Natural antibiotic resistance and contamination by antibiotic resistance determinants: the two ages in the evolution of resistance to antimicrobials

CS/PVP Hydrogel-Based Nanocapillary for Monitoring Bacterial Growth and Rapid Antibiotic Susceptibility Testing

Infection with drug-resistant bacteria poses a significant threat to human health. Judicious use of antibiotics could reduce the likelihood of bacterial resistance, which can be evaluated through antibiotic susceptibility testing (AST). This paper focuses on the application of a needle-like nanocapillary tip filled with chitosan (CS)/polyethylene pyrrolidone (PVP) hydrogel based on its specific pH-sensitive properties. The gel-filled nanocapillary has the potential to be used for electrical pH detection with a sensitivity of 3.06 nA/pH and a linear range from 7.3 to 4.3. Such sensitivity for pH measurement could be extended for monitoring of bacterial (such as Escherichia coli and Streptococcus salivarius) growth because of the relationship between pH and bacterial growth. Bacterial growth curves obtained using the hydrogel-filled nanocapillary showed good agreement with the OD600 method. Moreover, this device could be applied for rapid AST for tetracycline and norfloxacin on E. coli with minimum inhibitory concentrations of 2 and 0.125 μg/mL, respectively. This study expands the application of the hydrogel-based nanocapillary for bacterial research by monitoring changes in pH values.

Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations

Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.

On the antimicrobial properties and endurance of eugenol and 2-phenylphenol functionalized sol-gel coatings

Preventing microbiological surface contamination in public spaces is nowadays of high priority. The proliferation of a microbial infection may arise through air, water, or direct contact with infected surfaces. Chemical sanitization is one of the most effective approaches to avoid the proliferation of microorganisms. However, extended contact with chemicals for cleaning purposes such as chlorine, hydrogen peroxide or ethanol may lead to long-term diseases as well as drowsiness or respiratory issues, not to mention environmental issues associated to their use. As a potentially safer alternative, in the present work, the efficacy and endurance of the antimicrobial activity of different sol-gel coatings were studied, where one or two biocides were added to the coating matrix resulting on active groups exposed on the surface. Specifically, the coating formulations were synthesized by the sol-gel method. Using the alkoxide route with acid catalysis a hybrid silica-titania-methacrylate matrix was obtained where aromatic liquid eugenol was added with a double function: as a complexing agent for the chelation of the reaction precursor titanium isopropoxide, and as a biocide. In addition, 2-Phenylphenol, ECHA approved biocide, has also been incorporated to the coating matrix. The antibacterial effect of these coatings was confirmed on Gram-positive (Staphylococcus aureus) and Gram-negative bacteria (Escherichia coli). Additionally, the coatings were non cyto-toxic and displayed virucidal activity. The coating chemical composition was characterized by 29Si NMR, and ATR-FTIR. Furthermore, the thickness and the mechanical properties were characterized by profilometry and nanoindentation, respectively. Finally, the durability of the coatings was studied with tribology tests. Overall, our data support the efficacy of the tested sol-gel coatings and suggest that added features may be required to improve endurance of the antimicrobial effects on operational conditions.

A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch

Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.

High carriage of plasmid-mediated quinolone resistance (PMQR) genes by ESBL-producing and fluoroquinolone-resistant Escherichia coli recovered from animal waste dumps

BACKGROUND

There has been a rise in the consumption of fluoroquinolones in human and veterinary medicine recently. This has contributed to the rising incidence of quinolone resistance in bacteria. This study aimed at the determination of the antibiotic resistance profile of ESBL-producing and fluoroquinolone-resistant E. coli (FQEC) isolated from animal waste obtained from the waste dumps of an agricultural farm and their carriage of genes encoding PMQR.

METHODS AND RESULTS

Isolation of ESBL-producing E. coli from animal waste samples was done on CHROMagar ESBL, while presumptive isolates were purified, and identified via the detection of uidA gene. Susceptibility to a panel of ten antibiotics was done using the disc diffusion method, and detection of PMQR genes (qnrA, qnrB, qnrS, aac(6')-lb-cr, qepA and oqxAB) was done using monoplex and duplex PCR. Twenty-five ESBL-producing and FQEC were obtained from the cattle (6), piggery (7) and poultry (12) waste dumps of the farm. There was 100% resistance to cefpodoxime, cefotaxime, enrofloxacin, trimethoprim-sulfamethoxazole and penicillin by the isolates. The resistance to the other antibiotics was streptomycin (48%), ceftazidime (24%), while no isolate resisted amoxicillin-clavulanate and imipenem. The frequencies of PMQR genes detected were; qnrA (96%), oqxAB (96%), qnrB (92%), while  qnrS was detected in 88% (22) of the isolates. Aminoglycoside acetyltransferase (aac(6')-lb-cr) and quinolone efflux pump (qepA) were each detected in 20 (80%) of the isolates.

CONCLUSIONS

This study showed that animal wastes disposed indiscriminately into dumps could be a budding 'hotspot' for multidrug resistant, ESBL-producing and fluoroquinolone-resistant E. coli carrying multiple genes encoding resistance to fluoroquinolone antibiotics.

Unifying concepts in methanogenic, aerobic, and anammox sludge granulation

The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.

Postbiotic as Novel Alternative Agent or Adjuvant for the Common Antibiotic Utilized in the Food Industry

BACKGROUND

Antibiotic resistance is a serious public health problem as it causes previously manageable diseases to become deadly infections that can cause serious disability or even death. Scientists are creating novel approaches and procedures that are essential for the treatment of infections and limiting the improper use of antibiotics in an effort to counter this rising risk.

OBJECTIVES

With a focus on the numerous postbiotic metabolites formed from the beneficial gut microorganisms, their potential antimicrobial actions, and recent associated advancements in the food and medical areas, this review presents an overview of the emerging ways to prevent antibiotic resistance.

