Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies

Occurrence of integrons and antibiotic resistance genes in cryoconite and ice of Svalbard, Greenland, and the Caucasus glaciers

The prevalence of integrons and antibiotic resistance genes (ARGs) is a serious threat for public health in the new millennium. Although commonly detected in sites affected by strong anthropogenic pressure, in remote areas their occurrence, dissemination, and transfer to other ecosystems is poorly recognized. Remote sites are considered as a benchmark for human-induced contamination on Earth. For years glaciers were considered pristine, now they are regarded as reservoirs of contaminants, thus studies on contamination of glaciers, which may be released to other ecosystems, are highly needed. Therefore, in this study we evaluated the occurrence and frequency of clinically relevant ARGs and resistance integrons in the genomes of culturable bacteria and class 1 integron-integrase gene copy number in the metagenome of cryoconite, ice and supraglacial gravel collected on two Arctic (South-West Greenland and Svalbard) and two High Mountain (the Caucasus) glaciers. Altogether, 36 strains with intI1 integron-integrase gene were isolated. Presence of class 1 integron-integrase gene was also recorded in metagenomic DNA from all sampling localities. The mean values of relative abundance of intI1 gene varied among samples and ranged from 0.7% in cryoconite from Adishi Glacier (the Caucasus) to 16.3% in cryoconite from Greenland. Moreover, antibiotic-resistant strains were isolated from all regions. Genes conferring resistance to β-lactams (bla_SHV, bla_TEM, bla_OXA, bla_CMY), fluoroquinolones (qepA, qnrC), and chloramphenicol (cat, cmr) were detected in the genomes of bacterial isolates.

Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora

Mcr-1 and bla_NDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and bla_NDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and bla_NDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and bla_NDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and bla_NDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.

Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome

The widespread practice of applying sewage sludge to arable land makes use of nutrients indispensable for crops and reduces the need for inorganic fertilizer, however this application also provides a potential route for human exposure to chemical contaminants and microbial pathogens in the sludge. A recent concern is that such practice could promote environmental selection and dissemination of antibiotic resistant bacteria or resistance genes. Understanding the risks of sludge amendment in relation to antibiotic resistance development is important for sustainable agriculture, waste treatment and infectious disease management. To assess such risks, we took advantage of an agricultural field trial in southern Sweden, where land used for growing different crops has been amended with sludge every four years since 1981. We sampled raw, semi-digested and digested and stored sludge together with soils from the experimental plots before and two weeks after the most recent amendment in 2017. Levels of selected antimicrobials and bioavailable metals were determined and microbial effects were evaluated using both culture-independent metagenome sequencing and conventional culturing. Antimicrobials or bioavailable metals (Cu and Zn) did not accumulate to levels of concern for environmental selection of antibiotic resistance, and no coherent signs, neither on short or long time scales, of enrichment of antibiotic-resistant bacteria or resistance genes were found in soils amended with digested and stored sewage sludge in doses up to 12 metric tons per hectare. Likewise, only very few and slight differences in microbial community composition were observed after sludge amendment. Taken together, the current study does not indicate risks of sludge amendment related to antibiotic resistance development under the given conditions. Extrapolations should however be done with care as sludge quality and application practices vary between regions. Hence, the antibiotic concentrations and resistance load of the sludge are likely to be higher in regions with larger antibiotic consumption and resistance burden than Sweden.

Detection of microbial aerosols in hospital wards and molecular identification and dissemination of drug resistance of Escherichia coli

Antibiotic-resistant bacteria (ARB) present a global public health problem. Microorganisms are the main cause of hospital-acquired infections, and the biological contamination of hospital environments can cause the outbreak of a series of infectious diseases. Therefore, it is very important to understand the spread of antibiotic-resistant bacteria in hospital environments. This study examines the concentrations of aerobic bacteria and E. coli in ward environments and the airborne transmission of bacterial drug resistance. The results show that the three wards examined have an average aerobic bacterial concentration of 132 CFU∙m^-3 and an average inhalable aerobic bacterial concentration of 73 CFU∙m^-3, with no significant difference (P > 0.05) among the three wards. All isolated E. coli showed multi-drug resistance to not only third-generation cephalosporin antibiotics, but also quinolones, aminoglycosides, and sulfonamides. Furthermore, 51 airborne E. coli strains isolated from the air in the three wards and the corridor were screened for ESBLs, and 12 (23.53%) were ESBL-positive. The drug-resistance gene of the 12 ESBL-positive strains was mainly TEM gene, and the detection rate was 66.67% (8/12). According to a homology analysis with PFGE, 100% homologous E. coli from the ward at 5 m and 10 m outside the ward in the corridor shared the same drug-resistance spectrum, which further proves that airborne E. coli carrying a drug-resistance gene spreads out of the ward through gas exchange. This leads to biological pollution inside, outside, and around the ward, which poses a direct threat to the health of patients, healthcare workers, and surrounding residents. It is also the main reason for the antibiotic resistance in the hospital environment. More attention should be paid to comprehensive hygiene management in the surrounding environment of hospitals.

Molecular Epidemiology of Staphylococcus aureus Lineages in Wild Animals in Europe: A Review

Staphylococcus aureus is an opportunist pathogen that is responsible for numerous types of infections. S. aureus is known for its ability to easily acquire antibiotic resistance determinants. Methicillin-resistant S. aureus (MRSA) is a leading cause of infections both in humans and animals and is usually associated with a multidrug-resistant profile. MRSA dissemination is increasing due to its capability of establishing new reservoirs and has been found in humans, animals and the environment. Despite the fact that the information on the incidence of MRSA in the environment and, in particular, in wild animals, is scarce, some studies have reported the presence of these strains among wildlife with no direct contact with antibiotics. This shows a possible transmission between species and, consequently, a public health concern. The aim of this review is to better understand the distribution, prevalence and molecular lineages of MRSA in European free-living animals.

Contribution of antibiotics to the fate of antibiotic resistance genes in anaerobic treatment processes of swine wastewater: A review

Antibiotic resistance genes (ARGs) in water environment have become a global health concern. Swine wastewater is widely considered to be one of the major contributors for promoting the proliferation of ARGs in water environments. This paper comprehensively reviews and discusses the occurrence and removal of ARGs in anaerobic treatment of swine wastewater, and contributions of antibiotics to the fate of ARGs. The results reveal that ARGs' removal is unstable during anaerobic processes, which negatively associated with the presence of antibiotics. The abundance of bacteria carrying ARGs increases with the addition of antibiotics and results in the spread of ARGs. The positive relationship was found between antibiotics and the abundance and transfer of ARGs in this review. However, it is necessary to understand the correlation among antibiotics, ARGs and microbial communities, and obtain more knowledge about controlling the dissemination of ARGs in the environment.

