of aquaculture wastewater was quite different before and after wastewater treatment. The abundance changes of Saccharimonadales and Mycobacterium affect the removal of sulfonamide ARGs.

Typology of interventions for antimicrobial use and antimicrobial resistance in aquaculture systems in low- and middle-income countries

Indiscriminate antimicrobial use (AMU) in aquaculture to treat and prevent diseases is common and can lead to the emergence of antimicrobial-resistant micro-organisms, potentially impacting public health and connected ecosystems. This study aimed to develop a typology to classify and characterise interventions to reduce AMU in aquaculture and identify points of action. Seventeen aquaculture and animal health professionals in Asian and African countries were interviewed to gather information on characteristics of interventions in different contexts to develop a typology. Seven types of interventions were defined: (i) legislation and regulations; (ii) industry rules and standards; (iii) voluntary instruments; (iv) commercial technology and alternatives to antimicrobials; (v) on-farm management; (vi) learning and awareness-raising; and (vii) activities with co-benefits. Types were based on intervention function, scope of implementation, implementer, compulsion, strength of the intervention, AMU/antimicrobial resistance (AMR) objective and stakeholder to influence. For each type, examples were described and discussed. The most common interventions to address AMU and AMR were legislative and regulatory frameworks and voluntary instruments, including National Action Plans. Interventions addressing AMU/AMR specifically were scarce. Other interventions focused on indirect effect pathways to AMU and AMR reduction aiming to improve good aquaculture practices, disease prevention and improved management. Monitoring and evaluation of these interventions were found to be rare, only present for interventions driven by development projects and international agencies. The presented typology of existing strategies and interventions addressing AMU/AMR in aquaculture systems can guide evaluation of AMR-sensitive interventions that promote responsible AMU, and informs the design and implementation of future interventions.

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.

Prevalence, antibiotic susceptibility, and presence of drug resistance genes in Aeromonas spp. isolated from freshwater fish in Kelantan and Terengganu states, Malaysia

Background and Aim:

The emergence of antibiotic-resistant bacterial pathogens has been increasingly reported, which has resulted in a decreasing ability to treat bacterial infections. Therefore, this study investigated the presence of Aeromonas spp., including its antibiotic resistance in various fish samples, Oreochromis spp., Clarias gariepinus, and Pangasius hypophthalmus, obtained from Kelantan and Terengganu, Malaysia.

Materials and Methods:

In this study, 221 fish samples, of which 108 (Oreochromis spp., n=38; C. gariepinus, n=35; and P. hypophthalmus, n=35) were from Kelantan and 113 (Oreochromis spp., n=38; C. gariepinus, n=35; and P. hypophthalmus, n=40) were from Terengganu, were caught using cast nets. Then, samples from their kidneys were cultured on a Rimler Shott agar to isolate Aeromonas spp. Polymerase chain reaction (PCR) was used to confirm this isolation using specific gene primers for species identification. Subsequently, the isolates were tested for their sensitivity to 14 antibiotics using the Kirby–Bauer method, after which the PCR was conducted again to detect resistance genes: sul1, strA-strB, aadA, bla_TEM, bla_SHV, tetA-tetE, and tetM.

Results:

From the results, 61 isolates were identified as being from the genus Aeromonas using PCR, of which 28 were Aeromonas jandaei, 19 were Aeromonas veronii, seven were Aeromonas hydrophila, and seven were Aeromonas sobria. Moreover, 8, 12, and 8 of A. jandaei; 4, 3, and 12 of A. veronii; 6, 0, and 1 of A. hydrophila; and 3, 3, and 1 of A. sobria were obtained from Oreochromis spp., C. gariepinus, and P. hypophthalmus, respectively. In addition, the isolates showed the highest level of resistance to ampicillin (100%), followed by streptomycin (59.0%), each kanamycin and nalidixic acid (41.0%), neomycin (36.1%), tetracycline (19.7%), sulfamethoxazole (14.8%), and oxytetracycline (13.1%). Resistance to gentamicin and ciprofloxacin both had the same percentage (9.8%), whereas isolates showed the lowest resistance to norfloxacin (8.2%) and doxycycline (1.6%). Notably, all Aeromonas isolates were susceptible to chloramphenicol and nitrofurantoin. Results also revealed that the multiple antibiotic resistances index of the isolates ranged from 0.07 to 0.64, suggesting that the farmed fish in these areas were introduced to the logged antibiotics indiscriminately and constantly during their cultivation stages. Results also revealed that the sul1 gene was detected in 19.7% of the Aeromonas isolates, whereas the tetracycline resistance genes, tetA and tetE, were detected in 27.9% and 4.9% of the isolates, respectively. However, β-lactam resistance genes, bla_TEM and bla_SHV, were found in 44.3% and 13.1% of Aeromonas isolates, respectively, whereas strA-strB and aadA genes were found in 3.3% and 13.1% of the isolates, respectively.

Conclusion:

This study, therefore, calls for continuous surveillance of antibiotic-resistant Aeromonas spp. in cultured freshwater fish to aid disease management and better understand their implications to public health.

