Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment

Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.

The vertical migration of antibiotic-resistant genes and pathogens in soil and vegetables after the application of different fertilizers

The prevalence of bacterial resistance caused by the application of animal manure has become an important environmental issue. Herein, the vertical migration of antibiotic resistance genes (ARGs) and pathogens in soil and vegetables after the application of different fertilizers was explored. The results showed that the application of composted manure considerably enhanced the abundance of most ARGs and pathogens, especially in surface soil and pakchoi roots. Moreover, the soil ARGs increased partially from log 1.93 to log 4.65 after the application of composted manure, and six pathogens were simultaneously detected. It was observed that the increase in soil depth decreased most ARGs and pathogens by log 1.04-2.24 and 53.98 %~85.54 %, respectively. This indicated that ARGs and pathogens still existed in the deep soil (80-100 cm). Moreover, total organic carbon had a significant influence on the pathogen distribution, whereas bacterial communities primarily drove the vertical migration of ARGs rather than environmental factors. Although most of the ARG-host associations observed in the surface soil were disappeared in deep soil as revealed by network analysis, some co-occurrence pattern still occurred in deep soil, suggesting that some ARGs might be carried to deep soil by their host bacteria. These results were novel in describing the vertical migration of ARGs in the environment after the application of different fertilizers, providing ideas for curbing their migration to crops.

Reduction of antibiotic resistome in influent of a wastewater treatment plant (WWTP) via a chemically enhanced primary treatment (CEPT) process

Chemically enhanced primary treatment (CEPT) has been considered for maximizing wastewater energy recovery by enhancing the carbon captured through the primary treatment. However, evaluating the potential of CEPT as a primary treatment process for removing antibiotic resistance genes (ARGs) in the influent from a wastewater treatment plant (WWTP) has seldom been investigated. In this study, CEPT was conducted to assess simultaneous reduction of 13 major targeted ARGs and common pollutants in wastewater compared with primary sedimentation alone (non-CEPT). CEPT processes using three types of coagulants (PACl, FeCl₃ and alum) effectively reduced absolute abundance of ARGs and intI1 in the influent from municipal WWTP. Average log-removal of absolute abundance of ARGs was achieved up to 1.77 ± 0.41 along with 90% turbidity reduction compared to non-CEPT. Through the simultaneous reduction of ARGs and intI1 genes during a CEPT process, ARGs proliferation may be limited directly through reduction of antibiotic resistant bacteria or indirectly through decreasing the possibility of horizontal gene transfer by intI1 removal. Reduction of ARGs and intI1 was improved by increasing coagulants' doses: abundances of residual ARGs under optimal dose conditions were similar, regardless of the different characteristics of coagulant types. The strongly positive correlation between reduction of turbidity/total phosphorus (T-P) and ARGs was explored, identifying that turbidity or T-P might be suitable indicators linked with variations in the abundance of ARGs during CEPT. As a result, CEPT may prove promising in efforts to control ARGs flowing into a WWTP.

Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables

Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.

Treatment technologies to mitigate the harmful effects of recalcitrant fluoroquinolone antibiotics on the environ- ment and human health

Antibiotic proliferation in the environment and their persistent nature is an issue of global concern as they induce antibiotic resistance threatening both human health and the ecosystem. Antibiotics have therefore been categorized as emerging pollutants. Fluoroquinolone (FQs) antibiotics are an emerging class of contaminants that are used extensively in human and veterinary medicine. The recalcitrant nature of fluoroquinolones has led to their presence in wastewater, effluents and water bodies. Even at a low concentration, FQs can stimulate antibacterial resistance. The main sources of FQ contamination include waste from pharmaceutical manufacturing industries, hospitals and households that ultimately reaches the wastewater treatment plants (WWTPs). The conventional WWTPs are unable to completely remove FQs due to their chemical stability. Therefore, the development and implementation of more efficient, economical, convenient treatment and removal technologies are needed to adequately address the issue. This review provides an overview of the technologies available for the removal of fluoroquinolone antibiotics from wastewater including adsorptive removal, advanced oxidation processes, removal using non-carbon based nanomaterials, microbial degradation and enzymatic degradation. Each treatment technology is discussed on its merits and limitations and a comparative view is presented on the choice of an advanced treatment process for future studies and implementation. A discussion on the commercialization potential and eco-friendliness of each technology is also included in the review. The importance of metabolite identification and their residual toxicity determination has been emphasized. The last section of the review provides an overview of the policy interventions and regulatory frameworks that aid in retrofitting antibiotics as a central key focus contaminant and thereby defining the discharge limits for antibiotics and establishing safe manufacturing practices.

Antibiotic Resistance: One Health One World Outlook

Antibiotic resistance (ABR) is a growing public health concern worldwide, and it is now regarded as a critical One Health issue. One Health’s interconnected domains contribute to the emergence, evolution, and spread of antibiotic-resistant microorganisms on a local and global scale, which is a significant risk factor for global health. The persistence and spread of resistant microbial species, and the association of determinants at the human-animal-environment interface can alter microbial genomes, resulting in resistant superbugs in various niches. ABR is motivated by a well-established link between three domains: human, animal, and environmental health. As a result, addressing ABR through the One Health approach makes sense. Several countries have implemented national action plans based on the One Health approach to combat antibiotic-resistant microbes, following the Tripartite’s Commitment Food and Agriculture Organization (FAO)-World Organization for Animal Health (OIE)-World Health Organization (WHO) guidelines. The ABR has been identified as a global health concern, and efforts are being made to mitigate this global health threat. To summarize, global interdisciplinary and unified approaches based on One Health principles are required to limit the ABR dissemination cycle, raise awareness and education about antibiotic use, and promote policy, advocacy, and antimicrobial stewardship.

Carriage of ESBL-producing Enterobacterales in wastewater treatment plant workers and surrounding residents - the AWARE Study

To investigate whether wastewater treatment plant (WWTP) workers and residents living in close proximity to a WWTP have elevated carriage rates of ESBL-producing Enterobacterales, as compared to the general population. From 2018 to 2020, we carried out a cross-sectional study in Germany, the Netherlands, and Romania among WWTP workers (N = 344), nearby residents (living ≤ 300 m away from WWTPs; N = 431) and distant residents (living ≥ 1000 m away = reference group; N = 1165). We collected information on potential confounders via questionnaire. Culture of participants' stool samples was performed with ChromID®-ESBL agar plates and species identification with MALDI-TOF-MS. We used logistic regression to estimate the odds ratio (OR) for carrying ESBL-producing E. coli (ESBL-EC). Sensitivity analyses included stratification by country and interaction models using country as secondary exposure. Prevalence of ESBL-EC was 11% (workers), 29% (nearby residents), and 7% (distant residents), and higher in Romania (28%) than in Germany (7%) and the Netherlands (6%). Models stratified by country showed that within the Romanian population, WWTP workers are about twice as likely (aOR = 2.34, 95% CI: 1.22-4.50) and nearby residents about three times as likely (aOR = 3.17, 95% CI: 1.80-5.59) to be ESBL-EC carriers, when compared with distant residents. In stratified analyses by country, we found an increased risk for carriage of ESBL-EC in Romanian workers and nearby residents. This effect was higher for nearby residents than for workers, which suggests that, for nearby residents, factors other than the local WWTP could contribute to the increased carriage.

