Antimicrobial resistance due to the content of potentially toxic metals in soil and fertilizing products

Groundwater resistant gene accumulation in mining-agriculture complex zones: Insights from metagenomic analysis of subterranean mineral and terrestrial agricultural interactions

During the Mining-Agriculture Complex Areas, the mining and agriculture activities could lead to an excessive presence of sulfate content in the regional groundwater. Sulfate exhibits the potential to influence the positive accumulation of RGs, although its mechanisms remain inadequately explored. To address this gap, this study analyzed the RGs buildup mechanisms in the groundwater of the mining-agriculture complex area. Results showed a widespread presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), especially in coal-seams crevice groundwater. And iron and sulfur are primary environmental factors conducive to RGs accumulation through a synergistic interaction. Microbial annotation of gene sets sourced from coal-seams crevice groundwater samples unveiled part of sulfur-metabolizing microorganisms that were hosts of both ARGs and MRGs. Mechanistic insights revealed that iron may stimulates reactive oxygen species (ROS) generation, facilitating RGs accumulation, while adjusting sulfur metabolism and the synthesis of iron-sulfur clusters, thereby augmenting microbial growth which as predominant hosts of RGs, thereby intensifying the buildup of RGs.

Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

The role of heavy metal exposure on the microbiome in the etiology of gastrointestinal disorders: a scoping review

In recent years, epidemiological studies have increasingly recognized the significance of heavy metals as an important pathogenetic factor in many gastrointestinal diseases, particularly those associated with in gut microbiota functions. The toxicity of heavy metals towards essential intestinal microflora goes beyond causing dysbiotic disorders; it can also exacerbate intestinal infections, alter metabolic processes, and influence the development of antibiotic resistance. Since the negative effects of heavy metals are environmental in nature, there is a need to systematize the etiological role between the effects of heavy metals on the microbiome and possible nosological conditions for a more accurate approach to treatment and further research. Given the environmental origins of the abovementioned effects, there is a need to systematize the impact of heavy metals on the microbiome and their role in disease development to improve approaches to treatment and further research. We aimed to analyze the latest scientific evidence on the associations between heavy metals exposure and the intestinal microbiome and its role in the development of gastrointestinal disorders. For this scoping review we used PubMed and eLIBRARY.ru databases. We searched for keywords: «gut microbiota», «intestinal infections» (disorders), «antibiotic resistance» «heavy metals» in both Russian and English. Based on the research reviewed in this study, we can infer that heavy metals act as exogenous toxicants contributing to the development of dysbiotic, metabolic and trophic disorders of the gastrointestinal tract. They also influence the progression of infections and the development of antibiotic resistance in bacteria. Further studies should focus on exploring the toxicity of heavy metals in relation to specific populations of intestinal flora and associations with metal and antibiotic resistance. It is important to consider the therapeutic potential of microbiome modulation in the management of gastrointestinal diseases.

Studies on Antifungal Properties of Methacrylamido Propyl Trimethyl Ammonium Chloride Polycations and Their Toxicity In Vitro

The biological activity of polycations is usually associated with their biocidal properties. Their antibacterial features are well known, but in this work, observations on the antifungal properties of macromolecules obtained by methacrylamido propyl trimethyl ammonium chloride (MAPTAC) polymerization are presented. The results, not previously reported, make it possible to correlate antifungal properties directly with the structure of the macromolecule, in particular the molecular mass. The polymers described here have antifungal activity against some filamentous fungi. The strongest effect occurs for polymers with a mass of about 0.5 mDa which have confirmed activity against the multidrug-resistant species Scopulariopsis brevicaulis, Fusarium oxysporum, and Fusarium solani, as well as the dermatophytes Trichophyton mentagrophytes, Trichophyton rubrum, Trichophyton interdigitale, and Trichophyton tonsurans. In addition, this publication describes the effects of these macromolecular systems on serum and blood components and provides a preliminary assessment of toxicity on cell lines of skin-forming cells, i.e., fibroblasts and keratinocytes. Additionally, using a Franz diffusion chamber, a negligibly low transport of the active polymer through the skin was demonstrated, which is a desirable effect for externally applied antifungal drugs. IMPORTANCE Infectious diseases are a very big medical, social, and economic problem. Even before the COVID-19 pandemic, certain infections were among of the most common causes of death. The difficulties in the treatment of infectious diseases concern in particular fungal diseases, against which we have only a few classes of drugs represented by a few substances. The publication presents the preliminary results of the in vitro antifungal activity studies of four MAPTAC polymers on different fungal species and their cytotoxicity to human cells (fibroblasts and keratinocytes). The paper also compares these properties with analogous ones of two commonly used antifungal drugs, ciclopirox and terbinafine.

Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site

Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.

Rapid growth of antimicrobial resistance: the role of agriculture in the problem and the solutions

Abstract

The control of infectious diseases has always been a top medical priority. For years during the so-called antibiotic era, we enjoyed prolonged life expectancy and the benefits of superior pathogen control. The devastating failure of the medical system, agriculture and pharmaceutical companies and the general population to appreciate and safeguard these benefits is now leading us into a grim post-antibiotic era. Antimicrobial resistance (AMR) refers to microorganisms becoming resistant to antibiotics that were designed and expected to kill them. Prior to the COVID-19 pandemic, AMR was recognised by the World Health Organization as the central priority area with growing public awareness of the threat AMR now presents. The Review on Antimicrobial Resistance, a project commissioned by the UK government, predicted that the death toll of AMR could be one person every 3 seconds, amounting to 10 million deaths per year by 2050. This review aims to raise awareness of the evergrowing extensiveness of antimicrobial resistance and identify major sources of this adversity, focusing on agriculture’s role in this problem and its solutions.

Keypoints

• Widespread development of antibiotic resistance is a major global health risk.

• Antibiotic resistance is abundant in agricultural produce, soil, food, water, air and probiotics.

• New approaches are being developed to control and reduce antimicrobial resistance.

Factors promoting and limiting antimicrobial resistance in the environment - Existing knowledge gaps

The dissemination of multidrug-resistant bacteria strains and genes carrying antibiotic resistance is currently considered to be one of the most important global problem. The WHO calls for the need to contain the spread of Antimicrobial Resistance (AMR) from all possible sources. There have been many international actions grouping scientists studying this phenomenon, and quite a lot of scientific projects devoted to this problem have already been carried out. As well, so far several strategies have been developed that can inhibit the AMR spread. In this mini-review, we highlight overlooked aspects that seem to be crucial for creating a comprehensive picture of AMR, especially in the context of One Health approach.

Extraintestinal Pathogenic Escherichia coli: Beta-Lactam Antibiotic and Heavy Metal Resistance

Multiple-antibiotic-resistant (MAR) extra-intestinal pathogenic Escherichia coli (ExPEC) represents one of the most frequent causes of human nosocomial and community-acquired infections, whose eradication is of major concern for clinicians. ExPECs may inhabit indefinitely as commensal the gut of humans and other animals; from the intestine, they may move to colonize other tissues, where they are responsible for a number of diseases, including recurrent and uncomplicated UTIs, sepsis and neonatal meningitis. In the pre-antibiotic era, heavy metals were largely used as chemotherapeutics and/or as antimicrobials in human and animal healthcare. As with antibiotics, the global incidence of heavy metal tolerance in commensal, as well as in ExPEC, has increased following the ban in several countries of antibiotics as promoters of animal growth. Furthermore, it is believed that extensive bacterial exposure to heavy metals present in soil and water might have favored the increase in heavy-metal-tolerant microorganisms. The isolation of ExPEC strains with combined resistance to both antibiotics and heavy metals has become quite common and, remarkably, it has been recently shown that heavy metal resistance genes may co-select antibiotic-resistance genes. Despite their clinical relevance, the mechanisms underlining the development and spread of heavy metal tolerance have not been fully elucidated. The aim of this review is to present data regarding the development and spread of resistance to first-line antibiotics, such as beta-lactams, as well as tolerance to heavy metals in ExPEC strains.

