Antibiotic and heavy metal resistance in enterococci from coastal marine sediment

Novel insights into the co-selection of metal-driven antibiotic resistance in bacteria: a study of arsenic and antibiotic co-exposure

The simultaneous development of antibiotic resistance in bacteria due to metal exposure poses a significant threat to the environment and human health. This study explored how exposure to both arsenic and antibiotics affects the ability of an arsenite oxidizer, Achromobacter xylosoxidans CAW4, to transform arsenite and its antibiotic resistance patterns. The bacterium was isolated from arsenic-contaminated groundwater in the Chandpur district of Bangladesh. We determined the minimum inhibitory concentration (MIC) of arsenite, cefotaxime, and tetracycline for A. xylosoxidans CAW4, demonstrating a multidrug resistance (MDR) trait. Following this determination, we aimed to mimic an environment where A. xylosoxidans CAW4 was exposed to both arsenite and antibiotics. We enabled the strain to grow in sub-MIC concentrations of 1 mM arsenite, 40 µg/mL cefotaxime, and 20 µg/mL tetracycline. The expression dynamics of the arsenite oxidase (aioA) gene in the presence or absence of antibiotics were analyzed. The findings indicated that simultaneous exposure to arsenite and antibiotics adversely affected the bacteria's capacity to metabolize arsenic. However, when arsenite was present in antibiotics-containing media, it promoted bacterial growth. The study observed a global downregulation of the aioA gene in arsenic-antibiotic conditions, indicating the possibility of increased susceptibility through co-resistance across the entire bacterial population of the environment. This study interprets that bacterial arsenic-metabolizing ability can rescue the bacteria from antibiotic stress, further disseminating environmental cross-resistance. Therefore, the co-selection of metal-driven antibiotic resistance in bacteria highlights the need for effective measures to address this emerging threat to human health and the environment.

Co-selection mechanism for bacterial resistance to major chemical pollutants in the environment

Bacterial resistance is an emerging global public health problem, posing a significant threat to animal and human health. Chemical pollutants present in the environment exert selective pressure on bacteria, which acquire resistance through co-resistance, cross-resistance, co-regulation, and biofilm resistance. Resistance genes are horizontally transmitted in the environment through four mechanisms including conjugation transfer, bacterial transformation, bacteriophage transduction, and membrane vesicle transport, and even enter human bodies through the food chain, endangering human health. Although the co-selection effects of bacterial resistance to chemical pollutants has attracted widespread attention, the co-screening mechanism and co-transmission mechanisms remain unclear. Therefore, this article summarises the current research status of the co-selection effects and mechanism of environmental pollutants resistance, emphasising the necessity of studying the co-selection mechanism of bacteria against major chemical pollutants, and lays a solid theoretical foundation for conducting risk assessment of bacterial resistance.

Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment

Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00192-z.

Genomic insights into Enterococcus faecium isolates from marine bivalves highlight One Health concerns and healthcare linkages

Enterococci, especially Enterococcus faecium, are one of today's leading causes of multidrug-resistant infections in hospital settings. The marine environment may harbour enterococci, but its role as an evolutionary niche and as a vector for the spread of enterococci is sparsely investigated. Hence, by applying enterococci in bivalves as a sentinel tool, this study aimed to describe the prevalence of enterocooci along the Norwegian coast and in addition the phylogeny of E. faecium in particular. Enterococci in batch samples of marine bivalves, harvested from 86 different locations, were quantitatively examined by a culture-dependent most probable number (MPN) method. Isolates were identified by MALDI-TOF-MS prior to antimicrobial susceptibility testing by broth microdilution. In-detail analyses of a representative selection of E. faecium isolates (n=148) were done by Illumina whole-genome sequencing, and assembled genomes were compared to closed E. faecium genomes in the public databases and to genomes from commensal and clinical isolates from Norway. Diversity among E. faecium within the same batch sample of bivalves was also explored. Enterococci were detected in 287 of the 471 examined bivalve samples, but in low concentrations with a median value of <18 MPN /100 g. From positive samples, 479 isolates of enterococci were identified belonging to ten different species, where E. faecium (n=247), Enterococcus hirae (n=114) and Enterococcus faecalis (n=66) were most frequently found. Resistance towards one or more antimicrobial agents was observed in 197 isolates (41 %), none of the isolates showed acquired resistance to vancomycin or linezolid. Phylogenetic analyses revealed high diversity among the E. faecium isolates and showed that the marine niche is dominated by strains from the non-clinical setting belonging to clade A2 (n=85) and B (E. lactis) (n=60). Only three isolates belonged to the hospital-associated clade A1 (ST80 and ST117). Two of these clustered with one isolate from a hospitalized patient and one from a non-hospitalized person. This study demonstrated a high prevalence, but low concentrations of enterococci in bivalves, and low levels of antimicrobial resistance. E. faecium genomes showed high population diversity and that very few E. faecium isolates in bivalves may have arisen from the human healthcare system. A systematic surveillance of target micro-organisms applying methods examining multiple isolates from the same bivalve sample provides important data to assess the enterococcal phylogeny, antimicrobial resistance and the level of faecal pollution in the marine environment.