RESULTS

Presently, scientific literature confirms that plant-derived antimicrobials, RNA therapy, fecal microbiota transplantation, vaccines, nanoantibiotics, haemofiltration, predatory bacteria, immunotherapeutics, quorum-sensing inhibitors, phage therapies, and probiotics can be considered natural and efficient antibiotic alternative candidates. The investigations on appropriate probiotic strains have led to the characterization of specific metabolic byproducts of probiotics named postbiotics. Based on preclinical and clinical studies, postbiotics with their unique characteristics in terms of clinical (safe origin, without the potential spread of antibiotic resistance genes, unique and multiple antimicrobial action mechanisms), technological (stability and feasibility of largescale production), and economic (low production costs) aspects can be used as a novel alternative agent or adjuvant for the common antibiotics utilized in the production of animal-based foods.

CONCLUSION

Postbiotic constituents may be a new approach for utilization in the pharmaceutical and food sectors for developing therapeutic treatments. Further metabolomics investigations are required to describe novel postbiotics and clinical trials are also required to define the sufficient dose and optimum administration frequency of postbiotics.

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

What are the missing pieces needed to stop antibiotic resistance?

As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with the introduction of new antibiotics into the market in the golden age of antimicrobial discovery, nowadays few antibiotics are in the pipeline. Under these circumstances, a deep understanding on the mechanisms of emergence, evolution and transmission of antibiotic resistance, as well as on the consequences for the bacterial physiology of acquiring resistance is needed to implement novel strategies, beyond the development of new antibiotics or the restriction in the use of current ones, to more efficiently treat infections. There are still several aspects in the field of antibiotic resistance that are not fully understood. In the current article, we make a non-exhaustive critical review of some of them that we consider of special relevance, in the aim of presenting a snapshot of the studies that still need to be done to tackle antibiotic resistance.

Hepatoprotective Properties of Water Kefir: A Traditional Fermented Drink and Its Potential Role

The liver is extremely vulnerable to damage because of its role in metabolism. Toxin, metabolic syndrome, alcohol, microorganisms, and autoimmune diseases can be the cause of liver damage. While different etiologies can cause liver disease, pathophysiologically, there are similarities in the role of free radicals, inflammatory mediators, and gut microbiome during the disease development. Therefore, ingredients with antioxidant, antiinflammatory, and antidysbiotic properties have the potential to act as hepatoprotectors; and water kefir is one of them. Water kefir is a traditional fermented drink made from water kefir grains, sugar, and dried fruit. Water kefir is dominated by lactic acid bacteria and yeast as a fermented beverage, and several species of this group of microorganisms have been shown as probiotics. According to researches, water kefir has strong antioxidant, antiinflammatory, and hepatoprotective effects. Even so, there are still few researches reported about water kefir as a hepatoprotective agent. Several studies, on the other hand, showed promising results. This review discusses the relationship between the pathophysiology of liver disease and the pharmacological activity of water kefir and other probiotics in general, which leads to the potential prospect of water kefir research as a hepatoprotective agent.

Efflux systems as a target for anti-biofilm nanoparticles: perspectives on emerging applications

INTRODUCTION

Understanding the role of efflux pumps in biofilm resistance provides valuable insights for developing effective therapeutic strategies. Drugs designed for targeting efflux pumps in drug design holds promise for combating biofilm-related infections. Nanoparticles offer unparalleled advantages in designing drugs targeting efflux pumps.

AREAS COVERED

This review rigorously examines the existing body of knowledge on the prospective targeting of efflux pumps using metal-based nanoparticles. It includes and analyses the pertinent research findings sourced from the PubMed and SciFinder databases. It covers the experimental studies on efflux inhibition by nanoparticles and provides detailed analyses of their mechanisms of action, elucidating their interactions with the efflux system and their influence on biofilm formation and persistence.

EXPERT OPINION

The potential of nanoparticles to act as potent antibacterial agents through efflux pump inhibition remains tantalizing, although hindered by limited mechanistic understanding. From the burgeoning research landscape nanoparticles emerge as a novel direction for shaping antimicrobial drug design. Notably, beyond their contribution to drug resistance, efflux pumps play a pivotal role in biofilm development. The deliberate disruption of these pumps can effectively reduce biofilm adhesion and maturation. More details however are needed to exploit this potential.

Reduced selection for antibiotic resistance in community context is maintained despite pressure by additional antibiotics

Selection for antibiotic resistance at very low antibiotic concentrations has been demonstrated for individual antibiotics in single species experiments. Furthermore, selection in these focal strains is reduced when taking place in complex microbial community context. However, in the environment, bacteria are rarely exposed to single, but rather complex mixtures of selective agents. Here, we explored how the presence of a second selective agent affects selection dynamics between isogenic pairs of focal E. coli strains, differing exclusively in a single resistance determinant, in the absence and presence of a model wastewater community across a gradient of antibiotics. An additional antibiotic that exclusively affects the model wastewater community, but to which the focal strains are resistant to, was chosen as the second selective agent. This allowed exploring how inhibition alters the community's ability to reduce selection. In the presence of the community, the selection coefficient at specific antibiotic concentrations was consistently decreased compared to the absence of the community. While pressure through the second antibiotic significantly decreased the activity and diversity of the community, its ability to reduce selection was consistently maintained at levels comparable to those recorded in absence of the second antibiotic. This indicates that the observed effects of community context on selection dynamics are rather based on competitive or protective effects between the focal strains and a small proportion of bacteria within the community, than on general competition for nutrients. These findings have implications for our understanding of the evolution and selection for multi-drug resistant strains.