What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach

It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. It has been suggested that the environment constitutes an enormous recruitment ground for ARGs to pathogens, but its extent is practically unknown. We have constructed a model framework for resistance emergence and used available quantitative data on relevant processes to identify limiting steps in the appearance of ARGs in human pathogens. We found that in a majority of possible scenarios, the environment would only play a minor role in the emergence of novel ARGs. However, the uncertainty is enormous, highlighting an urgent need for more quantitative data. Specifically, more data is most needed on the fitness costs of ARG carriage, the degree of dispersal of resistant bacteria from the environment to humans, and the rates of mobilization and horizontal transfer of ARGs. This type of data is instrumental to determine which processes should be targeted for interventions to curb development and transmission of ARGs in the environment.

Antibiotic resistance genes in an urban stream before and after a state fair

The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG bla_TEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.

Effective Treatment Strategies for the Removal of Antibiotic-Resistant Bacteria, Antibiotic-Resistance Genes, and Antibiotic Residues in the Effluent From Wastewater Treatment Plants Receiving Municipal, Hospital, and Domestic Wastewater: Protocol for a Systematic Review

Background

The widespread and unrestricted use of antibiotics has led to the emergence and spread of antibiotic-resistant bacteria (ARB), antibiotic-resistance genes (ARGs), and antibiotic residues in the environment. Conventional wastewater treatment plants (WWTPs) are not designed for effective and adequate removal of ARB, ARGs, and antibiotic residues, and therefore, they play an important role in the dissemination of antimicrobial resistance (AMR) in the natural environment.

Objective

We will conduct a systematic review to determine the most effective treatment strategies for the removal of ARB, ARGs, and antibiotic residues from the treated effluent disposed into the environment from WWTPs that receive municipal, hospital, and domestic discharge.

Methods

We will search the MEDLINE, EMBASE, Web of Science, World Health Organization Global Index Medicus, and ProQuest Environmental Science Collection databases for full-text peer-reviewed journal articles published between January 2001 and December 2020. We will select only articles published in the English language. We will include studies that measured (1) the presence, concentration, and removal rate of ARB/ARGs going from WWTP influent to effluent, (2) the presence, concentration, and types of antibiotics in the effluent, and (3) the possible selection of ARB in the effluent after undergoing treatment processes in WWTPs. At least two independent reviewers will extract data and perform risk of bias assessment. An acceptable or narrative synthesis method will be followed to synthesize the data and present descriptive characteristics of the included studies in a tabular form. The study has been approved by the Ethics Review Board at the International Centre for Diarrhoeal Disease Research, Bangladesh (protocol number: PR-20113).

Results

This protocol outlines our proposed methodology for conducting a systematic review. Our results will provide an update to the existing literature by searching additional databases.

Conclusions

Findings from our systematic review will inform the planning of proper treatment methods that can effectively reduce the levels of ARB, ARGs, and residual antibiotics in effluent, thus lowering the risk of the environmental spread of AMR and its further transmission to humans and animals.

International Registered Report Identifier (IRRID)

PRR1-10.2196/33365

Characterization of enoxacin (ENO) during ClO2 disinfection in water distribution system: Kinetics, byproducts, toxicity evaluation and halogenated disinfection byproducts (DBPs) formation potential

Enoxacin (ENO) is widespread in water because it is commonly used as a human and veterinary antibiotic. However, little effort has been dedicated to revealing the transformation mechanisms of ENO destruction using ClO₂, especially within a water distribution system (WDS). To address this knowledge gap, the kinetics, byproducts, toxicity, and formation potential of halogenated disinfection byproducts (DBPs) associated with ENO destruction using ClO₂ in a pilot-scale PE pipe was explored for the first time. Statistical analyses showed that the destruction efficiency of ENO in the pilot-scale PE pipe was lower than that in deionized water (DI water), and the reactions in DI water followed the second-order kinetic model. Furthermore, pH has a significant effect on the destruction of ENO, and the removal ratio increased at a higher pH. Additionally, increasing the flow rate elevated the ENO removal efficiency; however, the influence of flow velocity was limited to ENO destruction. The ENO removal rates within the diverse pipes exhibited the following order: stainless steel pipe < PE pipe < ductile iron pipe. Nine possible intermediates were identified, and those that were formed by piperazine group cleavage represented the major primary byproducts of the entire destruction process. Additionally, the ENO destruction in a pilot-scale PE pipe had minimal influence on halogenated DBPs and chlorite formation. Finally, the toxicity evaluation illustrated that the presence of ENO increased the potential risk of water quality safety when treated with ClO₂.

The role of antibiotics and heavy metals on the development, promotion, and dissemination of antimicrobial resistance in drinking water biofilms

Antimicrobial resistance (AMR), as well as the development of biofilms in drinking water distribution systems (DWDSs), have become an increasing concern for public health and management. As bulk water travels from source to tap, it may accumulate contaminants of emerging concern (CECs) such as antibiotics and heavy metals. When these CECs and other selective pressures, such as disinfection, pipe material, temperature, pH, and nutrient availability interact with planktonic cells and, consequently, DWDS biofilms, AMR is promoted. The purpose of this review is to highlight the mechanisms by which AMR develops and is disseminated within DWDS biofilms. First, this review will lay a foundation by describing how DWDS biofilms form, as well as their basic intrinsic and acquired resistance mechanisms. Next, the selective pressures that further induce AMR in DWDS biofilms will be elaborated. Then, the pressures by which antibiotic and heavy metal CECs accumulate in DWDS biofilms, their individual resistance mechanisms, and co-selection are described and discussed. Finally, the known human health risks and current management strategies to mitigate AMR in DWDSs will be presented. Overall, this review provides critical connections between several biotic and abiotic factors that influence and induce AMR in DWDS biofilms. Implications are made regarding the importance of monitoring and managing the development, promotion, and dissemination of AMR in DWDS biofilms.

Antimicrobial resistance in integrated agroecosystems: State of the science and future opportunities

As the Journal of Environmental Quality (JEQ) celebrates 50 years of publication, the division of environmental microbiology is one of the newest additions to the journal. During this time, significant advances in understanding of the interconnected microbial community and impact of the microbiome on natural and designed environmental systems have occurred. In this review, we highlight the intractable challenge of antimicrobial resistance (AMR) on humans, animals, and the environment, with particular emphasis on the role of integrated agroecosystems and by highlighting contributions published in JEQ. From early studies of phenotypic resistance of indicator organisms in waters systems to current calls for integrating AMR assessment across "One Health," publications in JEQ have advanced our understanding of AMR. As we reflect on the state of the science, we emphasize future opportunities. First, integration of phenotypic and molecular tools for assessing environmental spread of AMR and human health risk continues to be an urgent research need for a one health approach to AMR. Second, monitoring AMR levels in manure is recommended to understand inputs and potential spread through agroecosystems. Third, baseline knowledge of AMR levels is important to realize the impact of manure inputs on water quality and public health risk; this can be achieved through background monitoring or identifying the source-related genes or organisms. And finally, conservation practices designed to meet nutrient reduction goals should be explored for AMR reduction potential.

Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H218O-based DNA-Stable isotope probing and metagenomics

The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H₂¹⁸O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.

Metagenomic Analysis Reveals the Fate of Antibiotic Resistance Genes in a Full-Scale Wastewater Treatment Plant in Egypt

Wastewater treatment plants (WWTPs) are recognized as hotspots for the dissemination of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in the environment. Our study utilized a high-throughput sequencing-based metagenomic analysis approach to compare the ARG abundance profiles of the raw sewage, treated effluent and activated sludge samples from a full-scale WWTP in Egypt. In addition, the difference in microbial community composition due to the treatment process was assessed. As a result, 578 ARG subtypes (resistance genes) belonging to 18 ARG types (antibiotic resistance classes) were identified. ARGs encoding for resistance against multidrug, aminoglycoside, bacitracin, beta-lactam, sulfonamide, and tetracycline antibiotics were the most abundant types. The total removal efficiency percentage of ARGs in the WWTP was found to be 98% however, the ARG persistence results indicated that around 68% of the ARGs in the influent could be found in the treated effluent. This finding suggests that the treated wastewater poses a potential risk for the ARG dissemination in bacterial communities of the receiving water bodies via horizontal gene transfer (HGT). The community composition at phylum level showed that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant phyla in all datasets. Although the relative abundance of several pathogenic bacteria in the influent declined to less than 1% in the effluent, the taxonomic assignments at species level for the effluent and sludge metagenomes demonstrated that clinically important pathogens such as Escherichia coli, Klebsiella pneumonia, and Aeromonas caviae were present. Overall, the results of this study would hopefully enhance our knowledge about the abundance profiles of ARGs and their fate in different wastewater treatment compartments that have never been examined before.

Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

Distribution of antimicrobial resistance across the overall environment of dairy farms - A case study

The environmental implications of antimicrobial resistance arising from food animal farm practice are still a knowledge gap. This study investigates the fate and transport of antimicrobial resistance genes related to the use of antibiotics on a dairy farm in Michigan. Manure, soil, animal feed, animal drinking water, surface and groundwater samples were taken and the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were subsequently measured using high parallel quantitative PCR targeting 136 genes. The total abundance and detected numbers of ARGs were found to be highest in the stagnant lagoon. Up to 44 ARG subtypes with high abundance were found in drinking water in pen which was very close to those in manure compost. The ARGs pattern clustered by soil depth although they were treated by different manure. ARGs and MGEs were detected in surface and groundwater surrounded by dairy farmlands, with the occurrence of carbapenemase-encoding KPC gene in two waters, which may be due to transport of ARGs through runoff or other sources. Overall, the results of the study suggest high prevalence of ARGs both inside and outside the animal raising area and their potential contribution to environmental ARGs.

Evaluation of Knowledge and Risk Perception about Antibiotic Resistance in Biology and Mathematics Young Students in Nîmes University in France

In response to the antimicrobial resistance issue, the World Health Organization developed and conducted a survey in 2015 dealing with habits, antibiotic use, awareness of appropriate use and sensitization to the issue of antibacterial resistance. In France, we conducted a similar survey to investigate the use of antibiotics and students' perceptions of the antibiotic resistance risk. Our results indicated that antibiotics are moderately taken (42% in the last six months), but mistakes remain in appropriate practices and knowledge. Many people still believe that the body develops resistance to antibiotics and 24% responded that antibiotics can be stopped before the end of the treatment if they feel better. Furthermore, only 14% said antibiotics could be used to treat gonorrhea while 57% indicated that influenza could be treated with antibiotics. We looked at risk perception as well, and noticed that students in biology were more aware of risk (mean score = 48.87) and health consequences (mean score = 40.33) than mathematics students (mean score = 44.11 and 37.44). They were more aware of the threat, had a better understanding of antibiotic resistance and their denial of this risk was less significant (mean score = 27.04 against 23.81). However, the importance of providing a minimum level of knowledge to young students has been emphasized, regardless of the field of expertise.

Epidemiology of mobile colistin resistance (mcr) genes in aquatic environments

Colistin is one of the last-line therapies against multidrug-resistant Gram-negative pathogens, especially carbapenemase-producing isolates, making resistance to this compound a major global public-health crisis. Until recently, colistin resistance in Gram-negative bacteria was known to arise only by chromosomal mutations. However, a plasmid-mediated colistin resistance mechanism was described in late 2015. This mechanism is encoded by different mobile colistin resistance (mcr) genes that encode phosphoethanolamine (pEtN) transferases. These enzymes catalyse the addition of a pEtN moiety to lipid A in the bacterial outer membrane leading to colistin resistance. MCR-producing Gram-negative bacteria have been largely disseminated worldwide. However, their environmental dissemination has been underestimated. Indeed, water environments act as a connecting medium between different environments, allowing them to play a crucial role in the spread of antibiotic resistance between the natural environment and humans and other animals. For a better understanding of the role of such environments as reservoirs and/or dissemination routes of mcr genes, this review discusses primarily the various water habitats contributing to the spread of antibiotic resistance. Thereafter, we provide an overview of existing knowledge regarding the global epidemiology of mcr genes in water environments. This review confirms the global distribution of mcr genes in several water environments, including wastewater from different origins, surface water and tap water, making these environments reservoirs and dissemination routes of concern for this resistance mechanism.

Prevalence and Quantitative Analysis of Antibiotic Resistance Genes (ARGs) in Surface and Groundwater in Meandering Part of the Kelani River Basin in Sri Lanka

Nearly 80% of the population in the Colombo district fulfill their major requirement from the Kelani river. Recent studies are interoperating: most groundwater and surface water in Sri Lanka are contaminated with waterborne pathogens and antibiotics. In the present study, nine antibiotic resistance genes (ARGs) were screened which were belonging to two common groups of antibiotic: penicillin - OPR D, bla _TEM , bla _OXA , amp a, and amp b - and tetracycline - tet A, tet M, tet B, and tet S. The results of the study reveled that the surface and groundwater of the entire lower part of the Kelani river basin were contaminated with TC and FC (98%). None of the penicillin and tetracycline group antibiotics were detected either surface or groundwater samples except the Kelani river mouth (amoxicillin (AMX) at 0.003 ± 0.001 µg/ml). The results showed that 5 to 15% of surface water samples were positive for penicillin resistance genes (bla _TEM , bla _OXA , OPR D, amp a, amp b) where ~ 10% of groundwater samples were positive against tetracycline resistance genes (tet A, tet M, tet S, tet B). Among the penicillin resistance genes, the bla _TEM (700.576 × 10² copy/ml) was recorded as the highest concentration where the highest tet A gene (439.875 × 10² copy/ml) was detected among the tetracycline resistance genes. Therefore, water quality management and regular monitoring are essential to maintain the quality of drinking water in the meandering part of the Kelani river basin to safeguard river water consumers.