Endophytic fungi mediates production of bioactive secondary metabolites via modulation of genes involved in key metabolic pathways and their contribution in different biotechnological sector

Endophytic fungi stimulate the production of an enormous number of bioactive metabolites in medicinal plants and affect the different steps of biosynthetic pathways of these secondary metabolites. Endophytic fungi possess a number of biosynthetic gene clusters that possess genes for various enzymes, transcription factors, etc., in their genome responsible for the production of secondary metabolites. Additionally, endophytic fungi also modulate the expression of various genes responsible for the synthesis of key enzymes involved in metabolic pathways of such as HMGR, DXR, etc. involved in the production of a large number of phenolic compounds as well as regulate the expression of genes involved in the production of alkaloids and terpenoids in different plants. This review aims to provide a comprehensive overview of gene expression related to endophytes and their impact on metabolic pathways. Additionally, this review will emphasize the studies done to isolate these secondary metabolites from endophytic fungi in large quantities and assess their bioactivity. Due to ease in synthesis of secondary metabolites and their huge application in the medical industry, these bioactive metabolites are now being extracted from strains of these endophytic fungi commercially. Apart from their application in the pharmaceutical industry, most of these metabolites extracted from endophytic fungi also possess plant growth-promoting ability, bioremediation potential, novel bio control agents, sources of anti-oxidants, etc. The review will comprehensively shed a light on the biotechnological application of these fungal metabolites at the industrial level.

Prevalence of Class 1 Integron and In Vitro Effect of Antibiotic Combinations of Multidrug-Resistant Enterococcus Species Recovered from the Aquatic Environment in the Eastern Cape Province, South Africa

Enterococci are regarded as a better indication of faecal pollution in freshwater and marine waters. Their levels in seawater are positively connected with swimming-related gastrointestinal disorders. This study used an Enterococcus-specific polymerase chain reaction (PCR) to characterize the isolates. Classes 1 and 2 integrons were examined for environmental Enterococcus isolates using a standard biological procedure. All strains were assessed against a panel of 12 antibiotics from various classes using disc diffusion methods. The microdilution method was used to work out the minimum inhibitory concentration (MIC) according to the CLSI guiding principles. The combination therapy of the resistant drugs was evaluated using a checkerboard assay and a time-dependent test for assessing their bactericidal or bacteriostatic activity. The gene diversity of the tested organisms was analyzed with the aid of Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR. In total, 57 Enterococcus spp. environmental samples were recovered, in which Enterococcus faecalis (33.33%) and Enterococcus faecium (59.65%) were the dominant species. Resistance to linezolid, ciprofloxacin, erythromycin, gentamicin, vancomycin, rifampicin, and tetracycline was prevalent. Fifty (50) strains tested positive for class 1 integron, more frequent in Enterococcus faecium and Enterococcus faecalis isolates, with no gene cassette array discovered. A combination of gentamicin (MIC 4 µg/mL) with vancomycin (MIC 256 µg/mL) antibiotics against Enterococcus faecalis showed antibacterial activity. In contrast, the combination of ciprofloxacin (1 µg/mL) with Ampicillin (16 µg/mL) antibiotics against Enterococcus faecalis showed a bacteriostatic effect. The ERIC-PCR analysis pointed out that most of the assessed isolates have close genetic similarities.