Enhanced detoxification of Cr6+ by Shewanella oneidensis via adsorption on spherical and flower-like manganese ferrite nanostructures

Maximizing the safe removal of hexavalent chromium (Cr6+) from waste streams is an increasing demand due to the environmental, economic and health benefits. The integrated adsorption and bio-reduction method can be applied for the elimination of the highly toxic Cr6+ and its detoxification. This work describes a synthetic method for achieving the best chemical composition of spherical and flower-like manganese ferrite (MnxFe3-xO4) nanostructures (NS) for Cr6+ adsorption. We selected NS with the highest adsorption performance to study its efficiency in the extracellular reduction of Cr6+ into a trivalent state (Cr3+) by Shewanella oneidensis (S. oneidensis) MR-1. MnxFe3-xO4 NS were prepared by a polyol solvothermal synthesis process. They were characterised by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray photoelectron spectrometry (XPS), dynamic light scattering (DLS) and Fourier transform-infrared (FTIR) spectroscopy. The elemental composition of MnxFe3-xO4 was evaluated by inductively coupled plasma atomic emission spectroscopy. Our results reveal that the oxidation state of the manganese precursor significantly affects the Cr6+ adsorption efficiency of MnxFe3-xO4 NS. The best adsorption capacity for Cr6+ is 16.8 ± 1.6 mg Cr6+/g by the spherical Mn0.22+Fe2.83+O4 nanoparticles at pH 7, which is 1.4 times higher than that of Mn0.8Fe2.2O4 nanoflowers. This was attributed to the relative excess of divalent manganese in Mn0.22+Fe2.83+O4 based on our XPS analysis. The lethal concentration of Cr6+ for S. oneidensis MR-1 was 60 mg L-1 (determined by flow cytometry). The addition of Mn0.22+Fe2.83+O4 nanoparticles to S. oneidensis MR-1 enhanced the bio-reduction of Cr6+ 2.66 times compared to the presence of the bacteria alone. This work provides a cost-effective method for the removal of Cr6+ with a minimum amount of sludge production.

Management of mung bean leaf spot disease caused by Phoma herbarum through Penicillium janczewskii metabolites mediated by MAPK signaling cascade

Vigna radiata L., an imperative legume crop of Pakistan, faces hordes of damage due to fungi; infecting host tissues by the appressorium. The use of natural compounds is an innovative concern to manage mung-bean fungal diseases. The bioactive secondary metabolites of Penicillium species are well documented for their strong fungi-static ability against many pathogens. Presently, one-month-old aqueous culture filtrates of Penicillium janczewskii, P. digitatum, P. verrucosum, P. crustosum, and P. oxalicum were evaluated to check the antagonistic effect of different dilutions (0, 10, 20, … and 60%). There was a significant reduction of around 7-38%, 46-57%, 46-58%, 27-68%, and 21-51% in Phoma herbarum dry biomass production due to P. janczewskii, P. digitatum, P. verrucosum, P. crustosum, and P. oxalicum, respectively. Inhibition constants determined by a regression equation demonstrated the most significant inhibition by P. janczewskii. Finally, using real-time reverse transcription PCR (qPCR) the effect of P. Janczewskii metabolites was determined on the transcript level of StSTE12 gene involved in the development and penetration of appressorium. The expression pattern of the StSTE12 gene was determined by percent Knockdown (%KD) expression that was found to be decreased i.e. 51.47, 43.22, 40.67, 38.01, 35.97, and 33.41% for P. herbarum with an increase in metabolites concentrations viz., 10, 20, 30, 40, 50 and 60% metabolites, respectively. In silico studies were conducted to analyze the role of Ste12 a transcriptional factor in the MAPK signaling pathway. The present study concludes a strong fungicidal potential of Penicillium species against P. herbarum. Further studies to isolate the effective fungicidal constituents of Penicillium species through GCMS analysis and determination of their role in signaling pathways are requisite.

Ethiopia's Antibiotic Footprint: Employing the Newly Emerging Digital Concept to Estimate Annual Consumption for the Country

Background The processes involving resistance development against antibiotics have historically been part of the Darwinian evolution. However, the increasing use of antibiotics in modern medicine has intensified the selection pressures with an acute gear-up, rather than as part of this very slow evolutionary process that selects for enhanced fitness for survival. Two major recommendations have been made in the past to tackle this challenge: (1) incentivizing the pharmaceutical industry to invest more in research and development endeavors so that they come up with new antibiotics, and (2) implementing antimicrobial stewardship programs in healthcare systems. Methodology In this study, the third and emerging approach, namely, documenting antibiotic footprint, was employed as a communication tool that targets individual consumers of antibiotics. Data obtained from the Ethiopian Pharmaceutical Supply Agency were curated to systematically compile antibiotic consumption at each of the agency's regional hubs. The exact geospatial locations of the hubs were generated and synchronized to depict the size of the antibiotic footprint infograph as proportional to the antibiotic consumption data at each hub. Moreover, the cumulative and per-capita consumption of these antibiotics at the country level (overall antibiotic footprint) were calculated by including estimated data for the livestock sector. Results A total of 698.2 tons of antibiotics were used in Ethiopia in 2018, and the per-capita consumption of antibiotics was 5.8 g per person. Extended-spectrum (J01CA) and beta-lactamase-resistant penicillins (J01CF) were the most commonly utilized classes of antibiotics which accounted for, respectively, 38.3% and 20.8% of all antibiotics used in the country's public health sector. Hubs in Addis Ababa (14%) and Hawassa (12%) topped the overall antibiotic consumption in the country. Contrarily, hubs in Gambella and Semera received relatively smaller quantities of antibiotics, with totals of 4.8 tons (0.9%) and 10.2 tons (1.9%), respectively. Conclusions This study shows that the newly emerging concept of the antibiotic footprint is a simple and suitable tool for public health policy communications targeting individual consumers of antibiotics. If implemented judicially, the concept of the antibiotic footprint has a huge potential to support global scientific efforts and collaborations in setting standards that help to reduce the overuse and misuse of antibiotics in the future.