Tracking antibiotic resistance gene transfer at all seasons from swine waste to receiving environments

Antibiotic resistance genes (ARGs) in livestock farms have attracted a growing attention with potential effects on human health. As one of the most important organic fertilizer, swine waste provided an ideal environment for understanding the dissemination and accumulation of ARGs in agricultural ecosystems. Here we conducted a year-round follow-up trace from swine waste to receiving environments, with the purpose of revealing the contamination profiles and ecological risks of ARGs at different seasons. Results indicated that a variety of common ARGs and even high-risk ARGs (i.e., bla_ampC, bla_OXA-1, bla_TEM-1 and mcr-1) were prevalent from swine waste to farmland soil, with changing in various degrees from season to season. Regarding the occurrence pattern of ARGs, tetracycline resistance genes (tet-ARGs) were predominant genes at four seasons in all fresh pig feces, swine manure, manured soil and wastewater. The levels of most ARGs in solid waste were reduced at a different degree via natural composting, and the removal effect was best in summer, while ARGs decreased poorly after wastewater treatment, especially in winter (up to 10^-1 copies/16S copies in the residual level), which increased the possibility of propagation to receiving environment. This concern was also validated by the investigation on farmland environment with long-term application of manure, where causing an increase in ARG abundances in soils (approximately 0.9-32.7 times). To our knowledge, this study is the first to demonstrate the distribution pattern of ARGs from swine waste to its receiving farmland environment at all seasons on this integrity chain.

UV filters as a driver of the antibiotic pollution in different water matrices

Antibiotic pollution is frequently detected in fresh waters and wastewaters where they represent an environmental risk for the development of global antibiotic resistance. Due to their excessive use in personal care products, UV filters have also been found to be pseudo-persistent in the aquatic environment. In contrast to antibiotics, which can undergo photodegradation, UV filters are compounds designed to stably absorb UV radiation. This study explored the light based remediation of representative antibiotics from seven classes of antibiotics (fluoroquinolones, tetracyclines, penicillins, macrolide, glycolpeptide, sulphonamides and trimethoprim) in order to assess whether antibiotic pollution persists longer in the presence of organic UV filters. We show that the presence of UV filters either completely supresses or significantly alters the photodegradation of antibiotics in water. Advanced technologies in wastewater treatment, such as the use of UV C radiation, both effectively minimise the effect of UV filters and degrade most of the tested antibiotics proving to be effective management strategy. However, the half-life of erythromycin and amoxicillin, widely used antibiotics from macrolide- and penicillin-like classes, is extended in the presence of UV filters, even during UV C irradiation. Overall, the UV filters present within environmental mixtures are identified as important drivers of mixture toxicity, as they prolong antibiotic contamination of aquatic and engineered environments. The ramification of such finding is that inadequate consideration of UV filters may result in an imperfect prediction of the solar and UV light-based remediation of antibiotics, lead to improper classification of antibiotics persistence in the environment and cause non-optimal chemical fate and transport model performance. Use of the more benign compounds and assessment of the UV filters were identified as feasible management options in minimizing the influence of UV filters onto the remediation of antibiotics in aquatic environments.

Antimicrobial Resistance Profiling of Biofilm Forming Non Typhoidal Salmonella enterica Isolates from Poultry and Its Associated Food Products from Pakistan

Salmonellosis caused by non-typhoidal Salmonella enterica from poultry products is a major public health concern worldwide. This study aimed at estimating the pathogenicity and antimicrobial resistance in S. enterica isolates obtained from poultry birds and their food products from different areas of Pakistan. In total, 95/370 (25.67%) samples from poultry droppings, organs, eggs, and meat were positive for Salmonella. The isolates were further identified through multiplex PCR (mPCR) as Salmonella Typhimurium 14 (14.7%), Salmonella Enteritidis 12 (12.6%), and other Salmonella spp. 69 (72.6%). The phenotypic virulence properties of 95 Salmonella isolates exhibited swimming and/or swarming motility 95 (100%), DNA degrading activity 93 (97.8%), hemolytic activity 92 (96.8%), lipase activity 87 (91.6%), and protease activity 86 (90.5%). The sopE virulence gene known for conferring zoonotic potential was detected in S. Typhimurium (92.8%), S. Enteritidis (100%), and other Salmonella spp. (69.5%). The isolates were further tested against 23 antibiotics (from 10 different antimicrobial groups) and were found resistant against fifteen to twenty-one antibiotics. All isolates showed multiple drug resistance and were found to exhibit a high multiple antibiotic-resistant (MAR) index of 0.62 to 0.91. The strong biofilm formation at 37 °C reflected their potential adherence to intestinal surfaces. There was a significant correlation between antimicrobial resistance and the biofilm formation potential of isolates. The resistance determinant genes found among the isolated strains were blaTEM-1 (59.3%), blaOxA-1 (18%), blaPSE-1 (9.5%), blaCMY-2 (43%), and ampC (8.3%). The detection of zoonotic potential MDR Salmonella in poultry and its associated food products carrying cephalosporin and quinolone resistance genes presents a major threat to the poultry industry and public health.

On-Farm Anaerobic Digestion of Dairy Manure Reduces the Abundance of Antibiotic Resistance-Associated Gene Targets and the Potential for Plasmid Transfer

The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets, and the horizontal transfer potential of extended-spectrum β-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying β-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/liter cefotaxime into a β-lactam-sensitive green fluorescent protein (GFP)-labeled Escherichia coli recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer of ESBL genes. Twenty-five transconjugants were sequenced, revealing six distinct plasmids, ranging in size from 40 to 180 kb. A variety of ESBL genes were identified: bla_CTX-M-1, bla_CTX-M-14, bla_CTX-M-15, bla_CTX-M-27, bla_CTX-M-55, and bla_PER-1. bla_CTX-M-15 was the most prevalent ESBL gene detected on plasmids harbored by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets, including sul1, str(A), str(B), erm(B), erm(F), intI1, aadA, incW, bla_PSE, and bla_OXA-20, were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure; however, erm(B) and erm(F) targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum β-lactams and other classes of antibiotics into E. coli CV601. IMPORTANCE Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have shown potential for reducing the abundance of antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria, E. coli, and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli strain CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry, and the potential for ESBL-carrying plasmid transfer.

Antibacterial Residue Excretion via Urine as an Indicator for Therapeutical Treatment Choice and Farm Waste Treatment

Many of the infectious diseases that affect livestock have bacteria as etiological agents. Thus, therapy is based on antimicrobials that leave the animal's tissues mainly via urine, reaching the environment through slurry and waste water. Once there, antimicrobial residues may lead to antibacterial resistance as well as toxicity for plants, animals, or humans. Hence, the objective was to describe the rate of antimicrobial excretion in urine in order to select the most appropriate molecule while reducing harmful effects. Thus, 62 pigs were treated with sulfamethoxypyridazine, oxytetracycline, and enrofloxacin. Urine was collected through the withdrawal period and analysed via LC-MS/MS. Oxytetracycline had the slowest rate of degradation (a half-life time of 4.18 days) and the most extended elimination period in urine (over 2 months), followed by enrofloxacin (a half-life time of 1.48 days, total urine elimination in ca. 3 weeks) and sulfamethoxypyridazine (a half-life time of 0.49 days, total urine elimination in ca. 1 week). Bacterial sensitivity and recommendations for responsible use are limiting when selecting the treatment. Nevertheless, with similar effectiveness, sulfamethoxypyridazine would be the choice, as waste treatment would only need to be implemented for 1 week after treatment. Thus, more in-depth knowledge regarding antibacterial elimination would improve resource management, while protecting animals and consumers' health.