A systematic review and meta-analysis on antimicrobial resistance in marine bivalves

Bivalves are filter-feeding animals able to accumulate contaminants and microorganisms, either of marine or terrestrial origin. The aim of this study was to describe the prevalence of antimicrobial resistance (AMR) in bacterial isolates from bivalves using a systematic review of the literature. Comprehensive searches of MEDLINE, EMBASE, and Web of Science were carried out, based upon a registered protocol (PROSPERO), and following the preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) guidelines. The methodological quality of the included studies was assessed using a modified Hoy checklist. Meta-analyses of prevalence were carried out using random-effects models. In total, 103 articles were selected from 1,280 records and were included in the final analysis. The studies were from Asia (n = 54), Europe (n = 27), South and North America (n = 10 and n = 6, respectively), Africa (n = 2), Oceania (n = 1), and multicentre and intercontinental (n = 3). The meta-analysis of multiple antibiotic resistance (MAR) index revealed Aeromonas spp. as the genus with the highest prevalence of AMR (37%), followed by Vibrio spp. (34%), Salmonella spp. (18%), and Escherichia coli (15%). Resistance to third/fourth/fifth generation cephalosporins and fluoroquinolones, two highest priority, critically important antimicrobials (HPCIA), was recorded in approximately 10% of E. coli isolates. Resistance to carbapenems was very low (<2%) in Salmonella spp. and in E. coli, but was found in 5% of Vibrio spp. and in more than a third of Aeromonas spp. isolates. In aquatic bacteria, resistance to carbapenems was higher in Asian than in European isolates. Our study shows the presence of antibiotic resistant bacteria (ARB), including bacteria resistant to HPCIA, in marine bivalves, posing a risk for consumers.

Antibiotic resistance and virulence genes in Enterococcus species isolated from raw and processed seafood

This study evaluated the antibiotic resistance characteristics and virulence genes of enterococci isolated from raw and processed seafood sold in the Marmara Region, Turkey. In this context, the enterococcal load was determined as between 1.0 and 2.5 log CFU/g in 39 of a total of 397 samples. It was determined that 117 strains isolated from the samples belonged to Enterococcus gallinarum, E. casseliflavus, E. durans, E. faecium, and E. faecalis species. Erythromycin, tetracycline, streptomycin, and gentamicin resistance was observed, whereas the tetM, ermB, aac(6')-aph(2'')-la genes were found in a majority of the isolates. It was also determined that the isolates carried the agg2 and gelE virulence genes. When all these results are evaluated, the presence of these isolates in aquatic products may pose a risk in terms of food safety and public health.

Metagenomic Characterization of Microbial Pollutants and Antibiotic- and Metal-Resistance Genes in Sediments from the Canals of Venice

The spread of fecal pollutants and antibiotic resistance in the aquatic environment represents a major public health concern and is predicted to increase in light of climate change consequences and the increasing human population pressure on the lagoon and coastal areas. The city of Venice (Italy) is affected by diverse microbial pollution sources, including domestic wastewaters that, due to the lack of modern sewage treatment infrastructure in the historical city center, are released into canals. The outflowing jets of its tidal inlets thus represent a source of contamination for the nearby beaches on the barrier island separating the lagoon from the sea. Metagenomic analyses of DNA extracted from sediment samples from six sites in the canals of the city’s historic center were undertaken to characterize the microbial community composition, the presence of fecal microbes as well as other non-enteric pathogens, and the content of genes related to antibiotic (AB) and heavy metal (HM) resistance, and virulence. The six sites hosted similar prokaryotic communities, although variations in community composition likely related to oxygen availability were observed. All sites displayed relatively high levels of fecal contamination, including the presence of Fecal Indicator Bacteria, sewage- and alternative feces-associated bacteria. Relatively high levels of other potential pathogens were also found. About 1 in 500 genes identified at these sites are related to AB and HM resistance; conversely, genes related to virulence were rare. Our data suggest the existence of widespread sediment microbial pollution in the canals of Venice, coupled with the prevalence of ARGs to antibiotics frequently used in humans as well as of HMRGs to toxic metals that still persists in the lagoon. All of this evidence raises concerns about the consequences on the water quality of the lagoon and adjacent marine areas and the potential risks for humans, deserving further studies.

