Multi-drug-resistant bacteria pose a significant threat to public health. The role of the environment in the overall rise in antibiotic-resistant infections and risk to humans is largely unknown. This study aimed to evaluate drivers of antibiotic-resistance levels across the River Thames catchment, model key biotic, spatial and chemical variables and produce predictive models for future risk assessment. Sediment samples from 13 sites across the River Thames basin were taken at four time points across 2011 and 2012. Samples were analysed for class 1 integron prevalence and enumeration of third-generation cephalosporin-resistant bacteria. Class 1 integron prevalence was validated as a molecular marker of antibiotic resistance; levels of resistance showed significant geospatial and temporal variation. The main explanatory variables of resistance levels at each sample site were the number, proximity, size and type of surrounding wastewater-treatment plants. Model 1 revealed treatment plants accounted for 49.5% of the variance in resistance levels. Other contributing factors were extent of different surrounding land cover types (for example, Neutral Grassland), temporal patterns and prior rainfall; when modelling all variables the resulting model (Model 2) could explain 82.9% of variations in resistance levels in the whole catchment. Chemical analyses correlated with key indicators of treatment plant effluent and a model (Model 3) was generated based on water quality parameters (contaminant and macro- and micro-nutrient levels). Model 2 was beta tested on independent sites and explained over 78% of the variation in integron prevalence showing a significant predictive ability. We believe all models in this study are highly useful tools for informing and prioritising mitigation strategies to reduce the environmentalresistome.
We subsequently conducted a principal component analysis (PCA) to visualize the ordination of ARGs abun- dance between sample types. ARGs profiles of human and animal stools appeared to be most strongly sepa- rated from the other sample types in both the first two principal components (PC1 and PC2) which accounted for the first and the second largest possible variance in our data set (Fig. 3a). Testing for potential differences confirmed that scores on PC1 significantly differed be- tween all sample types, except for human and animal samples. Also, the scores on PC2 are significantly differ- ent between most of the sample types, except for water and vegetables, indicating that the resistome differs be- tween sample types (Fig. 3c). In order to identify how the sample types differed in resistome composition, we next plotted the factor loadings (the correlation coeffi- cients between the ARGs abundance and sample types) of the PC1 and PC2. The plot shows that the abundance of mcr-1 , mcr-3 and CTX-M-1 genes are highly loaded on PC1 and abundance of bla NDM , bla OXA-48 , and mcr-5
Enterobacteriaceae [32, 50]. Only in recent years, Entero- bacteriaceae have been confirmed as indigenous com- ponents of the plant microbiome in other species [12, 26, 27, 60]. These pathogenic bacteria come also into focus for their potential role in the transfer of antibiotic resistance by mobile genetic elements [28, 34, 58]. The environmentalresistome has now been recognized as the origin and reservoir of antibiotic resistance genes and is considered to be dynamic and ever-expanding . With increasing resistances, the success of treatment options for infectious diseases, e.g., cases of sepsis, after major surgery or during cancer chemotherapy will be compromised [20, 22]. Wellington et al.  discussed an extensive anti- biotic resistance (AR) “pollution” in our environment. In a large-scale metagenomics-based study of anti- biotic resistances in the environment, Nesme et al.  depicted soil habitats as the most diverse reser- voir for AR across four different environmental clus- ters. Lettuce was also reported as a source of multi-resistant bacteria [17, 64], but such information thus far lacks for arugula. Therefore, we were inter- ested in the potential for antibiotic resistance in this unique ecosystem and hypothesized that the arugula resistome may be affected by its particular microbiome.
