Occurrence and abundance of clinically relevant antimicrobial resistance genes in environmental samples after the Brumadinho dam disaster, Brazil

Attenuation of water contamination in the Paraopeba River after the collapse of B1 tailings dam: Natural wash-off and dredging contributions

Following the B1 dam collapse at Córrego do Feijão Mine, actions were taken to address environmental damage and enhance the quality of water in the Paraopeba River. Natural processes in the river involve gradual reduction of contamination through dispersion and downstream transportation of tailings-a slow, nature-driven process. Dredging, a human intervention, aimed to expedite recovery. Hence, this study aimed to explore dredging's role in reducing contamination in the impacted Paraopeba River zone. Analysis revealed a direct link between dredging and post-collapse turbidity, though recent trends suggest a lessening impact on pre-collapse conditions. Distinct seasonal variations were observed in iron and manganese concentrations, peaking during wet seasons and displaying notable upstream-downstream disparities. An analysis of ratios (downstream/upstream) was conducted to understand and even predict the return to pre-collapse conditions. Wet season averages for iron and manganese decreased by around 90 % over time, with standard deviations reducing by about 48 % and 58 %, respectively. In the dry season, the averages decreased by over 100 %, indicating water quality improvements surpassing pre-collapse levels. Standard deviations also decreased significantly, by approximately 67 % and 79 %, respectively. Employing an exponential decay model revealed that the contribution of dredging in the dry period is negligible, but in the wet period the contribution can be estimated at 28.6 % in the case of iron and 25 % in the case of manganese. While the models performed well based on extensive data, some limitations occur in estimating dredging contribution rates. The model's sensitivity might overlook influential factors, underscoring the importance of considering sediment nature and dredged area extent in understanding water quality dynamics. Despite these potential limitations, this investigation provides crucial insights into the intricate relationship between dredging and water quality in the Paraopeba River. These findings pave the way for future studies aimed at deeper exploration and more accurate assessments of this association.

Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment

The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.

Patterns of antimicrobial resistance and metal tolerance in environmental Pseudomonas aeruginosa isolates and the genomic characterization of the rare O6/ST900 clone

Pseudomonas aeruginosa can harbor several virulence and antimicrobial resistance genes (ARGs). In this regard, virulent and multidrug-resistant (MDR) P. aeruginosa strains are closely related to severe infections. In addition, this species can also carry metal tolerance genes, selecting mainly antimicrobial-resistant strains. The action of several pollutants on the environment may favor the occurrence of antimicrobial-resistant and metal-tolerant strains. Therefore, the aim of this study was to characterize potentially pathogenic, antimicrobial-resistant, and/or metal-tolerant P. aeruginosa isolates from different environmental samples (waters, soils, sediments, or sands) and to perform a whole-genome sequence-based analysis of a rare clone from residual water. Environmental isolates carried virulence genes related to adherence, invasion, and toxin production, and 79% of the isolates harbored at least five virulence genes. In addition, the isolates were resistant to different antimicrobials, including important antipseudomonal agents, and 51% of them were classified as MDR, but only ARGs associated with aminoglycoside resistance were found. Furthermore, some isolates were tolerant mainly to copper, cadmium, and zinc, and presented metal tolerance genes related to these compounds. Whole-genome characterization of an isolate with unique phenotype with simultaneous resistance to antimicrobials and metals showed nonsynonymous mutations in different antimicrobial resistance determinants and revealed a classification of O6/ST900 clone as rare, potentially pathogenic, and predisposed to acquire multidrug resistance genes. Therefore, these results draw attention to the dissemination of potentially pathogenic, antimicrobial-resistant, and metal-tolerant P. aeruginosa isolates in environmental niches, alerting to a potential risk mainly to human health.

Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism

A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.