Decay of elevated antibiotic resistance genes in natural river sediments after sedimentation of wastewater particles

Large-scale wastewater treatment plants (WWTPs) discharge hundreds of tons of total suspended solids (TSS) into surface waters every year. Additionally, a comparable amount is released by sewer overflows during heavy rain events in case of combined sewer systems. Along with sedimentation, particle-attached microorganisms and their antibiotic resistance genes (ARGs) are herewith transported to the riverbed of the receiving water. To better understand the dynamics of this process, a particulate wastewater fraction was added into batch reactors, which were previously filled with natural river sediments and tap water. In parallel, antibiotics (ABs) (erythromycin, tetracycline, ciprofloxacin, roxithromycin, penicillin V, and sulfamethoxazole) were spiked to investigate their capability to select for resistance. The abundance of six ARGs (ermB, tetM, bla_TEM, sul1, CTX-M-32, and qnrS) as well as total bacteria (16S rDNA) was monitored in waters and in sediments for a duration of two months using quantitative PCR. Despite a continuous exposure to ABs (5 μg/L each), the abundance of ARGs remained unaffected. Addition of wastewater particles resulted in a sudden and strong increase of ARGs in waters (3-5 log units) and sediments (1-4 log units), however, elevated ARGs underwent a particular and complete decay. Our results indicate that the increased ARG abundances in receiving rivers are the result of a continuous import of ARGs from WWTP discharges or sewer overflow events. They further imply that elevated ARGs do not persist in receiving rivers, if this continuous import is removed. This seems to be the case merely for ARGs introduced by wastewater, given that a stable background concentration of ARGs was observed for the native population.

Effects of the novel concept 'outdoor veal calf' on antimicrobial use, mortality and weight gain in Switzerland

The aim of the intervention study 'outdoor veal calf' was to evaluate a novel concept for calf fattening which aimed at reducing antimicrobial use without compromising animal health. Management practices such as commingling of calves from multiple birth farms, crowding, and suboptimal barn climate are responsible for high antimicrobial use and mortality in the veal calf population. The risk of selecting bacteria resistant to antimicrobials and of economic losses is accordingly elevated. The 'outdoor veal calf' concept, implemented in nineteen intervention farms (IF), is based on three main measures: 1. purchased calves are transported directly from neighboring birth farms to the fattening facility instead of commingling calves in livestock dealer trucks; 2. each calf is vaccinated against pneumonia after arrival and completes a three-week quarantine in an individual hutch; and 3. the calves spend the rest of the fattening period in outdoor hutches in groups not exceeding 10 calves. The covered and bedded paddock and the group hutches provide shelter from cold weather and direct sunshine, constant access to fresh air is warranted. Nineteen conventional calf fattening operations of similar size served as controls (CF). Every farm was visited once a month for a one-year period, and data regarding animal health, treatments, and production parameters were collected. Treatment intensity was assessed by use of the defined daily dose method (TI_DDD in days per animal year), and calf mortality and daily weight gain were recorded in both farm groups. Mean TI_DDD was 5.3-fold lower in IF compared to CF (5.9 ± 6.5 vs. 31.5 ± 27.4 days per animal year; p < 0.001). Mortality was 2.1-fold lower in IF than in CF (3.1% ± 2.3 vs. 6.3 % ± 4.9; p = 0.020). Average daily gain did not differ between groups (1.29 ± 0.17 kg/day in IF vs. 1.35 ± 0.16 kg/day in CF; p = 0.244). A drastic reduction in antimicrobial use and mortality was achieved in the novel 'outdoor veal calf' system without compromising animal health. The principles of risk reduction used in designing the system can be used to improve management and animal health, decrease the need for antimicrobial treatments and thus selection pressure on bacteria in veal operations.

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

Antibiotic resistance genes identified in wastewater treatment plant systems - A review

The intensive use of antibiotics for human, veterinary and agricultural purposes, results in their continuous release into the environment. Together with antibiotics, antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are introduced into wastewater. Wastewater treatment plants (WWTPs) are believed to be probable hotspots for antibiotic resistance dissemination in the environment as they offer convenient conditions for ARB proliferation as well as for horizontal transfer of ARGs among different microorganisms. In fact, genes conferring resistance to all classes of antibiotics together with mobile genetic elements (MGEs) like plasmids, transposons, bacteriophages, integrons are detected in WWTPs in different countries. It seems that WWTPs with conventional treatment processes are capable of significant reduction of ARB but are not efficient in ARG removal. Implementation of advanced wastewater cleaning processes in addition to a conventional wastewater treatment is an important step to protect the aquatic environment. Growing interest in presence and fate of ARB and ARGs in WWTP systems resulted in the fact that knowledge in this area has increased staggeringly in the past few years. The main aim of the article is to collect and organize available data on ARGs, that are commonly detected in raw sewage, treated wastewater or activated sludge. Resistance to the antibiotics usually used in antibacterial therapy belonging to main classes like beta-lactams, macrolides, quinolones, sulfonamides, trimethoprim and tetracyclines was taken into account. The presence of multidrug efflux genes is also included in this paper. The occurrence of antibiotics may promote the selection of ARB and ARGs. As it is important to discuss the problem considering all aspects that influence it, the levels of antibiotics detected in influent and effluent of WWTPs were also presented.

Antimicrobial, antioxidant and cytotoxic evaluation of diazenyl chalcones along with insights to mechanism of interaction by molecular docking studies

BACKGROUND

In continuation of our work, new diazenyl chalcones scaffolds (C-18 to C-27) were efficiently synthesized from substituted acetophenone azo dyes (A-E) by base catalyzed Claisen-Schmidt condensation with different substituted aromatic/heteroaromatic aldehydes.

METHODOLOGY

The synthesized chalcones were assessed for their in vitro antimicrobial potential towards several pathogenic microbial strains by tube dilution method and further evaluated for antioxidant potential by DPPH assay. These derivatives were also assessed for the cytotoxicity towards the human lung cancer cell line (A549) and normal cell line (HEK) by MTT assay. The most active antimicrobial compounds were docked using Schrodinger v18.1 software with the various potential bacterial receptors to explore the mechanism of interaction.

RESULTS

The derivative C-22 exhibited high antibacterial activity with very low MIC (1.95-3.90 µg ml-1) and MBC (3.90-7.81 µg ml-1) values. The derivatives C-23, C-24 and C-27 have demonstrated good antioxidant potential (IC50 = 7-18 µg ml-1) correlated to the ascorbic acid (IC50 = 4.45 µg ml-1). The derivative C-25 had shown comparable cytotoxicity to camptothecin against A549 cell line. The docking studies predicted the bacterial dihydrofolate reductase (PDB ID: 3SRW) and bacterial DNA gyrase (PDB ID: 4ZVI) as the possible targets for most of the active antimicrobial compounds. These derivatives affirmed their safety by presenting less cytotoxicity towards HEK cells. Further the ADME prediction by qikprop module of the Schrodinger proved that these compounds exhibited drug-like attributes.

CONCLUSION

Hence, these compounds have shown their potential as lead for future expansion of novel antimicrobial and cytotoxic drugs.

Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes

Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.