Characterization of a fatty acid-binding protein from the Pacific oyster (Crassostrea gigas): pharmaceutical and toxicological implications

Pharmaceuticals and their metabolites constitute a class of xenobiotics commonly found in aquatic environments which may cause toxic effects in aquatic organisms. Several different lipophilic molecules, including some pharmaceuticals, can bind to fatty acid-binding proteins (FABPs), a group of evolutionarily related cytoplasmic proteins that belong to the intracellular lipid-binding protein (iLBP) family. An oyster FABP genome-wide investigation was not available until a recent study on gene organization, protein structure, and phylogeny of Crassostrea gigas iLBPs. Higher transcript levels of the C. gigas FABP2 gene were found after exposure to sewage and pharmaceuticals. Because of its relevance as a potential biomarker of aquatic contamination, in this study, recombinant FABP2 from C. gigas (CgFABP2) was successfully cloned, expressed, and purified, and in vitro and in silico assays were performed using lipids and pharmaceuticals. This is the first characterization of a protein from the iLBP family in C. gigas. Homology modeling and molecular docking were used to evaluate the binding affinities of natural ligands (palmitic, oleic, and arachidonic acids) and pharmaceuticals (ibuprofen, sodium diclofenac, and acetaminophen). Among the tested fatty acids, CgFABP2 showed preference for palmitic acid. The selected pharmaceuticals presented a biphasic-binding mode, suggesting a different binding affinity with a preference for diclofenac. Therefore, the approach using circular dichroism and in silico data might be useful for ligand-binding screening in an invertebrate model organism.

Antibiotic resistance genes are enriched with prolonged age of refuse in small and medium-sized landfill systems

Landfills are sites for the disposal of waste over decades. The dynamics of contaminants during landfill treatment influence the functions and environmental risks of the landfill systems, but the patterns of these dynamics are not fully characterized, especially for antibiotic resistant genes (ARGs), an emerging contaminant of global concern. Here, seventeen typical ARG subtypes were quantitatively investigated in refuse samples from small and medium-sized landfills with ages of <3 years, ~5 years, and 8-10 years. The abundance of ARGs, including tetM, tetX, blaPER, emrB, sul1 and sul2, increased significantly (p < 0.05), approaching 8- to 304-fold on average, from refuse of < 3years to that of 8-10 years, while there was no obvious change (p > 0.05) in abundance for other ARGs, including tetQ, tetW, ampC, blaCTX-M, blaSHV, emrA, mefA, qnrD, qnrS, and mexF. Accordingly, resistance to tetracyclines, macrolides, and sulfonamides increased with landfill age, while resistance to β-lactams and quinolones remained unchanged. The increase in ARG abundance with increasing refuse age was probably related with the increased horizontal gene transfer (HGT) (indicated by the increased abundance of mobile gene elements) and the enhanced co-selective pressure (suggested by the increased contents of heavy metals). These results indicated a potential risk from ARG enrichment with an increase in refuse age in small and medium-sized landfills, which should be managed to ensure landfill safety.

Antibiotic residues in the aquatic environment - current perspective and risk considerations

Antimicrobial resistance is a major concern for human and animal health, projected to deteriorate with time and given current trends of antimicrobial usage. Antimicrobial use, particularly in healthcare and agriculture, can result in the release of antimicrobials into surface waters, promoting the development of antibiotic resistance in the environment, and potentially leading to human health risks. This study reviews relevant literature, and investigates current European and Irish antimicrobial usage trends in humans and animals, as well as potential pathways that antibiotics can take into surface waters following use. Reported levels in the aquatic environment are summarized, with particular focus on Ireland. There are relatively few studies examining Irish water bodies or sewage effluent for antibiotic residues, however, five antibiotics, namely azithromycin, ciprofloxacin, clarithromycin, metronidazole, and trimethoprim, have been measured in Irish waters, in concentrations predicted to select for resistance. Numerous isolates of multi-drug resistant bacteria have also been found in water bodies throughout Ireland and Europe. The value of risk assessment methodologies in understanding risks posed by antibiotic residues is reviewed including the advantages and disadvantages of specific approaches. Hazard quotient and bespoke Monte Carlo approaches are predominant risk assessment tools used to examine antimicrobial release and their complex pathways. This study highlights the need for monitoring of antimicrobial releases and the potential for resistance development, persistence and transmission while highlighting the role of risk assessment methodologies in assessing potential human and environmental health impacts.

Effectively reducing antibiotic contamination and resistance in fishery by efficient gastrointestine-blood delivering dietary millispheres

The overuse of antibiotics during the medication treatment is inevitable in the extensively-applied intensive and semi-intensive aquaculture mode; the accompanied antibiotic contamination and antimicrobial resistance pose threats to the ecosystems and cause great loss to the aquaculture industry. To solve the problem, this work introduced the antibiotic-laden dietary millispheres (DMSs) with internal porous structure for the high availability, attractiveness and digestibility to fish. Two types of antibiotics with distinct solubilities - tetracycline chloride (TCH) and sulfadiazine (SDZ) were made into the DMSs, individually, which were then directly adopted in the feeding of fish. Carassius auratus was chosen as the target fish in this work. The mesocosm study demonstrate that, compared with the regular way of oral administration (feeding the mixture of antibiotics and commercial feed pellets), the DMSs could use much less (i.e. one order of magnitude lower) antibiotic dose to reach the equivalent antibiotic concentration in gastrointestine and blood. As a robust alternative, either TCH- or SDZ-laden DMSs achieved efficient drug delivery in vivo, which importantly facilitated the source reduction of antibiotics, the alleviation of antibiotic contamination in fishery and the control of antibiotic resistance especially in sediments.

Prevalence of Antibiotic-Resistant Bacteria ESKAPE among Healthy People Estimated by Monitoring of Municipal Wastewater

There is increasing attention toward factors that potentially contribute to antibiotic resistance (AR), as well as an interest in exploring the emergence and occurrence of antibiotic resistance bacteria (ARB). We monitored six ARBs that cause hospital outbreaks in wastewater influent to highlight the presence of these ARBs in the general population. We analyzed wastewater samples from a municipal wastewater treatment plant (MWWTP) and hospital wastewater (HW) for six species of ARB: Carbapenem-resistant Enterobacteria (CARBA), extended-spectrum β-lactamase producing Enterobacteria (ESBL), multidrug-resistant Acinetobacter (MDRA), multidrug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococci (VRE). We registered a high percentage of ARBs in MWWTP samples (>66%) for all ARBs except for MDRP, indicating a high prevalence in the population. Percentages in HW samples were low (<78%), and no VRE was detected throughout the study. CARBA and ESBL were detected in all wastewater samples, whereas MDRA and MRSA had a high abundance. This result demonstrated the functionality of using raw wastewater at MWWTP to monitor the presence and extent of ARB in healthy populations. This kind of surveillance will contribute to strengthening the efforts toward reducing ARBs through the detection of ARBs to which the general population is exposed.

