Antibiotic-resistance and virulence-related genes in commercially bottled natural mineral waters. - Related Documents




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373001.0000Antibiotic-resistance and virulence-related genes in commercially bottled natural mineral waters. BACKGROUND: To date, the presence of antibiotics resistant genes (ARGs) and virulence-related genes (VRGs) has been evidenced in several surface waters, including natural surface water and wastewater, as well as drinking water. Bottled natural mineral waters, which are by law labelled as microbiologically pure at source, from underground aquifers, natural resurgence deposits or well suction pumps, do not undergo purification treatment, and do not experience any chemical decontamination or disinfection treatment, as in the case of drinking water from municipal conduits. The present study aimed to evaluate the presence of ARGs and VRGs, as well as the composition of microbial communities, in commercially bottled natural mineral drinking water by molecular methods. The study involved the analysis of bottled drinking water from four commercial brands. Moreover, an investigation was conducted into the potential association of known mobile elements or insertion sequences with the highlighted ARGs and VRGs. METHODS: Four commercial brands of drinking mineral bottled water were selected for analysis. A volume of 100 L from each brand was filtered to recover the microbes present in the water. The microbes successfully recovered on the filter, in conjunction with eventually other particles with a diameter of 0.22 μm or greater, or associated nucleic acids, underwent a process of DNA extraction using specific extraction kit. The extracted cell-DNA was subjected to shotgun sequencing. RESULTS: Sequence analysis revealed the presence of microbial communities associated with the water samples analyzed. Furthermore, several ARGs and VRGs were identified and, for some of them, a putative taxonomic assignment at genus level was defined. CONCLUSIONS: The results indicated that bottled drinking water may represent a potential reservoir of antibiotic resistance and virulence genes, which could persist and be transferred to other bacteria commonly found in the same water sample, as well as to microorganisms colonizing the human consumer. The use of the new molecular methods, such as next generation sequencing (NGS), could be useful for improving current methodologies for drinking water analysis, also considering their potential role of reservoir of antibiotic resistance and virulence genes, as well as the presence of potentially pathogenic microbes that cannot be detected by conventional cultural methods.202540993512
346110.9998Metagenomics insights into bacterial diversity and antibiotic resistome of the sewage in the city of Belém, Pará, Brazil. INTRODUCTION: The advancement of antimicrobial resistance is a significant public health issue today. With the spread of resistant bacterial strains in water resources, especially in urban sewage, metagenomic studies enable the investigation of the microbial composition and resistance genes present in these locations. This study characterized the bacterial community and antibiotic resistance genes in a sewage system that receives effluents from various sources through metagenomics. METHODS: One liter of surface water was collected at four points of a sewage channel, and after filtration, the total DNA was extracted and then sequenced on an NGS platform (Illumina® NextSeq). The sequenced data were trimmed, and the microbiome was predicted using the Kraken software, while the resistome was analyzed on the CARD webserver. All ecological and statistical analyses were performed using the. RStudio tool. RESULTS AND DISCUSSION: The complete metagenome results showed a community with high diversity at the beginning and more restricted diversity at the end of the sampling, with a predominance of the phyla Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria. Most species were considered pathogenic, with an emphasis on those belonging to the Enterobacteriaceae family. It was possible to identify bacterial groups of different threat levels to human health according to a report by the U.S. Centers for Disease Control and Prevention. The resistome analysis predominantly revealed genes that confer resistance to multiple drugs, followed by aminoglycosides and macrolides, with efflux pumps and drug inactivation being the most prevalent resistance mechanisms. This work was pioneering in characterizing resistance in a sanitary environment in the Amazon region and reinforces that sanitation measures for urban sewage are necessary to prevent the advancement of antibiotic resistance and the contamination of water resources, as evidenced by the process of eutrophication.202439629213
345920.9998Diversity of antibiotic resistance gene variants at subsequent stages of the wastewater treatment process revealed by a metagenomic analysis of PCR amplicons. Wastewater treatment plants have been recognised as point sources of various antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) which are considered recently emerging biological contaminants. So far, culture-based and molecular-based methods have been successfully applied to monitor antimicrobial resistance (AMR) in WWTPs. However, the methods applied do not permit the comprehensive identification of the true diversity of ARGs. In this study we applied next-generation sequencing for a metagenomic analysis of PCR amplicons of ARGs from the subsequent stages of the analysed WWTP. The presence of 14 genes conferring resistance to different antibiotic families was screened by PCR. In the next step, three genes were selected for detailed analysis of changes of the profile of ARG variants along the process. A relative abundance of 79 variants was analysed. The highest diversity was revealed in the ermF gene, with 52 variants. The relative abundance of some variants changed along the purification process, and some ARG variants might be present in novel hosts for which they were currently unassigned. Additionally, we identified a pool of novel ARG variants present in the studied WWTP. Overall, the results obtained indicated that the applied method is sufficient for analysing ARG variant diversity.202338274111