Characteristics of resistome and bacterial community structure in constructed wetland during dormant period: A fullscale study from Annan wetland

As a green technology, constructed wetlands (CWs) can provide a low-cost solution for wastewater treatment. Either as a standalone treatment or integrated with conventional treatment, nutrients, antibiotic resistant bacteria (ARB)/antibiotic resistance genes (ARGs) can be removed by CW efficiently. While, few studies have focused on characteristics of resistome and bacterial community (BC) structure in CW during dormant period. Therefore, in this study, Annan CW (a full-scale hybrid CW) was selected to characterize resistome and BC during dormant period. The profiles of bacteria / ARGs were monitored in combination of shotgun sequencing and metagenomic assembly analysis. And multidrug ARGs are the most abundant in Annan CW, and surface flow wetland had the relatively high ARG diversity and abundance compared with subsurface flow wetland and the front pond. The most dominant phylum in CW is Proteobacteria, while the other dominant phylum in three parts have different order. COD, TP, TN, ARGs, and mobile genetic genes (MGEs) were removed by subsurface flow CW with better performance, but virulent factors (VFs) were removed by surface flow CW with better performance. Based on the spatiotemporal distribution of ARGs, the internal mechanism of ARGs dynamic variation was explored by the redundancy analysis (RDA) and variation partitioning analysis (VPA). BCs, MGEs and environmental factors (EFs) were responsible for 45.6 %, 28.3 % and 15.4 % of the ARGs variations. Among these factors, BCs and MGEs were the major co-drivers impacting the ARG profile, and EFs indirectly influence the ARG profile. This study illustrates the specific functions of ARG risk elimination in different CW components, promotes a better understanding of the efficiency of CWs for the reduction of ARG and ARB, contributing to improve the removal performance of constructed wetlands. And provide management advice to further optimize the operation of CWs during dormant period.

Cyanophages as an important factor in the early evolution of oxygenic photosynthesis

Cyanophages are viruses that infect cyanobacteria. An interesting feature of many of them is the presence of psbA and psbD, genes that encode D1 and D2 proteins, respectively. The D1 and D2 are core proteins of the photosystem II (PSII) in cyanobacteria, algae and plants and influence the proper function of oxygenic photosynthesis (OP) in all oxyphototrophs on Earth. The frequent occurrence of psbA and psbD in cyanophages raises the question whether these genes coevolved with hosts during the early stages of cyanophage and cyanobacterial evolution, or whether they are direct descendants of genes adopted from the genomes of cyanobacterial hosts. The phylogeny of D1/D2 proteins encoded in the genomes of selected cyanophages and oxyphototrophs was reconstructed. In addition, common ancestral sequences of D1 and D2 proteins were predicted for cyanophages and oxyphototrophs. Based on this, the reconstruction of the 3D structures of D1 and D2 proteins was performed. In addition, the ratio of non-synonymous to synonymous (d_N/d_S) nucleotide substitutions in the coding sequences (CDSs) of psbA and psbD was determined. The results of the predicted spatial structures of the D1 and D2 proteins and purifying selection for the CDSs of psbA and psbD suggest that they belong to the ancient proteins, which may have formed the primordial PSII. It cannot be ruled out that they involved in water oxidation in cyanobacteria-like organisms at early stages of the evolution of life on Earth and coevolved with ancient cyanophages. The data are also discussed in the context of the origin of viruses.

Trade-off for survival: Microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity

The environmental microbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen asa bioindicatororganism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native microbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.

Pharmaceuticals and other contaminants of emerging concern in Admiralty Bay as a result of untreated wastewater discharge: Status and possible environmental consequences

Considering how the impact of human activity in Antarctica is growing, the aim of this study was to conduct the first assessment of pharmaceuticals and personal care products (PPCPs), other emerging contaminants (ECs), and antibiotic resistance genes present in the western shore of the Admiralty Bay region of King George Island. In total, more than 170 substances were evaluated to assess the potential environmental risks they pose to the study area. The major evaluated source of pollutants in this study is discharged untreated wastewater. The highest PPCP concentrations in wastewater were found for naproxen (2653 ngL^-1), diclofenac (747 ngL^-1), ketoconazole (760 ngL^-1), ibuprofen (477 ngL^-1) and acetaminophen (332 ngL^-1). Moreover, the concentrations of benzotriazole (6340 ngL^-1) and caffeine (3310 ngL^-1) were also high. The Risk Quotient values indicate that azole antifungals (ketoconazole), anti-inflammatories (diclofenac, ibuprofen) and stimulants (caffeine) are the main groups responsible for the highest toxic burden. In addition, antibiotic resistance genes integrons (int 1) and sulphonamide resistance genes (sul 1-2) were detected in wastewater and seawater. These results indicate that regular monitoring of PPCPs and other ECs is of great importance in this environment. Additionally, the following mitigation strategies are suggested: (1) to create a centralised record of the medications prescribed and consumed in situ (to improve knowledge of potential contaminants without analysis); (2) to use more environmentally friendly substitutes both for pharmaceuticals and personal care products when possible (limiting consumption at the source); and (3) to apply advanced systems for wastewater treatment before discharge to the recipient (end-of-pipe technologies as a final barrier).

Isolation, Physiological Characterization, and Antibiotic Susceptibility Testing of Fast-Growing Bacteria from the Sea-Affected Temporary Meltwater Ponds in the Thala Hills Oasis (Enderby Land, East Antarctica)

Simple Summary

The characterization of microbial communities from Antarctic temporary meltwater ponds is limited, while they could serve as a source of biotechnologically interesting microorganisms. In this study, we characterized a set of bacteria isolated from the sea-affected temporary meltwater ponds in the East Antarctica area of the Vecherny region of the Thala Hills Oasis, Enderby Land. The isolated meltwater bacteria were identified as Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, where Proteobacteria and Actinobacteria were predominant. The isolated bacteria were able to grow in a relatively wide temperature range between 4 °C and 37 °C, with an optimal temperature range of 18–25 °C. Further, most of the isolates showed an ability to secrete lipases and proteases, and several of them were pigmented. Bacterial isolates from the genera Pseudomonas and Acinetobacter exhibited multi-resistance against β-lactams, sulfonamide, macrolide, diaminopyrimidines, and chloramphenicol antibiotics. This study shows that bacterial communities from the temporary meltwater ponds in East Antarctica consist of metabolically versatile bacteria that might be defined by their location near the sea and the close presence of animals, penguins and skuas in particular.

