Co-selection of antibiotic and metal(loid) resistance in gram-negative epiphytic bacteria from contaminated salt marshes

Plastiome: Plastisphere-enriched mobile resistome in aquatic environments

Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.

Modeling the impact of urban and hospital eco-exposomes on antibiotic-resistance dynamics in wastewaters

The emergence and selection of antibiotic resistance is a major public health problem worldwide. The presence of antibiotic-resistant bacteria (ARBs) in natural and anthropogenic environments threatens the sustainability of efforts to reduce resistance in human and animal populations. Here, we use mathematical modeling of the selective effect of antibiotics and contaminants on the dynamics of bacterial resistance in water to analyze longitudinal spatio-temporal data collected in hospital and urban wastewater between 2012 and 2015. Samples were collected monthly during the study period at four different sites in Haute-Savoie, France: hospital and urban wastewater, before and after water treatment plants. Three different categories of exposure variables were collected simultaneously: 1) heavy metals, 2) antibiotics and 3) surfactants for a total of 13 drugs/molecules; in parallel to the normalized abundance of 88 individual genes and mobile genetic elements, mostly conferring resistance to antibiotics. A simple hypothesis-driven model describing weekly antibiotic resistance gene (ARG) dynamics was proposed to fit the available data, assuming that normalized gene abundance is proportional to antibiotic resistant bacteria (ARB) populations in water. The detected compounds were found to influence the dynamics of 17 genes found at multiple sites. While mercury and vancomycin were associated with increased ARG and affected the dynamics of 10 and 12 identified genes respectively, surfactants antagonistically affected the dynamics of three genes. The models proposed here make it possible to analyze the relationship between the persistence of resistance genes in the aquatic environment and specific compounds associated with human activities from longitudinal data. Our analysis of French data over 2012-2015 identified mercury and vancomycin as co-selectors for some ARGs.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

Metal- and antibiotic-resistant heterotrophic plate count bacteria from a gold mine impacted river: the Mooi River system, South Africa

The Wonderfonteinspruit, South Africa, is highly impacted by a century of gold mining activities. The aim of this study was to investigate the physico-chemical properties of the Wonderfonteinspruit and the receiving Mooi River system, the levels of antimicrobial (metals and antibiotics) resistance characteristics and heterotrophic bacteria levels in these water systems. Various physico-chemical parameters were determined. R2A agar and R2A agar supplemented with antimicrobials were used to enumerate heterotrophic bacteria. Morphologically distinct antimicrobial-resistant isolates were purified and screened for antibiotic susceptibility by a disc diffusion method. Selected isolates were identified, and minimum inhibitory concentration ranges determined. Among the antimicrobial resistant isolates, 87% were resistant to at least one antibiotic. Of these, almost 50% were resistant to more than 3 antibiotic classes. A large proportion was resistant to all 7 antibiotics tested. Phyla detected were Proteobacteria, Firmicutes and Bacteriodetes. High MIC levels for metals and antibiotics were detected among all the genera. Results demonstrate potential impacts of physico-chemical properties on levels of antimicrobial-resistant bacteria. Metal-resistant bacteria were also resistant to multiple antibiotics, suggesting that metal pollution from mining may be responsible for co-selection and maintenance of antibiotic-resistant bacteria in this aquatic system.

Ecological risk under the dual threat of heavy metals and antibiotic resistant Escherichia coli in swine-farming wastewater in Shandong Province, China

Mineral elements and antibiotic-resistant bacterial pollutants in livestock and poultry farms' wastewater are often sources of ecological and public health problems. To understand the heavy-metal pollution status and the characteristics of drug-resistant Escherichia coli (E. coli) in swine-farm wastewater in Shandong Province and to provide guidance for the rational use of mineral-element additives, common antibiotics, and quaternary ammonium compound disinfectants on swine farms, 10 mineral elements were measured and E. coli isolated from wastewater and its resistance to 29 commonly used antibiotics and resistance genes was determined. Finally, phylogenetic and multi-locus sequence typing (MLST) analyses was performed on E. coli. The results showed serious pollution from iron and zinc, with a comprehensive pollution index of 708.94 and 3.13, respectively. It is worth noting that average iron levels in 75% (12/16) of the districts exceed allowable limits. Multidrug-resistant E. coli were found in every city of the province. The E. coli isolated from swine-farm wastewater were mainly resistant to tetracyclines (95.3%), chloramphenicol (77.8%), and sulfonamides (62.2%), while antibiotic resistance genes for quinolones, tetracyclines, sulfonamides, aminoglycosides, and β-lactams were all more than 60%. The clonal complex 10 (CC10) was prevalent, and ST10 and ST48 were dominant in E. coli isolates. Multidrug-resistant E. coli were widely distributed, with mainly A genotypes. However, the mechanism of the effect of iron on antibiotic resistance needs more study in this area. Thus, further strengthening the prevention and control of iron and zinc pollution and standardizing the use of antibiotics and mineral element additives in the swine industry are necessary.