high-throughput sequencing [9, 10], and epicPCR (emul- sion, paired isolation, and concatenation PCR) . Pure culture isolation, combined with whole-genome sequen- cing, has been and remains an important method to de- termine the phenotypic and genotypic correlations for ARBs and identify the MGEs with which they are associ- ated [12, 13]. However, only a limited fraction of bacteria in WWTPs can be cultured and isolated, which seriously limits the application of pure culture isolation to explore the environmentalresistome. High-throughput sequen- cing has greatly increased our knowledge of the diversity and abundance of ARGs in WWTPs [14, 15]. However, the information about the ARG-carrying species and the genetic contexts remains poorly understood, because of the short read length generated by Illumina sequencing. Although assembly of short reads might provide such in- formation, the frequent repetitive sequences flanking ARGs carried on MGEs usually hamper the effective as- sembly of genetic contexts of ARGs . EpicPCR was developed to link functional genes and phylogenetic markers, such as 16S rRNA in single cells, and has been used to identify the hosts of ARGs . However, this PCR-based method requires the sequence information of the target genes of interest, and only one functional tar- get gene can be sorted each time, although the phylo- genetic marker gene could be a universal one . Above all, a robust method is urgently required to re- solve both the genetic environments and the hosts of the ARGs in a high-throughput format.
widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype- based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. Conclusions: Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmentalresistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Keywords: Antibiotic resistance, Antibiotic resistance gene, Resistome, Mobile genetic element, Horizontal gene transfer, Human gut microbiome, Pathogen, Transmission, Metagenome, Bacterial genome
However, recent research has demonstrated that the utilization of organic com- pounds as fertilizers in agriculture soils can alter the selective pressure that drives anti- biotic resistance genes (ARGs) on soil-borne microbial communities . Soil ecosystems are considered to harbor a remarkable diversity of ARGs . According to Wright et al. , the collection of all the ARGs and their precursors in both patho- genic and non-pathogenic bacteria can be defined by the term ‘resistome’. The number of studies reporting the dynamics of resistome in the environment is growing . To date, the impacting activities often reported are associated to manure fertilization and wastewater utilization in agricultural practices [6, 7]. The discovery of new sources of anthropogenic practices that may affect ARGs in the environment is a challenging and timely topic, since the mechanisms regulating the spread of resistance and evolution of pathogens in environmentalresistome are widely unknown .
In the present study, a set of the DNA samples, extracted from the fecal samples collected during the pre- vious Phase 2b clinical study, were analyzed by whole- genome shotgun sequencing and alignment against the Comprehensive Antibiotic Resistance Database (CARD, https://card.mcmaster.ca/home). Some of the samples were also analyzed by qPCR and additional statistical analyses using clinical metadata and a linear model were performed to compare the change in the number of hits for AMR genes pre- to post-antibiotics. Here we report the ﬁ ndings of these analyses and demonstrate, consistent with its intended mechanism of action, ribaxamase appeared to reduce changes in the AMR gene pro ﬁ le (the resistome) in the GI tract of patients treated with ceftriaxone. Five-fold more AMR genes were signi ﬁ cantly changed in terms of hits in placebo-treated patients as compared with ribaxa- mase-treated patients, including genes relevant to the clin- ical study such as β– lactamase, vancomycin resistance, and macrolide resistance genes. A qPCR assay con ﬁ rmed these results for two representative genes.
Human GM has become a functional reservoir of anti- microbial resistance genes (ARGs) 17 that could potentially be acquired by opportunistic pathogens. 17,18 These patho- gens could translocate from the gut to various body sites through fecal contamination, gut barrier penetration, and medical services (such as catheter replacement). 19,20 Such pathogens could further complicate infections, especially in immune-compromised individuals (including pregnant women and infants), 21,22 and stress health care resources. Bacterial pathogens carrying ARGs could affect ovum implantation, pregnancy sustention, and delivery, and they could be life-threatening for both the mother and fetus. 23,24 To deal with emerging infectious diseases, a top priority is an effective strategy for pro ﬁ ling the GM resistome and documenting the abundance of antibio- tic-resistant bacteria in the human gut.
for antibiotic resistance genes, termed the gut resistome [13–17]. The use of antibiotics may favor the selection for antimicrobial resistance genes (ARGs) among mem- bers of the gut microbiota, thus increasing the likelihood of horizontal spread of ARGs between commensals and opportunistic pathogens co-residing in the gut . Dur- ing the administration of SDD, the gut resistome of patients is monitored by the cultivation of resistant bacteria from rectal swabs or feces, as part of routine diagnostics. However, methods that rely on microbial culture capture only a fraction of the gut resistome, since anaerobic commensals, which are the main reservoir of ARGs in the gut microbiota, are difficult to culture [18–20]. Thus, culture-independent methods are needed to comprehensively assess the impact of antibiotic prophylaxis on the microbiota and resistome of ICU patients.