Genomic Insights into Two Colistin-Resistant Klebsiella pneumoniae Strains Isolated from the Stool of Preterm Neonate During the First Week of Life

Background: Klebsiella pneumoniae is a major opportunistic pathogen frequently associated with nosocomial infections, and often poses a major threat to immunocompromised patients. In our previous study, two K. pneumoniae (K36 and B13), which displayed resistance to almost all major antibiotics, including colistin, were isolated. Both isolates were not associated with infection and isolated from the stools of two preterm neonates admitted to the neonatal intensive care unit (NICU) during their first week of life. Materials and Methods: In this study, whole genome sequencing was performed on these two clinical multidrug resistant K. pneumoniae. We aimed to determine the genetic factors that underline the antibiotic-resistance phenotypes of these isolates. Results: The strains harbored bla_SHV-27, bla_SHV-71, and oqxAB genes conferring resistance to cephalosporins, carbapenems, and fluoroquinolones, respectively, but not harboring any known plasmid-borne colistin resistance determinants such as mcr-1. However, genome analysis discovered interruption of mgrB gene by insertion sequences gaining insight into the development of colistin resistance. Conclusion: The observed finding that points to a scenario of potential gut-associated resistance genes to Gram negative (K. pneumoniae) host in the NICU environment warrants attention and further investigation.

Characteristics of tetracycline adsorption by cow manure biochar prepared at different pyrolysis temperatures

This study aimed to explore the feasibility of using cow manure biochar (CMBC) for adsorption of tetracycline for realizing farm waste treatment and recycling. Three kinds of pyrolysis-temperature CMBCs were prepared and characterized. There were significant differences in the specific surface area, pores structure, surface charge, and oxygen-containing functional groups. The effect of adsorption was not only related to the physicochemical properties of CMBC but also the dosage, solution pH, and ambient temperature. CMBC showed surface heterogeneity, and the adsorption of tetracycline was mainly chemical. Controlling the rate of adsorption was achieved by combining internal particle diffusion and liquid film diffusion. Furthermore, the adsorption was a spontaneous and endothermic process. The use of CMBC as an adsorbent for tetracycline represents a new method for treating and recycling waste in farms. These results could aid in further studies on the adsorption mechanism and optimizing the adsorption process.

Wild Nutria (Myocastor coypus) Is a Potential Reservoir of Carbapenem-Resistant and Zoonotic Aeromonas spp. in Korea

The emergence and spread of antibiotic-resistant Aeromonas spp. is a serious public and animal health concern. Wild animals serve as reservoirs, vectors, and sentinels of these bacteria and can facilitate their transmission to humans and livestock. The nutria (Myocastor coypus), a semi-aquatic rodent, currently is globally considered an invasive alien species that has harmful impacts on natural ecosystems and carries various zoonotic aquatic pathogens. This study aimed to determine the prevalence of antibiotic-resistant zoonotic Aeromonas spp. in wild invasive nutrias captured in Korea during governmental eradication program. Three potential zoonotic Aeromonas spp. (A. hydrophila, A. caviae, and A. dhakensis) were identified among isolates from nutria. Some strains showed unexpected resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems. In carbapenem-resistant isolates, the cphA gene, which is related to intrinsic resistance of Aeromonas to carbapenems, was identified, and phylogenetic analysis based on this gene revealed the presence of two major groups represented by A. hydrophila (including A. dhakensis) and other Aeromonas spp. These results indicate that wild nutrias in Korea are a potential reservoir of zoonotic and antibiotic-resistant Aeromonas spp. that can cause infection and treatment failure in humans. Thus, measures to prevent contact of wild nutrias with livestock and humans are needed.

Graphene oxide as a tool for antibiotic-resistant gene removal: a review

Environmental pollutants, including antibiotics (ATBs), have become an increasingly common health hazard in the last several decades. Overdose and abuse of ATBs led to the emergence of antibiotic-resistant genes (ARGs), which represent a serious health threat. Moreover, water bodies and reservoirs are places where a wide range of bacterial species with ARGs originate, owing to the strong selective pressure from presence of ATB residues. In this regard, graphene oxide (GO) has been utilised in several fields including remediation of the environment. In this review, we present a brief overview of resistant genes of frequently used ATBs, their occurrence in the environment and their behaviour. Further, we discussed the factors influencing the binding of nucleic acids and the response of ARGs to GO, including the presence of salts in the water environment or water pH, because of intrinsic properties of GO of not only binding to nucleic acids but also catalysing their decomposition. This would be helpful in designing new types of water treatment facilities.

Extended-spectrum beta-lactamase and ampicillin Class C beta lactamase-producing Escherichia coli from food animals: A review

Antimicrobial resistance has gained global notoriety due to its public health concern, the emergence of multiple drug-resistant bacteria, and lack of new antimicrobials. Extended-spectrum beta-lactamase (ESBL)/ampicillin Class C (AmpC)- producing Escherichia coli and other zoonotic pathogens can be transmitted to humans from animals either through the food chain, direct contact or contamination of shared environments. There is a surge in the rate of resistance to medically important antibiotics such as carbapenem, ESBL, aminoglycosides, and fluoroquinolones among bacteria of zoonotic importance. Factors that may facilitate the occurrence, persistence and dissemination of ESBL/AmpC-Producing E. coli in humans and animal includes; 1). o ral administration of antimicrobials to humans primarily (by physician and health care providers) and secondarily to animals, 2). importation of parent stock and day-old chickens, 3). farm management practice and lack of water acidification in poultry, 4). contamination of feed, water and environment, 5). contamination of plants with feces of animals. Understanding these key factors will help reduce the level of resistance, thereby boosting the therapeutic effectiveness of antimicrobial agents in the treatment of animal and human infections. This review highlights the occurrence, risk factors, and public health importance of ESBL/AmpC-beta-lactamase producing E. coli isolated from livestock.

Tracking changes in the occurrence and source of pharmaceuticals within the River Thames, UK; from source to sea

There is a growing interest in the occurrence and sources of pharmaceutical substances in the environment. This paper reports the first detailed transect of pharmaceutical occurrence along the River Thames, UK, from source to sea, undertaken during a period of high flow in 2016. In 37 samples a total of 41 pharmaceuticals and 2 lifestyle compounds (cocaine and sucralose) were detected. Total concentration of pharmaceuticals ranged from 0.0012 μg/l to 10.24 μg/l with a median of 2.6 μg/l. Sucralose concentrations varied from <0.01 to 5.9 μg/l with a median concentration of 1.93 μg/l and was detected in every sample except the groundwater-dominated sources of the Thames. Antimicrobials, including those on the surface water watch list (erythromycin, clarithromycin and azithromycin) were detected in every site downstream of the Thames source. Diclofenac, recently on the surface water watch list, was detected in 97% of Thames samples and above the proposed EQS of 0.1 μg/l in 12 samples. Distinct increases in concentration and number of pharmaceuticals were found downstream of the Oxford, Mogdon and Hogsmill wastewater treatment works (WWTW) but were more subdued downstream of the Crossness and Beckton WWTW due to the tidal nature of the Thames and combined sewer outflows. Sucralose was found to be an excellent tracer of wastewaters (treated and untreated) and can be used as a proxy for many pharmaceuticals. Paracetamol and ibuprofen were tracers of untreated wastewater inputs to the Thames due to their high biodegradation within WWTWs.