732530.9998Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa. Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.202439500921
346240.9998Environmental health of water bodies from a Brazilian Amazon Metropolis based on a conventional and metagenomic approach. AIMS: The present study aimed to use a conventional and metagenomic approach to investigate the microbiological diversity of water bodies in a network of drainage channels and rivers located in the central area of the city of Belém, northern Brazil, which is considered one of the largest cities in the Brazilian Amazon. METHODS AND RESULTS: In eight of the analyzed points, both bacterial and viral microbiological indicators of environmental contamination-physical-chemical and metals-were assessed. The bacterial resistance genes, drug resistance mechanisms, and viral viability in the environment were also assessed. A total of 473 families of bacteria and 83 families of viruses were identified. Based on the analysis of metals, the levels of three metals (Cd, Fe, and Mn) were found to be above the recommended acceptable level by local legislation. The levels of the following three physicochemical parameters were also higher than recommended: biochemical oxygen demand, dissolved oxygen, and turbidity. Sixty-three bacterial resistance genes that conferred resistance to 13 different classes of antimicrobials were identified. Further, five mechanisms of antimicrobial resistance were identified and viral viability in the environment was confirmed. CONCLUSIONS: Intense human actions combined with a lack of public policies and poor environmental education of the population cause environmental degradation, especially in water bodies. Thus, urgent interventions are warranted to restore the quality of this precious and scarce asset worldwide.202438627246
710750.9998A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms. The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.202236009027
328760.9998Antimicrobial resistance screening and profiles: a glimpse from the South African perspective. According to the Centre for Disease Dynamics Economics and Policy, South Africa represents a paradox of antibiotic management similar to other developing countries, with both overuse and underuse (resulting from lack of access) of antibiotics. In addition, wastewater reuse may contribute towards antibiotic resistance through selective pressure that increases resistance in native bacteria and on clinically relevant bacteria, increasing resistance profiles of the common pathogens. Sediments of surface water bodies and wastewater sludge provide a place where antibiotic resistance genes are transferred to other bacteria. Crop irrigation is thought to be a potential source of exposure to antibiotic-resistant bacteria through the transfer from the water or sludge into crops. The objectives of this study were to examine the antibiotic-resistance profiles of Escherishia coli from three agricultural locations in the Western Cape, South Africa. Using a classical microbiology culture approach, the resistance profiles of E. coli species isolated from river water and sediments, farm dams and their sediments and a passive algal wastewater treatment ponds and sediment used for crop irrigation were assessed for resistance to 13 commonly used antibiotics. Randomly selected E. coli isolates from the sediment and water were tested for resistance. 100% of E. coli isolates were resistant to sulphamethoxazole, highlighting its relevance in the South African context. In river water and farm dam samples, only the E. coli isolated from sediment were found to be resistant to fluoroquinolone or fluorifenicol. In the wastewater treatment ponds, the resistance profiles of E. coli isolated from sediments differed from those isolated from effluent, with 90% of the effluent isolates being resistant to ampicillin. Isolates from the sediment were less resistant (40%) to ampicillin, whereas all the isolates from the pond water and sediment samples were resistant to sulphamethoxazole. These results illustrate the importance of developing a better understanding of antibiotic resistance in agriculture and wastewater scenarios to ensure remedial measures take place where the greatest benefit can be realised especially in countries with limited financial and infrastructural resources. Moreover, the potential for passive algal treatment as an effective, feasible alternative for wastewater treatment is highlighted, with comparable resistance profiles and a reducing overall resistance in the sediment samples.202033328364
368270.9998Concentration of facultative pathogenic bacteria and antibiotic resistance genes during sewage treatment and in receiving rivers. Whereas the hygienic condition of drinking and bathing water by law must be monitored by culture-based methods, for quantification of microbes and antibiotic resistance in soil or the aquatic environment, often molecular genetic assays are used. For comparison of both methods, knowledge of their correlation is necessary. Therefore the population of total bacteria, Escherichia coli, enterococci and staphylococci during sewage treatment and in receiving river water was compared by agar plating and quantitative polymerase chain reaction (qPCR) assays. In parallel, all samples were investigated for clinically relevant antibiotic resistance genes. Whereas plating and qPCR data for total bacteria correlated well in sewage after primary treatment, qPCR data of river water indicated higher cell numbers for E. coli. It is unknown if these cells are 'only' not growing under standard conditions or if they are dead. Corresponding to the amount of non-culturable cells, the 'breakpoints' for monitoring water quality should be adapted. The abundances of clinically relevant antibiotic resistance genes in river water were in the same order of magnitude or even higher than in treated sewage. For estimation of the health risk it is important to investigate which species carry respective genes and whether these genes are disseminated via gene transfer.201627789876