Bacterial strains found in the soils of a municipal solid waste dumping site facilitated phosphate solubilization along with cadmium remediation

Phosphate solubilizing bacteria (PSB) that can withstand high cadmium (Cd) stress is a desired combination for bioremediation. This study evaluated the Cd bioremediation potential of four PSB strains isolated from the contaminated soils of a municipal solid waste (MSW) discarding site (Guwahati, India). PSB strains were cultured in Pikovskaya (PVK) media, which led to higher acid phosphatase (ACP) activity and the release of organic acid. Optical density (OD) measurements were performed to determine the growth pattern of PSB; furthermore, Cd uptake by PSB was evaluated using infrared spectroscopy (IR) and X-Ray Diffraction (XRD) analyses. The 16S rRNA taxonomic analysis revealed that all the four promising PSB strains belonged to either Bacillus sp. or Enterobacter sp. One strain (SM_SS8) demonstrated higher tolerance towards Cd (up to 100 mg L^-1). Flow cytometry analysis revealed 70.92%, 46.93% and 20.4% viability of SM_SS8 in 10, 50 and 100 mg L^-1, respectively in PVK media containing Cd. This study has therefore substantiated the bioremediation of Cd from polluted soil by the PSB isolates. Thus, experimental results revealed a potential combo benefit, phosphate solubilization along with Cd remediation.

Occurrence of antibiotic resistome in farmland soils near phosphorus chemical industrial area

Heavy metal pollution of soil surrounding phosphorus chemical industry has been a long-concerned problem; however, the occurrence of antibiotic resistance genes (ARGs) in farmland soils in its vicinity remains unexplored. In this study, variations of heavy metals, ARGs, mobile genetic elements (MGEs), and microbiome in surface soils of farmland along the prevailing downwind direction of a phosphorus chemical industrial zone were investigated. Cadmium (Cd) contents in soils close to the industrial zone (≤ 500 m away) were statistically higher than those at greater distances (1000 to 4000 m). A comparable ARG diversity was observed across soils, while the relative abundance of ARGs decreased markedly with increasing distance in the range of 1000 m. The soil in closest proximity to the industrial zone (20 m away) exhibited divergent compositions of ARGs, MGEs, and bacterial community from the other soils at farther locations (500 to 4000 m away). Variation partitioning analysis revealed that Cd and MGEs levels were the primary factors controlling ARG distribution. Structural equation modeling further indicated that the direct effect of Cd on ARG abundance was stronger than its indirect effect via affecting MGEs and microbiome. The observed prevalence of ARGs in farmland soils highlights the necessity of including resistome in the framework for environmental risk assessment of phosphorus chemical manufacturing.

Co-occurrence of antimicrobial and metal resistance genes in pig feces and agricultural fields fertilized with slurry

Antimicrobial resistance constitutes a global challenge to public health. The common addition of Zn, Cu and other metals to animal feed and the widespread presence of metal ions in livestock and their receiving environments may be a factor that facilitates the proliferation of antimicrobial resistance via co-selection of antimicrobial resistance genes (ARGs) and metal resistance genes (MRGs). However, the extent of co-selection is not yet fully understood. In this study, we used a metagenomic approach to profile ARGs, MRGs and mobile genetic elements (MGEs) known to constitute potential ARG and MRG vectors of transmission, and we determined the concentration of metal ions to assess the interrelationships between the occurrence of ARGs, MRGs and metal concentrations in samples from pig farms in China. Samples analyzed included fresh pig feces, soils fertilized with treated slurry, and sediments from aquatic environments, where effluent from treated slurry was discharged. Resistance genes to tetracycline and zinc were the most commonly observed ARGs and MRGs for all three types of samples. Significant correlations were observed between the abundance of ARGs and MRGs, and between ARGs/MRGs and MGEs, and between metal and ARGs/MGEs as documented by Pearson's correlation analysis (r > 0.9, P < 0.001). Further network analysis revealed significant co-occurrence between specific ARGs and MRGs, between ARGs/MRGs and MGEs, and between specific metals (Zn, Cr, and Mn) and ARGs and MGEs. Collectively, our findings demonstrate a high level of co-occurrence of antimicrobial and metal resistance genes in slurry from pig farms and their surrounding environments. The results suggest that metals added to pig feed might facilitate co-selection of ARGs and MGEs in the pig production environments, thereby resulting in a bigger pool of mobile ARGs.