Brumadinho dam collapse induces changes in the microbiome and the antibiotic resistance of the Paraopeba River (Minas Gerais, Brazil)

The rupture of the Córrego do Feijão dam in Brumadinho (January 25, 2019) caused serious damage to the Paraopeba River and compromised the quality of its waters for human consumption. However, the possible effects of the dam collapse on the river microbiome and its antibiotic resistance profiles are unknown. The present study aims to analyse the possible shifts in microbial diversity and enhancement of antibiotic resistance in the Paraopeba River. To this end, two sampling campaigns (February and May 2019) were performed to obtain water across the entire Paraopeba River (eight sampling locations: Moeda, Brumadinho, Igarapé, Juatuba, Varginha, Angueretá, Retiro Baixo and Três Marias; ~464 km). This sampling scheme enabled determining the effects of the disaster on the river microbiome. Total DNA and microbial isolation were performed with these water samples. The 16S rRNA-based microbiome analyses (n = 24; 2.05 million 16S rRNA reads) showed changes in microbial diversity immediately after the disaster with the presence of metal-indicating bacteria (Acinetobacter, Bacillus, Novosphingobium, and Sediminibacterium). Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification of bacterial isolates (n = 170) also disclosed possible indicators of faecal contamination across the Paraopeba (Cloacibacterium, Bacteroides, Feaecalibacterium, Bifidobacterium, Citrobacter, Enterobacter, Enterococcus and Escherichia). Antibiotic resistance increased significantly to ampicillin, ampicillin/sulbactam, amoxicillin/clavulanate, ceftriaxone, and cefalotin among isolates obtained in May after the disaster. The effects of toxic mud on microbiomes were felt at all points sampled up to Anguereta. The ore mud may have exacerbated the growth of different antibiotic-resistant, metal-resistant, and faecal-indicating bacteria in the Paraopeba River.

Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond

Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO₄^2- concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.

A partial least squares-path model of environmental degradation in the Paraopeba River, for rainy seasons after the rupture of B1 tailings dam, Brumadinho, Brazil

The present study aimed to investigate the rupture of B1 tailings dam of Córrego do Feijão mine, which drastically affected the region of Brumadinho (Minas Gerais, Brazil). The contamination of water resources reached 155.3 km from the dam site. In the river channel, high concentrations of Mn, Al, As and Fe were detected and correlated to the spillage of the tailings in the river. The presence of the tailings also affected the chlorophyll-a content in the water, as well as the reflectance of riparian forests. With the increase of metal(oid) concentrations above permitted levels, water management authorities suspended the use of Paraopeba River as resource in the impacted areas, namely the drinking water supply to the Metropolitan region of Belo Horizonte. This study aimed to evaluate possible links between tailings distribution, river water quality, and environmental degradation, which worked as latent variables in partial least squares regression models. The latent variables were represented by numerous physical and chemical parameters of water and sediment, measured four times in 22 locations during the rainy season of 2019, in addition to stream flow and to NDVI evaluated in satellite images processed daily. The modeling results suggested a relationship between river flow turbulence and increased arsenic release from sand fractions, as well as desorption of Mn from metal oxides, both representing causes of water quality reduction. They also revealed increasing iron concentrations affecting the forest NDVI (greening), which was interpreted as environmental degradation. The increase of chlorophyll-a concentrations (related with turbidity decreases), as well as the increase of river flows (responsible for dilution effects), seemed to work out as attenuators of degradation. Although applied to a specific site, our modeling approach can be transposed to equivalent dam failures and climate contexts, helping water resource management authorities to decide upon appropriate recovery solutions.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update

Background

Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane.

Results and discussion

Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI₂ conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins.

Conclusion

The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.