Pseudomonas fluorescens Complex and Its Intrinsic, Adaptive, and Acquired Antimicrobial Resistance Mechanisms in Pristine and Human-Impacted Sites

Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, pathogenic opportunistic microorganisms. The records of antimicrobial-resistant P. fluorescens are quite scattered, which hinders the recognition of patterns. This review compiles published data on antimicrobial resistance in species belonging to the P. fluorescens complex, which were identified through phylogenomic analyses. Additionally, we explored the occurrence of clinically relevant antimicrobial resistance genes in the genomes of the respective species available in the NCBI database. Isolates were organized into two categories: strains isolated from pristine sites and strains isolated from human-impacted or metal-polluted sites. Our review revealed that many reported resistant phenotypes in this complex might be related to intrinsic features, whereas some of them might be ascribed to adaptive mechanisms such as colistin resistance. Moreover, a few studies reported antimicrobial resistance genes (ARGs), mainly β-lactamases. In-silico analysis corroborated the low occurrence of transferable resistance mechanisms in this Pseudomonas complex. Both phenotypic and genotypic assays are necessary to gain insights into the evolutionary aspects of antimicrobial resistance in the P. fluorescens complex and the possible role of these ubiquitous species as reservoirs of clinically important and transmissible ARGs.

Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture

Increasing use of feed and medicine in mariculture could cause negative environmental impacts such as habitat modification, microbial disease development and antibiotic resistance. Here we investigated contamination of antibiotics and antibiotic resistance genes (ARGs), and composition of microbial community in grouper mariculture systems in Hainan province, China. Results showed detection of various antibiotic residues with the dominance of fluoroquinolones and tetracyclines in the six grouper cultivation systems. The concentrations of the detected antibiotics in the grouper mariculture water were significantly higher than those in the original seawater. Some of the detected antibiotics such as enrofloxacin, ciprofloxacin, ofloxacin, oxytetracycline and erythromycin in the mariculture water and/or sediment would pose high resistance selection risks. Sulfonamides resistance genes sul1 and sul2 were found to be predominant in water and sediment, while tetracycline resistance genes were prevalent in fish gill and gut. The dominant bacterial phyla in water and sediments were Bacteroides, Actinomycetes, and Proteobacteria, while the dominant ones in fish gill and gut were the Proteobacteria. Genera of Vibrio and Mycobacterium in the core microbiota were important zoonotic pathogens, and there was a significant positive correlation between Vibrio and ARGs. Phyla of Proteobacteria, Actinomyces, and Cyanobacteria were positively correlated to ARGs, indicating that these microorganisms are potential hosts of ARGs. The putative functions of microbiome related to antibiotic resistance and human diseases were significantly higher in fish than in the mariculture environment. This study suggests that mariculture system is a reservoir of ARGs, and the use of antibiotics in mariculture could induce the increase of antibiotic resistance and the prevalence of opportunistic pathogens.

Co-Selection of Heavy Metal and Antibiotic Resistance in Soil Bacteria from Agricultural Soils in New Zealand

Accumulation of trace elements (including heavy metals) in soil from usage of superphosphate fertilisers induces resistance of soil bacteria to trace elements of environmental concern (TEoEC) and may co-select for resistance to antibiotics (Ab). This study aimed to investigate selection of co-resistance of soil bacteria to Cd, Zn and Hg, and Ab in soils with varied management histories. Genetic diversity of these bacteria and horizontal transfer of Cd resistance genes (cadA and czcA) were also investigated. Soils with either pastoral and arable management histories and either high levels of Cd and Zn, or indigenous bush with background levels of these TEoEC from the Waikato region, New Zealand were sampled. Plate culturing with a range of TEoEC and Ab concentrations, Pollution Induced Community Tolerance (PICT) assay, antibiotic sensitivity, terminal restriction fragment length polymorphism (TRFLP) and horizontal gene transfer (HGT) analyses were employed to investigate co-selection of TEoEC and Ab resistance. Higher levels of bacterial resistance to TEoEC and Ab correlated with higher levels of TEoEC in soil. Bacterial community structures were altered in soils with high TEoEC levels. Cd resistance genes were transferred from donor bacterial isolates, to recipients and the transconjugants also had resistance to Zn and/or Hg and a range of Ab.