Incidence of antimicrobial resistance genes and class 1 integron gene cassettes in multidrug-resistant motile Aeromonas sp. isolated from ornamental guppy (Poecilia reticulata)

Aeromonas sp. are opportunistic pathogenic bacteria which are associated with various diseases in ornamental fish, aquaculture raised species and wild fisheries. In our study, antimicrobial resistance patterns, antimicrobial resistance genes and class 1 integron gene cassettes of 52 guppy-borne Aeromonas sp. were examined. The isolates were identified as A. veronii (n = 34), A. dhakensis (n = 10), A. hydrophila (n = 3), A. caviae (n = 3) and A. enteropelogenes (n = 2) by gyrB gene sequencing. Every isolate was resistant to at least four antimicrobials in disc diffusion test. The resistance to amoxicillin, nalidixic acid and oxytetracycline was 100% among the tested isolates. 92·30, 76·92, 71·15, 51·92, 51·92 and 50·00% of the isolates were resistant to ampicillin, rifampicin, imipenem, cephalothin, tetracycline and trimethoprim respectively. The multiple antibiotic resistance index values ranged from 0·28 to 0·67. PCR amplification of antimicrobial resistance genes implied the occurrence of tetracycline resistance (tetA (65·39%), tetE (25·00%) and tetB (15·38%)), plasmid-mediated quinolone resistance (qnrS (26·92%) and qnrB (17·31%)) and aminoglycoside resistance (aphaAI-IAB (7·69%) and aac (6')-Ib (3·84%)) genes in the isolates. The IntI gene was positive for 36·54% of the isolates and four class 1 integron gene cassette profiles (aadA2, qacE2-orfD, aadA2-catB2 and dfrA12-aadA2) were identified. These data suggest that ornamental guppy can be a reservoir of multidrug-resistant Aeromonas sp. which comprise different antimicrobial resistance genes and class 1 integrons. SIGNIFICANCE AND IMPACT OF THE STUDY: Antimicrobial resistance genes and integron gene cassettes of ornamental fish-borne aeromonads are poorly studied. The antimicrobial resistance patterns, antimicrobial resistance genes and class 1 integron gene cassettes of Aeromonas sp. isolated from ornamental guppy were characterized for the first time in Korea. The incidence of different antimicrobial resistance genes and class 1 integron gene cassettes were observed in multidrug-resistant Aeromonas isolates. This result suggests that better management practices are necessary to prevent and address the serious consequences of indiscriminate and inappropriate antimicrobial use, and the distribution of multidrug-resistant bacteria.

Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals

In 2016, the Austrian Agency for Health and Food Safety started a pilot project to investigate antimicrobial resistance in surface water. Here we report on the characterisation of carbapenem resistant and ESBL-producing K. pneumoniae isolates from Austrian river water samples compared to 95 clinical isolates recently obtained in Austrian hospitals. Ten water samples were taken from four main rivers, collected upstream and downstream of major cities in 2016. For subtyping and comparison, public core genome multi locus sequence typing (cgMLST) schemes were used. The presence of AMR genes, virulence genes and plasmids was extracted from whole genome sequence (WGS) data. In total three ESBL-producing strains and two carbapenem resistant strains were isolated. WGS based comparison of these five water isolates to 95 clinical isolates identified three clusters. Cluster 1 (ST11) and cluster 2 (ST985) consisted of doublets of carbapenem resistant strains (one water and one clinical isolate each). Cluster 3 (ST405) consisted of three ESBL-producing strains isolated from one water sample and two clinical specimens. The cities, in which patient isolates of cluster 2 and 3 were collected, were in concordance with the water sampling locations downstream from these cities. The genetic concordance between isolates from river water samples and patient isolates raises concerns regarding the release of wastewater treatment plant effluents into surface water. From a public health perspective these findings demand attention and strategies are required to minimize the spread of multiresistant strains to the environment.

Genomic Characterization of Arcobacter butzleri Isolated From Shellfish: Novel Insight Into Antibiotic Resistance and Virulence Determinants

Arcobacter (A.) butzleri is an emerging pathogenic microorganism, whose taxonomy has been recently suggested to be emended to the Aliarcobacter (Al.) butzleri comb. nov. Despite extensive taxonomic analysis, only few fragmented studies have investigated the occurrence and the prevalence of virulence and antibiotic resistance determinants of this species in strains isolated from shellfish. Herein we report for the first time the whole genome sequencing and genomic characterization of two A. butzleri strains isolated from shellfish, with particular reference to the antibiotic, heavy metals and virulence determinants. This study supported the taxonomic assignment of these strains to the Al. butzleri species, and allowed us to identify antibiotic and metal resistance along with virulence determinants, also additional to those previously reported for the only two A. butzleri strains from different environments genomically characterized. Moreover, both strains showed resistance to β-lactams, vanocomycin, tetracycline and erythromycin and susceptibility to aminoglycosides and ciprofloxacin. Beside enlarging the availability of genomic data to perform comparative studies aimed at correlating phenotypic differences associated with ecological niche and geographic distribution with the genetic diversity of A. butzleri spp., this study reports the endowment of antibiotic and heavy metal resistance and virulence determinants of these shellfish-isolated strains. This leads to hypothesize a relatively high virulence of A. butzleri isolated from shellfish and prompt the need for a wider genomic analysis and for in vitro and in vivo studies of more strains isolated from this and other ecological niches, to unravel the mechanism of pathogenicity of this species, and the potential risk associated to their consumption.

Prevalence and characterization of carbapenem-resistant bacteria in water bodies in the Los Angeles-Southern California area

Carbapenems are β-lactam antibiotics used in healthcare settings as last resort drugs to treat infections caused by antibiotic-resistant bacteria. Carbapenem-resistant bacteria are increasingly being isolated from healthcare facilities; however, little is known about their distribution or prevalence in the environment, especially in the United States, where their distribution in water environments from the West Coast has not been studied before. The aim of this study was to determine the prevalence of carbapenem-resistant bacteria and carbapenemase genes in water bodies from the Los Angeles area (California, USA). All samples that were analyzed contained carbapenem-resistant bacteria with a frequency of between 0.1 and 324 carbapenem-resistant cfu per 100 mls of water. We identified 76 carbapenem-resistant or -intermediate isolates, most of which were also resistant to noncarbapenem antibiotics, as different strains of Enterobacter asburiae, Aeromonas veronii, Cupriavidus gilardii, Pseudomonas, and Stenotrophomonas species. Of them, 52 isolates were carbapenemase-producers. Furthermore, PCR and sequence analysis to identify the carbapenemase gene of these carbapenemase-producing isolates revealed that all Enterobacter asburiae isolates had a blaIMI-2 gene 100% identical to the reference sequence, and all Stenotrophomonas maltophlia isolates had a blaL1 gene 83%-99% identical to the reference blaL1 . Our findings indicate that water environments in Southern California are an important reservoir of bacteria-resistant to carbapenems and other antibiotics, including bacteria carrying intrinsic and acquired carbapenemase genes.

