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

Antimicrobial resins with quaternary ammonium salts as a supplement to combat the antibiotic resistome in drinking water treatment plants

The increasing finding of pathogens and antibiotic resistance genes (ARGs) in drinking water has become one of the most challenging global health threats worldwide. However, conventional disinfection strategies in drinking water treatment plants (DWTPs) require further optimization in combating the antibiotic resistome. Here, we show that antimicrobial resins with quaternary ammonium salts (AMRs-QAS) exhibit great potentials in diminishing specific potential pathogens that relatively resist chlorine or UV disinfection in DWTPs, and comprehensive analyses using microscopy and fluorescence techniques revealed that the antimicrobial capacity of AMRs-QAS mainly proceed via the bacterial adsorption and cell membrane dissociation. Moreover, a total of 15 among 30 selected ARGs, as well as 4 selected potential pathogens including Pseudomonas aeruginosa, Bacillus subtilis, Escherichia coli and Staphylococcus aureus were all detected in the source water. Coupling the AMRs-QAS with 0.2 mg/L chlorine resulted in higher removal efficiencies than chlorination (2 mg/L) or UV disinfection (400 mJ cm^-2) for all the detected pathogens and ARGs in drinking water and significantly decreased the relative abundances of Pseudomonas aeruginosa, Bacillus subtilis, Escherichia coli, as well as all the detected ARGs (p < 0.05). Co-occurrences of pathogens and ARGs were revealed by a correlation network and possibly accounts for the ARGs removal. This coupled disinfection strategy overcomes the limitations of individual disinfection methods, i.e. the enrichment of specific pathogens and ARGs among bacterial populations, and provides an alternative for minimizing health risks induced by the antibiotic resistome in DWTPs.

Fate of two strains of extended-spectrum beta-lactamase producing Escherichia coli in constructed wetland microcosm sediments: survival and change in antibiotic resistance profiles

Free water surface constructed wetlands (FWS CW) are efficient technologies to limit the transfer of antibiotic resistant bacteria (ARB) originating from urban effluents into the aquatic environment. However, the decrease in ARB from inflow to outflow through the FWS CW may be explained by their transfer from the water body to the sediment. To investigate the behavior of ARB in the sediment of a FWS CW, we inoculated three microcosms with two strains of extended-spectrum beta-lactamase producing Escherichia coli (ESBL E. coli) belonging to two genotypes. Microcosms were composed of two sediments collected at two locations of an FWS CW from which the strains were isolated. Phragmites were planted in one of the microcosms. The survival curves of the two strains were close regardless of the genotype and the type of sediment. After a rapid decline, both strains were able to survive at low level in the sediments for 50 days. Their fate was not affected by the presence of phragmites. Changes in the bla content and antibiotic resistance of the inoculated strains were observed after three weeks of incubation, indicating that FWS CW sediments are favorable environments for spread of antibiotic resistance genes and for the acquisition of new antibiotic resistance.

Environmental pharmacology: source, impact and solution

Environmental pharmacology is the knowledge, study and the methods implemented for amalgamating the presence of pharmaceutical products and their metabolites in the environment. Pharmaceutical and house care products and their metabolites gain access to the environment through various means and affect the flora and fauna and modulate the ecosystem. The effect on wildlife, biofilms and human are being studied to gain knowledge of sources and causations. Potential risks of development of acute and chronic toxicity, carcinogenicity, interference with hormone and immune systems and drug resistance are of major concern. They may alter the genome and can affect future generations leaving them vulnerable to disease. There are regulations in good manufacturing practices and disposal which take into account the environmental risks but the knowledge for stakeholders and their implementation is very restricted. Ecopharmacology and ecopharmacovigilance are propagators of green healthcare. A strategy towards human health risk assessment and ecotoxicological hazard evaluation must be developed and risk minimization measures to be sought for and applied.

Policy options for reducing antibiotics and antibiotic-resistant genes in the environment

Responses to the threat posed by antimicrobial resistance have been inadequate. Most attention has focused on the emergence of resistant organisms in human medicine and in agriculture. Much less attention has been given to antibiotic contamination of the environment. To assist health advocates to engage with this issue, we review the evidence on the role of agriculture, aquaculture, domestic waste and pharmaceutical manufacturing in the spread of antibiotic resistance, concluding that all of these activities pose a potentially serious threat. We then examine ways that this threat might be mitigated by specific measures, such as improved wastewater treatment processes, reduction of manufacturing emissions, consideration of environmental impacts in procurement and drug approval decisions, and better manure management. We conclude by placing this problem within the growing literature on commercial determinants of health, stressing the need for effective legislation and regulation developed independent of vested interests.

The enzyme toilet rim block 'pCure' does not efficiently remove drug residues in a hospital setting - exemplifying the importance of on-site implementation testing

Introduction: Negative environmental effects of active pharmaceutical ingredients (APIs) are increasingly recognized, especially concerning antibiotics, and hospitals are important point sources. “pCure” is a toilet rim block containing API-degrading enzymes; the producing company claims positive in vitro results but no implementation studies have been performed. Materials and methods: In a university hospital setting, 16 weeks were randomized to installation or no installation of pCure in all 261 toilets connected to the same cesspit where sewage water was sampled daily. Ninety-six samples were analyzed for 102 APIs using liquid chromatography/tandem mass spectrometry. Results and Discussion: Fifty-one APIs were detected with a large variation in levels but no significant differences in the initial statistical analysis. More statistical testing of API level ratios (pCure installed/not installed) yielded some cases of significant decrease. Differences were small and not consistent when comparing means and medians. We cannot exclude a small pCure effect but clearly pCure has no effect of biological importance. Conclusion: pCure is not useful to reduce drug residue discharge in a hospital setting. In a bigger perspective, our study exemplifies that products claiming to reduce an environmental problem need to be tested in on-site implementation studies by independent researchers before reaching the market.

Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance

Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms.