Abstract

In this study, for the first time, we report the identification and characterization of culturable fast-growing bacteria isolated from the sea-affected temporary meltwater ponds (MPs) in the East Antarctica area of the Vecherny region (−67.656317, 46.175058) of the Thala Hills Oasis, Enderby Land. Water samples from the studied MPs showed alkaline pH (from 8.0 to 10.1) and highly varied total dissolved solids (86–94,000 mg/L). In total, twenty-nine bacterial isolates were retrieved from the studied MPs. The phylogenetic analysis based on 16S rRNA gene sequence similarities showed that the isolated bacteria belong to the phyla Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes and the twelve genera Pseudomonas, Shewanella, Acinetobacter, Sporosarcina, Facklamia, Carnobacterium, Arthrobacter, Brachybacterium, Micrococcus, Agrococcus, Leifsonia, and Flavobacterium. Most of the isolated bacteria were psychrotrophs and showed the production of one or more extracellular enzymes. Lipolytic and proteolytic activities were more prevalent among the isolates. Five isolates from the Actinobacteria phylum and one isolate from the Bacteroidetes phylum had strong pigmentation. Antibiotic susceptibility testing revealed that most of the isolates are resistant to at least one antibiotic, and seven isolates showed multi-resistance.

An Overview of Human T-Lymphotropic Virus Type 1 Lung Injury

Previous studies have demonstrated the development of pulmonary impairment in individuals infected with human T-lymphotropic virus type 1 (HTLV-1). Complications, such as alveolitis and bronchiectasis, were found in individuals who developed tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP-HAM) due to chronic inflammation. These patients exhibited increased levels of lymphocytes (CD4+ and CD25+), cytokines (IL-2, IL-12, and IFN-γ), inflammatory chemokines (MIP-1α and IP-10), and cell adhesion molecules (ICAM-1) in the bronchoalveolar lavage fluid, with the result of chronic inflammation and lung injury. The main lesions observed at Chest high-resolution computed tomography were centrilobular nodules, parenchymal bands, lung cysts, bronchiectasis, ground-glass opacity, mosaic attenuation, and pleural thickening. It can lead to progressive changes in pulmonary function with the development of restrictive and obstructive diseases. Recent studies suggest a causal relationship between HTLV-1 and pulmonary diseases, with intensification of lesions and progressive decrease in pulmonary function. This summary updates a previous publication and addresses the general lack of knowledge regarding the relationship between TSP-HAM and pulmonary disease, providing direction for future work and the management of these individuals.

Knowledge, Attitude and Beliefs of Nurses Regarding Antibiotic use and Prevention of Antibiotic Resistance

Introduction

Resistance to antibiotics is a threat confronting health care system worldwide. Nurses play a significant role in combating this threat.

Objectives

The present study examined the knowledge and attitude of nurses towards antibiotic use and prevention of antibiotic resistance.

Methods

The research involved a cross-sectional study conducted in a multi-cultural tertiary healthcare setting. The participants were 341 nurses. A structured self-administered questionnaire with a good validity and reliability (α = 0.7) was used.

Results

The nurses surveyed showed moderate awareness of antibiotic resistance and a fair attitude towards its prevention. There was no significant correlation of demographic features with their overall knowledge and attitude ( p > 0.05).

Conclusions

Nurses perform a crucial part in infection control, but often lack knowledge of methods to prevent antibiotic resistance. This paucity highlights the importance of tailored interventions to help nurses improve their awareness of antibiotic resistance and create a favorable attitude towards its prevention.

Antibiotic Use in Livestock and Residues in Food-A Public Health Threat: A Review

The usage of antibiotics has been, and remains, a topic of utmost importance; on the one hand, for animal breeders, and on the other hand, for food safety. Although many countries have established strict rules for using antibiotics in animal husbandry for the food industry, their misuse and irregularities in compliance with withdrawal periods are still identified. In addition to animal-origin foods that may cause antibiotic residue problems, more and more non-animal-origin foods with this type of non-compliance are identified. In this context, we aim to summarize the available information regarding the presence of antibiotic residues in food products, obtained in various parts of the world, as well as the impact of consumption of food with antibiotic residues on consumer health. We also aim to present the methods of analysis that are currently used to determine antibiotic residues in food, as well as methods that are characterized by the speed of obtaining results or by the possibility of identifying very small amounts of residues.

Distribution, Diversity and Antibiotic Resistance of Pseudomonas spp. Isolated from the Water Dams in the North of Tunisia

Natural environment is one of the important reservoirs to disseminate antibiotic resistance, most of the antibiotics resistance researches were focused on clinical isolates. Thus, this work aimed to analyze surface water samples collected from dams and rivers in the north of Tunisia. Pseudomonas species were confirmed using biochemical and molecular identifications. Resistance was studied by testing their susceptibility against 19 antibiotics using the disc diffusion method moreover the virulence factors were studied by PCR targeting 13 genes. 104 isolates were confirmed as Pseudomonas genera distributed into 21 species. The most abundant species is P. aeruginosa (22.11%), followed by P. protegens (12.5%). No resistance phenotypes were observed towards imipenem, meropenem, ceftazidime, colistin, ciprofloxacin and amikacin. A high resistance level was observed against cefoxitin (94.23%), amoxicillin-clavulanic acid (67.31%), nalidixic acid (62.5%), streptomycin (57.69%), ticarcillin (43.27%), fosfomycin (64.42%) and tetracycline (23.08%). A low rate of resistance was observed against cefotaxime (16.35%) and gentamicin (7.69%). The majority (70.19%) of isolates were Multidrug-resistant (MDR). 12 of virulence genes were found in all P. aeruginosa isolates. Our results showed that Pseudomonas isolates could be an important reservoir of antibiotic resistance from environment sites.