Remote Sensing Approach for Monitoring Coastal Wetland in the Mekong Delta, Vietnam: Change Trends and Their Driving Forces

Coastal wetlands in the Mekong Delta (MD), Vietnam, provide various vital ecosystem services for the region. These wetlands have experienced critical changes due to the increase in regional anthropogenic activities, global climate change, and the associated sea level rise (SLR). However, documented information and research on the dynamics and drivers of these important wetland areas remain limited for the region. The present study aims to determine the long-term dynamics of wetlands in the south-west coast of the MD using remote sensing approaches, and analyse the potential factors driving these dynamics. Wetland maps from the years 1995, 2002, 2013, and 2020 at a 15 m spatial resolution were derived from Landsat images with the aid of a hybrid classification approach. The accuracy of the wetland maps was relatively high, with overall accuracies ranging from 86–93%. The findings showed that the critical changes over the period 1995/2020 included the expansion of marine water into coastal lands, showing 129% shoreline erosion; a remarkable increase of 345% in aquaculture ponds; and a reduction of forested wetlands and rice fields/other crops by 32% and 73%, respectively. Although mangrove forests slightly increased for the period 2013/2020, the overall trend was also a reduction of 5%. Our findings show that the substantial increase in aquaculture ponds is at the expense of mangroves, forested wetlands, and rice fields/other crops, while shoreline erosion significantly affected coastal lands, especially mangrove forests. The interaction of a set of environmental and socioeconomic factors were responsible for the dynamics. In particular, SLR was identified as one of the main underlying drivers; however, the rapid changes were directly driven by policies on land-use for economic development in the region. The trends of wetland changes and SLR implicate their significant effects on environment, natural resources, food security, and likelihood of communities in the region sustaining for the long-term. These findings can assist in developing and planning appropriate management strategies and policies for wetland protection and conservation, and for sustainable development in the region.

Comparative study on the bacterial diversity and antibiotic resistance genes of urban landscape waters replenished by reclaimed water and surface water in Xi'an, China

Pathogenic bacteria and antibiotic resistance genes (ARGs) in urban landscape waters may pose a potential threat to human health. However, the investigation of their occurrence in the urban landscape waters replenished by reclaimed water (RW) and surface water (SW) is still insufficient. The water samples collected from six urban landscape waters replenished by RW or SW were used to analyze bacterial diversity using high-throughput sequencing of 16S rRNA gene and to detect 18 ARGs and 2 integron-integrase genes by means of quantitative PCR array. Results indicated that Proteobacteria was the dominant phylum in all six urban landscape waters. The bacterial species richness was lower in urban landscape waters replenished by RW than that by SW. Sulfonamide resistance genes (sulI and sulIII) were the major ARGs in these urban landscape waters. No significant difference in the relative abundance of sulfonamide resistance genes, tetracycline resistance genes, and most of beta-lactam resistance genes was observed between RW-replenished and SW-replenished urban landscape waters. By contrast, the relative abundance of bla_ampC gene and qnrA gene in RW-replenished urban landscape waters was significantly higher than that in SW-replenished urban landscape waters (p < 0.05), which suggested that use of RW may increase the amount of specific ARGs to urban landscape waters. Interestingly, among six urban landscape waters, RW-replenished urban landscape waters had a relatively rich variety of ARGs (12-15 of 18 ARGs) but a low relative abundance of ARGs (458.90-1944.67 copies/16S × 10⁶). The RW replenishment was found to have a certain impact on the bacterial diversity and prevalence of ARGs in urban landscape waters, which provide new insight into the effect of RW replenishment on urban landscape waters.

Systems-thinking approach to identify and assess feasibility of potential interventions to reduce antibiotic use in tilapia farming in Egypt

Antibiotics are used in aquaculture to maintain the health and welfare of stocks; however, the emergence and selection of antibiotic resistance in bacteria poses threats to humans, animals and the environment. Mitigation of antibiotic resistance relies on understanding the flow of antibiotics, residues, resistant bacteria and resistance genes through interconnecting systems, so that potential solutions can be identified and issues around their implementation evaluated. Participatory systems-thinking can capture the deep complexity of a system while integrating stakeholder perspectives. In this present study, such an approach was applied to Nile tilapia (Oreochromis niloticus) production in the Nile Delta of Egypt, where disease events caused by antibiotic-resistant pathogens have been reported. A system map was co-produced with aquaculture stakeholders at a workshop in May 2018 and used to identify hotspots of antibiotic use, exposure and fate and to describe approaches that would promote fish health and thus reduce antibiotic use. Antibiotics are introduced into the aquaculture system via direct application for example in medicated feed, but residues may also be introduced into the system through agricultural drainage water, which is the primary source of water for most fish farms in Egypt. A follow-up survey of stakeholders assessed the perceived feasibility, advantages and disadvantages of potential interventions. Interventions that respondents felt could be implemented in the short-term to reduce antibiotic usage effectively included: more frequent water exchanges, regular monitoring of culture water quality parameters, improved storage conditions for feed, use of probiotics and greater access to farmer and service providers training programmes. Other potential interventions included greater access to suitable and rapid diagnostics, high quality feeds, improved biosecurity measures and genetically-improved fish, but these solutions were expected to be achieved as long-term goals, with cost being of one of the noted barriers to implementation. Identifying feasible and sustainable interventions that can be taken to reduce antibiotic use, and understanding implementation barriers, are important for addressing antibiotic resistance and ensuring the continued efficacy of antibiotics. This is vital to ensuring the productivity of the tilapia sector in Egypt. The approach taken in the present study provides a means to identify points in the system where the effectiveness of interventions can be evaluated and thus it may be applied to other food production systems to combat the problem of antibiotic resistance.