Characterization of antibiotic resistance genes in the sediments of an urban river revealed by comparative metagenomics analysis

The over-use of antibiotics causes growing concerns about human health risks induced by increasing rates of antimicrobial resistance. Riverine systems are considered generally as a natural reservoir of antibiotic resistance genes (ARGs). In this study, several methods including high-throughput sequencing-based metagenomics approach, statistical analysis and network analysis were applied jointly to characterize the wide-spectrum profile of ARGs in the sediments of an urban river in Beijing. Furthermore, contribution of human activities for the presence of ARGs was identified through comparative studies on the metagenomic profiling of ARGs between the river sediments and pristine niches (remote Antarctic soils and deep sea sediments). In total, 442 ARG subtypes belonging to 22 ARG types were detected in the human-impacted river sediments with an abundance range of 1.1 × 10^-1-8.1 × 10^-1 copy of ARG per copy of 16S-rRNA gene. The most abundant and diverse ARGs were commonly associated with antibiotics that have been extensively used in that area, likely indicating the spread of ARGs in river environments because of the selective pressure resulting from antibiotic use. As a whole, anthropogenic activities were the dominant contributor of major ARG types, for example, occupying 100% for sulfonamide-ARGs, 97% for beta-lactam-ARGs, 94% for aminoglycoside-ARGs and 64% for tetracycline-ARGs. This study provides insights into the role of human activities in accelerating the dissemination and proliferation of ARGs in urban river environment and draws attention to controlling the use and discharge of antibiotics for protection of public health.

Prevalence and distribution of antibiotic resistance in marine fish farming areas in Hainan, China

Antibiotic resistance represents a global health crisis for humans, animals, and for the environment. Transmission of antibiotic resistance through environmental pathways is a cause of concern. In this study, quantitative PCR and culture-dependent bacteriological methods were used to detect the abundance of antibiotic resistance genes (ARGs) and the quantity of culturable heterotrophic antibiotic-resistant bacteria (ARB) in marine fish farming areas. The results indicated that sul and tet family genes were widely distributed in marine fish farming areas of Hainan during both rearing and harvesting periods. Specifically, sul1 and tetB were the most dominant ARGs. The total abundance of ARGs increased significantly from the rearing to the harvesting period. A total of 715 ARB strains were classified into 24 genera, within these genera Vibrio, Acinetobacter, Pseudoalteromonas, and Alteromonas are opportunistic pathogens. High bacterial resistance rate to oxytetracycline (OT) was observed. The numbers of OT- and enrofloxacin-resistant bacteria dropped significantly from rearing the period to the harvesting. The co-occurrence pattern showed that Ruegeria and tetB could be indicators of ARB and ARGs, respectively, which were found in the same module. Redundancy analysis indicated that salinity was positively correlated with the most dominant ARB, and was negatively correlated with the most dominant ARGs. These findings demonstrated the prevalence and persistence of ARGs and ARB in marine fish farming areas in China.

Antibiotic resistance in grass and soil

Antibiotic resistance is currently one of the greatest threats to human health. The global overuse of antibiotics in human medicine and in agriculture has resulted in the proliferation and dissemination of a multitude of antibiotic resistance genes (ARGs). Despite a large proportion of antibiotics being used in agriculture, little is understood about how this may contribute to the overall antibiotic resistance crisis. The use of manure in agriculture is a traditional and widespread practice and is essential for returning nutrients to the soil; however, the impact of continuous manure application on the environmental microbiome and resistome is unknown. The use of antibiotics in animal husbandry in therapeutic and sub-therapeutic doses creates a selective pressure for ARGs in the gut microbiome of the animal, which is then excreted in the faeces. Therefore, the application of manure to agricultural land is a potential route for the transmission of antibiotic-resistant bacteria from livestock to crops, animals and humans. It is of vital importance to understand the mechanisms behind ARG enrichment and its maintenance both on the plant and within the soil microbiome to mitigate the spread of this resistance to animals and humans. Understanding this link between human health, animal health, plant health and the environment is crucial to inform implementation of new regulations and practice regarding antibiotic use in agriculture and manure application, aimed at ensuring the antibiotic resistance crisis is not aggravated.

The impact of municipal sewage sludge stabilization processes on the abundance, field persistence, and transmission of antibiotic resistant bacteria and antibiotic resistance genes to vegetables at harvest

Biosolids were obtained from four Ontario municipalities that vary in how the sewage sludge is treated. These included a Class B biosolids that was anaerobically digested, a Class A biosolids that were heat treated and pelletized (Propell), and two Class A biosolids that were stabilized using either the N-Viro (N-Rich) or Lystek (LysteGro) processes. Viable enteric indicator or pathogenic bacteria in the biosolids were enumerated by plate count, gene targets associated with antibiotic resistance or horizontal gene transfer were detected by PCR, and a subset of these gene targets were quantified by qPCR. Following application at commercial rates to field plots, the persistence of enteric bacteria and gene targets in soil was followed during the growing season. Carrots, radishes and lettuce were sown into the amended and unamended control plots, and the diversity and abundance of gene targets they carried at harvest determined. All three Class A biosolids carried fewer and less abundant antibiotic resistance genes than did the Class B biosolids, in particular the very alkaline N-Viro product (N-Rich). Following application, some gene targets (e.g. int1, sul1, strA/B, aadA) that are typically associated with mobile gene cassettes remained detectable throughout the growing season, whereas others (e.g. ermB, ermF, bla_OXA20) that are not associated with cassettes became undetectable within three weeks or less. At harvest a larger number of gene targets were detected on the carrots and radishes than in the lettuce. Overall, land application of Class A biosolids will entrain fewer viable bacteria and genes associated with antibiotic resistance into crop ground than will amendment with Class B biosolids.

Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater

With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move toward standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit and ZR Fecal DNA MiniPrep), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA. Annotated sequences obtained from the DNA extracted using the three kits shared similar taxonomy and ARG profiles. Overall, it was found that the DNA yield and purity, and diversity of ARGs captured were all highest when applying the FastDNA SPIN Kit for Soil for all three WWTP sample types investigated here (influent, activated sludge, effluent). Quantitative polymerase chain reaction of 16S rRNA genes confirmed the same trend as DNA extraction yields and similar recovery of a representative Gram-negative bacterium (Escherichia coli). Moreover, sample fixation in ethanol, deep-freezing and overseas shipment had no discernable effect on ARG profiles, as compared to fresh samples. This approach serves to inform future efforts toward global comparisons of ARG distributions in WWTPs.