The purpose of our research is to clarify the relationship between environm ental actions, environmental consciousness, and the extent to which environmental labels are recognized. There are significant differences in the individual perception of environmental problems, and it is important to encourage environmental actions while taking into consideration these differences. Then in this research, we assumed a relationship between actions that are conscious of environmental problems (environmental actions), and the extent to which commonly known environmental labels are recognized, and how consciousness of environmental problems fluctuates high or low (environmental consciousness); and conducted an online questionnaire survey to investigate these issues. To illustrate concrete environmental actions, we took advantage of the registrat ion for energy visualization provided by a power company (through the “electric household account book), and efforts to reduce electricity usage (reduction efforts) and the agreement on power peak shift (peak shift agreement).
Analysis of the antibiotic resistance genes of C. gilardii W2-2 and comparison with other C. gilardii strains reveals a large and complex resistome within this species. Two of the major concerns about C. gilardii as an emerging pathogen are its innate resistance to multiple antibiotics and its ability to acquire new resistances during therapy, often requiring a combination of multiple drugs and changes in therapy during the treatment of patients (11, 13–17). However, no C. gilardii clinical isolate has been sequenced to date, nor is there any knowledge about the antibiotic resistance mechanisms found in this species, except for a recent report of a transposon containing the mcr-5 colistin resistance gene identiﬁed ﬁrst in a Salmonella enterica serovar Paratyphi plasmid and then, using BLAST analysis, in chromosome 1 of C. gilardii CR3 (18). Therefore, we studied in more detail the antibiotic resistance in our C. gilardii water isolate, further analyzed its genome to identify its antibiotic resistance determinants, and used comparative genomic studies to determine how extended and conserved these determinants are within C. gilardii.
Sequences were quality filtered using Trimmomatic v0.32  and human-derived reads removed using BBMap v35.40 (comparing reads to the NCBI human ref- erence genome release GRCh38) . Contigs were de novo assembled using IDBA-UD v1.1.1 , followed by identification of open-reading frames using MetaGene- Mark v3.26 . A non-redundant gene catalogue was constructed using CDHIT v4.6  and resistome com- position annotated by BLASTP search to the Comprehen- sive Antibiotic Resistance Database (CARD) v1.1.7 . Quantification of gene hits was determined by SOAP v2.20  and normalised to counts per million reads.
This study involved sample isolates collected from a local pig slaughterhouse (Jaén, Spain), which is representative of those in the region and receives animals from multiple suppliers and geographic locations. Different samples were collected with sterile swabs from the animals’ backs (A; or equivalent surfaces) and also environmental surfaces (S) from the following zones (Figure 1): “animal arrival” (MA, MS), stabling and corral showers (CA, CS), anesthesia (AA, AS), “scalding and depilating” (PA, PS), “scorching and whip” (FA, FS), evisceration (several samples) and extraction of lard (MNT1, MNT2), “weight and classification” (BA, BS) and sale (EA, ES). For animal products, only the surface was swabbed. The samples were immediately stored and transported to the laboratory under refrigerated conditions.