From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches

With increasing reports on antimicrobial resistance (AMR) in humans, animals and the environment, we are at risk of returning to a pre-antibiotic era. Therefore, AMR is recognized as one of the major global health threats of this century. Antibiotics are used extensively in farming systems to treat and prevent infections in food animals or to increase their growth. Besides the risk of a transfer of AMR between the human and the animal sector, there is another yet largely overlooked sector in the One Health triad. Human-dominated ecosystems such as agricultural soils are a major sink for antibiotics and AMR originating from livestock farming. This review summarizes current knowledge on the prevalence of AMR at the interface of animal and agricultural production and discusses the potential implications for human health. Soil resistomes are augmented by the application of manure from treated livestock. Subsequent transfer of AMR into plant microbiomes may likely play a critical role in human exposure to antibiotic resistance in the environment. Based on the knowledge that is currently available we advocate that more attention should be paid to the role of environmental resistomes in the AMR crisis.

Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups

The rapid emergence of antimicrobial resistance (AMR) is a major concern for wildlife and ecosystem health globally. Genetic determinants of AMR have become indicators of anthropogenic pollution due to their greater association with humans and rarer presence in environments less affected by humans. The objective of this study was to determine the distribution and frequency of the class 1 integron, a genetic determinant of AMR, in both the faecal microbiome and in Escherichia coli isolated from neonates of three pinniped species. Australian sea lion (Neophoca cinerea), Australian fur seal (Arctocephalus pusillus doriferus) and long-nosed fur seal (Arctocephalus forsteri) pups from eight breeding colonies along the Southern Australian coast were sampled between 2016-2019. DNA from faecal samples (n = 309) and from E. coli (n = 795) isolated from 884 faecal samples were analysed for class 1 integrons using PCRs targeting the conserved integrase gene (intI) and the gene cassette array. Class 1 integrons were detected in A. p. doriferus and N. cinerea pups sampled at seven of the eight breeding colonies investigated in 4.85% of faecal samples (n = 15) and 4.52% of E. coli isolates (n = 36). Integrons were not detected in any A. forsteri samples. DNA sequencing of the class 1 integron gene cassette array identified diverse genes conferring resistance to four antibiotic classes. The relationship between class 1 integron carriage and the concentration of five trace elements and heavy metals was also investigated, finding no significant association. The results of this study add to the growing evidence of the extent to which antimicrobial resistant bacteria are polluting the marine environment. As AMR determinants are frequently associated with bacterial pathogens, their occurrence suggests that these pinniped species are vulnerable to potential health risks. The implications for individual and population health as a consequence of AMR carriage is a critical component of ongoing health investigations.

Recent Advances in Understanding the Influence of Zinc, Copper, and Manganese on the Gastrointestinal Environment of Pigs and Poultry

Simple Summary

Pigs and poultry, similar to humans, need regular consumption of zinc, copper, and manganese for normal functioning. To ensure adequate dietary intake, and prevent deficiency, their diets are supplemented with sufficient, often excessive, levels of these minerals or even at higher levels, which have been associated with improvements in their health and/or growth. However, if provided in excess, mineral quantities beyond those required are simply excreted from the animal, which is associated with negative consequences for the environment and even the development of antimicrobial resistance. Therefore, it is of great interest to better understand the dynamics of zinc, copper, and manganese in the intestine of pigs and poultry following consumption of supplemented diets, and how the requirements and benefits related to these minerals can be optimized and negative impacts minimized. The intestine of pigs and poultry contains vast numbers of microorganisms, notably bacteria, that continually interact with, and influence, their host. This review explores the influence of zinc, copper, and manganese on these interactions and how novel forms of these minerals have the potential to maximize their delivery and benefits, while limiting any negative consequences.