Leaching assessment of cemented bauxite tailings through wetting and drying cycles of durability test

Disposal of mine tailings can cause negative environmental effects by releasing contaminants to surface and underground water. Alkali activation is a promising technique for immobilizing metals in stabilization/solidification of these wastes. This study evaluates the leaching behavior of cemented bauxite tailings (BT) submitted to weathering conditions. The alkali-activated binder was composed of sugar cane bagasse ash, carbide lime, and sodium hydroxide solution. Comparisons of the durability and leaching behavior of BT stabilized with alkali-activated binder and high initial strength Portland cement were performed. The durability results for alkali-activated were similar to the Portland cement, showing an average difference of 16%. Portland cement showed favorable results in the encapsulation of heavy metals like Cd and Hg, while the alkali-activated cement on Al, Cr, and Se. For Ba, Fe, Mn, and Zn immobilization, both types of cement presented an equal performance. The durability and leaching behavior of stabilized bauxite tailings is governed by the cement content and porosity of the blends, as well as their pH.

A partial least squares-path model of causality among environmental deterioration indicators in the dry period of Paraopeba River after the rupture of B1 tailings dam in Brumadinho (Minas Gerais, Brazil)

This study investigated the collapse of B1 mine-tailings dam that occurred in 25 January 2019 and severely affected the Brumadinho region (Minas Gerais state, Brazil) socially, economically and environmentally. As regards water resources, the event impacted the Paraopeba River in the first 155.3 km counted from the dam site, meaning nearly half the main water course downstream of B1. In the impacted sector, high concentrations of tailings-related Al, Fe, Mn, P in river sediment-tailings mixtures and water were detected, as well as changes to the reflectance of riparian forests. In the river water, the metal concentrations raised significantly above safe levels. For caution, the water management authorities declared immediate suspension of Paraopeba River as drinking water source to the Metropolitan Region of Belo Horizonte (6 million people), irrespective of representing nearly 30% of all supply. In this study, the main purpose was to assess potential links between tailings distribution, river water composition and reflectance of forest vegetation, which worked out as latent variables in regression models. The latent variables were represented by numerous physical and chemical parameters, measured 4 times in 22 sites during the dry period of 2019. The modeling results suggested the release of aluminum and phosphorus from sand fractions in the mine tailings as major cause of water contamination. The NDVI changes were interpreted as environmental deterioration. Changes in redox potential may have raised manganese concentrations in surface water further affecting the forest NDVI. Distance from the B1 dam and dissolved calcium appear to attenuate deterioration. Overall, the regressions allowed robust prognoses of environmental deterioration in the Paraopeba River under low flow conditions. More importantly, they can be transposed to similar dam ruptures helping environmental authorities to decide upon measures that can bring the affected rivers to pre-rupture conditions.

Antibiotic-resistant bacteria and antibiotic resistance genes in uranium mine: Distribution and influencing factors

Both heavy metals and radiation could affect the proliferation and dissemination of emerging antibiotic resistance pollutants. As an environmental medium rich in radioactive metals, the profile of antibiotic resistance in uranium mine remains largely unknown. A uranium mine in Guangdong province, China was selected to investigate the distribution and influencing factors of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) including intracellular ARGs (iARGs), adsorbed-extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs). The result indicated that sulfonamide and tetracycline ARB could be generally detected in mining area with the absolute concentrations of 7.70 × 10²-5.18 × 10⁵ colony forming unit/g. The abundances of aeARGs in mine soil were significantly higher than those of iARGs (p < 0.05), highlighting the critical contribution of aeARGs to ARGs spread. The feARGs in mine drainage and its receiving river were abundant (3.38 × 10⁴-1.86 × 10⁷ copies/mL). ARB, aeARGs, and iARGs may correlate with nitrogen species and heavy metals (e.g., U and Mn), and feARGs presented a significant correlation with chemical oxygen demand (p < 0.05). These findings demonstrate the occurrence of ARB and ARGs in uranium mine for the first time, thereby contributing to the assessment and control of the ecological risk of antibiotic resistance in radioactive environments.