High Prevalence of Cefotaxime Resistant Bacteria in Grazing Beef Cattle: A Cross Sectional Study

Although the over-use of antibiotics during food animal production is a potential driver of antimicrobial resistant microorganisms (ARMs), a high prevalence of cefotaxime resistant bacteria (CRB) has been observed in grazing animals raised without antibiotic supplementation. In this cross-sectional study, the prevalence and concentration of CRB in beef cattle on grazing farms were investigated. Fecal samples from the recto-anal junction of cattle (n = 840) and environmental samples (n = 258) were collected from 17 farms in North and Central Florida in the United States, and a survey of farm characteristics, animal husbandry practices, and antibiotic usage was conducted. CRB were detected in fecal samples from 47.4% of all cattle, with the prevalence ranging from 21.1 to 87.5% on farms, and significantly higher (P < 0.001) in calves compared to adult cows (54.1 vs. 41.8%). Environmental samples had a higher prevalence than fecal samples (P < 0.001), with CRB detected in 88.6% of water, 98.7% of soil, and 95.7% of forage samples. Compared to the concentration (log CFU/g) of CRB in fecal samples (2.95, 95% CI: 2.89, 3.02), the concentration of CRB was higher (P < 0.001) in soil and forage samples (5.37, 95% CI: 5.16, 5.57) and lower (P < 0.001) in water samples (1.08, 95% CI: 0.82, 1.36). Soil microbiota from farms with high prevalence of CRB clustered closer together and the proportion of Phylum Proteobacteria was higher on farms with high prevalence of CRB resistance. Large farming operations were associated with a 58% higher likelihood of CRB detection in fecal samples. Regular cleaning of drinking troughs and the addition of ionophores to feed were associated with CRB reduction in fecal samples. Taken together, the widespread of CRB into both cattle seldom treated with cephalosporin antibiotics and the surrounding environment suggests the environment is a natural source of antimicrobial resistance in beef cattle.

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer

The composting of fresh manure is an effective way to inactivate pathogens and reduce the levels of antibiotics and some antibiotic resistance genes (ARGs) prior to its application on agricultural land as organic fertilizer. However, some ARGs could still exist and even be enriched after composting. This study investigated whether converting composted pig manure into biochar could reduce the dissemination of ARGs into the soil in comparison with a compost amendment. We performed a pot experiment using pakchoi (Brassica chinensis), with two pig manure-based composts and the biochar derived from composted pig manure, as organic fertilizers. The distributions of the antibiotic resistome, mobile genetic elements (MGEs) and bacterial community composition in soils during cultivation were evaluated by high-throughput qPCR and Illumina sequencing. The total ARGs and MGEs abundance in the biochar-treated soils were significantly lower than those in the compost-amended soils during cultivation. The total ARGs abundance in the biochar-amended soils was similar to that in the control soils during cultivation. Thus, the dissemination of ARGs from animal waste to the environment can be effectively mitigated by converting manure into biochar.

Effectiveness of zinc oxide-assisted photocatalysis for concerned constituents in reclaimed wastewater: 1,4-Dioxane, trihalomethanes, antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs)

Microbial and emerging chemical contaminants are unwanted constituents in reclaimed wastewater, due to the health concerns of using the water for agricultural irrigation, aquifer recharges, and potable water. Removal of these contaminants is required but it is currently challenging, given that there is no simple treatment technology to effectively remove the mixture of these contaminants. This study examined the effectiveness of ZnO-assisted photocatalytic degradation of several constituents, including 1,4-dioxane, trihalomethanes (THMs), triclosan (TCS), triclocarban (TCC), antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), under low intensity of UV exposure. E. coli with an ARGs-carrying circular plasmid (pUC19) was used as a model antibiotic resistant bacterium. Our results show that commercial zinc oxide (C-ZnO) assisted photodegradation of 1,4-dioxane, and dehalogenation of THMs, TCS, and TCC, while tetrapodal zinc oxide (T-ZnO) enhanced the dehalogenation of TCS and TCC. Additionally, T-ZnO assisted the photocatalytic inactivation of the E. coli within 6 h and caused structural changes in the plasmid DNA (pUC19) with additional UV exposure, resulting in non-functional AGR-containing plasmids. These results also suggest that higher UV dose is required not only to inactivate ARB but also to damage ARGs in the ARB in order to decrease risks in promoting ARB population in the environment. Overall, our results implicated that, under low UV intensity, ZnO-assisted photocatalysis is a promising alternative to simultaneously remove biological and emerging chemical contaminants in treated wastewater for safe reuse.

Occurrence of enterococci harbouring clinically important antibiotic resistance genes in the aquatic environment in Gauteng, South Africa

The development of antibiotic resistance and dissemination of its determinants is an emerging public health problem as it compromises treatment options of infections that were, until recently, treatable. Investigation of outbreaks of vancomycin resistant enterococci (VRE) suggests that the environment serves as a significant reservoir for antibiotic resistance genes (ARGs). However, there is a paucity of data regarding the presence of ARGs in the water sources in South Africa. In this study, water samples collected from wastewater treatment plants (WWTPs), surface water and hospital sewage were screened for enterococci harbouring genes conferring resistance to four classes of antibiotics. Enterococci isolates harbouring ARGs were detected in raw influent and treated wastewater discharge from WWTPs and hospital sewage water. Plasmid and transposon encoded ermB (macrolide), tetM and tetL (tetracycline) as well as aph(3')-IIIa (aminoglycosides) genes were frequently detected among the isolates, especially in E. faecalis. The presence of enterococci harbouring ARGs in the treated wastewater suggest that ARGs are discharged into the environment where their proliferation could be perpetuated. Among the enterococci clonal complexes (CCs) recovered from wastewater were E. faecium CC17 (ST18), which is frequently associated with hospital outbreaks and a novel E. faecalis sequence type (ST), ST780.

A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: Application to an urban river in Beijing

River is considered generally as a natural reservoir of antibiotic resistance genes (ARGs) in environments. For the prevention and control of ARG risks, it is critical to comprehensively characterize the antibiotic resistomes and their associations in riverine systems. In this study, we proposed a metagenomic framework for identifying antibiotic resistomes in river sediments from multiple categories, including ARG potential, ARG hosts, pathogenicity potential, co-selection potential and gene transfer potential, and applied it to understand the presence, hosts, and co-occurrence of ARGs in the sediments of an urban river in Beijing. Results showed that a total of 203 ARG subtypes belonging to 21 ARG types were detected in the river sediments with an abundance range of 107.7-1004.1×/Gb, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone and sulfonamide resistance genes. Host-tracking analysis identified Dechloromonas, Pseudoxanthomonas, Arenimonas, Lysobacter and Pseudomonas as the major hosts of ARGs. A number of ARG-carrying contigs (ACCs) were annotated as fragments of pathogenic bacteria and carried multiple multidrug-ARGs. In addition, various biocide/metal resistance genes (B/MRGs) and mobile genetic elements (MGEs), including prophages, plasmids, integrons and transposons, were detected in the river sediments. More importantly, the co-occurrence analysis via ACCs showed a strong association of ARGs with B/MRGs and MGEs, indicating high potential of co-selection and active horizontal transmission for ARGs in the river environment, likely driven by the frequent impact of anthropogenic activities in that area.