Diversity of metal and antibiotic resistance genes in Enterococcus spp. from the last century reflects multiple pollution and genetic exchange among phyla from overlapping ecosystems

Arsenic (As), mercury (Hg), and copper (Cu) are among the major historical and contemporary metal pollutants linked to global anthropogenic activities. Enterococcus have been considered indicators of fecal pollution and antibiotic resistance for years, but its largely underexplored metallome precludes understanding their role as metal pollution bioindicators as well. Our goal was to determine the occurrence, diversity, and phenotypes associated with known acquired genes/operons conferring tolerance to As, Hg or Cu among Enterococcus and to identify their genetic context (381 field isolates from diverse epidemiological and genetic backgrounds; 3547 enterococcal genomes available in databases representing a time span during 1900-2019). Genes conferring tolerance to As (arsA), Hg (merA) or Cu (tcrB) were used as biomarkers of widespread metal tolerance operons. Different variants of metal tolerance (MeT) genes (13 arsA, 6 merA, 1 tcrB) were more commonly recovered from the food-chain (arsA, tcrB) or humans (merA), and were shared with 49 other bacterial taxa. Comparative genomics analysis revealed that MeT genes occurred in heterogeneous operons, at least since the 1900s, with an increasing accretion of antibiotic resistance genes since the 1960's, reflecting diverse antimicrobial pollution. Multiple MeT genes were co-located on the chromosome or conjugative plasmids flanked by elements with high potential for recombination, often along with antibiotic resistance genes. Phenotypic analysis of some isolates carrying MeT genes revealed up to 128× fold increase in the minimum inhibitory concentrations to metals. The main distribution of functional MeT genes among Enterococcus faecium and Enterococcus faecalis from different sources, time spans, and clonal lineages, and their ability to acquire diverse genes from multiple taxa bacterial communities places these species as good candidates to be used as model organisms in future projects aiming at the identification and quantification of bioindicators of metal polluted environments by anthropogenic activities.

Industrialization as a source of heavy metals and antibiotics which can enhance the antibiotic resistance in wastewater, sewage sludge and river water

The spread of antibiotic resistance is closely related with selective pressure in the environment. Wastewater from industrialized regions is characterized by higher concentrations of these pollutants than sewage from less industrialized areas. The aim of this study was to compare the concentrations of contaminants such as antibiotics and heavy metals (HMs), and to evaluate their impact on the spread of genes encoding resistance to antimicrobial drugs in samples of wastewater, sewage sludge and river water in two regions with different levels of industrialization. The factors exerting selective pressure, which significantly contributed to the occurrence of the examined antibiotic resistance genes (ARGs), were identified. The concentrations of selected gene copy numbers conferring resistance to four groups of antibiotics as well as class 1 and 2 integron-integrase genes were determined in the analyzed samples. The concentrations of six HMs and antibiotics corresponding to genes mediated resistance from 3 classes were determined. Based on network analysis, only some of the analyzed antibiotics correlated with ARGs, while HM levels were correlated with ARG concentrations, which can confirm the important role of HMs in promoting drug resistance. The samples from a wastewater treatment plant (WWTP) located an industrialized region were characterized by higher HM contamination and a higher number of significant correlations between the analyzed variables than the samples collected from a WWTP located in a less industrialized region. These results indicated that treated wastewater released into the natural environment can pose a continuous threat to human health by transferring ARGs, antibiotics and HMs to the environment. These findings shed light on the impact of industrialization on antibiotic resistance dissemination.

Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle

The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity. However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T=LMG 30557T) as a novel species with the name Pseudooceanicola algae.