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.

A Novel Mobile Element ICERspD18B in Rheinheimera sp. D18 Contributes to Antibiotic and Arsenic Resistance

Antibiotics and organoarsenical compounds are frequently used as feed additives in many countries. However, these compounds can cause serious antibiotic and arsenic (As) pollution in the environment, and the spread of antibiotic and As resistance genes from the environment. In this report, we characterized the 28.5 kb genomic island (GI), named as ICERspD18B, as a novel chromosomal integrative and conjugative element (ICE) in multidrug-resistant Rheinheimera sp. D18. Notably, ICERspD18B contains six antibiotic resistance genes (ARGs) and an arsenic tolerance operon, as well as genes encoding conjugative transfer proteins of a type IV secretion system, relaxase, site-specific integrase, and DNA replication or partitioning proteins. The transconjugant strain 25D18-B4 was generated using Escherichia coli 25DN as the recipient strain. ICERspD18B was inserted into 3'-end of the guaA gene in 25D18-B4. In addition, 25D18-B4 had markedly higher minimum inhibitory concentrations for arsenic compounds and antibiotics when compared to the parental E. coli strain. These findings demonstrated that the integrative and conjugative element ICERspD18B could mediate both antibiotic and arsenic resistance in Rheinheimera sp. D18 and the transconjugant 25D18-B4.

Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment

Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.

Secondary Effects of Antibiotics on Microbial Biofilms

Biofilms are assemblages of microorganisms attached to each other, or to a surface, and encased in a protective, self-produced matrix. Such associations are now recognized as the predominant microbial growth mode. The physiology of cells in biofilms differs from that of the planktonic cells on which most research has been conducted. Consequently, there are significant gaps in our knowledge of the biofilm lifestyle. Filling this gap is particularly important, given that biofilm cells may respond differently to antibiotics than do planktonic cells of the same species. Understanding the effects of antibiotics on biofilms is of paramount importance for clinical practice due to the increased levels of antibiotic resistance and resistance dissemination in biofilms. From a wider environmental perspective antibiotic exposure can alter the ecology of biofilms in nature, and hence disrupt ecosystems. Biofilm cells display increased resilience toward antibiotics. This resilience is often explained by mechanisms and traits such as decreased antibiotic penetration, metabolically inactive persister cells, and intrinsic resistance by members of the biofilm community. Together, these factors suggest that cells in biofilms are often exposed to subinhibitory concentrations of antimicrobial agents. Here we discuss how cells in biofilms are affected by the presence of antibiotics at subinhibitory concentrations, and the possible ramifications of such secondary effects for healthcare and the environment.

Molecular profiling of multidrug-resistant river water isolates: insights into resistance mechanism and potential inhibitors

Polluted waters are an important reservoir for antibiotic resistance genes and multidrug-resistant bacteria. This report describes the microbial community, antibiotic resistance genes, and the genetic profile of extended spectrum β-lactamase strains isolated from rivers at, Pune, India. ESBL-producing bacteria isolated from diverse river water catchments running through Pune City were characterized for their antibiotic resistance. The microbial community and types of genes which confer antibiotic resistance were identified followed by the isolation of antibiotic-resistant bacteria on selective media and their genome analysis. Four representative isolates were sequenced using next generation sequencing for genomic analysis. They were identified as Pseudomonas aeruginosa, Escherichia coli, and two isolates were Enterobacter cloacae. The genes associated with the multidrug efflux pumps, such as tolC, macA, macB, adeL, and rosB, were detected in the isolates. As MacAB-TolC is an ABC type efflux pump responsible for conferring resistance in bacteria to several antibiotics, potential efflux pump inhibitors were identified by molecular docking. The homology model of their MacB protein with that from Escherichia coli K12 demonstrated structural changes in different motifs of MacB. Molecular docking of reported efflux pump inhibitors revealed the highest binding affinity of compound MC207-110 against MacB. It also details the potential efflux pump inhibitors that can serve as possible drug targets in drug development and discovery.

Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications

The use of irrigation water sourced from reclamation facilities and untreated surface water bodies may be a practical solution to attenuate the burden on diminishing groundwater aquifers. However, comprehensive microbial characterizations of these water sources are generally lacking, especially with regard to variations through time and across multiple water types. To address this knowledge gap we used a shotgun metagenomic approach to characterize the taxonomic and functional variations of microbial communities within two agricultural ponds, two freshwater creeks, two brackish rivers, and three water reclamation facilities located in the Mid-Atlantic, United States. Water samples (n = 24) were collected from all sites between October and November 2016, and filtered onto 0.2 μm membrane filters. Filters were then subjected to total DNA extraction and shotgun sequencing on the Illumina HiSeq platform. From these data, we found that Betaproteobacteria dominated the majority of freshwater sites, while Alphaproteobacteria were abundant at times in the brackish waters. One of these brackish sites was also host to a greater abundance of the bacterial genera Gimesia and Microcystis. Furthermore, predicted microbial features (e.g. antibiotic resistance genes (ARGs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) arrays) varied based on specific site and sampling date. ARGs were found across samples, with the diversity and abundance highest in those from a reclamation facility and a wastewater-impacted freshwater creek. Additionally, we identified over 600 CRISPR arrays, containing ∼2600 unique spacers, suggestive of a diverse and often site-specific phage community. Overall, these results provide a better understanding of the complex microbial community in untreated surface and reclaimed waters, while highlighting possible environmental and human health impacts associated with their use in agriculture.