Bacteria and Antibiotic Resistance Genes (ARGs) in PM2.5 from China: Implications for Human Exposure

Airborne transmission is one of the environmental dissemination pathways of antibiotic resistance genes (ARGs), and has critical implications for human exposure through inhalation. In this study, we focused on three regions of China to reveal some unique spatiotemporal features of airborne bacteria and ARGs in fine aerosols (PM_2.5): (1) greater seasonal variations in the abundance of bacteria and ARGs in temperate urban Beijing than in the subtropical urban areas of the Yangtze River Delta (YRD) and Pearl River Delta (PRD) regions, with regional disparities in bacterial communities; (2) geographical fingerprints of ARG profiles independent of seasonal cycles and land-use gradients within each region; (3) region-independent associations between the targeted ARGs and limited bacterial genera; (4) common correlations between ARGs and mobile genetic elements (MGEs) across regions; and (5) PM_2.5 at the higher end of ARG enrichment across various environmental and human media. The spatiotemporally differentiated bacterial communities and ARG abundances, and the compositions, mobility, and potential hosts of ARGs in the atmosphere have strong implications for human inhalational exposure over spatiotemporal scales. By comparing other contributing pathways for the intake of ARGs (e.g., drinking water and food ingestion) in China and the U.S.A., we identified the region-specific importance of inhalation in China as well as country-specific exposure scenarios. Our study thus highlights the significance of inhalation as an integral part of the aggregate exposure pathways of environmentally disseminated ARGs, which, in turn, may help in the formulation of adaptive strategies to mitigate the exposure risks in China and beyond.

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.

Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities

The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.

Abundances of Tetracycline Resistance Genes and Tetracycline Antibiotics during Anaerobic Digestion of Swine Waste

The impact of anaerobic digestion of animal waste on the persistence of antibiotic resistance genes (ARGs) and antibiotics is not widely studied. Two identical, 800-L digesters seeded with swine slurry were followed up to 100 d in three separate trials. The trials received varying amounts of antibiotic-free corn ( L.) mixed with water to maintain the digestion process. Biogas production, seven tetracycline resistance () genes, and three tetracyclines and their transformation products were measured. Biogas production proportionally increased as the feeding loads increased between trials. In Trial 1, log gene copies showed small but statistically significant ( < 0.01) increases during digestion. In Trial 2, anaerobic digestion did not have a significant ( > 0.05) effect except for significant reductions in B ( < 0.0001) and G ( = 0.0335) log gene copies. In Trial 3, which received the highest amount of corn mix, log copies of the 16S ribosomal RNA and the genes significantly ( < 0.0001) reduced over time during digestion. Up to 36 μg L tetracycline, 112 μg L chlortetracycline, 11.9 mg L isochlortetracycline, and 30 μg L 4-epitetracycline were detected both in the liquid and solid digestates. Results of this study revealed that although anaerobic digestion of swine waste can produce useful biogas, it does not result in complete removal of bacteria, ARGs, and antibiotics regardless of differences in the feeding loads between trials. Further effluent and sludge treatments are required prior to their downstream use in crop production to minimize emergence and environmental dissemination of antimicrobial-resistant bacteria through animal manure.

Inactivation of antibiotic-resistant bacteria by chlorine dioxide in soil and shifts in community composition

Antibiotic-resistant bacteria are common widespread in soil and the most resistant species isStaphylococcus aureus.Sphingomonas,ArthrobacterandMassiliaare sensitive to ClO₂.MicromonosporaceaeandThaumarchaeotaare more resistant to ClO₂.

Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: An emerging health threat

Misuse/over use of antibiotics increases the threats to human health since this is a main reason behind evolution of antibiotic resistant bacterial pathogens. However, metals such as mercury, lead, zinc, copper and cadmium are accumulating to critical concentration in the environment and triggering co-selection of antibiotic resistance in bacteria. The co-selection of metal driven antibiotic resistance in bacteria is achieved through co-resistance or cross resistance. Metal driven antibiotic resistant determinants evolved in bacteria and present on same mobile genetic elements are horizontally transferred to distantly related bacterial human pathogens. Additionally, in marine environment persistent pollutants like microplastics is recognized as a vector for the proliferation of metal/antibiotics and human pathogens. Recently published research confirmed that horizontal gene transfer between phylogenetically distinct microbes present on microplastics is much faster than free living microbes. Therefore, microplastics act as an emerging hotspot for metal driven co-selection of multidrug resistant human pathogens and pose serious threat to humans which do recreational activities in marine environment and ingest marine derived foods. Therefore, marine environment co-polluted with metal, antibiotics, human pathogens and microplastics pose an emerging health threat globally.

Evaluation of antibiotic resistant lactose fermentative opportunistic pathogenic Enterobacteriaceae bacteria and blaTEM-2 gene in cephalosporin wastewater and its discharge receiving river

This study investigated the concentration of cephalosporin, the resistant levels of lactose fermentative opportunistic pathogenic Enterobacteriaceae bacteria (LFOPEB) against seven antibiotics and one cephalosporin-resistant gene in cephalosporin wastewater (CPWW) treatment plant and its discharge receiving river. Although large numbers of bacteria have been removed during the CPWW treatment process, the antibiotic resistant rates of the isolates to β-lactam antibiotics significantly increased (p = 0.032) after treatment, while the percentage of resistant LFOPEB to non-β-lactam antibiotics did not change dramatically. Furthermore, the discharge of the effluent of CPWW treatment plant (CPWW_eff) led to an obvious increase in the percentages of β-lactam antibiotic-resistant LFOPEB and relative abundance of the blaTEM-2 gene in the downstream receiving river (RW_down) in comparison with those in the upstream receiving river (RW_up). The antibiotic resistant phenotypes of isolates in the influent of CPWW treatment plant (CPWW_in), CPWW_eff and RW_down appeared to be seriously affected by the cephalosporin residues, which suggested that main antibiotic resistance phenotypes in antibiotic contaminated water were closely associated with its antibiotic composition. Therefore, CPWW treatment process has been proved to result in selective growth of ARB and proliferation of ARG. Besides, CPWW_eff was also proved to be an important supplier of ARB and ARG to the receiving river.