Molecular detection of Shiga toxin-producing and antibiotic-resistant Escherichia coli isolates from buffaloes in southwest of Iran

Three hundred fifteen bacteriological samples were obtained from feces and both external and visceral cavity surfaces of carcasses of 105 healthy buffalo slaughtered in southwest of Iran. Confirmed Escherichia coli isolates were examined for antimicrobial resistance phenotypically and were screened for stx₁, stx₂, and eae genes and their subtypes and assessment of antimicrobial resistance genes by regular PCR and RFLP techniques. One hundred forty-five E. coli were isolated from feces (96 isolates) and external (37) and internal (12) surfaces of carcasses. Results showed that the prevalence of STEC, EPEC, and EHEC pathotypes was 2.8%, 0.7%, and 0.7% respectively. Among 6 (4.13%) positive isolates for examined genes, 4 (2.8%) isolates were positive for stx1, 3 (2.1%) for stx2, and 2 (1.4%) for eae gene. The detected genes were classified into stx₁a (4 isolates), stx₂a, stx₂b, stx₂c, eae-β, and unknown subtypes. The most prevalent antibiotic resistance gene was sulII (11.03%). The tetB, qnrB, floR, bla_TEM, bla_SHV, and aad_A genes were found to a lesser extent, and all isolates were negative for bla_CTX-15, bla_OXA, aac(3)-I, tetA, cat1, qnrA, sulI, dhfrI, and dhfrV genes. Twelve combination patterns of antibiotic-resistant genes were observed. Maximum phenotypically resistance rate was against doxycycline (91.83%), and the minimum was against ceftazidime and florfenicol (2.75%). E. coli isolates from feces and carcasses of slaughtered buffalo can be considered a mild reservoir for stx and eae genes. However, healthy buffaloes could be considered a potential reservoir of multiple antibiotic resistance genes in E. coli isolates.

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

Although antibiotic resistance represents a significant and growing public health concern, the contribution of bacteriophages (phages) to the mobilization of antibiotic resistance genes (ARGs) in the environment has not been extensively studied. Recent studies, however, suggest that phages play an important role in the acquisition, maintenance, and spread of ARGs than previously expected. This Opinion article offers an update on the contribution of phages to environmental antibiotic resistance. A better understanding of the mechanisms and factors that promote antibiotic resistance may significantly contribute to the implementation of control strategies.

Control of bacterial pathogens isolated from water using Actinomycetes extracts at Egerton University, Kenya

Diseases are the worst enemy to man currently. This study was aimed at isolating pathogenic bacteria from water obtained from shallow wells in Dundori Kenya. Also, the study aimed at testing the isolates for sensitivity to antibiotic metabolites previously extracted from Actinomycetes isolates from soils of Egerton University. Water samples were collected from shallow wells randomly selected from Dundori and abbreviated as A, B, C, D, and E. Bacterial pathogens were isolated from the water samples using the membrane filtration technique. The isolates were characterized using biochemical means. Antimicrobial sensitivity testing was carried out using Kirby Bauer disk diffusion method. Data analysis was carried out using the Statistical Package for Social Sciences (SPSS). Comparison of means was carried out using one way ANOVA. Shallow wells B, D and E were highly contaminated with pathogenic bacteria. Biochemical characterization of the isolates indicated that the most common isolates were Vibrio cholera, Klebsiella pneumoniae, Proteus sp, Escherichia coli, and Staphylococcus aureus. There was no significant difference between the zones of inhibition produced by the antibiotic metabolites (F=2.149 P=1340) when tested against the test isolates. There were no significant differences between the MIC's of the antibiotic metabolites on the bacterial pathogens (F=2.01 P=0.15). Water from some shallow wells in Dundori is highly contaminated with Klebsiella pneumoniae, Escherichia coli, Proteus sp., Vibrio cholerae and Staphylococcus aureus. The pathogens can effectively be controlled using antibiotics from the Actinomycetes. There is a need to sensitize the residents of the study area on ways of preventing seepage of contaminants into the shallow wells.

Microbial diversity and antibiotic resistance in a final effluent-receiving lake

Wastewater treatment plants have been recognised as hotspots for antibiotic resistance genes and antibiotic-resistant bacteria which enter the environment. However, the persistence of these genes and bacteria in receiving ecosystems remains poorly understood. The aim of the study was to evaluate the effect of final effluent release on microbial diversity and the antibiotic resistance gene pool in a final effluent-receiving lake. The numbers of total culturable heterotrophs and unculturable bacteria (represented as the 16S rRNA gene copy number) were significantly reduced during the treatment process. The number of ampicillin-resistant bacteria was higher in the sediment than in water samples, suggesting accumulation of ampicillin-resistant bacteria in freshwater sediments. Using an exogenous method, we captured 56 resistance plasmids which were further characterised. Next-generation sequencing revealed that the microbial phyla represented in the studied metagenomes were typical of corresponding environments. The highest relative abundance of antibiotic resistance genes was observed in the final effluent, suggesting that a considerable number of genes were released from the wastewater treatment plant. However, the lowest relative abundance and lowest diversity of the genes in the lake water, compared to the other studied metagenomes, suggest a negligible effect of treated sewage release on antibiotic resistance within water microbial communities of the lake. Furthermore, uncontrolled sewage dumping into this reservoir in the past as well as lower quality of the water upstream of the lake indicated that the wastewater treatment plant protected the studied ecosystem.

High-throughput profiling of antibiotic resistance gene dynamic in a drinking water river-reservoir system

The rapid construction of reservoir in river basin generates a river-reservoir system containing an environmental gradient from river system to reservoir system in modern aquatic environment worldwide. Profiles of antibiotic resistance genes (ARGs) in river-reservoir system is essential to better understand their dynamic mechanisms in aquatic eco-environment. In this study, we investigated the diversity, abundance, distribution of ARGs and mobile genetic elements (MGEs) in a representative river-reservoir system using high-throughput quantitative PCR, as well as ranked the factors (e.g. antibiotics, bacterial biomass, bacteria communities, and MGEs) influencing the patterns of ARGs based on structural equation models (SEMs). Seasonal variations in absolute abundance of ARGs and MGEs exhibited similar trends with local rainfall, suggesting that seasonal runoff induced by the rainfall potentially promote the absolute abundance of ARGs and MGEs. In contrast, environmental gradient played more important roles in the detected number, relative abundance, distribution pattern of ARGs and MGEs in the river-reservoir system. Moreover, environmental gradient also made the co-occurrence patterns associated with ARGs subtypes, MGEs and bacteria genera in river system different from those in reservoir system. The SEMs revealed that MGEs contributed the most to shape the ARG profiles. Overall, our findings provide novel insights into the mechanisms of environmental gradient on ARGs dynamics in river-reservoir system, probably via influencing the MGEs, antibiotics, pathogenic bacteria community and nonpathogenic bacteria community.