Antibiotic resistance in fecal sludge and soil in Ho Chi Minh City, Vietnam

This study investigated the prevalence of antibiotic-resistant bacteria and genes in fecal sludge and soil in Ho Chi Minh City, Vietnam, and identified the factors contributing to the survival of antibiotic-resistant bacteria in soil. Sludge and soil samples (n = 24 and 55, respectively) were collected from residential septic systems and environmental reservoirs (i.e., canals, rivers, and parks) in twelve districts of Ho Chi Minh City and tested against a library of 12 antibiotic-resistant genes and 1 integron gene. The susceptibility of isolated Escherichia coli from sludge and soil (n = 104 and 129, respectively) was tested against nine antibiotics. Over 60% of sludge and soil samples harbored sul1, ere(A), intI1, cmIA, and tet(A) genes. The three most common phenotypic resistances found in E. coli isolated from sludge and soil were to ampicillin, tetracycline, and sulfamethoxazole/trimethoprim. In a temporal microcosm study of antibiotic-susceptible and multi-drug-resistant E. coli inoculated in soil, temperature (21.4 vs. 30 °C), resistance phenotype, and soil background microbial community were associated with E. coli decay rates over 73 days. This is the first study that provides insights into the high prevalence of antibiotic resistance in septic systems and environmental reservoirs in Ho Chi Minh City, Vietnam. Findings highlight that the fecal sludge and soil environments in Vietnam are likely reservoirs for dissemination of and human exposure to antibiotic resistance.

Extended-spectrum beta-lactamase-producing Escherichia coli harbouring sul and mcr-1 genes isolates from fish gut contents in the Mekong Delta, Vietnam

This study investigated the existence of sulfonamides and colistin resistance genes among extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli recovered from fish gut in Vietnam and evaluated the susceptibility patterns of the ESBL-producing E. coli to relevant antimicrobials. A total of 88 ESBL-producing E. coli isolates were analysed for the presence of the ESBLs, sul (1, 2, 3) and mcr (1-3) genes by PCR. Antimicrobial resistance phenotypes of isolates were determined by disc diffusion. Results showed that: (i) A high prevalence of 94·3% of sulfonamide resistance was observed in 88 isolates. Moreover, the existence of 2·3% of ESBL-producing E. coli harbouring mcr-1 gene were detected; (ii) The phylogenetic types A and B1 were most frequent, and the bla_CTX-M group1 and bla_TEM genes encoding ESBL were detected in 47·7% of the isolates; (iii) ESBL-producing E. coli harbouring mcr-1 gene exhibited resistance to 11 antibiotics. The existence of mcr-1 and sul1,2,3 genes and the extremely high level of multiple drug resistance in all ESBL-producing E. coli isolates obtained from sampled fish in Vietnam is a major concern. Therefore, it is imperative to monitor ESBL-producing E. coli in the river waters of Vietnam.

Identifying hotspots for antibiotic resistance emergence and selection, and elucidating pathways to human exposure: Application of a systems-thinking approach to aquaculture systems

Aquaculture systems are highly complex, dynamic and interconnected systems influenced by environmental, biological, cultural, socio-economic and human behavioural factors. Intensification of aquaculture production is likely to drive indiscriminate use of antibiotics to treat or prevent disease and increase productivity, often to compensate for management and husbandry deficiencies. Surveillance or monitoring of antibiotic usage (ABU) and antibiotic resistance (ABR) is often lacking or absent. Consequently, there are knowledge gaps for the risk of ABR emergence and human exposure to ABR in these systems and the wider environment. The aim of this study was to use a systems-thinking approach to map two aquaculture systems in Vietnam - striped catfish and white-leg shrimp - to identify hotspots for emergence and selection of resistance, and human exposure to antibiotics and antibiotic-resistant bacteria. System mapping was conducted by stakeholders at an interdisciplinary workshop in Hanoi, Vietnam during January 2018, and the maps generated were refined until consensus. Thereafter, literature was reviewed to complement and cross-reference information and to validate the final maps. The maps and component interactions with the environment revealed the grow-out phase, where juveniles are cultured to harvest size, to be a key hotspot for emergence of ABR in both systems due to direct and indirect ABU, exposure to water contaminated with antibiotics and antibiotic-resistant bacteria, and duration of this stage. The pathways for human exposure to antibiotics and ABR were characterised as: occupational (on-farm and at different handling points along the value chain), through consumption (bacterial contamination and residues) and by environmental routes. By using systems thinking and mapping by stakeholders to identify hotspots we demonstrate the applicability of an integrated, interdisciplinary approach to characterising ABU in aquaculture. This work provides a foundation to quantify risks at different points, understand interactions between components, and identify stakeholders who can lead and implement change.