Wildlife and Antibiotic Resistance

Antibiotic resistance is a major human health problem. While health care facilities are main contributors to the emergence, evolution and spread of antibiotic resistance, other ecosystems are involved in such dissemination. Wastewater, farm animals and pets have been considered important contributors to the development of antibiotic resistance. Herein, we review the impact of wildlife in such problem. Current evidence supports that the presence of antibiotic resistance genes and/or antibiotic resistant bacteria in wild animals is a sign of anthropic pollution more than of selection of resistance. However, once antibiotic resistance is present in the wild, wildlife can contribute to its transmission across different ecosystems. Further, the finding that antibiotic resistance genes, currently causing problems at hospitals, might spread through horizontal gene transfer among the bacteria present in the microbiomes of ubiquitous animals as cockroaches, fleas or rats, supports the possibility that these organisms might be bioreactors for the horizontal transfer of antibiotic resistance genes among human pathogens. The contribution of wildlife in the spread of antibiotic resistance among different hosts and ecosystems occurs at two levels. Firstly, in the case of non-migrating animals, the transfer will take place locally; a One Health problem. Paradigmatic examples are the above mentioned animals that cohabit with humans and can be reservoirs and vehicles for antibiotic resistance dissemination. Secondly, migrating animals, such as gulls, fishes or turtles may participate in the dissemination of antibiotic resistance across different geographic areas, even between different continents, which constitutes a Global Health issue.

Assessing the inhibitory activity of culture supernatants against foodborne pathogens of two psychrotrophic bacteria isolated from river trout

There is a need for new natural products with antimicrobial activity to treat multidrug resistant bacteria that can cause human illness. Some of them are foodborne pathogens. Two different Gram-negative psychrotrophic strains were isolated from healthy trout river samples (Salmotrutta). Based on phenotypic characterization, proteomics, genotyping and phylogenetic analyses of 16 rRNA gene, strains TCPS12 and TCPS13 were identified as Shewanellabaltica and Pseudomonasfragi, respectively. Both of them produced an exopolysaccharide that showed antimicrobial activity against four foodborne pathogens. P. fragi supernatant (AS13) showed higher antimicrobial activity than S. baltica supernatant (AS12) against all tested pathogens. The stability of the antimicrobial activity of AS13 was assessed against Enterococcus faecalis ATCC 29212 under different conditions. This solution was stable when exposed for 30 min to temperatures ranging from 40 to 100 °C. In addition, it retained its activity within a pH range of 2–8 during 2 h of incubation, showing higher activity at pH 6. Serine proteases and α-amylase inactivated significantly the antimicrobial activity of AS13, suggesting that the active molecule could most likely be a glycoprotein. These products are interesting for their possible application as biopreservatives in the food industry.

Origanum vulgare L. essential oil inhibits virulence patterns of Candida spp. and potentiates the effects of fluconazole and nystatin in vitro

Background

Recurrence and resistance of Candida spp. infections is associated with the ability of these microorganisms to present several virulence patterns such as morphogenesis, adhesion, and biofilm formation. In the search for agents with antivirulence activity, essential oils could represent a strategy to act against biofilms and to potentiate antifungal drugs.

Objective

To evaluate the antivirulence effect of Origanum vulgare L. essential oil (O-EO) against Candida spp. and to potentiate the effect of fluconazole and nystatin.

Methods

The effect of O-EO was evaluated on ATCC reference strains of C. albicans and non-albicans Candida species. Minimum inhibitory concentration (MIC) was determined through broth microdilution assay. Adhesion to microplates was determined by crystal violet (CV) assay. An adapted scratch assay in 24-well was used to determine the effect of essential oil on biofilms proliferation. Viability of biofilms was evaluated by MTT reduction assay and through a checkerboard assay we determined if O-EO could act synergistically with fluconazole and nystatin.

Results

MIC for C. albicans ATCC-90029 and ATCC-10231 was 0.01 mg/L and 0.97 mg/L, respectively. For non-albicans Candida strains MIC values were 2.6 mg/L for C. dubliniensis ATCC-CD36 and 5.3 mg/L for C. krusei ATCC-6258. By using these concentrations, O-EO inhibited morphogenesis, adhesion, and proliferation at least by 50% for the strains assayed. In formed biofilms O-EO decreased viability in ATCC 90029 and ATCC 10231 strains (IC50 7.4 and 2.8 mg/L respectively). Finally, we show that O-EO interacted synergistically with fluconazole and nystatin.

Conclusions

This study demonstrate that O-EO could be considered to improve the antifungal treatment against Candida spp.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03518-z.

Biotechnological synthesis of Pd-based nanoparticle catalysts

Palladium metal nanoparticles are excellent catalysts used industrially for reactions such as hydrogenation and Heck and Suzuki C-C coupling reactions. However, the global demand for Pd far exceeds global supply, therefore the sustainable use and recycling of Pd is vital. Conventional chemical synthesis routes of Pd metal nanoparticles do not meet sustainability targets due to the use of toxic chemicals, such as organic solvents and capping agents. Microbes are capable of bioreducing soluble high oxidation state metal ions to form metal nanoparticles at ambient temperature and pressure, without the need for toxic chemicals. Microbes can also reduce metal from waste solutions, revalorising these waste streams and allowing the reuse of precious metals. Pd nanoparticles supported on microbial cells (bio-Pd) can catalyse a wide array of reactions, even outperforming commercial heterogeneous Pd catalysts in several studies. However, to be considered a viable commercial option, the intrinsic activity and selectivity of bio-Pd must be enhanced. Many types of microorganisms can produce bio-Pd, although most studies so far have been performed using bacteria, with metal reduction mediated by hydrogenase or formate dehydrogenase enzymes. Dissimilatory metal-reducing bacteria (DMRB) possess additional enzymes adapted for extracellular electron transport that potentially offer greater control over the properties of the nanoparticles produced. A recent and important addition to the field are bio-bimetallic nanoparticles, which significantly enhance the catalytic properties of bio-Pd. In addition, systems biology can integrate bio-Pd into biocatalytic processes, and processing techniques may enhance the catalytic properties further, such as incorporating additional functional nanomaterials. This review aims to highlight aspects of enzymatic metal reduction processes that can be bioengineered to control the size, shape, and cellular location of bio-Pd in order to optimise its catalytic properties.