Prediction of the intestinal resistome by a three-dimensional structure-based method

The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens.

Removal of antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in municipal wastewater by membrane bioreactor systems

Antibiotic residues, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are considered new classes of water contaminants due to their potential adverse effects on aquatic ecosystems and human health. This paper provides comprehensive data on the occurrences of 19 antibiotics, bacteria resistant to 10 antibiotics, and 15 ARGs in raw influent and different treatment stages of conventional activated sludge (CAS) and membrane bioreactor (MBR) systems. Seventeen out of the 19 target antibiotics were detected in raw influent with concentrations of up to ten micrograms per liter. Concentrations of antibiotics measured in the secondary effluent were much lower compared to those in the raw influent. Among the antibiotics, amoxicillin, azithromycin, ciprofloxacin, chloramphenicol, meropenem, minocycline, oxytetracycline, sulfamethazine and vancomycin had highest removal by CAS or MBR systems with median removal efficiency (RE) > 70%, while trimethoprim and lincomycin were recalcitrant in the CAS system with median RE <50%. Similarly, the target ARB and ARGs were omnipresent in the raw influent samples with average concentrations as high as 2.6 × 10⁶ CFU/mL and 2.0 × 10⁷ gene copies/mL, respectively. The concentrations of ARB in secondary effluent of the CAS system declined relative to the raw influent (i.e. lower than raw influent by 2-3 orders of magnitude) and no ARB were detected in the MF permeate of the MBR system. For ARGs, their concentrations in secondary effluent/MF permeate ranged from below method quantification limit (<MQL) to 10⁴ gene copies/mL. It is noteworthy that several ARGs, i.e. bla_KPC, bla_NDM, bla_SHV, ermB, intI1, sul1 and tetO, were still found in the MF permeate of the MBR system at average concentrations up to 10³ copies/mL. In conclusion, MBR outperformed CAS in the elimination of ARB, ARGs and most target antibiotics.

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.

Mechanisms of bacterial multiresistance to antibiotics

Multiple drug resistance (MDR) to widening range of antibiotics emerging in increasing variety of pathogenic bacteria is a serious threat to the health of mankind nowadays. This is partially due to an uncontrolled usage of antibiotics not only in clinical practice, but also in various branches of agriculture. MDR is affected by two mechanisms: (1) accumulation of resistance genes as a result of intensive selection caused by antibiotics, and (2) active horizontal transfer of resistance genes. To unveil the reasons of bacterial multiresistance to antibiotics, it is necessary to understand the mechanisms of antibiotics action as well as the ways how either resistance to certain antibiotics emerge or resistance genes accumulate and transfer among bacterial strains. Current review is devoted to all these problems.

Exploring the differences of antibiotic resistance genes profiles between river surface water and sediments using metagenomic approach

To better understand the potential genic communication and dissemination of antibiotic resistance genes (ARGs) in different environmental matrices, the differences of ARG profiles between river surface water and sediments were explored. Metagenomic analysis was applied to investigate the comprehensive ARG profiles in water and sediment samples collected from the highly human-impacted catchment of the Beijiang River and its river source. A total of 135 ARG subtypes belonging to 18 ARG types were identified. Generally, ARGs in surface water were more diverse and abundant than those in sediments. ARG profiles in the surface water and sediment samples were distinct from each other, but some ARGs were shared by the surface water and sediments. Results revealed that multidrug and bacitracin resistance genes were the predominant ARGs types in both surface water (0.30, 0.17 copies/cell) and sediments (0.19, 0.15 copies/cell). 73 ARG subtypes were shared by the water and sediment samples and had taken over 90% of the total detected ARG abundance. Most of the shared ARGs are resistant to the clinically relevant antibiotics. Furthermore, significant correlations between the ARGs and 21 shared genera or mobile genetic elements (MGEs) (plasmids and integrons) were found in surface water and sediments, suggesting the important role of genera or MGEs in shaping ARGs profiles, propagation and distribution. These findings provide deeper insight into mitigating the propagation of ARGs and the associated risks to public health.

Extensive Genetic Commonality among Wildlife, Wastewater, Community, and Nosocomial Isolates of Escherichia coli Sequence Type 131 (H30R1 and H30Rx Subclones) That Carry blaCTX-M-27 or blaCTX-M-15

Escherichia coli sequence type 131 (ST131) is currently one of the leading causes of multidrug-resistant extraintestinal infections globally. Here, we analyzed the phenotypic and genotypic characteristics of 169 ST131 isolates from various sources (wildlife, wastewater, companion animals, community, and hospitals) to determine whether wildlife and the environment share similar strains with humans, supporting transmission of ST131 between different ecological niches. Susceptibility to 32 antimicrobials was tested by disc diffusion and broth microdilution. Antibiotic resistance genes, integrons, plasmid replicons, 52 virulence genes, and fimH-based subtypes were detected by PCR and DNA sequencing. Genomic relatedness was determined by pulsed-field gel electrophoresis (PFGE). The genetic context and plasmid versus chromosomal location of extended-spectrum beta-lactamase and AmpC beta-lactamase genes was determined by PCR and probe hybridization, respectively. The 169 ST131 study isolates segregated predominantly into bla_CTX-M-15H30Rx (60%) and bla_CTX-M-27H30R1 (25%) subclones. Within each subclone, isolates from different source groups were categorized into distinct PFGE clusters; genotypic characteristics were fairly well conserved within each major PFGE cluster. Irrespective of source, the bla_CTX-M-15H30Rx isolates typically exhibited virotype A (89%), an F2:A1:B- replicon (84%), and a 1.7-kb class 1 integron (92%) and had diverse structures upstream of the bla_CTX-M region. In contrast, the bla_CTX-M-27H30R1 isolates typically exhibited virotype C (86%), an F1:A2:B20 replicon (76%), and a conserved IS26-ΔISEcp1-bla_CTX-M-like structure. Despite considerable overall genetic diversity, our data demonstrate significant commonality between E. coli ST131 isolates from diverse environments, supporting transmission between different sources, including humans, environment, and wildlife.

Effect of chlorine on cultivability of Shiga toxin producing Escherichia coli (STEC) and β-lactamase genes carrying E. coli and Pseudomonas aeruginosa

The worldwide spread of toxin-producing and multi-drug resistant bacteria in water, food and the environment is considered a major threat to human health. Drinking water quality is controlled by inspection of fecal indicators presence whereby viable contaminants will be efficiently reduced by chlorination which is a common process for disinfection. However, the all-out efficiency is arguable, because bacterial regrowth has been documented after disinfection. In this study, we investigated the stability of Shiga toxin producing Escherichia coli (STEC) and β-lactamase expressing E. coli and Pseudomonas aeruginosa isolates, both equipped with multiple or single β-lactamase resistance genes. The aim of the study was to analyze the efficiency of chlorine (Cl₂) disinfection against shigatoxigenic or β-lactamase producing bacteria. Cl₂ reacts with the bacterial cells after first contact. Counts of antibiotic resistant E. coli were lower after short than upon extended Cl₂ treatment. P. aeruginosa counts decreased moderately upon 15-60 min treatment with 1.2 mg Cl₂/l, while cells adapted to tap water were not cultivable anymore. We assume that the bacterial physiology changed to a temporary non-cultivatable state at first Cl₂ contact followed by resuscitation of some cells at later stages. STEC viability went down continuously at low Cl₂ concentrations and these toxigenic E. coli isolates exhibited slightly increased stability to Cl₂ treatment compared with non-toxigenic E. coli. Controlling the efficiency of disinfection, realistic counts of cultivatable cells are achieved after extended Cl₂ action.