Abstract

Zinc, copper, and manganese are prominent essential trace (or micro) minerals, being required in small, but adequate, amounts by pigs and poultry for normal biological functioning. Feed is a source of trace minerals for pigs and poultry but variable bioavailability in typical feed ingredients means that supplementation with low-cost oxides and sulphates has become common practice. Such trace mineral supplementation often provides significant ‘safety margins’, while copper and zinc have been supplemented at supra-nutritional (or pharmacological) levels to improve health and/or growth performance. Regulatory mechanisms ensure that much of this oversupply is excreted by the host into the environment, which can be toxic to plants and microorganisms or promote antimicrobial resistance in microbes, and thus supplying trace minerals more precisely to pigs and poultry is necessary. The gastrointestinal tract is thus central to the maintenance of trace mineral homeostasis and the provision of supra-nutritional or pharmacological levels is associated with modification of the gut environment, such as the microbiome. This review, therefore, considers recent advances in understanding the influence of zinc, copper, and manganese on the gastrointestinal environment of pigs and poultry, including more novel, alternative sources seeking to maintain supra-nutritional benefits with minimal environmental impact.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations

Coastal sands are important natural recreational facilities that have become hotspots for tourism and economic development. However, these sands harbour diverse microbial assemblages that play a critical role in the balance between public health and ecology. In this study, targeted high-throughput sequencing analysis was used to identify sand-borne bacterial populations at four public beaches in Durban. The effect of heavy metal in shaping the distribution of bacterial metacommunities was determined using canonical correspondence analysis (CCA), while the functional gene profiles were predicted using PICRUSt2 analysis. Sequences matching those of the bacterial phylum Proteobacteria were the most abundant in all samples, followed by those of the phyla Firmicutes, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Genus-level taxonomic analysis showed the presence of 1163 bacterial genera in all samples combined. The distribution of bacterial communities was shaped by heavy metal concentrations, with the distribution of Flavobacteria, Bacteroidia, and Deltaproteobacteria influenced by Pb and Zn, while B and Cr influenced the distribution of Clostridia and Gammaproteobacteria, respectively. Identified antibiotic resistance genes included the peptidoglycan biosynthesis gene II, III, IV, and V, as well as the polymyxin resistance gene, while the virulence genes included the sitA, fimB, aerobactin synthase, and pilL gene. Our findings demonstrate that beach sand-borne bacteria are reservoirs of virulence and antibiotic resistance genes. Contamination of beach sands with heavy metals selects for both heavy metal resistance and antibiotic resistance in beach sand bacterial communities. Children and immunocompromised people engaging in recreational activities on beaches may be exposed to higher risk of infection.

Development, spread and persistence of antibiotic resistance genes (ARGs) in the soil microbiomes through co-selection

Bacterial pathogens resistant to multiple antibiotics are emergent threat to the public health which may evolve in the environment due to the co-selection of antibiotic resistance, driven by poly aromatic hydrocarbons (PAHs) and/or heavy metal contaminations. The co-selection of antibiotic resistance (AMR) evolves through the co-resistance or cross-resistance, or co-regulatory mechanisms, present in bacteria. The persistent toxic contaminants impose widespread pressure in both clinical and environmental setting, and may potentially cause the maintenance and spread of antibiotic resistance genes (ARGs). In the past few years, due to exponential increase of AMR, numerous drugs are now no longer effective to treat infectious diseases, especially in cases of bacterial infections. In this mini-review, we have described the role of co-resistance and cross-resistance as main sources for co-selection of ARGs; while other co-regulatory mechanisms are also involved with cross-resistance that regulates multiple ARGs. However, co-factors also support selections, which results in development and evolution of ARGs in absence of antibiotic pressure. Efflux pumps present on the same mobile genetic elements, possibly due to the function of Class 1 integrons (Int1), may increase the presence of ARGs into the environment, which further is promptly changed as per environmental conditions. This review also signifies that mutation plays important role in the expansion of ARGs due to presence of diverse types of anthropogenic pollutants, which results in overexpression of efflux pump with higher bacterial fitness cost; and these situations result in acquisition of resistant genes. The future aspects of co-selection with involvement of systems biology, synthetic biology and gene network approaches have also been discussed.