Influence of clay mineral content on mechanical properties and microfabric of tailings

Clay mineral content has an important influence on the mechanical behaviour of tailings, and this mechanical behaviour significantly affects the stability of tailings dams. X-ray fluorescence (XRF) and X-ray diffraction (XRD) tests were carried out on tailings from three different regions. The chemical and mineral composition of the tailings are analyzed. The strength and failure deformation of the tailings were studied by laboratory triaxial compression tests. The effect of clay content on the behaviour of tailings was investigated. The microfabric of tailings sample was examined with the scanning electron microscope (SEM) and nitrogen adsorption tests. The results show that the confining pressure corresponding to the samples exhibiting strain hardening increases with the increase of the content of clay minerals. The cohesion of tailings increases linearly, and the specific surface area decreases as the content of clay minerals increases. Nitrogen adsorption test results reveal from a microscopic point of view that changes in pore structure are associated with the content of clay minerals. The higher the content of clay minerals is, the higher the proportion of micropores is (aggregated interior). Macroscopically, the overall porosity decreases and the size of the pores increases with clay content, which will directly affect the mechanical properties of tailings.

Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America

Mining dam disasters contribute to the contamination of aquatic environments, impacting associated ecosystems and wildlife. A multidrug-resistant Escherichia coli strain (B2C) was isolated from a river water sample in Brazil after the Mariana mining dam disaster. The genome was sequenced using the Illumina MiSeq platform, and de novo assembled using Unicycler. Resistome, virulome, and plasmidome were predicted using bioinformatics tools. Data analysis revealed that E. coli B2C belonged to sequence type ST219 and phylogroup E. Strikingly, a broad resistome (antibiotics, hazardous heavy metals, and biocides) was predicted, including the presence of the clinically relevant bla_CTX-M-2 extended-spectrum β-lactamase (ESBL) gene, qacE∆1 efflux pump gene, and the mer (mercury resistance) operon. SNP-based analysis revealed that environmental E. coli B2C was clustered along to ESBL-negative E. coli strains of ST219 isolated between 1980 and 2021 from livestock in the United States of America. Acquisition of clinically relevant genes by ST219 seems to be a recent genetic event related to anthropogenic activities, where polluted water environments may contribute to its dissemination at the human-animal-environment interface. In addition, the presence of genes conferring resistance to heavy metals could be related to environmental pollution from mining activities. Antimicrobial resistance genes could be essential biomarkers of environmental exposure to human and mining pollution.

Application of Multispectral Remote Sensing for Mapping Flood-Affected Zones in the Brumadinho Mining District (Minas Gerais, Brasil)

The collapse of the tailing “Dam B1” of the Córrego do Feijão Mine (Brumadinho, Brasil) that occurred in January 2019 is considered a large socio-environmental flood-disaster where numerous people died and the local flora and fauna were seriously affected, including agricultural areas of the Paraopeba River. This study aims to map the land area affected by the flood by using multispectral satellite images. To pursue this aim, Level-2A multispectral images from the European Space Agency’s Sentinel-2 sensor were acquired before and after the tailing dam collapse in the period 2019–2021. The pre- and post-failure event analysis allowed us to evidence drastic changes in the vegetation rate, as well as in the nature of soils and surficial waters. The spectral signatures of the minerals composing the mining products allowed us to highlight the effective area covered by the flood and to investigate the evolution of land properties after the disaster. This technique opens the possibility for quickly classifying areas involved in floods, as well as obtaining significant information potentially useful for monitoring and planning the reclamation and restoration activities in similar cases worldwide, representing an additional tool for evaluating the environmental issues related to mining operations in large areas at high temporal resolution.

Removal of cephalexin and erythromycin antibiotics, and their resistance genes, by microalgae-bacteria consortium from wastewater treatment plant secondary effluents

Antibiotics have become a concern in the aquatic environments owing to the potential development of bacterial resistances. Thus, this study evaluated the removal of cephalexin (CEP) and erythromycin (ERY) from a local wastewater treatment plant (WWTP) effluent, mediated by microalgae-bacteria consortium. Likewise, the removal of correlated antibiotics resistance genes bla_TEM and ermB was also assessed. The incubation results showed that the added concentrations of selected antibiotics did not restrain the consortium growth. Moreover, CEP and ERY were almost completely removed after the cultivation period, reaching total removals of 96.54% and 92.38%, respectively. The symbiotic interaction between microalgae and bacteria plays a role in the kinetics removal of CEP and ERY. The abundance of bla_TEM and ermB was reduced by 0.56 and 1.75 logs, respectively. Lastly, our results suggest that technology based on natural microalgae-bacteria consortium could be a potential alternative to improve the quality of WWTP effluents.