A School-Based Educational Intervention for School-Aged Children and Caregivers about Rational Use of Antibiotics in Urban Areas of Shaanxi Province: A Study Protocol for a Randomized Controlled Research

(1) Background: Antibiotic resistance is an imperative public health issue globally. Major factors that are resulting in this trend are the irrational and excessive use of antibiotics. Children account for a greater population of antibiotics use, therefore, an educational intervention on the rational use of antibiotics for children and caregivers will be beneficial. (2) Methods: A randomized controlled and parallel group study of fifth grade children and their caregivers will be evaluated in four primary schools in Baoji and Weinan of the Shaanxi Province. Two primary schools will be randomly selected for the educational intervention and two schools will serve as a control group. In the intervention arm, educational interventions will be conducted among caregivers and their children. The intervention measures include interactive training sessions, booklets, and printed or electronic educational materials that will be given to the caregivers or the school-aged children. In the control arm, no interventions will be implemented. Baseline data collected from June, 2018 and the intervention will last for three months. Knowledge-Attitude-Practice (KAP) questionnaires will be used to evaluate the caregivers’ knowledge, their attitude, and their practice. Knowledge-Retention questionnaires will be used to assess the children’s knowledge about microbes, antibiotics, and hygiene. (3) Discussion: This study is a unique comprehensive intervention targeting both children and their caregivers. We hypothesize a decrease in the irrational use of antibiotics among the studied population. Hence, this result would provide evidence for policy makers and educational departments for the implementation of similar interventions on the rational use of antibiotics.

Persistence of bacterial pathogens, antibiotic resistance genes, and enterococci in tidal creek tributaries

Intertidal creeks form the primary hydrologic link between estuaries and land-based activities on barrier islands. Fecal indicators Enterococcus spp. (Entero1), pathogens Shigella spp. (ipaH), Salmonella spp. (invA), E. coli of EHEC/EPEC groups (eaeA), E. coli of EAEC, EIEC, and UPEC groups (set1B), E. coli of STEC group (stx1); and tetracycline resistance genes (tet(B), tet(C), tet(D), tet(E), tet(K), tet(Q), tet(W), and tet(X); TRG) were detected in the headwater of Oakdale Creek (Sapelo Island, GA) receiving runoffs from Hog Hammock village. Excavation of drainage ditches around the village caused a high increase in the incidence of the above determinants. Water samples were collected from the headwater, transferred to diffusion chambers, submersed in the headwater, saltmarsh, and mouth of the creek; and the determinants were monitored for 3 winter months. With some exceptions, their persistence decreased in order headwater > saltmarsh > mouth. Genes associated with Enterococcus spp. were the most persistent at all the sites, following in the headwater with determinants for Salmonella spp. and E. coli of EAEC, EIEC, and UPEC groups. In the mouth, the most persistent gene was eaeA indicating EHEC, EPEC, and STEC. Tet(B) and tet(C) persisted the longest in headwater and saltmarsh. No TRG persisted after 11 days in the mouth. Most determinants revealed correlations with temperature and pH, and inverse correlations with dissolved oxygen. Decay rates of the above determinants varied in the range of -0.02 to -0.81/day, and were up to 40 folds higher in the saltmarsh and mouth than in the headwater. Our data demonstrated that water parameters could to some extent predict a general trend in the fate of virulence and antibiotic resistance determinants in tidal creek tributaries but strongly suggested that their persistence in these tributaries cannot be predicted from that of enterococci, or extrapolated from one biological contaminant to another.

Occurrence and Distribution of Tetracycline Antibiotics and Resistance Genes in Longshore Sediments of the Three Gorges Reservoir, China

The widespread use of antibiotics and the induced antibiotic resistance genes have attracted much attention in recent years. The longshore sediments in the water-level-fluctuating zone of the Three Gorges Reservoir were selected to investigate the spatial-temporal distribution of antibiotics and antibiotic resistance genes in two different operation stages (low-water level in summer and high-water level in winter). Three kinds of tetracycline antibiotics (tetracycline, oxytetracycline, and chlortetracycline) and three kinds of tetracycline resistance genes [tet(A), tet(C), and tet(M)] were analyzed and quantified. The results showed that the distribution of tetracyclines and resistance genes in riverine, transition and lacustrine zones showed a certain regularity, and the tetracycline antibiotics concentration and the total abundance of the tetracycline resistance genes were highest in the transition zone, and then the riverine zone. Meanwhile, there were significant seasonal variations of tetracycline and the resistance genes. The concentrations of the tetracycline and resistance genes were higher in summer than those in winter, while the relative abundance of resistance genes was higher in winter. It was suggested that the different seasonal distribution of antibiotics and resistance genes may be correlated with the reservoir operation in the Three Gorges Reservoir and the higher use of antibiotics in winter. In addition, Pearson correlation analysis showed that the concentrations of the tetracycline, class 1 integron and 16S rRNA were positively correlated with the abundance of the tetracycline resistance genes.

Integrating microbial biomass, composition and function to discern the level of anthropogenic activity in a river ecosystem

Anthropogenic activities (e.g., wastewater discharge and pesticide and fertilizer use) have considerable impact on the biotic properties of natural aquatic ecosystems, especially the microbial community and function. Microbes can respond to anthropogenic activities and are thus potential indicators of activity levels. Several reports have documented the impacts of anthropogenic activities on the variations in the microbial community, but the direct use of microbial community indices to discern anthropogenic activity levels remains limited. Here, we integrated flow cytometry, 16S rRNA sequencing, and natural organic matter metabolism determination to investigate microbial biomass, composition, and function in three areas along a gradient of anthropogenic disturbance (less-disturbed mountainous area, wastewater-discharge urban area, and pesticide and fertilizer used agricultural area) in a river ecosystem. Multiple statistical methods were used to explore the causal relationships between changes in environmental factors and microbial variation. Results showed that anthropogenic activities (e.g., wastewater discharge, pesticide and fertilizer use) facilitated bacterial production, affected dominant species distribution, and accelerated natural organic matter (NOM) metabolic rate by microbes. After screening the possible factors influencing the microbial community, we determined that cyanobacterial concentration could be a diagnostic indicator of nutrient levels. We also developed a NOM metabolic index to quantitatively reflect the holistic influence of nutrients and xenobiotics.