Antibiotic Resistance in Wastewater Treatment Plants and Transmission Risks for Employees and Residents: The Concept of the AWARE Study

Antibiotic resistance has become a serious global health threat. Wastewater treatment plants may become unintentional collection points for bacteria resistant to antimicrobials. Little is known about the transmission of antibiotic resistance from wastewater treatment plants to humans, most importantly to wastewater treatment plant workers and residents living in the vicinity. We aim to deliver precise information about the methods used in the AWARE (Antibiotic Resistance in Wastewater: Transmission Risks for Employees and Residents around Wastewater Treatment Plants) study. Within the AWARE study, we gathered data on the prevalence of two antibiotic resistance phenotypes, ESBL-producing E. coli and carbapenemase-producing Enterobacteriaceae, as well as on their corresponding antibiotic resistance genes isolated from air, water, and sewage samples taken from inside and outside of different wastewater treatment plants in Germany, the Netherlands, and Romania. Additionally, we analysed stool samples of wastewater treatment plant workers, nearby residents, and members of a comparison group living ≥1000 m away from the closest WWTP. To our knowledge, this is the first study investigating the potential spread of ESBL-producing E. coli, carbapenemase-producing Enterobacteriaceae, and antibiotic resistance genes from WWTPs to workers, the environment, and nearby residents. Quantifying the contribution of different wastewater treatment processes to the removal efficiency of ESBL-producing E. coli, carbapenemase-producing Enterobacteriaceae, and antibiotic resistance genes will provide us with evidence-based support for possible mitigation strategies.

Horizontal and vertical gene transfer drive sediment antibiotic resistome in an urban lagoon system

Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes (ARGs) in urban aquatic ecosystems. However, limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems. Here, we employed high-throughput quantitative PCR (HT-qPCR) to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon, China. The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments, highlighting the role of anthropogenic activities in ARG pollution. Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-, Deltaproteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes and Synergistetes were the potential hosts of ARGs. The partial least squares-path modeling (PLS-PM) analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles, via biotic factors, respectively. The horizontal (mediated by mobile genetic elements) and vertical (mediated by prokaryotic communities) gene transfer may directly contribute the most to drive the abundance and composition of ARGs, respectively. Furthermore, the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes. Overall, this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.

Tracking high-risk β-lactamase gene (bla gene) transfers in two Chinese intensive dairy farms

Extended-spectrum β-lactam antibiotics are critically important antibiotics for humans, but their use in food-animals poses a potential threat for public health. This paper addressed the occurrence of high-risk β-lactamase genes (bla genes) in intensive dairy farms, and assessed the effects of different waste treatment technologies at dairies on the propagation and dissemination of bla genes. Results showed that ESBL genes (bla_TEM-1, bla_OXA-1), ampC β-lactamase genes (bla_ampC) and carbapenemase genes (bla_GES-1, bla_NDM) were prevalent in dairy cow waste, and even prevailed through each processing stage of solid manure and dairy wastewater. Significant levels of bla genes were present in the final lagoon (from 10⁴ to 10⁶ copies/mL, representing from 10% to 151%, of raw influent levels), raising the possibility of dissemination to the receiving environment. This concern was validated by the investigation on farmland that had long-term undergone wastewater irrigation, where causing an increase in bla gene levels in soils (approximately 1-3 orders of magnitude). More troublesomely, considerable levels of certain bla genes were still observed in the bedding material (up to 10⁵ and 10⁷ copies/g), which would directly threaten the dairy cow health. Otherwise, correlation analysis showed that both bacterial community and environmental factors played important roles in the bla genes abundances in dairy farms. This study demonstrated the prevalence of high-risk bla genes in dairy farms, and also underscored that dairy waste was a non-ignored great source of multidrug resistance for their surroundings.

Relating the prevalence of plasmid-mediated AmpC beta-lactamase genes to aquatic environmental factors

It is important that environmental parameters that may affect the prevalence of AmpC beta-lactamase genes are investigated to devise frameworks for their surveillance, management and prevention. The aim of this study was thus to determine which environmental parameters are associated with the prevalence of clinically relevant AmpC beta-lactamase genes in aquatic systems. River water was sampled from seven sites in the Crocodile West River, South Africa. Physical-chemical parameters, metal levels and beta-lactam levels were measured. Environmental DNA was extracted from the water samples and six AmpC beta-lactamase gene groups (ACC, ACT/MIR, BIL/LAT/CMY, DHA, FOX, MOX/CMY) were quantified using quantitative PCR. Additionally, 16S rRNA gene metabarcoding analyses were performed on eDNA for each site and metabolic pathways were predicted using PICRUST2. Network analysis was performed to establish co-occurrences of AmpC genes with environmental factors. Quantification results indicated that AmpC gene copy numbers were significantly high (Kruskal Wallis H Test, p < 0.05) at Sites 1-3 of the Crocodile West River. In contrast, no significant changes regarding environmental factors were observed across the seven sites. Results of network analysis indicated that the AmpC gene groups had limited associations with all the environmental parameters, except for some key bacterial families, specifically Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. A significant positive correlation between population density and AmpC genes suggested that in more densely populated areas more faecal pollution will be prevalent which is associated with high AmpC gene levels. Areas such as these are also likely to be linked with more antibiotic use which supports the notion that pre-selection of AmpC genes occurs before entering the aquatic environment. Moreover, it was demonstrated that prevalent selectors of AmpC genes do not ensure that continuous selection occurs in an aquatic environment. This information could be vital in future detection and management of AmpC genes in aquatic systems.

Spatiotemporal variations and source tracking of antibiotics in an ecological aquaculture farm in Southern China

Although the occurrence and distribution of antibiotics in aquatic environments and reared organisms have been widely reported, the spatiotemporal variations and sources of antibiotics throughout the rearing period of aquaculture remain unclear. In this study, the concentrations and spatiotemporal variations of antibiotics in water sources, pond water, sediment, feed, and reared shrimp samples during three rearing periods in an ecological shrimp farm in Southern China were investigated. The water, sediment, and feed samples were found to contain twelve, nine, and four types of antibiotics, respectively, and the concentration of erythromycin-H₂O was the highest among these antibiotics. No target antibiotics were detected in the reared shrimp samples from this typical shrimp farm, which employed ecological rearing with no antibiotic use throughout the rearing processes. The total concentrations of antibiotics in water source were 1.96-40.58 times higher than those in pond water. A significant decrease in the total antibiotic concentrations of the pond water was observed, while a significant increase was observed in sediment during each rearing period (p < 0.05), suggesting that antibiotics transferred from the water phase to the sediment phase in the farm. Redundancy analysis demonstrated that the chemical oxygen demand was negatively correlated with the concentration of the target antibiotics in the water samples during three rearing periods (p < 0.05). The results of calculations conducted using the concentrations of antibiotics in the water source, pond water, sediment, and feed samples detected in this study indicated that the water source was likely to be the main source of antibiotics in the rearing ponds. This study can provide a better understanding of the spatiotemporal variations and sources of antibiotics in aquaculture.