Prevalence of extended-spectrum β-lactamase-producing Escherichia coli and residual antimicrobials in the environment in Vietnam

Emergence and spread of antimicrobial-resistant bacteria, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, have become serious problems worldwide. Recent studies conducted in Vietnam revealed that ESBL-producing E. coli are widely distributed in food animals and people. CTX-M-9 and CTX-M-1 are the most prevalent β-lactamases among the identified ESBLs. Furthermore, most of the ESBL-producing E. coli isolates were multi-drug resistant. Residual antimicrobials such as sulfamethoxazole, trimethoprim, sulfadimidine, cephalexin, and sulfadiazine were also detected at a high level in both animal meats and environmental water collected from several cities, including Ho Chi Minh city and Can Tho city. These recent studies indicated that improper use of antimicrobials in animal-originated food production might contribute to the emergence and high prevalence of ESBL-producing E. coli in Vietnam. Although clonal ESBL-producing E. coli was not identified, CTX-M-55 gene-carrying plasmids with similar sizes (105-139 kb) have been commonly detected in the ESBL-producing E. coli strains isolated from various food animals and human beings. This finding strongly suggests that horizontal transfer of the CTX-M plasmid among various E. coli strains played a critical role in the emergence and high prevalence of ESBL-producing E. coli in Vietnam.

Antibiotic resistome profile based on metagenomics in raw surface drinking water source and the influence of environmental factor: A case study in Huaihe River Basin, China

The contamination with antibiotic resistance genes (ARGs) in raw drinking water source may pose a direct threat to human health. In this study, metagenomics sequencing and analysis were applied to investigate the ARG pattern in 12 drinking water sources in upper and middle reach of Huaihe River Basin, China. Based on the redundant analysis and multi-linear regression model, location, specific microbial taxa, number of livestock and health facilities significantly influenced the ARG profile in drinking water sources. Besides the cluster effect of ARG in samples from plain and bedrock mountain areas, the samples from fracture aquifer areas also showed a distinctive biogeographic pattern with that from porous aquifer areas. Putative ARGs host Opitutus and Flavobacterium were the enriched biomarkers in plain and fracture aquifer area respectively, which mainly carried bacitracin, multidrug, beta-lactam and tetracycline ARGs. This result illuminated that both natural background and anthropogenic activities in the watershed influenced the ARG profile in natural freshwater system significantly. The low MGEs abundance and absence of pathogen revealed a low ARG dissemination risk in sampled drinking water sources, while Polynucleobacter was an abundant ARGs host and was significantly related to the ARG profile, which indicated that specific bacteria was responsible for ARGs propagation and accumulation in surface freshwater system. Further researches are needed to assess human exposure to raw drinking water source and the potential risk, as well as the species interaction in microbial community and its impact on ARG propagation under oligotrophic condition.

Simultaneous remediation of sediments contaminated with sulfamethoxazole and cadmium using magnesium-modified biochar derived from Thalia dealbata

In situ remediation and assessment of sediments contaminated with both antibiotics and heavy metals remains a technological challenge. In this study, MgCl₂-modified biochar (BCM) was obtained at 500 °C through slow pyrolysis of Thalia dealbata and used for remediation of sediments contaminated by sulfamethoxazole (SMX) and Cd. The BCM showed greater surface area (110.6 m² g^-1) than pristine biochar (BC, 7.1 m² g^-1). The SMX sorption data were well described by Freundlich model while Langmuir model was better for the Cd²⁺ sorption data. The addition of 5.0% BCM significantly increased the sorption of SMX (by 50.8-58.6%) and Cd (by 24.2-25.6%) on sediments in both single and binary systems as compared with 5.0% BC. SMX sorption in sediments was significantly improved by addition of Cd²⁺, whereas SMX has no influence on Cd sorption on sediments. The addition of BCM distinctly decreased both SMX (by 51.4-87.2%) and Cd concentrations (by 56.2-91.3%) in overlying water, as well as in TCLP extracts (by 55.6-86.1% and 58.2-91.9% for SMX and Cd, respectively), as compared with sediments without biochar. Both germination rate and root length of pakchoi increased with increasing doses of BCM in contaminated sediments, 5.0% BCM showed greater promotion on pakchoi growth than 5.0% BC. Overall, BCM in the sediments does not only decrease the bioavailability of SMX and Cd, but it also diminishes the phytotoxicity, and thereby shows great application potential for in situ remediation of sediments polluted with antibiotics and heavy metals.