U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids

Ten infrequently monitored antibiotics in biosolids were examined in archived American sewage sludges (n = 79) collected as part of the 2006/2007 U.S. Environmental Protection Agency (EPA) Targeted National Sewage Sludge Survey. This study inspected the occurrence of amoxicillin, ampicillin, erythromycin, furazolidone [proxy metabolite: 3-(2-nitrobenzylidenamino)-2-oxazolidinone (NP-AOZ)], nalidixic acid, oxolinic acid, oxytetracycline, spiramycin, sulfadimidine, and sulfadimethoxine in sewage sludges after nearly a decade in frozen storage. Six antibiotics were detected at the following average concentrations (ng/g dry weight): amoxicillin (1.0), nalidixic acid (19.1), oxolinic acid (2.7), erythromycin (0.6), oxytetracycline (4.5), and ampicillin (14.8). The remaining four were not detected in any samples (<method detection limit, ng/g dry weight): sulfadimethoxine (<0.5), sulfadimidine (<1.0), spiramycin (<2.0), and NP-AOZ (<20.0). This study provides the first data on spiramycin, NP-AOZ, and nalidixic acid in U.S. sewage sludges. This study also provides new data on the losses of 5 antibiotics during long term frozen storage (-20 °C) in comparison to the 2006/2007 U.S. EPA Targeted National Sewage Sludge Survey.

High abundances of class 1 integrase and sulfonamide resistance genes, and characterisation of class 1 integron gene cassettes in four urban wetlands in Nigeria

There is little information about environmental contamination with antibiotic resistance genes (ARG) in Sub-Saharan Africa, home to about 1 billion people. In this study we measured the abundance of three genes (sul1, sul2, and intI1) used as indicators of environmental contamination with ARGs in the sediments of four urban wetlands in southwestern Nigeria by qPCR. In addition, we characterised the variable regions of class 1 integrons in sulfamethoxazole/trimethoprim (SMX/TRI)-resistant bacteria isolated from the wetlands by PCR and DNA sequencing. The indicator ARGs were present in all wetlands with mean absolute copy numbers/gram of sediment ranging between 4.7x106 and 1.2x108 for sul1, 1.1x107 and 1x108 for sul2, and 5.3x105 and 1.9x107 for intI1. The relative abundances (ARG/16S rRNA copy number) ranged from about 10-3 to 10-1. These levels of ARG contamination were similar to those previously reported for polluted environments in other parts of the world. The integrase genes intI1 and intI2 were detected in 72% and 11.4% SMX/TRI-resistant isolates, respectively. Five different cassette array types (dfrA7; aadA2; aadA1|dfrA1; acc(6')lb-cr|arr3|dfrA27; arr3|acc(6')lb-cr|dfrA27) were detected among 34 (59.6%) intI1-positive isolates. No gene cassettes were found in the nine intI2-positive isolates. These results show that African urban ecosystems impacted by anthropogenic activities are reservoirs of bacteria harbouring transferable ARG.

A novel microfluidic system enables visualization and analysis of antibiotic resistance gene transfer to activated sludge bacteria in biofilm

Antibiotic resistance genes (ARGs) in environment have become a growing public concern, due to their potential to be obtained by pathogens and their duplication along cell division. Horizontal gene transfer (HGT) was reported to be responsible for ARGs dissemination in microbes, but the HGT feature in environmental biofilm was still unclear due to insufficient assay tools. To address this challenge, we applied a novel microfluidic system to cultivate thin biofilm by continuous supply of nutrients and close contact between cells. Resembling the living state of biofilm in open environment, this chip visualized the transfer of ARG-encoded plasmids RP4 and pKJK5 to the receptors, e.g., activated sludge bacteria. The average plasmid transfer frequency per receptor (T/R) from RP4-hosted Pseudomonas putida KT2440 to activated sludge bacteria was quantified to be 2.5 × 10^-3 via flow cytometry, and T/R for pKJK5-hosted Escherichia coli MG1655 was 8.9 × 10^-3, while the corresponding average frequencies per donor (T/D) were diverse for the two host strains as 4.3 × 10^-3 and 1.4 × 10^-1 respectively. The difference between T/R and T/D was explained by the plasmid transfer kinetics, implying specific purposes of the two calculations. Finally, we collected the transconjugants by fluorescent activated cell sorting and further sequenced their 16S rDNA. Bacteria from phyla Proteobacteria and Firmicutes were found more susceptible to be transconjugants than those from Bacteroidetes. Our work demonstrated that microfluidic system was advantageous in biofilm HGT study, which can provide more insights into environmental ARG control.

blaNDM-1-producing Vibrio parahaemolyticus and V. vulnificus isolated from recreational beaches in Lagos, Nigeria

Twenty-six strains of Vibrio parahaemolyticus and 14 strains of V. vulnificus isolated from selected beaches in Lagos State, Nigeria, were examined for virulence and antimicrobial resistance genes. The V. parahaemolyticus isolates were further serotyped and subjected to pulsed field gel electrophoresis (PFGE). Five strains of V. vulnificus and one of V. parahaemolyticus carried the New Delhi-metallo-beta-lactamase gene bla_NDM-1, seven strains carried bla_TEM, and four strains of V. vulnificus and one of V. parahaemolyticus carried bla_CMY. Real-time PCR assay for detection of virulence genes tdh and trh in the V. parahaemolyticus isolates showed that five isolates were positive for tdh, two for trh, and one isolate carried both genes. Ten V. parahaemolyticus serogroups and 23 pulsotypes were identified from 26 isolates based on O and K antigens typing and PFGE. Five of the isolates belong to the pandemic strains O1:Kut and O3:K6, and three belonged to the highly virulent O4:Kut serotype. Nineteen of the isolates showed distinct PFGE banding patterns. These results highlighted the importance of Nigerian recreational beaches as reservoirs of antimicrobial resistance genes of global public health interest, such as bla_NDM-1.

Evaluation of the leaching of florfenicol from coated medicated fish feed into water

Florfenicol is one of the most-used antimicrobial agents in global fish farming. Nevertheless, in most countries, its use is not conducted in accordance with good practices. The aim of this work was to evaluate the leaching of florfenicol from coated fish feed into the water. Analytical methods were developed and validated for the quantitation of florfenicol in medicated feed and water by UHPLC-MS/MS. Florfenicol residues in the water were quantified after 5- and 15-min exposures of the medicated feed in the water at 22 and 28 °C and at pH 4.5 and 8.0. The influence of pellet size and three coating agents (vegetable oil, carboxymethylcellulose, and low-methoxylated pectin) on the leaching of the drug was also assessed. Pellet size, coating agent, water temperature, and time of exposure significantly (p < 0.05) affected florfenicol leaching, while water pH did not interfere with the leaching. Coating with vegetable oil was the most efficient method to reduce florfenicol leaching, while coating with carboxymethylcellulose presented the highest leaching (approximately 60% after 15 min at 28 °C). Thus, the coating agent has a significant effect on the florfenicol leaching rate and, consequently, on the necessary dose of the drug to be administered. Moreover, it is worth mentioning that higher florfenicol leaching will pose a greater risk to environmental health, specifically in terms of the development of bacteria resistant to florfenicol. Additional studies are needed with other polymers and veterinary drugs used in medicated feed for fish farming.