Antibiotic Discovery and Resistance: The Chase and the Race

The history of antimicrobial resistance (AMR) evolution and the diversity of the environmental resistome indicate that AMR is an ancient natural phenomenon. Acquired resistance is a public health concern influenced by the anthropogenic use of antibiotics, leading to the selection of resistant genes. Data show that AMR is spreading globally at different rates, outpacing all efforts to mitigate this crisis. The search for new antibiotic classes is one of the key strategies in the fight against AMR. Since the 1980s, newly marketed antibiotics were either modifications or improvements of known molecules. The World Health Organization (WHO) describes the current pipeline as bleak, and warns about the scarcity of new leads. A quantitative and qualitative analysis of the pre-clinical and clinical pipeline indicates that few antibiotics may reach the market in a few years, predominantly not those that fit the innovative requirements to tackle the challenging spread of AMR. Diversity and innovation are the mainstays to cope with the rapid evolution of AMR. The discovery and development of antibiotics must address resistance to old and novel antibiotics. Here, we review the history and challenges of antibiotics discovery and describe different innovative new leads mechanisms expected to replenish the pipeline, while maintaining a promising possibility to shift the chase and the race between the spread of AMR, preserving antibiotic effectiveness, and meeting innovative leads requirements.

Antimicrobial resistance in integrated agroecosystems: State of the science and future opportunities

As the Journal of Environmental Quality (JEQ) celebrates 50 years of publication, the division of environmental microbiology is one of the newest additions to the journal. During this time, significant advances in understanding of the interconnected microbial community and impact of the microbiome on natural and designed environmental systems have occurred. In this review, we highlight the intractable challenge of antimicrobial resistance (AMR) on humans, animals, and the environment, with particular emphasis on the role of integrated agroecosystems and by highlighting contributions published in JEQ. From early studies of phenotypic resistance of indicator organisms in waters systems to current calls for integrating AMR assessment across "One Health," publications in JEQ have advanced our understanding of AMR. As we reflect on the state of the science, we emphasize future opportunities. First, integration of phenotypic and molecular tools for assessing environmental spread of AMR and human health risk continues to be an urgent research need for a one health approach to AMR. Second, monitoring AMR levels in manure is recommended to understand inputs and potential spread through agroecosystems. Third, baseline knowledge of AMR levels is important to realize the impact of manure inputs on water quality and public health risk; this can be achieved through background monitoring or identifying the source-related genes or organisms. And finally, conservation practices designed to meet nutrient reduction goals should be explored for AMR reduction potential.

ARGuing the case for (or against) probiotics

Antibiotic resistance is one of the leading medical challenges with which we are currently faced. Antibiotics, while powerful medical tools, also wreak havoc on the endogenous microbiota. Many believe that probiotics can restore the microbiota following antibiotic treatment and might even suppress the spread of antibiotic-resistance genes, but a recent study (Montassier et al.) suggests otherwise.

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants

BACKGROUND

Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.

RESULTS

Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.

CONCLUSION

Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills. Video abstract.

Antibiotic Resistance Genes in Lemur Gut and Soil Microbiota Along a Gradient of Anthropogenic Disturbance

The overuse of man-made antibiotics has facilitated the global propagation of antibiotic resistance genes in animals, across natural and anthropogenically disturbed environments. Although antibiotic treatment is the most well-studied route by which resistance genes can develop and spread within host-associated microbiota, resistomes also can be acquired or enriched via more indirect routes, such as via transmission between hosts or via contact with antibiotic-contaminated matter within the environment. Relatively little is known about the impacts of anthropogenic disturbance on reservoirs of resistance genes in wildlife and their environments. We therefore tested for (a) antibiotic resistance genes in primate hosts experiencing different severities and types of anthropogenic disturbance (i.e., non-wildlife animal presence, human presence, direct human contact, and antibiotic treatment), and (b) covariation between host-associated and environmental resistomes. We used shotgun metagenomic sequencing of ring-tailed lemur (Lemur catta) gut resistomes and associated soil resistomes sampled from up to 10 sites: seven in the wilderness of Madagascar and three in captivity in Madagascar or the United States. We found that, compared to wild lemurs, captive lemurs harbored greater abundances of resistance genes, but not necessarily more diverse resistomes. Abundances of resistance genes were positively correlated with our assessments of anthropogenic disturbance, a pattern that was robust across all ten lemur populations. The composition of lemur resistomes was site-specific and the types of resistance genes reflected antibiotic usage in the country of origin, such as vancomycin use in Madagascar. We found support for multiple routes of ARG enrichment (e.g., via human contact, antibiotic treatment, and environmental acquisition) that differed across lemur populations, but could result in similar degrees of enrichment. Soil resistomes varied across natural habitats in Madagascar and, at sites with greater anthropogenic disturbance, lemurs and soil resistomes covaried. As one of the broadest, single-species investigations of wildlife resistomes to date, we show that the transmission and enrichment of antibiotic resistance genes varies across environments, thereby adding to the mounting evidence that the resistance crisis extends outside of traditional clinical settings.