Potential application of Pseudomonas stutzeri W228 for removal of copper and lead from marine environments

High concentrations of metals in the environment alter bacterial diversity, selecting resistant and tolerant species. The study evaluated the selection of a potential bacterial strain from Sepetiba Bay-Rio de Janeiro, Brazil marine sediments to remove Cu and Pb. The bacterial strain isolated from the sediments was used in three different bioassays: (1) Cu at concentrations of 0 (control), 6 and 50 μg.mL^-1; (2) Pb at concentrations of 0 (control), 6 and 50 μg.mL^-1; (3) Cu + Pb in concentrations of 3 μg.mL^-1 Cu + 3 μg.mL^-1 Pb (6 μg.mL^-1) and 25 μg.mL^-1 Cu + 25 μg.mL^-1 Pb (50 μg.mL^-1). The number of cells and the enzymatic activities of dehydrogenases and esterases were quantified. Results of taxonomic identification indicated the selection of the Pseudomonas stutzeri W228 strain, showing a greater degree of similarity (±73%) with the database used. There was no significant variation in the number of cells, 10⁸ cells.mL^-1, which represents a high biomass production in the presence of stressors. However, we observed a reduction in dehydrogenase activity at all tested concentrations of Cu, Pb and Cu + Pb. The activity of esterase increased, indicating a higher energy demand to complete the bacterial life cycle. The study showed significant results for the absorption of Pb by the extracellular polymeric substances (EPS) and the efflux of Cu. The capacity of Pb absorption by EPS can be considered a resistance mechanism, as well as the efflux of Cu, so that the available EPS sites could be occupied by the most toxic ions demonstrating that Pseudomonas stutzeri is resistant to Pb and Cu.

Detection of Heavy Metal Tolerance among different MLSB Resistance Phenotypes of Methicillin-Resistant S. aureus (MRSA)

Methicillin-resistant Staphylococcus aureus (MRSA) strains are widespread globally. Besides their virulence factors, the co-occurrence of antimicrobial and metal resistance has been reported. This study was designed to evaluate the antibiotic resistance and resistance phenotypes, investigate the occurrence of virulence factors, and detect heavy metal tolerance among MRSA strains. Antibiogram profiling was done as recommended by CLSI instructions. Resistance phenotypes were detected by D test, followed by characterization of enzymatic activities and biofilm formation assay. Antibacterial activity of different heavy metals was tested, and predictable synergistic assay was performed. Among MRSA strains collected, high resistance to ampicillin and amoxicillin/clavulanate (100%) and high susceptibility to clindamycin (70%) were obtained. Resistance phenotypes were detected as S, constitutive MLSB, inducible MLSB, and MS by percentages of 10%, 30%, 30% and 30% respectively. Virulence factors like lipolytic (50%) and hemolytic (70%) activity, and biofilm formation ability (100%) were detected. High resistance towards potassium and magnesium was observed. MTC of 500 ppm was detected for all isolates in case of cobalt and iron. In case of zinc and copper, MTC was detected as 500 ppm except for one isolate which was highly resistant, and 500 ppm for all isolates except for two isolates which were highly sensitive respectively. Magnesium in different concentrations (500 and 2000 ppm) showed synergistic activity with erythromycin and clindamycin. Results reveal high heavy metal tolerance among antibiotic resistant MRSA strains, in addition to the presence of virulence factors. Upcoming studies must be focused on the combination of sub-inhibitory concentration of different heavy metals with the available antibiotics.