Pollution from azithromycin-manufacturing promotes macrolide-resistance gene propagation and induces spatial and seasonal bacterial community shifts in receiving river sediments

Effluents from antibiotic manufacturing may contain high concentrations of antibiotics, which are the main driving force behind the selection and spread of antibiotic resistance genes in the environment. However, our knowledge about the impact of such effluent discharges on the antibiotic resistome and bacterial communities is still limited. To gain insight into this impact, we collected effluents from an azithromycin-manufacturing industry discharge site as well as upstream and downstream sediments from the receiving Sava river during both winter and summer season. Chemical analyses of sediment and effluent samples indicated that the effluent discharge significantly increased the amount of macrolide antibiotics, heavy metals and nutrients in the receiving river sediments. Quantitative PCR revealed a significant increase of relative abundances of macrolide-resistance genes and class 1 integrons in effluent-impacted sediments. Amplicon sequencing of 16S rRNA genes showed spatial and seasonal bacterial community shifts in the receiving sediments. Redundancy analysis and Mantel test indicated that macrolides and copper together with nutrients significantly correlated with community shift close to the effluent discharge site. The number of taxa that were significantly increased in relative abundance at the discharge site decreased rapidly at the downstream sites, showing the resilience of the indigenous sediment bacterial community. Seasonal changes in the chemical properties of the sediment along with changes in effluent community composition could be responsible for sediment community shifts between winter and summer. Altogether, this study showed that the discharge of pharmaceutical effluents altered physicochemical characteristics and bacterial community of receiving river sediments, which contributed to the enrichment of macrolide-resistance genes and integrons.

Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods

Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.

A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals

The occurrence of antibiotic resistance genes (ARGs) as emerging contaminants is of continued concern for human health. Antibiotics used in aquaculture have promoted the evolution and spread of ARGs. This study aimed to investigate the occurrence of 37 ARGs conferring resistance to six classes of antibiotics in 94 aquatic animals from five cities in southeast coast of China. The results showed that floR, sulII, sulI, strB, strA, aadA, and tetS were identified as the prominent ARGs with the high detection frequencies ranging from 30.9 to 51.1% in total samples. Then relative expression amount of seven prominent ARGs quantified by qPCR, ranging from 0.003 to 0.065. The tetS was the most abundant ARG among the seven ARGs. Though aadA was the second highest detection frequency of ARGs, it was the lowest expression amount ARG. The occurrences and abundances of ARGs in freshwater aquatic animals were greater than those in marine, reflecting the discrepancy of cultivation pattern between the freshwater and marine aquaculture. Shanghai was considered as the most prevalent site with 16 ARGs, and Ningbo merely contained 9 ARGs without of β-lactam ARGs and quinolone ARGs, showing variations of ARGs with geographical location. Eight kinds of sulfonamides and one chloramphenicol residues were further measured in samples from Shanghai. Interestingly, no target antibiotics were found, but sulfonamides resistance genes (sulI, sulII) and chloramphenicol resistance genes (floR) persisted at aquatic animals in the absence of selection pressure. Our research firstly shows comprehensive information on the ARGs in skin microbiota of aquatic animals, which could provide useful information and a new insight for better understanding on the ARGs dissemination in aquatic animals.

Antibiotics and antibiotic resistance genes in global lakes: A review and meta-analysis

Lakes are an important source of freshwater, containing nearly 90% of the liquid surface fresh water worldwide. Long retention times in lakes mean pollutants from discharges slowly circulate around the lakes and may lead to high ecological risk for ecosystem and human health. In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. The occurrence and distribution of antibiotics and ARGs in global freshwater lakes are summarized to show the pollution level of antibiotics and ARGs and to identify some of the potential risks to ecosystem and human health. Fifty-seven antibiotics were reported at least once in the studied lakes. Our meta-analysis shows that sulfamethoxazole, sulfamerazine, sulfameter, tetracycline, oxytetracycline, erythromycin, and roxithromycin were found at high concentrations in both lake water and lake sediment. There is no significant difference in the concentration of sulfonamides in lake water from China and that from other countries worldwide; however, there was a significant difference in quinolones. Erythromycin had the lowest predicted hazardous concentration for 5% of the species (HC₅) and the highest ecological risk in lakes. There was no significant difference in the concentration of sulfonamide resistance genes (sul1 and sul2) in lake water and river water. There is surprisingly limited research on the role of aquatic biota in propagation of ARGs in freshwater lakes. As an environment that is susceptible to cumulative build-up of pollutants, lakes provide an important environment to study the fate of antibiotics and transport of ARGs with a broad range of niches including bacterial community, aquatic plants and animals.

Living in uncertainty due to floods and pollution: the health status and quality of life of people living on an unhealthy riverbank

BACKGROUND

People living on the banks of polluted rivers with yearly flooding lived in impoverished and physically unhealthy circumstances. However, they were reluctant to move or be relocated to other locations where better living conditions were available. This study aimed to investigate the health status, quality of life (QoL), happiness, and life satisfaction of the people who were living on the banks of one of the main rivers in Jakarta, Indonesia, the Ciliwung.

METHODS

Respondents were 17 years and older and recruited from the Bukit Duri community (n = 204). Three comparison samples comprised: i) a socio-demographically matched control group, not living on the river bank (n = 204); ii) inhabitants of Jakarta (n = 305), and iii) the Indonesian general population (n = 1041). Health status and QoL were measured utilizing EQ-5D-5L, WHOQOL-BREF, the Happiness Scale, and the Life Satisfaction Index. A visual analogue scale question concerning respondents' financial situations was added. MANOVA and multivariate regression analysis were used to analyze the differences between the Ciliwung respondents and the three comparison groups.