Multiple sequence types, virulence determinants and antimicrobial resistance genes in multidrug- and colistin-resistant Escherichia coli from agricultural and non-agricultural soils

In soils, the presence of clinically relevant bacteria carrying ARGs, including extended-spectrum β-lactamase- and plasmid-mediated AmpC β-lactamase-encoding genes, is an underestimated public health problem that requires more attention. For this investigation, 300 samples from agricultural and non-agricultural soils were used to obtain 41 MDR E. coli isolates, standing out the resistance to β-lactams, fluoroquinolones and colistin. Virulence genes related to diarrheagenic E. coli and extraintestinal pathogenic E. coli were detected. Several ARGs were found, highlighting the presence of at least one β-lactamase-encoding gene (bla_TEM, bla_CMY, bla_SHV, bla_OXA-1-like, bla_CTX-M-2, and/or bla_CTX-M-15) in each isolate. Among the fluoroquinolone-resistant E. coli isolates, the plasmid-mediated quinolone resistance genes (qnrB and oqxA) and substitutions in the quinolone resistance-determining regions were detected. Some isolates were resistant to colistin (MICs of 4-8 mg/L) and, although no mcr-like gene was detected, substitutions in the two-component systems involving PhoP/PhoQ and PmrA/PmrB were found. Furthermore, the E. coli isolates presented plasmids and class 1 integrons, the last one detected in all isolates. The ARGs bla_TEM, aadA and dfrA and the lpfA virulence-associated gene presented statistically significant differences (P < 0.05) in agricultural soils, while the bla_OXA-1-like gene presented a statistically significant difference in non-agricultural soils. Thirty-eight sequence types (STs) were identified among the isolates, spotlighting the 20 different STs that carried bla_CMY and bla_CTX-M-type genes and those commonly reported in infections worldwide. The occurrence of virulent, multidrug- and colistin-resistant E. coli isolates in soils could lead to contamination of surrounding environments and food, increasing the risk of human and animal exposure. Therefore, this study contributes to a better understanding of E. coli in soils and reinforces the importance of the One Health approach to antimicrobial resistance surveillance.

The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance

Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.

Ubiquitousness of Haloferax and Carotenoid Producing Genes in Arabian Sea Coastal Biosystems of India

This study presents a comparative analysis of halophiles from the global open sea and coastal biosystems through shotgun metagenomes (n = 209) retrieved from public repositories. The open sea was significantly enriched with Prochlorococcus and Candidatus pelagibacter. Meanwhile, coastal biosystems were dominated by Marinobacter and Alcanivorax. Halophilic archaea Haloarcula and Haloquandratum, predominant in the coastal biosystem, were significantly (p < 0.05) enriched in coastal biosystems compared to the open sea. Analysis of whole genomes (n = 23,540), retrieved from EzBioCloud, detected crtI in 64.66% of genomes, while cruF was observed in 1.69% Bacteria and 40.75% Archaea. We further confirmed the viability and carotenoid pigment production by pure culture isolation (n = 1351) of extreme halophiles from sediments (n = 410 × 3) sampling at the Arabian coastline of India. All red-pigmented isolates were represented exclusively by Haloferax, resistant to saturated NaCl (6 M), and had >60% G + C content. Multidrug resistance to tetracycline, gentamicin, ampicillin, and chloramphenicol were also observed. Our study showed that coastal biosystems could be more suited for bioprospection of halophiles rather than the open sea.