Progress on the usage of the rotifer Brachionus plicatilis in marine ecotoxicology: A review

The rotifer, Brachionus plicatilis, is a widely used model species in marine ecotoxicology for evaluating pollutions, toxins, and harmful algae. In this paper, the marine ecotoxicology of Brachionus plicatilis was reviewed, including toxicity measurements of harmful algae species and environmental stresses. In addition, marine pollution involving pesticides, heavy metals, drugs, petroleum, and petrochemicals were addressed. Methods for measuring toxicity were also discussed. The standard acute lethal assay and the chronic population dynamics test were indicated as common methods of toxicity evaluating using B. plicatilis. Research on other biomarkers, such as behaviour, enzyme activity, or gene expression, are also reported here, with potential applications for fast detection or the scientific exploration of underlying molecular mechanisms. It is suggested that the methods selected should reflect the experimental purpose. Additionally, series assays should be conducted for comprehensive evaluation of ecotoxicity as well as to elucidate the correct mechanisms. Genetic methods, such as transcriptomics, were suggested as useful tools for exploring the toxicity mechanism using the rotifer B. plicatilis.

Dissemination and conservation of cadmium and arsenic resistance determinants in Listeria and other Gram-positive bacteria

Metal homeostasis in bacteria is a complex and delicate balance. While some metals such as iron and copper are essential for cellular functions, others such as cadmium and arsenic are inherently cytotoxic. While bacteria regularly encounter essential metals, exposure to high levels of toxic metals such as cadmium and arsenic is only experienced in a handful of special habitats. Nonetheless, Listeria and other Gram-positive bacteria have evolved an impressively diverse array of genetic tools for acquiring enhanced tolerance to such metals. Here, we summarize this fascinating collection of resistance determinants in Listeria, with special focus on resistance to cadmium and arsenic, as well as to biocides and antibiotics. We also provide a comparative description of such resistance determinants and adaptations in other Gram-positive bacteria. The complex coselection of heavy metal resistance and other types of resistance seems to be universal across the Gram-positive bacteria, while the type of coselected traits reflects the lifestyle of the specific microbe. The roles of heavy metal resistance genes in environmental adaptation and virulence appear to vary by genus, highlighting the need for further functional studies to explain the mystery behind the array of heavy metal resistance determinants dispersed and maintained among Gram-positive bacteria.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.

Carbapenem resistant Enterobacteriaceae from port areas in São Paulo State (Brazil): Isolation and molecular characterization

Coastal areas with important economic activities have high levels of contamination by metals, pathogenic bacteria, among other contaminants. The emergence of antibiotic-resistant bacteria is a global problem of public health. Carbapenem resistant Enterobacteriaceae (CRE) are a serious threat. The occurrence of carbapenem resistant bacteria was investigated in waters and sediments of a Brazilian coastal area, characterized by high levels of contamination. The samples of water and sediment were collected in two areas of the coast of São Paulo (Brazil). The study involved the characterization of the molecular mechanisms associated with the carbapenem resistance phenotype. No genes were detected for β-lactamases but the absence and/or presence of mutations in outer membrane proteins (OMPs) may justify the detected phenotype. The presented results show the need for further studies that allow a review of the current legislation and the importance of the reevaluation of monitoring policies of these environments.

Antibiotic-Resistant Enterococcus Species in Marine Habitats: A Review

Antibiotic-resistant Enterococcus (ARE) are among leading causes of nosocomial infections worldwide. Enterococcus spp. are ubiquitous in sewage, which can contaminate surface waters via many pathways, providing a route of exposure for humans. This review focuses on ARE in marine and estuarine habitats, including marine animals. Phylogenetic confirmation of the genus Enterococcus and intermediate or full resistance to clinically relevant antibiotics were inclusion criteria. The proportion of resistant isolates varied greatly among antibiotics, for example, 24.2% for ampicillin and 2.4% for vancomycin. The water column contained the highest proportion of ARE observations (18.8%), followed by animal feces and tissues (14.8%), sediment (9.4%), and sand (2.0%). The proportion of multidrug-resistant isolates was the greatest in animal tissue and fecal samples, followed by water and sediments. This review indicates that clinically relevant ARE are present in marine/estuarine habitats and that animals may be important reservoirs.