Genome analysis of two multidrug-resistant Escherichia coli O8:H9-ST48 strains isolated from lettuce

Vegetables may become contaminated with antibiotic-resistant bacteria from farm-to-fork. Here we report draft genome sequences of two multidrug-resistant Escherichia coli isolated from lettuce. Whole genomes of strains Y15 V.22 and Y15 V.54 were sequenced. Available tools were used to inspect for virulence factors (VF), metals tolerance, resistome and mobilome features. The predicted genome sizes were 5,4 Mb and 6,2 Mb for Y15 V.22 and Y15 V.54, respectively, both with 50.7% GC content, ST48 and serotype O8:H9. Resistome analysis showed genes encoding resistance to β-lactams, sulphonamides, trimethoprim, tetracyclines and macrolides. Cobalt, cadmium, zinc and copper tolerance determinants were identified in both. VF detected included genetic determinants related to toxin production, adherence and invasion. SNPs and VF content analysis showed a close relatedness to ETEC. Putative genomic islands, prophage and CRISPR sequences were predicted. The genome sequences here reported will aid in understanding antibiotic resistance transfer between vegetables consumed raw and humans.

Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria

Environmental health is a critical concern, continuously contaminated by physical and biological components (viz., anthropogenic activity), which adversely affect on biodiversity, ecosystems and human health. Nonetheless, environmental pollution has great impact on microbial communities, especially bacteria, which try to evolve in changing environment. For instance, during the course of adaptation, bacteria easily become resistance to antibiotics and heavy metals. Antibiotic resistance genes are now one of the most vital pollutants, provided as a source of frequent horizontal gene transfer. In this review, the environmental cause of multidrug resistance (MDR) that was supposed to be driven by either heavy metals or combination of environmental factors was essentially reviewed, especially focussed on the correlation between accumulation of heavy metals and development of MDR by bacteria. This kind of correlation was seemed to be non-significant, i.e. paradoxical. Gram-positive bacteria accumulating much of toxic heavy metal (i.e. highly stress tolerance) were unlikely to become MDR, whereas Gram-negative bacteria that often avoid accumulation of toxic heavy metal by efflux pump systems were come out to be more prone to MDR. So far, other than antibiotic contaminant, no such available data strongly support the direct influence of heavy metals in bacterial evolution of MDR; combinations of factors may drive the evolution of antibiotic resistance. Therefore, Gram-positive bacteria are most likely to be an efficient member in treatment of industrial waste water, especially in the removal of heavy metals, perhaps inducing the less chance of antibiotic resistance pollution in the environment.

Acceleration of emergence of E. coli antibiotic resistance in a simulated sublethal concentration of copper and tetracycline co-contaminated environment

An environment co-contaminated with metals and antibiotics ultimately exposes bacteria to these metals and antibiotics simultaneously. This study aims to explore the efficacy of sublethal concentrations of copper ions contaminated with tetracycline regarding antibiotic resistance in a sensitive strain of E. coli K12. The study proved that a copper ions and tetracycline co-contaminated environment could considerably enhance the mutation frequencies of chloramphenicol and polymyxin B resistance in antibiotic susceptible E. coli; however, the equivalent copper ions and tetracycline alone showed weaker effects. Results also demonstrated that an environment co-contaminated with relatively high sublethal concentrations of copper ion and tetracycline co-contaminated environment could induce much higher antibiotic resistance than the low sublethal and control groups. Whole-genome characterization results indicated that variability existed within the genotype and phenotype involved in antibiotic resistance. Additionally, the evolved resistant strains displayed hereditary resistance after 5 round culture cycles in LB broth over 5 days. Results implied that co-contamination with metals and antibiotics environment could strengthen resistance and contribute to the induction and dissemination of antibiotic resistance in metal and antibiotic co-contaminated environment.