"Barcode" cell sensor microfluidic system: Rapid and sample-to-answer antimicrobial susceptibility testing applicable in resource-limited conditions

Many rapid antimicrobial susceptibility testing (AST) methods have been proposed to contain clinical antimicrobial resistance (AMR) and preserve the effectiveness of remaining antimicrobials. However, far fewer methods have been proposed to test AMR in resource-limited conditions, such as for frequent safety screenings of water/food/public facilities, urgent surveys of massive samples during a pandemic, or AMR tests in low-income countries. Rapid AST methods realized thus far have a variety of drawbacks when used for such surveys, e.g., high cost and the requirement of expensive instruments such as microscopy. A more reasonable strategy would be to screen samples via onsite testing first, and then send any sample suspected to contain AMR bacteria for advanced testing. Accordingly, a cost-efficient AST is demanded, which can rapidly process a large number of samples without using expensive equipment. To this end, current work demonstrates a novel "barcode" cell sensor based on an adaptive linear filter array as a fully automatic and microscope-free method for counting very small volumes of cells (~1.00 × 10⁴ cells without pre-incubation), wherein suspended cells concentrate into microbars with length proportional to the number of cells. We combined this sensor with an on-chip culture approach we had demonstrated for rapid and automated drug exposure and realized a low-cost and resource-independent platform for portable AST, from which results can be obtained simply through a cell phone. This method has a much shorter turnaround time (2-3 h) than that of standard methods (16-24 h). Thanks to its microscopy-free analysis, affordability, portability, high throughput, and user-friendliness, our "barcode" AST system has the potential to fulfill the various demands of AST when advanced facilities are not available, making it a promising new tool in the fight against AMR.

Appearance of mcr-9, blaKPC, cfr and other clinically relevant antimicrobial resistance genes in recreation waters and sands from urban beaches, Brazil

The co-occurrence of mcr-like and carbapenemase-encoding genes have been reported mainly in humans and animals, whereas, in the environment, studies are gradually increasing due to the One Health approach. In this study, we investigated antimicrobial resistance genes (ARGs) in water and sand samples from marine environments in Brazil. Total DNA from 56 samples (33 sands and 23 waters) was obtained and 27 different ARGs were detected, highlighting the presence of mcr-9, bla_KPC and cfr genes. Additionally, the microbiological analysis revealed that sand samples of all analyzed beaches were not recommended for primary use, whereas water samples from most beaches were classified as unsuitable for bathing. The presence of clinically relevant ARGs in urban beaches suggests the presence of antimicrobial-resistant bacteria. Furthermore, to the best of our knowledge, this is the first report of mcr-9 and cfr genes in the environment from Brazil and recreational areas worldwide.

Occurrence of multidrug-resistant Enterococcus faecium isolated from environmental samples

Enterococcus species are present in the microbiota of humans and animals and have also been described in the environment. Among the species, Enterococcus faecium is one of the main pathogens associated with nosocomial infections worldwide. Enterococcus faecium isolates resistant to different classes of antimicrobials have been increasingly reported, including multidrug-resistant (MDR) isolates in environmental sources, which is worrying. Therefore, this study aimed to characterize E. faecium isolates obtained from soil and water samples regarding antimicrobial resistance and virulence determinants. A total 40 E. faecium isolates were recovered from 171 environmental samples. All isolates were classified as MDR, highlighting the resistance to the fluoroquinolones class, linezolid and vancomycin. Furthermore, high-level aminoglycoside resistance and high-level ciprofloxacin resistance were detected in some isolates. Several clinically relevant antimicrobial resistance genes were found, including vanC1, ermB, ermC, mefAE, tetM, tetL, ant(6')-Ia, ant(4')-Ia, aph(3')-IIIa and aac(6')-Ie-aph(2″)-Ia. Three virulence genes were detected among the MDR E. faecium isolates, such as esp, gelE and ace. The results of this study contribute to a better understanding of MDR E. faecium isolates carrying antimicrobial resistance and virulence genes in environmental sources and report for the first time in the world the presence of vanC1-producing E. faecium isolated from soil.