Tossed 'good luck' coins as vectors for anthropogenic pollution into aquatic environment

Superstition has it that tossing coins into wells or fountains brings good luck, thereby causing a potential accumulation of microbially contaminated metal particles in the water. Here, we characterized the microbiota and the resistance profile in biofilm on such coins and their surrounding sediments. The study site was a tidal marine lake within a touristic center located in a natural reserve area. Notwithstanding the fact that coin-related biofilms were dominated by typical marine taxa, coin biofilms had specific microbial communities that were different from the communities of the surrounding sediment. Moreover, the communities were different depending on whether the coin were made mainly of steel or of copper. Sequences affiliated with putative pathogens were found on every third coin but were not found in the surrounding sediment. Antibiotic resistance genes (ARGs) were detected on most of the coins, and interestingly, sediments close to the area where coins accumulate had a higher frequency of ARGs. We suggest that the surface of the coins might offer a niche for ARGs and faecal bacteria to survive, and, thus, tossed coins are a potential source and vector for ARGs into the surrounding environment.

Water environments: metal-tolerant and antibiotic-resistant bacteria

The potential threat of both metals and antibiotics to the environment and human health has raised significant concerns in the last decade. Metal-resistant and antibiotic-resistant bacteria are found in most environments, including water, and the risk posed to humans and animals due to the spread of antibiotic-resistant bacteria and antibiotic-resistant genes in the environment is increasing. Bacteria have developed the ability to tolerate metals even at notable concentrations. This ability tends to favor the selection of antibiotic-resistant strains, even in pristine water environments, with the potential risk of spreading this resistance to human pathogens. In this mini-review, we focus on investigations performed in marine and freshwater environments worldwide, highlighting the presence of co-resistance to metals and antibiotics.

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.

Selection and dissemination of antimicrobial resistance in Agri-food production

Public unrest about the use of antimicrobial agents in farming practice is the leading cause of increasing and the emergences of Multi-drug Resistant Bacteria that have placed pressure on the agri-food industry to act. The usage of antimicrobials in food and agriculture have direct or indirect effects on the development of Antimicrobial resistance (AMR) by bacteria associated with animals and plants which may enter the food chain through consumption of meat, fish, vegetables or some other food sources. In addition to antimicrobials, recent reports have shown that AMR is associated with tolerance to heavy metals existing naturally or used in agri-food production. Besides, biocides including disinfectants, antiseptics and preservatives which are widely used in farms and slaughter houses may also contribute in the development of AMR. Though the direct transmission of AMR from food-animals and related environment to human is still vague and debatable, the risk should not be neglected. Therefore, combined global efforts are necessary for the proper use of antimicrobials, heavy metals and biocides in agri-food production to control the development of AMR. These collective measures will preserve the effectiveness of existing antimicrobials for future generations.

Substratum-associated microbiota

This survey of 2018 literature on substratum-associated microbiota presents brief highlights on research findings from primarily freshwaters, but includes those from a variety of aquatic ecosystems. Coverage of topics associated with benthic algae and cyanobacteria, though not comprehensive, includes new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metal contaminants, nuisance, bloom-forming and harmful algae, bioassessment, and bioremediation. Coverage of bacteria, also not comprehensive, focused on methylation of mercury, metal contamination, toxins, and other environmental pollutants, including oil, as well as the use of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. Additionally, we cover trends in recent and emerging topics on substratum-associated microbiota of relevance to the Water Environment Federation. PRACTITIONER POINTS: This review of literature from 2018 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Topics covered that focus on algae and cyanobacteria include findings on new methods, taxa new to science, nutrient dynamics, trophic interactions, herbicides and other pollutants, metal contaminants, nuisance, bloomforming and harmful algae, bioassessment, and bioremediation. Topics covered that focus on bacteria include findings on methylation of mercury, metal contamination, toxins and other environmental pollutants, including oil, as well as the us e of benthic bacteria as bioindicators, in bioassessment tools and in biomonitoring. A brief presentation of new, noteworthy and emerging topics on substratum-associated microbiota, build on those from 2017, to highlight those of particular relevance to the Water Environment Federation.