Changes of Antibiotic Resistance Phenotype in Outbreak-Linked Salmonella enterica Strains after Exposure to Human Simulated Gastrointestinal Conditions in Chicken Meat

Fifteen outbreak-linked Salmonella enterica strains in chicken meat were evaluated under simulated human gastrointestinal conditions for their resistance and susceptibility to 11 antibiotics from seven antibiotic classes. The MIC of each antibiotic was determined by microdilution in broth before and after the exposure of each strain to a continuous system simulating the conditions in the human mouth, esophagus-stomach, duodenum, and ileum. Strains were inoculated onto chicken breast (9 g; inoculated at 5 log CFU/g) prior to exposure. Data were interpreted according Clinical and Laboratory Standards Institute breakpoints. After the in vitro digestion, 12 Salmonella strains with reduced susceptibility to ciprofloxacin (CIP) changed to CIP resistant. The ceftriaxone (CTX)-intermediate Salmonella Newport strain changed to CTX resistant. The ampicillin (AMP)-susceptible Salmonella Heidelberg strain changed to AMP resistant, and the sulfamethoxazole-trimethoprim (SXT)-susceptible strains of Salmonella serovars Typhimurium, Agona, Newport, Albany, and Corvallis changed to SXT resistant. The Salmonella Heidelberg, Salmonella Newport, Salmonella Albany, and Salmonella Corvallis strains had the highest frequency of changes in antibiotic susceptibility with new resistant phenotypes to AMP and CIP, CTX and SXT, CIP and SXT, and CIP and SXT, respectively. Conditions imposed by a simulated gastrointestinal environment changed the susceptibility of S. enterica strains to clinically relevant antibiotics and should be considered in the selection of therapies for human salmonellosis.

Reservoirs and Transmission Pathways of Resistant Indicator Bacteria in the Biotope Pig Stable and along the Food Chain: A Review from a One Health Perspective

The holistic approach of “One Health” includes the consideration of possible links between animals, humans, and the environment. In this review, an effort was made to highlight knowledge gaps and various factors that contribute to the transmission of antibiotic-resistant bacteria between these three reservoirs. Due to the broad scope of this topic, we focused on pig production and selected “indicator bacteria”. In this context, the role of the bacteria livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and extended spectrum beta-lactamases carrying Escherichia coli (ESBL-E) along the pig production was particularly addressed. Hotspots of their prevalence and transmission are, for example, pig stable air for MRSA, or wastewater and manure for ESBL-E, or even humans as vectors in close contact to pigs (farmers and veterinarians). Thus, this review focuses on the biotope “stable environment” where humans and animals are both affected, but also where the end of the food chain is not neglected. We provide basic background information about antibiotics in livestock, MRSA, and ESBL-bacteria. We further present studies (predominantly European studies) in tabular form regarding the risk potentials for the transmission of resistant bacteria for humans, animals, and meat differentiated according to biotopes. However, we cannot guarantee completeness as this was only intended to give a broad superficial overview. We point out sustainable biotope approaches to try to contribute to policy management as critical assessment points in pig housing conditions, environmental care, animal health, and food product safety and quality as well as consumer acceptance have already been defined.

Characterization of the Microbiome at the World's Largest Potable Water Reuse Facility

Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 10⁶ copies in source, unchlorinated wastewater feed to 5.49 × 10¹ copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature.

Detection of the carbapenemase gene blaVIM-5 in members of the Pseudomonas putida group isolated from polluted Nigerian wetlands

There are increasing concerns about possible dissemination of clinically relevant antibiotic resistance genes, including genes encoding for carbapenemases in the environment. However, little is known about environmental distribution of antibiotic resistance in Africa. In this study, four polluted urban wetlands in Nigeria were investigated as potential reservoirs of carbapenem-resistant bacteria (CRB). CRB were isolated from the wetlands, characterized by Blue-Carba test, MIC determinations and whole genome sequencing (WGS). Nine of 65 bacterial isolates identified as members of the Pseudomonas putida group (P. plecoglossicida and P. guariconensis, respectively) harboured the metallo-beta-lactamase gene bla_VIM-5. WGS revealed the bla_VIM-5 in three novel Tn402-like class 1 integron structures containing the cassette arrays aadB|bla_VIM-5|bla_PSE-1, aadB|bla_VIM-5|aadB|bla_PSE-1, and bla_VIM-5|aadB|tnpA|bla_PSE-1|smr2|tnpA, respectively. Strains carrying the aadB|bla_VIM-5|bla_PSE-1 cassette also carried an identical integron without bla_VIM-5. In addition_, the strains harboured another Tn402-like class 1 integron carrying bcr2, several multidrug resistance efflux pumps, and at least one of ampC, aph(3”)-lb, aph(6)-ld, tetB, tetC, tetG, floR, and macAB. This is the first report of a carbapenemase gene in bacteria from environmental sources in Nigeria and the first report of bla_VIM-5 in environmental bacteria isolates. This result underscores the role of the Nigerian environment as reservoir of bacteria carrying clinically relevant antibiotic resistance genes.

Human and veterinary antibiotics during composting of sludge or manure: Global perspectives on persistence, degradation, and resistance genes

Wastewater treatment plant effluent, sludge and manure are the main sources of contamination by antibiotics in the whole environment compartments (soil, sediment, surface and underground water). One of the major consequences of the antibiotics discharge into the environment could be the prevalence of a bacterial resistance to antibiotic. In this review, four groups of antibiotics (Tetracyclines, Fluoroquinolones, Macrolides and Sulfonamides) were focused for the background on their wide spread occurrence in sludge and manure and for their effects on several target and non-target species. The antibiotics concentrations range between 1 and 136,000 μg kg^-1 of dry matter in sludge and manure, representing a potential risk for the human health and the environment. Composting of sludge or manure is a well-known and used organic matter stabilization technology, which could be effective in reducing the antibiotics levels as well as the antibiotic resistance genes. During sludge or manure composting, the antibiotics removals range between 17-100%. The deduced calculated half-lives range between 1-105 days for most of the studied antibiotics. Nevertheless, these removals are often based on the measurement of concentration without considering the matter removal (lack of matter balance) and very few studies are emphasized on the removal mechanisms (biotic/abiotic, bound residues formation) and the potential presence of more or less hazardous transformation products. The results from the few studies on the fate of the antibiotic resistance genes during sludge or manure composting are still inconsistent showing either decrease or increase of their concentration in the final product. Whether for antibiotic or antibiotic resistance genes, additional researches are needed, gathering chemical, microbiological and toxicological data to better understand the implied removal mechanisms (chemical, physical and biological), the interactions between both components and the environmental matrices (organic, inorganic bearing phases) and how composting process could be optimized to reduce the discharge of antibiotics and antibiotic resistance genes into the environment.