Detailed characterization, antibiotic resistance and seasonal variation of hospital wastewater

This study investigates the presence of the different classes of micro-pollutants such as pharmaceutical active compounds (PhACs) (20 antibiotics, 8 analgesics and anti-inflammatories, 5 cytostatic agents, 7 β-blockers, 4 lipid regulators, 13 psychiatrics, 1 antidiabetic, 1 receptor antagonist, 1 local anaesthetic, 1 antihypertensive and their 5 metabolites), hormones (8 compounds), X-ray contrast agents (6 compounds), benzotriazoles (3 compounds) and pesticides (6 compounds), and antibiotic resistance in hospital wastewater (HWW) of a medical faculty in Istanbul, Turkey. In addition, the seasonal variations of the selected PhACs and X-ray contrast agents and antibiotic resistance were evaluated for 2 years in a total of eight samples. In the PhACs, sulfamethoxazole and its metabolite (4 N-acethyl-sulfamethoxazole) in the antibiotic group and paracetamol in the analgesic and anti-inflammatory group were found at 100% of frequency and the highest concentrations as 35, 43 and 210 μg/L, respectively. The mean concentrations of psychiatric compounds were found less than 0.25 μg/L except carbamazepine (1.36 μg/L). Bisphenol A in hormone group had the highest concentration up to 14 μg/L. In the hormone group compounds, 17-α-Ethinylestradiol and 17-β-Estradiol were detected at lower mean concentrations of 0.2 and 0.05 μg/L, respectively. 1H-benzotriazole had the highest concentration with the mean concentration of 24.8 μg/L in benzotriazole group compounds. The compounds in X-ray contrast agents group were noted as compounds detected at the highest concentration in HWW up to 3000 μg/L. Antibiotic resistance against azithromycin, clindamycin and trimethoprim-sulfamethoxazole antibiotics was observed around 50% in the winter period. The seasonal variation was detected for the most of the investigated PhACs, especially in antibiotic group which was in line with those significant differences in antibiotic resistance rates in the studied antibiotics between winter and summer seasons.

Nano-Al2O3 can mediate transduction-like transformation of antibiotic resistance genes in water

The prevalence of various antibiotic resistance genes (ARGs) and resistant bacteria has caused global public health risks. The carrier transport mediated by phages or membrane vesicles is an important way for horizontal transfer of ARGs. Nano metal oxide particles (NMOPs), which can enter cell through the cell membrane, may be used as the carriers of genes. However, whether they can be used as transmembrane delivery vectors for the horizontal ARG transfer remains unknown. Here, we set up a model of MONPs-mediated transfer of ARGs, and demonstrate that NMOPs, especially for nano-Al₂O₃, can act as carriers mediating the transduction-like ARG transformation in water. The highest transfer rate mediated by nano-Al₂O₃ is 4.53 × 10⁴ cfu/mmol, and it is 10⁴ times higher than that of control. Nano-Al₂O₃ can combine with plasmid coding for ARGs to form high-density package and prevent ARGs from degradation by endonuclease. The results of superresolution fluorescence microscopy and transmission electron microscopy show that nano-Al₂O₃ can carry ARGs for transmembrane transport. Genome-wide transcription microarray and qPCR indicate that SOS response was closely related to transduction-like ARG transformation mediated by nano-Al₂O₃. This study is the first to demonstrate that as a new transmembrane carrier, nano-Al₂O₃ can also cause ARGs diffusion in water.

Metagenomic analysis of microbiota and antibiotic resistome in household activated carbon drinking water purifiers

Existing drinking water treatment systems have limited ability to control emerging contaminants such as antibiotic resistance genes (ARGs). Household activated carbon water purifiers (HWPs) are convenient measures to assure drinking water quality. However, ARGs distribution in HWPs has not been reported. Here, ARGs, mobile genetic elements (MGEs) and bacteria communities were profiled in tap water (TW), filter water (FW) and activated carbon (AC) biofilm from six kinds of HWPs after 80 days operation, using metagenomics. Results showed that the bacteria community diversities in FW and AC were higher than those in TW. A total of 88, 116 and 80 ARG subtypes were detected in TW, AC and FW, respectively. The AC structure was an important factor influencing the bacterial communities and ARG profiles in FW. The network analysis revealed the co-occurrence patterns between ARGs and bacteria. SourceTracker analyses showed AC biofilms were important contributors of microbes (29-79%) and ARGs (17-53%) in FW. Moreover, MGEs e.g. pBBta01, pMKMS02 and pMFLV01 plasmids, and ISMysp3 had significant co-occurrence patterns with ARGs in the AC biofilms. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.

Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments From Conventional and Organic Livestock Farms

The application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the crop.

Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation

Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and understand the data has limited its adoption at a wider scale. Additionally, the time needed to obtain actionable information is often seen as an impairment for the application and use of the information generated via WGS. Ongoing work towards standardization of wet lab including sequencing protocols, following guidelines from the regulatory authorities and international standardization efforts make the technology more and more accessible. However, data analysis and results interpretation guidelines are still subject to initiatives coming from distinct groups and institutions. There are multiple bioinformatics software and pipelines developed to handle such information. Nevertheless, little consensus exists on a standard way to process the data and interpret the results. Here, we want to present the constraints we face in an industrial setting and the steps we consider necessary to obtain high quality data, reproducible results and a robust interpretation of the obtained information. All of this, in a time frame allowing for data-driven actions supporting factories and their needs.

Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater

The free-floating extracellular DNA (exDNA) fraction of microbial ecosystems harbors antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Natural transformation of these xenogenetic elements can generate microbial cells resistant to one or more antibiotics. Isolating and obtaining a high yield of exDNA is challenging due to its low concentration in wastewater environments. Profiling exDNA is crucial to unravel the ecology of free-floating ARGs and MGEs and their contribution to horizontal genetransfer. We developed a method using chromatography to isolate and enrich exDNA without causing cell lysis from complex wastewater matrices like influent (9 µg exDNA out of 1 L), activated sludge (5.6 µg out of 1 L), and treated effluent (4.3 µg out of 1 L). ARGs and MGEs were metagenomically profiled for both the exDNA and intracellular DNA (iDNA) of activated sludge, and quantified by qPCR in effluent water. qPCR revealed that ARGs and MGEs are more abundant in the iDNA fraction while still significant on exDNA (100-1000 gene copies mL^-1) in effluent water. The metagenome highlighted that exDNA is mainly composed of MGEs (65%). According to their relatively low abundance in the resistome of exDNA, ARGs uptake by natural transformation is likely not the main transfer mechanism. Although ARGs are not highly abundant in exDNA, the prevalence of MGEs in the exDNA fraction can indirectly promote antibiotic resistance development. The combination of this method with functional metagenomics can help to elucidate the transfer and development of resistances in microbial communities. A systematic profiling of the different DNA fractions will foster microbial risk assessments across water systems, supporting water authorities to delineate measures to safeguard environmental and public health.