Tomatidine Is a Lead Antibiotic Molecule That Targets Staphylococcus aureus ATP Synthase Subunit C

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of deadly hospital-acquired infections. The discovery of anti-Staphylococcus antibiotics and new classes of drugs not susceptible to the mechanisms of resistance shared among bacteria is imperative. We recently showed that tomatidine (TO), a steroidal alkaloid from solanaceous plants, possesses potent antibacterial activity against S. aureus small-colony variants (SCVs), the notoriously persistent form of this bacterium that has been associated with recurrence of infections. Here, using genomic analysis of in vitro-generated TO-resistant S. aureus strains to identify mutations in genes involved in resistance, we identified the bacterial ATP synthase as the cellular target. Sequence alignments were performed to highlight the modified sequences, and the structural consequences of the mutations were evaluated in structural models. Overexpression of the atpE gene in S. aureus SCVs or introducing the mutation found in the atpE gene of one of the high-level TO-resistant S. aureus mutants into the Bacillus subtilis atpE gene provided resistance to TO and further validated the identity of the cellular target. FC04-100, a TO derivative which also possesses activity against non-SCV strains, prevents high-level resistance development in prototypic strains and limits the level of resistance observed in SCVs. An ATP synthesis assay allowed the observation of a correlation between antibiotic potency and ATP synthase inhibition. The selectivity index (inhibition of ATP production by mitochondria versus that of bacterial ATP synthase) is estimated to be >10⁵-fold for FC04-100.

Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia

The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.

Occurrence of intracellular and extracellular antibiotic resistance genes in coastal areas of Bohai Bay (China) and the factors affecting them

Coastal areas are the transition zones between ocean and land where intracellular antibiotic resistance genes (iARGs) and extracellular antibiotic resistance genes (eARGs) could spread among marine organisms, and between humans and marine organisms. However, little attention has been paid to the combined research on iARGs and eARGs in marine environment. In this context, we collected water and sediment samples from the coastal areas of the Bohai Bay in China and performed molecular and chemical analyses. The results of quantitative real-time PCR (qPCR) showed that the relative abundance of eARGs was up to 4.3 ± 1.3 × 10^-1 gene copies/16S rRNA copies in the water samples and 2.6 ± 0.3 × 10^-3 gene copies/16S rRNA copies in the sediment samples. Also, the abundance of eARGs was significantly higher than that of iARGs. Furthermore, the average abundances of antibiotic resistance genes (ARGs, include iARGs and eARGs) were the highest in both the water and sediment samples from the estuaries. The results of liquid chromatography-mass spectrometry showed that the concentrations of antibiotics in estuaries and areas near the mariculture site were higher than that in the other sites. The class 1 integron gene (int1) and sul1 in the intracellular DNA were significantly correlated in the water samples. Moreover, significant correlation between int1 and sul2 in the extracellular DNA was also found in the sediment samples. The combination of sulfamerazine and tetracycline as well as the combination of sulfamethazine and dissolved oxygen can both explain the abundance of ARGs, implying the combined effects of multiple stresses on ARGs.

Ecotoxicity and antibiotic resistance of a mixture of hospital and urban sewage in a wastewater treatment plant

Hospital and urban effluents are a source of diverse pollutants such as organic compounds, heavy metals, detergents, disinfectants, pharmaceuticals, and microorganisms resistant to antibiotics. Usually, these two types of effluent are mixed in the sewage network, but a pilot site in France now allows studying them separately or mixed to understand more about their characteristics and the phenomena that occur following their mixing. In this study, their ecotoxicity (Daphnia magna mobility, Pseudokirchneriella subcapitata growth, Brachionus calyciflorus reproduction, and SOS Chromotest) and antibiotic resistance (integron quantification) were assessed during mixing and treatment steps. The main results of this study are (i) the ecotoxicity and antibiotic resistance potentials of hospital wastewater are higher than in urban wastewater and (ii) mixing two different effluents does not lead to global synergistic or antagonistic effects on ecotoxicity and antibiotic resistance potential. The global additivity effect observed in this case must be confirmed by other studies on hospital and urban effluents on other sites to improve knowledge relating to this source of pollution and its management.

Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon

Extended-spectrum beta-lactamases (ESBLs) have been recurrently reported in both human and veterinary medicine, and carbapenemases have also emerged in these two sectors. Such resistance phenotypes were increasingly reported in the environment, which both receives and further disseminates multidrug-resistant (MDR) bacteria. Here, we report the high contamination of water samples (68.2%; 15/22) collected in estuaries in Lebanon. From these 15 contaminated sites, a total of 21 ESBL-producing (mostly harbouring the bla_CTX-M-15 gene) and four carbapenemase-producing (two bla_OXA-48 and two bla_OXA-244) Enterobacteriaceae were recovered. ESBL contamination was also identified in water samples collected from rural wells and spring water, although at a lower frequency. Indeed, 1.9% (3/155) and 6.1% (7/115) of the wells and springs were contaminated, respectively, and all identified isolates were CTX-M-15-producing E. coli. Interestingly, sequence types (STs) previously associated both with animal and human reservoirs were detected (ST38, ST10 and ST131), suggesting a complex source of contamination. This situation is alarming since water drawn from wells or springs is directly intended for human consumption in Lebanon without any further treatment. Moreover, even though water from estuaries is not intended for human consumption, it is used to water animals and irrigate crops. Consequently, water contamination by ESBLs and carbapenemases in Lebanon is potentially a major risk to public health. Part of this work was presented at the 7th Symposium on Antimicrobial Resistance in Animals and the Environment (ARAE).

Modeling the Emergence of Antibiotic Resistance in the Environment: an Analytical Solution for the Minimum Selection Concentration

Environmental antibiotic risk management requires an understanding of how subinhibitory antibiotic concentrations contribute to the spread of resistance. We develop a simple model of competition between sensitive and resistant bacterial strains to predict the minimum selection concentration (MSC), the lowest level of antibiotic at which resistant bacteria are selected. We present an analytical solution for the MSC based on the routinely measured MIC, the selection coefficient (sc) that expresses fitness differences between strains, the intrinsic net growth rate, and the shape of the bacterial growth dose-response curve with antibiotic or metal exposure (the Hill coefficient [κ]). We calibrated the model by optimizing the Hill coefficient to fit previously reported experimental growth rate difference data. The model fit varied among nine compound-taxon combinations examined but predicted the experimentally observed MSC/MIC ratio well (R² ≥ 0.95). The shape of the antibiotic response curve varied among compounds (0.7 ≤ κ ≤ 10.5), with the steepest curve being found for the aminoglycosides streptomycin and kanamycin. The model was sensitive to this antibiotic response curve shape and to the sc, indicating the importance of fitness differences between strains for determining the MSC. The MSC can be >1 order of magnitude lower than the MIC, typically by the factor sc^κ This study provides an initial quantitative depiction and a framework for a research agenda to examine the growing evidence of selection for resistant bacterial communities at low environmental antibiotic concentrations.