Deciphering the factors influencing the discrepant fate of antibiotic resistance genes in sludge and water phases during municipal wastewater treatment

The discrepant fate of antibiotic resistance genes (ARGs) in sludge and water phases was investigated in a municipal wastewater treatment plant, and a lab-scale A²O-MBR was operated to provide background value of ARGs. The influencing factors of ARGs including microbial community, co-selection from heavy metals, biomass and horizontal gene transfer were concerned. Results showed that iA²O (inversed A²O) showed better ARGs reduction, and longer SRT (sludge retention time) increased ARGs relative abundance while reduced the gene copies of ARGs in the effluent, but significantly increased the ARGs in sludge phase. Compared to background value, the most enriched ARG was tetX in water phase, while it was intI1 in sludge phase. There existed higher abundance of multi-resistant bacteria in sludge phase, and microbial community determined the fate of ARGs in both water and sludge phase, while the direct effects from horizontal gene transfer should not be overlooked especially in water phase.

Quantification of multi-antibiotic resistant opportunistic pathogenic bacteria in bioaerosols in and around a pharmaceutical wastewater treatment plant

Pharmaceutical wastewater treatment plants (WWTPs) are thought to be a "seedbed" and reservoirs for multi-antibiotic resistant pathogenic bacteria which can be transmitted to the air environment through aeration. We quantified airborne multi-antibiotic resistance in a full-scale plant to treat antibiotics-producing wastewater by collecting bioaerosol samples from December 2014 to July 2015. Gram-negative opportunistic pathogenic bacteria (GNOPB) were isolated, and antibiotic susceptibility tests against 18 commonly used antibiotics, including 11 β-lactam antibiotics, 3 aminoglycosides, 2 fluoroquinolones, 1 furan and 1 sulfonamide, were conducted. More than 45% of airborne bacteria isolated from the pharmaceutical WWTP were resistant to three or more antibiotics, and some opportunistic pathogenic strains were resistant to 16 antibiotics, whereas 45.3% and 50.3% of the strains isolated from residential community and municipal WWTP showed resistance to three or more antibiotics. The calculation of the multiple antibiotic resistance (MAR) index demonstrated that the air environment in the pharmaceutical WWTP was highly impacted by antibiotic resistance, while the residential community and municipal WWTP was less impacted by antibiotic resistance. In addition, we determined that the dominant genera of opportunistic pathogenic bacteria isolated from all bioaerosol samples were Acinetobacter, Alcaligenes, Citrobacter, Enterobacter, Escherichia, Klebsiella, Pantoea, Pseudomonas and Sphingomonas. Collectively, these results indicate the proliferations and spread of antibiotic resistance through bioaerosols in WWTP treating cephalosporin-producing wastewater, which imposed a potential health risk for the staff and residents in the neighborhood, calling for administrative measures to minimize the air-transmission hazard.

Antibiotic Residue in the Aquatic Environment: Status in Africa

Information on the presence of antibiotics is sparse for all types of water in Africa, including groundwater, surface water, effluent of wastewater treatment plants (WWTPs) and municipal potable water. With the relatively high sales of different antibiotics to treat infectious diseases in the human population of Africa, the residual of the antibiotics is bound to be released through excretion via urine or fecal matter in parallel to the high sales. This article reviews the published analysis on the occurrence of antibiotics in the environment particularly in the aquatic environment in some countries in Africa. In general, sulfamethoxazole was the most commonly detected in Africa surface water (with eight reports from four countries) at a concentration range of 0.00027 – 39 μgL-1. Wastewater analysis is believed to give an early warning for preventing epidemics. Thus, we discuss the associated level of antibiotic resistance to some prevalent diseases in Africa whose aetiological agents can develop antibiotic resistance due to exposure to antibiotic residue in water. This is important because of rising population of immuno-deficient African residents ravaged by HIV/AIDS, poor nutrition and less efficient sanitation systems.

Increased occurrence of heavy metals, antibiotics and resistance genes in surface soil after long-term application of manure

The purpose of this study was to investigate the impact of long-term application of pig manure on the accumulation of heavy metals, antibiotics and ARGs in surface soil sampled from the Jiaxing long-term field experimental site with three manure treatments, N-PM (0 kg/ha/y, dw), L-PM (7720 kg/ha/y, dw), and H-PM (11,580 kg/ha/y, dw), in 2013 and 2014. The results showed that most serious metal pollution of Zn and Cu was recorded in all manured samples in both years, and their contents exceeded the soil quality standards. Among the three tetracyclines, chlortetracycline was the predominant antibiotic detected with a range of 3.04-98.03 μg·kg^-1 in 2013 and 28.67-344.74 μg·kg^-1 in 2014 after long-term pig manure application. Q-PCR results showed that the average accumulation of ribosomal protection protein genes (tetM, tetO, tetQ and tetW) was lower than most of the efflux pump genes (tetA and tetG). The abundance of tet and sul genes of those sites with manure application was significantly higher than that of sites without manure application in both years. Metagenomics analysis of ARGs revealed that the abundance of multidrug resistance genes was the most abundant subtype, followed by fluoroquinolone, bacitracin, sulfonamide and tetracycline. There was a positive correlation between the levels of ARGs; soil organic matter, antibiotics, Cu, As, and Zn levels in both years. These results may shed light on the mechanism underlining the effects of long-term manure application on the occurrence and dissemination of ARGs in surface soil.