The combined exposure of microplastics and toxic contaminants in the floodplains of north India: A review

Microplastics in aquatic ecosystem are an emerging environmental threat, primarily aggregating into sediments and living biota besides providing active transportation to toxic pollutants. Recent studies have revealed that a microplastic surface cannot be considered as "inert" and therefore the rate and stage of degradation of microplastic will determine its capability in adsorbing and transporting the solute to longer distances. Our concern is driven by the fact that there has been an absence of widescale research in India despite a country with one of the longest networks of rivers and a 7500 km long active coastline. Anthropogenic pollutants are expected to increase and the situation will further worsen when more persistent organic pollutants (POCs) and geogenic contaminants will find its sink via monsoon runoff. Studies on aquatic species including COD, daphnia magna and zebrafish suggest strong links of bio-accumulation, suspecting to a more serious situation for the coastal India where there is an almost three times increase in the density of the microplastics as the monsoon progresses. Evidences also suggests that microplastics can adsorb known carcinogens as well as endocrine disrupting chemicals leaving our aquatic life exposed to higher mortality. Our review is a first ever scientific attempt in compiling these evidences through researches done in this field to understand the risk that the major floodplains of North India are currently facing. We have adapted the theories and inferences of the available research to predict and postulate a probable mechanism that could explain the severity of the situation in India.

Dry cow therapy and early lactation udder health problems-Associations and risk factors

Mastitis remains the most expensive disease of dairy cows, and antibiotic dry cow therapy (DCT) at dry-off is an important part of mastitis control. Regardless of the infection status, blanket DCT is administered to all quarters of all cows, which is controversial due to the worldwide problem of antimicrobial resistance. Even though selective DCT of only infected cows is a more sustainable approach, choosing animals for treatment is not always straightforward. Our aim was to evaluate whether the herd-level DCT approach is associated with early lactation udder health problems, taking into account the cow characteristics. The information source was 2015-2017 Dairy Herd Improvement data with 7461 multiparous cows from 241 Finnish dairy herds. Information on the herd-level DCT approach was obtained from farmers' questionnaire responses in 2017, and the three different approaches were selective DCT, blanket DCT, and no DCT. The statistical tool for the data analysis was a generalized linear mixed model with a random herd effect for binary outcomes and a linear mixed model with a random herd effect for a continuous outcome. The two binary outcomes were the odds of having high milk somatic cell count (SCC ≥ 200 000 cells/mL) on the first test-day within 5-45 days in milk (DIM) and the odds of mastitis treatment in early lactation up to 45 DIM. The third outcome was the mean milk lnSCC (× 1000 cells/mL) within 120 DIM. Selective DCT was the prevailing treatment practice in our data. Blanket DCT was associated with lower SCC after calving. Cows more likely to have high SCC after calving were older cows, cows with high average SCC during the previous lactation, and cows with high milk yield near dry-off. A mastitis treatment in the early lactation was more likely if, during the previous lactation, the cow had high average SCC, high peak milk production, or high milk yield near dry-off. Our findings indicate that DCT is still effective in mastitis control. Cows with high milk yield, especially near dry-off, and cows with persistently high SCC require attention when considering next lactation udder health.

The effects of synergistic blend of organic acid or antibiotic growth promoter on performance and antimicrobial resistance of bacteria in grow-finish pigs

This study was carried out to evaluate the effect of Selacid Green Growth (GG) or antibiotic growth promoter (AGP) on the performance and economics of grow–finish (GF) pigs. The Selacid GG is a blend of short-chain fatty acids (formic acid, acetic acid, lactic acid, propionic acid, citric acid, and sorbic acid), buffered organic acid (ammonium formate), and a combination of medium-chain fatty acids (C8, C10, and C12). A total of 312 grower pigs (Yorkshire × Landrace × Duroc) with initial body weight (BW) of 26.5 ± 0.92 kg were used in a 90-d feeding trial. The pigs were allocated randomly to three treatments consisting of eight replicate pens with 13 pigs each. The treatments tested included a 1) negative control (control): basal diet without colistin and Selacid GG, 2) positive control (AGP): basal diet with colistin (20 g/ton), and 3) Feed additive (Selacid GG): basal diet with Selacid GG (2 kg/ton). The results showed that, over the entire period of the experiment, the dietary supplementation of Selacid GG elicited a similar effect as AGP on feed cost and on all growth parameters measured (P > 0.05). In relation to the control group, Selacid GG significantly improved the final BW (+3.4 kg or 3.6%), average daily gain (+39 g/pig or 5.3%), and gain:feed (+30 g or 8.1%) of pigs (P < 0.05). In addition, the feeding of Selacid GG reduced feed cost (−0.078 USD) per kilogram BW gain. The average daily feed intake was not affected by dietary treatments (P > 0.05). Escherichia coli was prevalent in 46 out of 48 fecal samples tested. All E. coli isolates were resistant to colistin, amox-colistin, ciprofloxacin, and enrofloxacin. The number of E. coli isolates resistant to amoxicillin/clavulanic, cefotaxime, ceftiofur, and norfloxacin was significantly reduced, whereas the inhibitory zones of amocxillin/clavulanic acid were increased; and the susceptibility of E. coli to amoxcillin/clavulanic, cefotaxime, ceftiofur, ciprofloxacin, nofloxacin, and flumequin was increased when Selacid GG was added in the feeds (P < 0.05). The findings of the study suggest that Selacid GG is a cost-effective product with the same efficacy as AGP in promoting the growth and economic performance of GF pigs. The product is safe and can be added to the diet of GF pigs without developing resistance to selected antibiotics.

Role prediction of Gram-negative species in the resistome of raw cow's milk

Extended use of antibiotics in dairy farming for therapeutic and prophylactic reasons, but also the higher prevalence of antibiotic resistant bacteria (ARB) in the farm environment raised the concern of consuming raw cow's milk and its derived products. The aim of this study was to predict by shotgun metagenomic analyses the presence of antibiotic resistance genes (ARGs) mainly correlated with Gram-negative bacteria in antibiotic residue free raw cow's milk derived exclusively from healthy animal from South Tyrol (Northern Italy), chosen as a model system. Assessment of shotgun metagenomic data of reconstructed scaffolds, revealed the existence of Pseudomonas spp. as the most abundant Gram-negative species in the raw cow's milk samples bearing ARGs. Besides, ARGs also linked to lactic acid bacteria such as Lactococcus sp. and Lactobacillus sp. ARGs correlated to microbiome found in milk samples conferred resistance towards aminoglycoside-streptothricin, beta-lactamase, macrolide, tetracycline, carbapenem, cephalosporin, penam, peptide, penem, fluoroquinolone, chloramphenicol and elfamycin antibiotics. Further bioinformatic processing included de-novo reassembly of all metagenomic sequences from all milk samples in one, to reconstruct metagenome assembled genomes (MAGs), which were further used to investigate mobile genetic elements (MGE). Analyses of the reconstructed MAGs showed that, MAG 9 (Pseudomonas sp1.) contained the oriT gene (origin of transfer gene) needed for transferring virulent factors. Although the presence of Pseudomonas is common in raw cow's milk, pasteurization treatment reduces their survivability. Nevertheless, attention should be paid on Pseudomonas spp. due to their intrinsic resistance to antibiotics and their capability of transferring virulent factors to other bacteria.