740280.9998Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits. Reducing antibiotic use is a necessary step toward less antibiotic resistance in livestock, but many antibiotic resistance genes can persist for years, even in an antibiotic-free environment. In this study, we investigated the potential of three fecal complex microbial communities from antibiotic-naive does to drive the microbiota of kits from antibiotic-exposed dams and outcompete bacteria-carrying antibiotic-resistant genes. The fecal complex microbial communities were either orally delivered or simply added as fresh fecal pellets in four to five nests that were kept clean from maternal feces. Additionally, four nests were cleaned for the maternal feces and five nests were handled according to the common farm practice (i.e., cleaning once a week) as controls. At weaning, we measured the relative abundance of 26 antibiotic resistance genes, the proportion of Enterobacteriaceae resistant to tetracycline and sulfonamide antibiotics, and the taxonomic composition of the microbiota by sequencing the 16S rRNA genes of one kit per nest. Changing the surrounding microbes of the kits can hinder the transmission of antibiotic resistance genes from one generation to the next, but the three communities widely differed in their ability to orient gut microbes and in their impact on antibiotic resistance genes. The most efficient delivery of the microbial community reduced the proportion of resistant Enterobacteria from 93 to 9%, decreased the relative abundance of eight antibiotic resistance genes, and changed the gut microbes of the kits at weaning. The least efficient did not reduce any ARG or modify the bacterial community. In addition, adding fecal pellets was more efficient than the oral inoculation of the anaerobic suspension derived from these fecal pellets. However, we were unable to predict the outcome of the exclusion from the data of the donor does (species composition and abundance of antibiotic resistance genes). In conclusion, we revealed major differences between microbial communities regarding their ability to exclude antibiotic resistance genes, but more work is needed to understand the components leading to the successful exclusion of antibiotic resistance genes from the gut. As a consequence, studies about the impact of competitive exclusion should use several microbial communities in order to draw general conclusions.201931333614
387590.9998Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications. A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.202539752189
3723100.9997Hospital Antibiotics Usage: Environmental Hazard and Promotion of Antibiotic Resistant Bacteria. INTRODUCTION: Hospitals constitute a particular source of drug residues emission, especially antibiotics considered as the most critical therapeutic classes used in hospitals. Thus, the hospital wastewater can widely spread both types of emerging pollutants, antibiotic residues and antibiotic resistance bacteria. For this reason, antibiotics usage must be monitored. This study was conducted to investigate potential antibiotic compounds which can present potential environmental hazard and promote antibiotic resistance. METHODS: The consumption-based approach was adopted to calculate predicted antibiotic concentrations in hospital wastewaters. In the process, we assessed the antibiotics potential environmental hazard, with the hazard quotient between predicted concentrations and predicted no effect concentrations intended to be protective of ecological species. In order to evaluate the hospital contribution to antibiotic resistance bacteria promotion, we also compared predicted concentrations with predicted no effect concentrations as theoretical selective resistance bacteria. RESULTS: The highest expected concentrations in hospital wastewater were found for Penicillins and Cephalosporins being the most prescribed antibiotics in our context. We noted that among this class, Ampicillin is the most hazardous compound followed by Imipenem and Gentamicin as exclusive hospital use antibiotics, in spite of their low consumption. The results showed also that Ampicillin, Amoxicillin, and Ceftriaxone had a high ratio of potential antibiotic resistance bacteria promotion, confirming the correlation found previously between abundance of resistant bacteria and the corresponding effluent antibiotic concentrations. Nevertheless, the promotion of resistance selection can also be attributed to Imipenem and Ciprofloxacin as little-used antibiotics and occur at low to moderate levels in hospital wastewater. CONCLUSION: This study identified the profile antibiotics consumption and their potential environmental hazard contribution and antibiotic resistant bacteria promotion. It can help decision-makers make appropriate management decisions, especially preventive measures related to antibiotic use pattern, as neither dilution nor treatment can eliminate antibiotic residues and antibiotic resistance genes.202234113952