RESULTS

The Ciliwung respondents reported lower physical QoL on WHOQOL-BREF and less personal happiness than the matched controls but rated their health (EQ-5D-5L) and life satisfaction better than the matched controls. Similar results were obtained by comparison with the Jakarta inhabitants and the general population. Bukit Duri inhabitants also perceived themselves as being in a better financial situation than the three comparison groups even though their incomes were lower.

CONCLUSIONS

The recent relocation to a better environment with better housing might improve the former Ciliwung inhabitants' quality of life and happiness, but not necessarily their perceived health, satisfaction with life, and financial situations.

The prevalence and diversity of AmpC β-lactamase genes in plasmids from aquatic systems

This study aimed to investigate the presence and diversity of AmpC β-lactamase and integrase genes among DNA (genomic and plasmid) from bacterial populations in selected aquatic systems. Following an enrichment step, DNA was isolated and subjected to polymerase chain reaction (PCR) and digital droplet PCR. The intI1 gene and AmpC β-lactamase genes were present in genomic and plasmid DNA from all sites in the Mooi, Crocodile and Marico Rivers, with the exception of intI1 in the Marico River. Digital droplet PCR demonstrated that copy numbers varied considerably (0.0 to 29.38 copies per picogram of DNA). Some samples in which ampC was not detected, intI1 was present. Amplicons of ampC genes were subjected to restriction digest using HindIII. Samples where the restriction markers were absent were purified by cloning followed by plasmid extraction, PCR amplification, and sequencing of individual AmpC gene fragments. Phylogenetic analysis identified all positive AmpC genes as Class C β-lactamases, comprising of ampC, CMY- and ACT-families. Detecting AmpC and intl1 genes on plasmids suggests a high risk of horizontal gene transfer and potential dissemination of these and other antibiotic resistance genes surrounding immediate aquatic environments. Consequences of β-lactamase diversity in aquatic ecosystems are relatively unexplored in South African aquatic ecosystems.

Influence of Long-Term Feeding Antibiotics on the Gut Health of Zebrafish

The use of antibiotics for anti-infection and growth promotion has caused the overuse of antibiotics in aquaculture. However, the benefit or risk of the long-term use of antibiotics on fish growth or health has not been fully addressed. In the present study, zebrafish were fed with sulfamethoxazole (SMX) or oxytetracycline (OTC) at the therapeutic concentrations (100 and 80 mg/kg body weight per day, respectively) for 6 weeks to mimic the long-term use of antibiotics. The digestive enzyme activities were higher in both antibiotic treatments, and higher oxygen consumption rate was found in OTC treated group. As a result, SMX increased the weight gain of zebrafish, and OTC treatment did not show significant prompting effect on growth. The mortality was higher in SMX or OTC treated group on 2nd-4th day after exposure to Aeromonas hydrophila. Lower alkaline phosphatase (AKP) and acid phosphatase (ACP) activities were found in OTC treated group, while higher malondialdehyde (MDA) content was found in the intestine of both SMX and OTC treated zebrafish. Furthermore, feeding OTC decreased the intestinal microbial richness. This study revealed that long-term use of legal aquaculture concentrations of antibiotics caused systemic adverse effects on fish gut health; stringent policy for use of antibiotics in fish is urgent.

[Antibiotic Residue in Environmental Water in Vietnam]

　The increasing prevalence of antimicrobial resistance (AMR) has caused intractable infections worldwide. Nearly 50% of the healthy population of Southeast Asia carries extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. The overuse of antimicrobial agents in the agriculture, aquaculture, and medical care sectors causes environmental pollution, facilitating the spread of AMR. However, there is a lack of data pertaining to antimicrobial residues in environmental water in such regions. We investigated a total of 49 chemicals, including β-lactams, sulfonamides, quinolones, and tetracyclines. Water samples were collected from rivers in city centers, and ponds in livestock and aquaculture farms, in Ha Noi, Thai Binh, and Can Tho in Vietnam. We detected antimicrobial agents at 87 of 111 sampling sites (78.4%). Among the target analytes, sulfamethoxazole, sulfamethazine, trimethoprim, cephalexin, and ofloxacin were detected frequently. The residual levels of each antimicrobial agent ranged from 0.1 to 10000 ng/L. Moreover, we detected multi-drug resistant E. coli in fishes sampled from these rivers, suggesting unwanted effects of antimicrobial residues in the environment.

A probabilistic approach to assess antibiotic resistance development risks in environmental compartments and its application to an intensive aquaculture production scenario

Estimating antibiotic pollution and antibiotic resistance development risks in environmental compartments is important to design management strategies that advance our stewardship of antibiotics. In this study we propose a modelling approach to estimate the risk of antibiotic resistance development in environmental compartments and demonstrate its application in aquaculture production systems. We modelled exposure concentrations for 12 antibiotics used in Vietnamese Pangasius catfish production using the ERA-AQUA model. Minimum selective concentration (MSC) distributions that characterize the selective pressure of antibiotics on bacterial communities were derived from the European Committee on Antimicrobial Susceptibility Testing (EUCAST) Minimum Inhibitory Concentration dataset. The antibiotic resistance development risk (RDR) for each antibiotic was calculated as the probability that the antibiotic exposure distribution exceeds the MSC distribution representing the bacterial community. RDRs in pond sediments were nearly 100% for all antibiotics. Median RDR values in pond water were high for the majority of the antibiotics, with rifampicin, levofloxacin and ampicillin having highest values. In the effluent mixing area, RDRs were low for most antibiotics, with the exception of amoxicillin, ampicillin and trimethoprim, which presented moderate risks, and rifampicin and levofloxacin, which presented high risks. The RDR provides an efficient means to benchmark multiple antibiotics and treatment regimes in the initial phase of a risk assessment with regards to their potential to develop resistance in different environmental compartments, and can be used to derive resistance threshold concentrations.