Distribution characteristics and potential risks of heavy metals and antimicrobial resistant Escherichia coli in dairy farm wastewater in Tai'an, China

Heavy metals and antimicrobial resistant bacteria in livestock and poultry environments can cause declines in production and significant economic losses, leading to potential environmental and public health issues. In this study, the heavy metal pollution status of livestock breeding water bodies in the Dawen river basin of Shandong Province in China was evaluated, and a total of 10 heavy metals were measured. In addition, antimicrobial susceptibility tests were conducted for Escherichia coli strains isolated from the water samples. The results showed that among all the metals, copper, zinc, and iron were detected at each sampling point, followed by nickel (detection rate of 95.74%), arsenic (detection rate of 89.36%), selenium (detection rate of 68.09%), lead (detection rate of 27.66%), and mercury (detection rate of 12.77%). Cadmium and hexavalent chromium were not detected. The contents of nine heavy metals were below the existing water standard values in China, whereas the iron pollution index in the water body in the study area was large and may pose a potential risk. A total of 17 E. coli isolates showed different resistance to β-lactams, aminoglycosides, tetracyclines, quinolone antibiotics and chloramphenicol, but were mainly resistant to β-lactams and tetracyclines. The detection rate of the tetA resistance gene was relatively high, indicating the overuse of cephalosporins and tetracyclines. The results of the present study might provide evidence of metal pollution and theoretical basis on the treatment of colibacillosis in the livestock industries.

Selection of antibiotic resistance by metals in a riverine bacterial community

Antibiotic resistance is a health challenge across human, animal and environmental settings. In the environment, metals may contribute to antibiotic resistance selection. This study aimed to investigate the role of copper and zinc in the selection of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in a riverine bacterial community. Using a microcosm approach, bacteria in water samples were exposed to 50 μg L^-1 and 100 μg L^-1 of copper and zinc, for 20 days. The prevalence of ARB was determined from colony forming units counts in media with and without antibiotics. A significant increase in the prevalence of cefotaxime-resistant (from 2.3% in control to 9.5% in Cu50 and 16.8% in Cu100) and tetracycline-resistant bacteria (from 0.03% to 0.23% in Cu100) was observed in communities exposed to copper. Zinc exposure resulted in an increase in the prevalence of cefotaxime-resistant bacteria (from 24.6% to 91.3% in Zn50 and 72.4% in Zn100) and of kanamycin-resistant bacteria (from 6.1% to 24.1% in Zn50 and 43% in Zn100). Cefotaxime- and kanamycin-resistant bacteria belonged to genera intrinsically resistant to these compounds. DGGE profiling confirmed that metal exposure altered the structure and diversity of bacterial communities. Changes in the abundance of genes usually associated with mobile genetic elements (bla_CTX-M, bla_TEM, tet(A) and intI1) were not detected after exposure. Results demonstrated the selection of bacteria intrinsically resistant to antibiotics imposed by copper and zinc exposure, suggesting an important role played by cross-resistance mechanisms.

Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co-selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim's Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co-occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment.

Comparison of Microbiomes and Resistomes in Two Karst Groundwater Sites in Chongqing, China

Karst groundwater is an important water resource, as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in karst groundwater, two karst water samples were chosen for metagenome and metatranscriptome study, namely the 37^th spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes, and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database, three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed.

Efflux proteins MacAB confer resistance to arsenite and penicillin/macrolide-type antibiotics in Agrobacterium tumefaciens 5A

Antibiotic and arsenic (As) contaminations are worldwide public health problems. Previously, the bacterial ABC-type efflux protein MacAB reportedly conferred resistance to macrolide-type antibiotics but not to other metal(loid)s. In this study, the roles of MacAB for the co-resistance of different antibiotics and several metal(loid)s were analyzed in Agrobacterium tumefaciens 5A, a strain resistant to arsenite [As(III)] and several types of antibiotics. The macA and macB genes were cotranscribed, and macB was deleted in A. tumefaciens 5A and heterologously expressed in Escherichia coli AW3110 and E. coli S17-1. Compared to the wild-type strain 5A, the macB deletion strain reduced bacterial resistance levels to several macrolide-type and penicillin-type antibiotics but not to cephalosporin-type antibiotics. In addition, the macB deletion strain showed lower resistance to As(III) but not to arsenate [As(V)], antimonite [Sb(III)] and cadmium chloride [Cd(II)]. The mutant strain 5A-ΔmacB cells accumulated more As(III) than the cells of the wild-type. Furthermore, heterologous expression of MacAB in E. coli S17-1 showed that MacAB was essential for resistance to macrolide, several penicillin-type antibiotics and As(III) but not to As(V). Heterologous expression of MacAB in E. coli AW3110 reduced the cellular accumulation of As(III) but not of As(V), indicating that MacAB is responsible for the efflux of As(III). These results demonstrated that, in addition to macrolide-type antibiotics, MacAB also conferred resistance to penicillin-type antibiotics and As(III) by extruding them out of cells. This finding contributes to a better understanding of the bacterial resistance mechanisms of antibiotics and metal(loid)s.