In this study, a catalog of antibiotic resistome in drink- ing water was established and the host-tracking of ARGs was conducted via a large-scale survey using metage- nomic approach. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range from 2.8 × 10 −2 to 4.2 × 10 −1 capc. The highest abundance was observed in northern China. The dominant ARGs in the drinking water samples include bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes. Moreover, metagenomic assembly based host- tracking revealed that 80% of the ARG-carrying contigs originating from Pseudomonas spp. carried multidrug re- sistance genes. The findings of this study should propel the global surveillance and risk assessment of ARGs in drinking water onto the agendas of water supply author- ities. This will aid to prevent both the proliferation of ARGs in drinking water and their horizontal transfer to
Version: Accepted Version
Zheng, F., Zhu, D., Giles, M. et al. (4 more authors) (2019) Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome. The Science of The Total Environment, 680. pp. 70-78. ISSN 0048-9697
In addition to clinical or nosocomial transfer of antimicrobial resistance, due to issues such as patient non-compliance and improper prescribing practices (Berglund 2015), environmental transmission of both ARB and ARGs has been well documented (Pruden et al. 2013; Bengtsson-Palme 2017; Hiltunen et al. 2017). In fact, evidence suggests that the environment is not only a reservoir for antimicrobial resistance, but the source itself (Davies and Davies 2010; O’Toole 2014; Berglund 2015). Resistance genes are increasingly thought of as a separate class of contaminant and risk factor due to their ability to undergo gene transfer after bacterial death and presence in a variety of environmental contexts (Pruden et al. 2006; Liss et al. 2016). Current examples of ARG surveillance include cattle and swine manures (Zhu et al. 2013; Udikovic-Kolic et al. 2014; Wichmann et al. 2014; Ross and Topp 2015; Noyes et al. 2016; Qian et al. 2016), municipal solid wastes (Ross and Topp 2015; Ju et al. 2016), wastewater effluents (Pruden et al. 2013), and even paper currency (Jalali et al. 2015). Generally, these efforts have found that manure treatments without composting can lead to significant increases in ARGs in soils (Zhu et al. 2013; Udikovic-Kolic et al. 2014; Ross and Topp 2015), but thermophilic composting or anaerobic digestion can reduce the overall load of resistance in these materials (Qian et al. 2016; Liao et al. 2017).
Junior Eco-Club is an organization of children who engage in environmental activities, with support from the Ministry of the Environment of Japan. The national club meeting in Kitakyushu, Fukuoka on March 30, 2008 was a great success, draw- ing some 12,800 visitors in spite of drizzly weather. Toppan took part in the meeting by hold- ing a card-making workshop, inviting about 80 children to press paper and make postcards from Cartocans. Many of the parents asked Toppan about Cartocan and reported their impressions and opinions. The workshop was originally orga- nized at the request of the host as a venue to raise the environmental awareness among chil- dren. Ultimately, however, it provided Toppan with the opportunity to introduce the environmental benefits of Cartocan not only to children, but also to their parents. This made the workshop all the more meaningful for Toppan.
demand. I had planned already to include the following contemporary conflict, which now looks to me even more significant. In the late 1990s, in the region of Intag (Cotocachi, province of Imbabura) in northern Ecuador, Mitsubishi was defeated by a local non-governmental organization, Decoin, with help from Ecuadorian and international groups, in its plans to start mining for copper. I know this case first-hand, because of my relation with Accion Ecologica (Quito) which helped Decoin. The idea was to relocate one hundred families to make way for open-cast mining, bringing in thousand of miners in order to extract a large reserve of copper. This is a beautiful and fragile area of cloud forest and agriculture, with a mestizo population. Rio Tinto had already shown interest, but its previous incursions in Ecuador (at Salinas in Bolivar, at Molleturo in Azuay) ended in retreats. A Mitsubishi subsidiary, Bishi Metals, started in the early 1990s some preliminary work in Intag. After many meetings with the authorities, on May 12, 1997, a large gathering of members of affected communities resorted to direct action. Most of the company’s goods were inventoried and removed from the area (and later given back to the company), and the remaining equipment was burnt with no damage to persons. The government of Ecuador reacted by bringing a court case for terrorism (a rare event in Ecuador) against two community leaders and the leader of Decoin but the case was dismissed by the courts one year later. Attempts to bring in Codelco to mine (the Chilean national copper company) were also defeated, when Accion Ecologica from Quito sent one activist, Ivonne Ramos, to downtown Santiago to demonstrate with support from Chilean environmentalists on the occasion of a state visit of the president of Ecuador, and she was arrested. The publicity convinced Codelco to withdraw. Accion Ecologica also organized a visit by women belonging to the Intag communities, to copper mining areas in Peru, like Cerro de Pasco, La Oroya and Ilo. The women did their own interviews in those areas, and came back to Intag with their own impressions, carrying sad miners’ music and lyrics which became an immediate hit in Intag. These triumphant local women still deny to this day that they are environmentalists, or, God forbid, ecofeminists. 4 Today there are several initiatives for alternative forms of development in Intag, one of them being the export of “organic” coffee to Japan arranged through environmental networks first contacted in the fight against Mitsubishi. But the copper ore is still there, underground, and the world demand for copper (despite calls for the “dematerialization” of the economy) keeps increasing.