Unpacking factors influencing antimicrobial use in global aquaculture and their implication for management: a review from a systems perspective

Global seafood provides almost 20% of all animal protein in diets, and aquaculture is, despite weakening trends, the fastest growing food sector worldwide. Recent increases in production have largely been achieved through intensification of existing farming systems, resulting in higher risks of disease outbreaks. This has led to increased use of antimicrobials (AMs) and consequent antimicrobial resistance (AMR) in many farming sectors, which may compromise the treatment of bacterial infections in the aquaculture species itself and increase the risks of AMR in humans through zoonotic diseases or through the transfer of AMR genes to human bacteria. Multiple stakeholders have, as a result, criticized the aquaculture industry, resulting in consequent regulations in some countries. AM use in aquaculture differs from that in livestock farming due to aquaculture's greater diversity of species and farming systems, alternative means of AM application, and less consolidated farming practices in many regions. This, together with less research on AM use in aquaculture in general, suggests that large data gaps persist with regards to its overall use, breakdowns by species and system, and how AMs become distributed in, and impact on, the overall social-ecological systems in which they are embedded. This paper identifies the main factors (and challenges) behind application rates, which enables discussion of mitigation pathways. From a set of identified key mechanisms for AM usage, six proximate factors are identified: vulnerability to bacterial disease, AM access, disease diagnostic capacity, AMR, target markets and food safety regulations, and certification. Building upon these can enable local governments to reduce AM use through farmer training, spatial planning, assistance with disease identification, and stricter regulations. National governments and international organizations could, in turn, assist with disease-free juveniles and vaccines, enforce rigid monitoring of the quantity and quality of AMs used by farmers and the AM residues in the farmed species and in the environment, and promote measures to reduce potential human health risks associated with AMR.

Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters

Antibiotic resistance genes (ARGs) in urban rivers are a serious public health concern in regions with poorly planned, rapid development. To gain insights into the predominant factors affecting the fate of ARGs in a highly polluted urban river in eastern China, a total of 285 ARGs, microbial communities, and 20 physicochemical parameters were analyzed for 17 sites. A total of 258 unique ARGs were detected using high-throughput qPCR, and the absolute abundance of total ARGs was positively correlated with total organic carbon and total dissolved nitrogen concentrations (P < 0.01). ARG abundance and diversity were greatly altered by microbial community structure. Variation partitioning analysis showed that the combined effects of multiple factors contributed to the profile and dissemination of ARGs, and variation of microbial communities was the major factor affecting the distribution of ARGs. The disparate distribution of some bacteria, including Bacteroides from mammalian gastrointestinal flora, Burkholderia from zoonotic infectious diseases, and Zoogloea from wastewater treatment, indicates that the urban river was strongly influenced by point-source pollution. Results imply that microbial community shifts caused by changes in water quality may lead to the spread of ARGs, and point-source pollution in urban rivers requires greater attention to control the transfer of ARGs between environmental bacteria and pathogens.

Consumption of edible ice contaminated with Acinetobacter, Pseudomonas, and Stenotrophomonas is a risk factor for fecal colonization with extended-spectrum β-lactamase-producing Escherichia coli in Vietnam

Although Vietnamese residents frequently harbor extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E), it is unclear which foods/beverages are risk factors for acquiring these bacteria. The aim of this study was to evaluate the frequency with which edible ice served in restaurants is contaminated with antibiotic-resistant bacteria, and thereby clarify whether this product poses a risk for ESBL-E carriage in humans. Ice from restaurants in Vietnam and Japan was screened for bacteria capable of growing on agar containing cefotaxime (BG-CTX). Of the 119 BG-CTX strains isolated in Vietnam, 40%, 39%, and 12% were identified as Pseudomonas spp., Acinetobacter spp., and Stenotrophomonas maltophilia, respectively. Meanwhile, of the six such strains isolated in Japan, five were identified as Acinetobacter spp. and one as Pseudomonas spp. More than 10% of the Acinetobacter isolates exhibited cefotaxime, ceftazidime, and sulfa/trimethoprim resistance, while 21% of Pseudomonas and 14% of S. maltophilia isolates exhibited meropenem and sulfa/trimethoprim resistance, respectively. Subsequent multiplex polymerase chain reaction (PCR) analyses detected ESBL-encoding genes in 10% of the BG-CTX. Notably, feces harvested from mice administered water contaminated with BG-CTX contained E. coli harboring the bla_CTX-M-9 gene. In conclusion, our findings indicate that consumption of contaminated edible ice is a risk factor for human ESBL-E carriage.