Response of antibiotic resistance to the co-existence of chloramphenicol and copper during bio-electrochemical treatment of antibiotic-containing wastewater

Concerns have been raised regarding co-selection for antibiotic resistance among microorganisms exposed to antibiotics and metals. As a promising approach for treating antibiotics and heavy metal-containing wastewater, a bio-electrochemical system (BES) can be used for antibiotic and heavy metal removal. This study determined the fate of antibiotic resistance genes (ARGs) in a BES when exposed to chloramphenicol (CAP) and Cu²⁺. The ARGs encoding the efflux pump (cmlA, floR, and tetC), the class 1 integron integrase-encoding gene, and the sul1 gene were analyzed. The results indicated that the co-existence of CAP and different concentrations of Cu²⁺ had significant influence on the relative abundances of the ARGs. The changes in the bacterial community structure and the results of a quantitative correlation analysis between the bacterial community and the ARGs confirmed that the shift in the potential hosts was the key reason for the changes of the ARGs. This study sheds new light on the mechanisms of ARGs variations in BES under the co-selection pressure of antibiotics and heavy metals.

Extended Spectrum Beta-Lactamase-Producing Gram-Negative Bacteria Recovered From an Amazonian Lake Near the City of Belém, Brazil

Aquatic systems have been described as antibiotic resistance reservoirs, where water may act as a vehicle for the spread of resistant bacteria and resistance genes. We evaluated the occurrence and diversity of third generation cephalosporin-resistant gram-negative bacteria in a lake in the Amazonia region. This water is used for human activities, including consumption after appropriate treatment. Eighteen samples were obtained from six sites in October 2014. Water quality parameters were generally within the legislation limits. Thirty-three bacterial isolates were identified as Escherichia (n = 7 isolates), Acinetobacter, Enterobacter, and Klebsiella (n = 5 each), Pseudomonas (n = 4), Shigella (n = 3), and Chromobacterium, Citrobacter, Leclercia, Phytobacter (1 isolate each). Twenty nine out of 33 isolates (88%) were resistant to most beta-lactams, except carbapenems, and 88% (n = 29) were resistant to antibiotics included in at least three different classes. Among the beta-lactamase genes inspected, the bla_CTX–M was the most prevalent (n = 12 positive isolates), followed by bla_TEM (n = 5) and bla_SHV (n = 4). bla_CTX–M–15 (n = 5), bla_CTX–M–14 (n = 1) and bla_CTX–M–2 (n = 1) variants were detected in conserved genomic contexts: bla_CTX–M–15 flanked by ISEcp1 and Orf477; bla_CTX–M–14 flanked by ISEcp1 and IS903; and bla_CTX–M–2 associated to an ISCR element. For 4 strains the transfer of bla_CTX–M was confirmed by conjugation assays. Compared with the recipient, the transconjugants showed more than 500-fold increases in the MICs of cefotaxime and 16 to 32-fold increases in the MICs of ceftazidime. Two isolates (Escherichia coli APC43A and Acinetobacter baumannii APC25) were selected for whole genome analysis. APC43A was predicted as a E. coli pathogen of the high-risk clone ST471 and serotype O154:H18. bla_CTX–M–15 as well as determinants related to efflux of antibiotics, were noted in APC43A genome. A. baumannii APC25 was susceptible to carbapenems and antibiotic resistance genes detected in its genome were intrinsic determinants (e.g., bla_OXA–208 and bla_ADC–like). The strain was not predicted as a human pathogen and belongs to a new sequence type. Operons related to metal resistance were predicted in both genomes as well as pathogenicity and resistance islands. Results suggest a high dissemination of ESBL-producing bacteria in Lake Água Preta which, although not presenting characteristics of a strongly impacted environment, contains multi-drug resistant pathogenic strains.

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml⁻¹, chloramphenicol 0–24 μg ml⁻¹, and vancomycin 0–24 μg ml⁻¹). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.