Co-optimization of sponge-core bioreactors for removing total nitrogen and antibiotic resistance genes from domestic wastewater

Inadequate sanitation can lead to the spread of infectious diseases and antimicrobial resistance (AMR) via contaminated water. Unfortunately, wastewater treatment is not universal in many developing and emerging countries, especially in rural and peri-urban locations that are remote from central sewers. As such, small-scale, more sustainable treatment options are needed, such as aerobic-Denitrifying Downflow Hanging Sponge (DDHS) bioreactors. In this study, DDHS reactors were assessed for such applications, and achieved over 79% and 84% removal of Chemical Oxygen Demand and Ammonium, respectively, and up to 71% removal of Total Nitrogen (TN) from domestic wastes. Elevated TN removals were achieved via bypassing a fraction of raw wastewater around the top layer of the DDHS system to promote denitrification. However, it was not known how this bypass impacts AMR gene (ARG) and mobile genetic element (MGE) levels in treated effluents. High-throughput qPCR was used to quantify ARG and MGE levels in DDHS bioreactors as a function of percent bypass (0, 10, 20 and 30% by volume). All systems obtained over 90% ARG reduction, although effluent ARG and TN levels differed among bypass regimes, with co-optimal reductions occurring at ~20% bypass. ARG removal paralleled bacterial removal rate, although effluent bacteria tended to have greater genetic plasticity based on higher apparent MGE levels per cell. Overall, TN removal increased and ARG removal decreased with increasing bypass, therefore co-optimization is needed in each DDHS application to achieve locally targeted TN and AMR effluent levels.

Sunlight-mediated inactivation of health-relevant microorganisms in water: a review of mechanisms and modeling approaches

Health-relevant microorganisms present in natural surface waters and engineered treatment systems that are exposed to sunlight can be inactivated by a complex set of interacting mechanisms. The net impact of sunlight depends on the solar spectral irradiance, the susceptibility of the specific microorganism to each mechanism, and the water quality; inactivation rates can vary by orders of magnitude depending on the organism and environmental conditions. Natural organic matter (NOM) has a large influence, as it can attenuate radiation and thus decrease inactivation by endogenous mechanisms. Simultaneously NOM sensitizes the formation of reactive intermediates that can damage microorganisms via exogenous mechanisms. To accurately predict inactivation and design engineered systems that enhance solar inactivation, it is necessary to model these processes, although some details are not yet sufficiently well understood. In this critical review, we summarize the photo-physics, -chemistry, and -biology that underpin sunlight-mediated inactivation, as well as the targets of damage and cellular responses to sunlight exposure. Viruses that are not susceptible to exogenous inactivation are only inactivated if UVB wavelengths (280-320 nm) are present, such as in very clear, open waters or in containers that are transparent to UVB. Bacteria are susceptible to slightly longer wavelengths. Some viruses and bacteria (especially Gram-positive) are susceptible to exogenous inactivation, which can be initiated by visible as well as UV wavelengths. We review approaches to model sunlight-mediated inactivation and illustrate how the environmental conditions can dramatically shift the inactivation rate of organisms. The implications of this mechanistic understanding of solar inactivation are discussed for a range of applications, including recreational water quality, natural treatment systems, solar disinfection of drinking water (SODIS), and enhanced inactivation via the use of sensitizers and photocatalysts. Finally, priorities for future research are identified that will further our understanding of the key role that sunlight disinfection plays in natural systems and the potential to enhance this process in engineered systems.

MALDI-TOF MS Identification and Clustering Applied to Enterobacter Species in Nosocomial Setting

Enterobacter microorganisms cause important bacterial infections in humans. Recently, carbapenem resistant isolates carrying the blaKPC gene were described and their clonal transmission in different nosocomial outbreaks reported. In this study, the relative numbers of Enterobacter species, their antimicrobial susceptibility along 3 years of observation and the identification ability of the two most common MALDI-TOF platforms were evaluated. A clustering analysis was performed to identify changes in the microbial population within the nosocomial environment. Enterobacter were identified using two platforms (MALDI-TOF Biotyper and VITEK MS). Antimicrobial susceptibility was tested by Vitek2 Compact and MIC₅₀ and MIC₉₀ was evaluated using GraphPad software. Clustering analysis was performed by MALDI-TOF and a dendrogram was built with both platforms and compared. The most frequent species isolated were Enterobacter cloacae and Enterobacter aerogenes with a gradual increase of Enterobacter asburiae in 2017. MALDI-TOF platforms showed a very good sensitivity and specificity except for E. asburiae identification that was reliable only by MALDI-TOF MS Biotyper. An increase of resistance for Enterobacter, confirmed by the isolation of extended spectrum beta-lactamase (ESBL) strains and the emergence of E. cloacae multidrug-resistant (MDR) and carbapenem resistant strains, was observed. A clonal route of transmission involving general surgery and geriatric wards was evidenced as previously described for Klebsiella pneumoniae MDR strains in the same nosocomial setting. These data represent an important source of information about the spreading of Enterobacter in the nosocomial environment.

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance

There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.

Tracking antibiotic resistome during wastewater treatment using high throughput quantitative PCR

Wastewater treatment plants (WWTPs) contain diverse antibiotic resistance genes (ARGs), and thus are considered as a major pathway for the dissemination of these genes into the environments. However, comprehensive evaluations of ARGs dynamic during wastewater treatment process lack extensive investigations on a broad spectrum of ARGs. Here, we investigated the dynamics of ARGs and bacterial community structures in 114 samples from eleven Chinese WWTPs using high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis. Significant shift of ARGs profiles was observed and wastewater treatment process could significantly reduce the abundance and diversity of ARGs, with the removal of ARGs concentration by 1-2 orders of magnitude. Whereas, a considerable number of ARGs were detected and enriched in effluents compared with influents. In particular, seven ARGs mainly conferring resistance to beta-lactams and aminoglycosides and three mobile genetic elements persisted in all WWTPs samples after wastewater treatment. ARGs profiles varied with wastewater treatment processes, seasons and regions. This study tracked the footprint of ARGs during wastewater treatment process, which would support the assessment on the spread of ARGs from WWTPs and provide data for identifying management options to improve ARG mitigation in WWTPs.

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always

BACKGROUND

Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments.

RESULTS

This study shows that the diversity and abundance of known antibiotic resistance genes can generally predict the diversity and abundance of undescribed resistance genes. However, the extent of this predictability is dependent on the type of environment investigated. Furthermore, it is shown that carefully selected small sets of resistance genes can describe total resistance gene diversity remarkably well.

CONCLUSIONS

The results of this study suggest that knowledge gained from large-scale quantifications of known resistance genes can be utilized as a proxy for unknown resistance factors. This is important for current and proposed monitoring efforts for environmental antibiotic resistance and has implications for the design of risk ranking strategies and the choices of measures and methods for describing resistance gene abundance and diversity in the environment.