3683110.9997Small and large-scale distribution of four classes of antibiotics in sediment: association with metals and antibiotic resistance genes. Antibiotic chemicals and antibiotic resistance genes enter the environment via wastewater effluents as well as from runoff from agricultural operations. The relative importance of these two sources, however, is largely unknown. The relationship between the concentrations of chemicals and genes requires exploration, for antibiotics in the environment may lead to development or retention of resistance genes by bacteria. The genes that confer resistance to metal toxicity may also be important in antibiotic resistance. In this work, concentrations of 19 antibiotics (using liquid chromatography tandem mass spectrometry), 14 metals (using inductively coupled plasma-mass spectrometry), and 45 metal, antibiotic, and antibiotic-resistance associated genes (using a multiplex, microfluidic quantitative polymerase chain reaction method) were measured in 13 sediment samples from two large rivers as well as along a spatial transect in a wastewater effluent-impacted lake. Nine of the antibiotics were detected in the rivers and 13 were detected in the lake. Sixteen different resistance genes were detected. The surrounding land use and proximity to wastewater treatment plants are important factors in the number and concentrations of antibiotics detected. Correlations among antibiotic chemical concentrations, metal concentrations, and resistance genes occur over short spatial scales in a lake but not over longer distances in major rivers. The observed correlations likely result from the chemicals and resistance genes arising from the same source, and differences in fate and transport over larger scales lead to loss of this relationship.201830043816
3245120.9997From Metagenomes to Functional Expression of Resistance: floR Gene Diversity in Bacteria from Salmon Farms. Background. The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. Methods. Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover floR gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. Results. Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The floR gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference floR. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the floR sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. Conclusions. This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms.202540001366
7405130.9997Microbial Diversity and Antimicrobial Resistance Profile in Microbiota From Soils of Conventional and Organic Farming Systems. Soil is one of the biggest reservoirs of microbial diversity, yet the processes that define the community dynamics are not fully understood. Apart from soil management being vital for agricultural purposes, it is also considered a favorable environment for the evolution and development of antimicrobial resistance, which is due to its high complexity and ongoing competition between the microorganisms. Different approaches to agricultural production might have specific outcomes for soil microbial community composition and antibiotic resistance phenotype. Therefore in this study we aimed to compare the soil microbiota and its resistome in conventional and organic farming systems that are continually influenced by the different treatment (inorganic fertilizers and pesticides vs. organic manure and no chemical pest management). The comparison of the soil microbial communities revealed no major differences among the main phyla of bacteria between the two farming styles with similar soil structure and pH. Only small differences between the lower taxa could be observed indicating that the soil community is stable, with minor shifts in composition being able to handle the different styles of treatment and fertilization. It is still unclear what level of intensity can change microbial composition but current conventional farming in Central Europe demonstrates acceptable level of intensity for soil bacterial communities. When the resistome of the soils was assessed by screening the total soil DNA for clinically relevant and soil-derived antibiotic resistance genes, a low variety of resistance determinants was detected (resistance to β-lactams, aminoglycosides, tetracycline, erythromycin, and rifampicin) with no clear preference for the soil farming type. The same soil samples were also used to isolate antibiotic resistant cultivable bacteria, which were predominated by highly resistant isolates of Pseudomonas, Stenotrophomonas, Sphingobacterium and Chryseobacterium genera. The resistance of these isolates was largely dependent on the efflux mechanisms, the soil Pseudomonas spp. relying mostly on RND, while Stenotrophomonas spp. and Chryseobacterium spp. on RND and ABC transporters.201931105678
3458140.9997MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage. Wastewater treatment plants (WWTPs) functioned as the intersection between the human society and nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistance genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype, and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION sequencing to quantify the resistance genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples. Our pipeline could deliver the results within 30 h from sample collection and the resistome quantification was consistent to that based on the Illumina platform. Additionally, the long nanopore reads not only enabled a simultaneous identification of the carrier populations of ARGs detected, but also facilitated the genome reconstruction of a representative MAR strain, from which we identified an instance of chromosomal integration of environmental resistance gene obtained by plasmid exchange with a porcine pathogen. This study demonstrated the utilization of MinION sequencing in quick monitoring and simultaneous phylogenetic tracking of environmental ARGs to address potential health risk associated with them.201729163399