Patterns of sediment-associated fecal indicator bacteria in an urban estuary: Benthic-pelagic coupling and implications for shoreline water quality

Estuarine and coastal waterways are commonly monitored for fecal and sewage contamination to protect recreator health and ecosystem functions. Such monitoring programs commonly rely on cultivation-based counts of fecal indicator bacteria (FIB) in water column samples. Recent studies demonstrate that sediments and beach sands can be heavily colonized by FIB, and that settling and resuspension of colonized particles may significantly influence the distribution of FIB in the water column. However, measurements of sediment FIB are rarely incorporated into monitoring programs, and geographic surveys of sediment FIB are uncommon. In this study, the distribution of FIB and the extent of benthic-pelagic FIB coupling were examined in the urbanized, lower Hudson River Estuary. Using cultivation-based enumeration, two commonly-measured FIB, enterococci and Escherichia coli, were widely distributed in both sediment and water, and were positively correlated with each other. The taxonomic identity of FIB isolates from water and sediment was confirmed by DNA sequencing. The geometric mean of FIB concentration in sediment was correlated with both the geometric mean of FIB in water samples from the same locations and with sediment organic carbon. These two positive associations likely reflect water as the FIB source for underlying sediments, and longer FIB persistence in the sediments compared to the water, respectively. The relative representation of other fecal associated bacterial genera in sediment, determined by 16S rRNA gene sequencing, increased with the sequence representation of the two FIB, supporting the value of these FIB for assessing sediment contamination. Experimental resuspension of sediment increased shoreline water column FIB concentrations, which may explain why shoreline water samples had higher average FIB concentrations than samples collected nearby but further from shore. In combination, these results demonstrate extensive benthic-pelagic coupling of FIB in an urbanized estuary and highlight the importance of sediment FIB distribution and ecology when interpreting water quality monitoring data.

Characterization of phosphate solubilizing bacteria isolated from heavy metal contaminated soils and their potential for lead immobilization

Phosphate solubilizing bacteria (PSB) were isolated from heavy metal contaminated soils and their potentials for lead (Pb) immobilization in soil were studied in this paper. 53 PSB strains were isolated and their minimum inhibitory concentrations (MICs) for lead were determined. The results showed that strains B3, B4, B10, F2-1 and L1-5 had relatively high lead resistant capabilities with MICs ranged from 0.5 to 8 mM, and were identified as species of Leclercia adecarboxylata and Pseudomonas putida by 16S rRNA. The most efficient PSB strains could solubilize 200 mg L^-1 of P, and phosphate solubilizing capacity of those PSBs was related to the concentrations of organic acids, acid phosphatase activity and pH. Furthermore, the growth pattern of L1-5 strain with the presence of Pb(NO₃)₂ was observed and a mechanism of biomineralization of lead ions in bacteria biomass was determined by FT-IR and XRD analyses. Results showed that high concentration of lead can inhibit the growth of PSBs, and L1-5 isolate can transform lead ions into lead hydroxyapatite and pyromorphite. The PSBs, which possessing the properties of immobilizing lead through phosphate solubilization and biomineralization could be exploited for bioremediation of Pb polluted soils in future.

Coexistence and association between heavy metals, tetracycline and corresponding resistance genes in vermicomposts originating from different substrates

Coexistence of antibiotics/heavy metals and the overexpression of resistance genes in the vermicompost has become an emerging environmental issue. Little is known about the interaction and correlation between chemical pollutants and biological macromolecular compounds. In this study, three typical vermicompost samples were selected from the Yangtze River Delta region in China to investigate the antibiotic, heavy metal and corresponding antibiotic resistance genes (ARGs) and heavy metal resistance genes (HRGs). The results indicated the prevalence of tetracycline (TC), copper (Cu), zinc (Zn), cadmium (Cd), corresponding TC-resistance genes (tetA, tetC, tetW, tetM, tetO, and tetS) and HRGs (copA, pcoA, cusA, czcA, czcB, and czcR) in the three vermicompost samples. In addition, the ARG level was positively associated with the water-soluble TC fraction in the vermicompost, and it was same between the HRG abundance and exchangeable heavy metal content (p < 0.05). Moreover, a positive correlation was found between ARG and HRG abundance in the vermicompost samples, suggesting a close regulation mechanism involving the expression of both genes. The result obtained here could provide new insight into the controlling risk of heavy metals, TC, and relevant resistance genes mixed contamination in the vermicompost.