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

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

Resistance to Metals Used in Agricultural Production

Metals and metalloids have been used alongside antibiotics in livestock production for a long time. The potential and acute negative impact on the environment and human health of these livestock feed supplements has prompted lawmakers to ban or discourage the use of some or all of these supplements. This article provides an overview of current use in the European Union and the United States, detected metal resistance determinants, and the proteins and mechanisms responsible for conferring copper and zinc resistance in bacteria. A detailed description of the most common copper and zinc metal resistance determinants is given to illustrate not only the potential danger of coselecting antibiotic resistance genes but also the potential to generate bacterial strains with an increased potential to be pathogenic to humans. For example, the presence of a 20-gene copper pathogenicity island is highlighted since bacteria containing this gene cluster could be readily isolated from copper-fed pigs, and many pathogenic strains, including Escherichia coli O104:H4, contain this potential virulence factor, suggesting a potential link between copper supplements in livestock and the evolution of pathogens.

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract

Antibiotic resistance is a global public health issue and metal exposure can co-select for antibiotic resistance. We examined genome sequences of three multi-drug and metal resistant bacteria: one Shewanella sp., and two Vibrio spp., isolated from the gut of the mummichog fish (Fundulus heteroclitus). Our primary goal was to understand the mechanisms of co-selection. Phenotypically, the strains showed elevated resistance to arsenate, mercury, and various types of β-lactams. The genomes contained genes of public health concern including one carbapenemase (bla_OXA-48). Our analyses indicate that the co-selection phenotype is mediated by chromosomal resistance genes and cross-resistance. No evidence of co-resistance was found; most resistance genes were chromosomally located. Moreover, the identification of many efflux pump gene homologs indicates that cross-resistance and/or co-regulation may further contribute to resistance. We suggest that the mummichog gut microbiota may be a source of clinically relevant antibiotic resistance genes.

Fate of antibiotic resistance genes and metal resistance genes during thermophilic aerobic digestion of sewage sludge

This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed. Partial redundancy analysis (RDA) showed that shifts in temperature were the key factors affecting a decrease in ARGs. Shifts in temperature led to decreased amounts of ARGs by reducing resistome and bacterial diversity, rather than by lowering horizontal transfer potential via intI1 or co-resistance via MRGs.

Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters

Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.

-Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

Antibacterial activity of oxytetracycline photoproducts in marine aquaculture's water

Oxytetracycline (OTC) is one of the most used antibiotics in aquaculture. The main concern related to its use is the bacterial resistance, when ineffective treatments are applied for its removal or inactivation. OTC photo-degradation has been suggested as an efficient complementary process to conventional methods used in intensive fish production (e.g.: ozonation). Despite this, and knowing that the complete mineralization of OTC is difficult, few studies have examined the antibacterial activity of OTC photoproducts. Thus, the main aim of this work is to assess whether the OTC photoproducts retain the antibacterial activity of its parent compound (OTC) after its irradiation, using simulated sunlight. For that, three Gram-negative bacteria (Escherichia coli, Vibrio sp. and Aeromonas sp.) and different synthetic and natural aqueous matrices (phosphate buffered solutions at different salinities, 0 and 21‰, and three different samples from marine aquaculture industries) were tested. The microbiological assays were made using the well-diffusion method before and after OTC has been exposed to sunlight. The results revealed a clear effect of simulated sunlight, resulting on the decrease or elimination of the antibacterial activity for all strains and in all aqueous matrices due to OTC photo-degradation. For E. coli, it was also observed that the antibacterial activity of OTC is lower in the presence of sea-salts, as demonstrated by comparison of halos in aqueous matrices containing or not sea-salts.

Antibiotic and metal resistance in a ST395 Pseudomonas aeruginosa environmental isolate: A genomics approach

We analyzed the resistome of Pseudomonas aeruginosa E67, an epiphytic isolate from a metal-contaminated estuary. The aim was to identify genetic determinants of resistance to antibiotics and metals, assessing possible co-selection mechanisms. Identification was based on phylogenetic analysis and average nucleotide identity value calculation. MLST affiliated E67 to ST395, previously described as a high-risk clone. Genome analysis allowed identifying genes probably involved in resistance to antibiotics (e.g. beta-lactams, aminoglycosides and chloramphenicol) and metals (e.g. mercury and copper), consistent with resistance phenotypes. Several genes associated with efflux systems, as well as genetic determinants contributing to gene motility, were identified. Pseudomonas aeruginosa E67 possesses an arsenal of resistance determinants, probably contributing to adaptation to a polluted ecosystem. Association to mobile structures highlights the role of these platforms in multi-drug resistance. Physical links between metal and antibiotic resistance genes were not identified, suggesting a predominance of cross-resistance associated with multidrug efflux pumps.