4654150.9997Early Bacterial Colonization and Antibiotic Resistance Gene Acquisition in Newborns. Several studies have recently identified the main factors contributing to the bacterial colonization of newborns and the dynamics of the infant microbiome development. However, most of these studies address large time periods of weeks or months after birth, thereby missing on important aspects of the early microbiome maturation, such as the acquisition of antibiotic resistance determinants during postpartum hospitalization. The pioneer bacterial colonization and the extent of its associated antibiotic resistance gene (ARG) dissemination during this early phase of life are largely unknown. Studies addressing resistant bacteria or ARGs in neonates often focus only on the presence of particular bacteria or genes from a specific group of antibiotics. In the present study, we investigated the gut-, the oral-, and the skin-microbiota of neonates within the first 72 h after birth using 16S rDNA sequencing approaches. In addition, we screened the neonates and their mothers for the presence of 20 different ARGs by directed TaqMan qPCR assays. The taxonomic analysis of the newborn samples revealed an important shift of the microbiota during the first 72 h after birth, showing a clear site-specific colonization pattern in this very early time frame. Moreover, we report a substantial acquisition of ARGs during postpartum hospitalization, with a very high incidence of macrolide resistance determinants and mecA detection across different body sites of the newborns. This study highlights the importance of antibiotic resistance determinant dissemination in neonates during hospitalization, and the need to investigate the implication of the mothers and the hospital environment as potential sources of ARGs.202032754449
7407160.9997Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile. BACKGROUND: Aquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance. RESULTS: The taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site. CONCLUSIONS: Our results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities' risk for antibiotic resistance, and that a human-influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.202439523335
6574170.9997Exploiting microplastics and the plastisphere for the surveillance of human pathogenic bacteria discharged into surface waters in wastewater effluent. Discharge from wastewater treatment plants (WWTPs) is a well-characterised source of human pathogens and antimicrobial resistance genes entering the environment. However, determining whether pathogens released from effluent into surface waters are viable, and consequently pose a risk to human health, is hindered by the use of transient grab-sampling monitoring approaches. Here we present a novel surveillance system using low-cost microparticles (polyethylene, cork and rubber) deployed upstream and downstream of a WWTP effluent pipe, that exploits the ability of bacterial pathogens to form biofilms. Using quantitative culture-based and molecular methods, viable E. coli, Klebsiella spp., Citrobacter spp., and Enterococcus spp. were identified after only 24-hour of deployment. Moreover, these pathogens were continually present at each timepoint (2, 4, 6, 8, 10, 14 and 23 days) as biofilm communities matured, with all pathogens detected at higher concentrations downstream of the WWTP effluent pipe. Long-read whole genome sequencing revealed a suite of plasmids, virulence genes and antimicrobial resistance genes in bacterial pathogens isolated from biofilms formed downstream of the effluent pipe. Furthermore, recognising that pathogens are typically present at proportionally low concentrations within mixed biofilm communities, total biofilm pathogenicity was confirmed using a Galleria mellonella infection model. Full-length 16S rRNA gene sequencing revealed that human pathogens present in microplastic biofilms (the 'plastisphere') dominated the microbial community of infected G. mellonella larvae within 24 hr, suggesting these bacteria remained highly virulent. Overall, this study demonstrated the efficacy of an easy-to-deploy system for the surveillance and rapid detection of pathogenic bacteria being discharged from point-source pollution. We envisage that if used as part of an integrated environmental management approach, this approach could help to reduce the public and environmental health risks of human pathogens and antimicrobial resistance genes, by monitoring viable human pathogens entering surface waters.202540184703
3148180.9997Analysis of antibiotic resistance genes in pig feces during the weaning transition using whole metagenome shotgun sequencing. Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.202337093913
3681190.9997A closer look at the antibiotic-resistant bacterial community found in urban wastewater treatment systems. The conventional biological treatment process can provide a favorable environment for the maintenance and dissemination of antibiotic-resistant bacteria and the antibiotic resistance genes (ARG) they carry. This study investigated the occurrence of antibiotic resistance in three wastewater treatment plants (WWTP) to determine the role they play in the dissemination of ARGs. Bacterial isolates resistant to tetracycline were collected, and tested against eight antibiotics to determine their resistance profiles and the prevalence of multiple antibiotic resistance. It was found that bacteria resistant to tetracycline were more likely to display resistance to multiple antibiotics compared to those isolates that were not tetracycline resistant. Polymerase chain reaction (PCR) was used to identify the tetracycline resistance determinants present within the bacterial communities of the WWTPs and receiving waters, and it was found that ARGs may not be released from the treatment process. Identification of isolates showed that there was a large diversity of species in both the tetracycline-resistant and tetracycline-sensitive populations and that the two groups were significantly different in composition. Antibiotic resistance profiles of each population showed that a large diversity of resistance patterns existed within genera suggesting that transmission of ARG may progress by both horizontal gene and vertical proliferation.201829484827