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.

Escherichia coli Antibiotic Resistance Patterns from Co-Grazing and Non-Co-Grazing Livestock and Wildlife Species from Two Farms in the Western Cape, South Africa

Although limited, studies have found conflicting results on whether co-grazing results in significant antibiotic resistance transfer between species. This type of farming system can act as a vector in the geographical spread of antibiotic-resistant bacteria in the environment. The aim of this study was to determine the antibiotic-resistant patterns between co-grazing and non-co-grazing livestock and wildlife species in South Africa. Escherichia coli was isolated from the faeces of various wildlife and livestock species from two farms in South Africa and was tested for antibiotic resistance using the Kirby–Bauer disk diffusion method against chloramphenicol, nalidixic acid, ampicillin, streptomycin, sulphafurazole, and tetracycline. A selection of some common antibiotic-resistant genes (blaCMY, aadA1, sul1, sul2, tetA, and tetB) were detected using PCR. The E. coli isolates from wildlife and livestock that co-grazed showed no significant differences in antibiotic resistance patterns. However, this was not the case for tetracycline resistance as the livestock isolates were significantly more resistant than the co-grazing wildlife isolates. The E. coli isolates from the non-co-grazing livestock and wildlife had significant differences in their antibiotic susceptibility patterns; the wildlife E. coli isolates were significantly more resistant to sulphafurazole and streptomycin than the livestock isolates, whilst those isolated from the cattle were significantly more resistant to ampicillin than the wildlife and sheep isolates. The results of this study suggest that there could be an exchange of antibiotic-resistant bacteria and genes between livestock and wildlife that co-graze.

Antimicrobial Resistance Glides in the Sky-Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic Potential

Antimicrobial resistance (AMR) is one of the most important global health concerns; therefore, the identification of AMR reservoirs and vectors is essential. Attention should be paid to the recognition of potential hazards associated with wildlife as this field still seems to be incompletely explored. In this context, the role of free-living birds as AMR carriers is noteworthy. Therefore, we applied methods used in AMR monitoring, supplemented by colistin resistance screening, to investigate the AMR status of Escherichia coli from free-living birds coming from natural habitats and rescue centers. Whole-genome sequencing (WGS) of strains enabled to determine resistance mechanisms and investigate their epidemiological relationships and virulence potential. As far as we know, this study is one of the few that applied WGS of that number (n = 71) of strains coming from a wild avian reservoir. The primary concerns arising from our study relate to resistance and its determinants toward antimicrobial classes of the highest priority for the treatment of critical infections in people, e.g., cephalosporins, quinolones, polymyxins, and aminoglycosides, as well as fosfomycin. Among the numerous determinants, bla _CTX-M-15, bla _CMY-2, bla _SHV-12, bla _TEM-1B, qnrS1, qnrB19, mcr-1, fosA7, aac(3)-IIa, ant(3")-Ia, and aph(6)-Id and chromosomal gyrA, parC, and parE mutations were identified. Fifty-two sequence types (STs) noted among 71 E. coli included the global lineages ST131, ST10, and ST224 as well as the three novel STs 11104, 11105, and 11194. Numerous virulence factors were noted with the prevailing terC, gad, ompT, iss, traT, lpfA, and sitA. Single E. coli was Shiga toxin-producing. Our study shows that the clonal spread of E. coli lineages of public and animal health relevance is a serious avian-associated hazard.

Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq

Hfq is a bacterial regulator with key roles in gene expression. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, thanks to its binding to small regulatory noncoding RNAs. This property is of primary importance for bacterial adaptation and survival in hosts. Small RNAs and Hfq are, for instance, involved in the response to antibiotics. Previous work has shown that the E. coli Hfq C-terminal region (Hfq-CTR) self-assembles into an amyloid structure. It was also demonstrated that the green tea compound EpiGallo Catechin Gallate (EGCG) binds to Hfq-CTR amyloid fibrils and remodels them into nonamyloid structures. Thus, compounds that target the amyloid region of Hfq may be used as antibacterial agents. Here, we show that another compound that inhibits amyloid formation, apomorphine, may also serve as a new antibacterial. Our results provide an alternative in order to repurpose apomorphine, commonly used in the treatment of Parkinson’s disease, as an antibiotic to block bacterial adaptation to treat infections.

Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome

BACKGROUND

Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets.

RESULTS

The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 108 16S rRNA gene copies ng-1 DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential.

CONCLUSIONS

Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.

Treated wastewater irrigation promotes the spread of antibiotic resistance into subsoil pore-water

In the present study, we investigated the impact of treated wastewater (TWW) irrigation on the prevalence of antibiotic resistance genes (ARGs) in subsoil pore-water, a so-far under-appreciated matrix. We hypothesized that TWW irrigation increases ARG prevalence in subsoil pore-water. This hypothesis was tested using a multiphase approach, which consisted of sampling percolated subsoil pore-water from lysimeter-wells of a real-scale TWW-irrigated field, operated for commercial farming practices, and controlled, laboratory microcosms irrigated with freshwater or TWW. We monitored the abundance of six selected ARGs (sul1, bla_OXA-58, tetM, qnrS, bla_CTX-M-32 and bla_TEM), the intI1 gene associated with mobile genetic elements and an indicator for anthropogenic pollution and bacterial abundance (16S rRNA gene) by qPCR. The bacterial load of subsoil pore water was independent of both, irrigation intensity in the field study and irrigation water type in the microcosms. Among the tested genes in the field study, sul1 and intI1 exhibited constantly higher relative abundances. Their abundance was further positively correlated with increasing irrigation intensity. Controlled microcosm experiments verified the observed field study results: the relative abundance of several genes, including sul1 and intI1, increased significantly when irrigating with TWW compared to freshwater irrigation. Overall, TWW irrigation promoted the spread of ARGs and intI1 in the subsoil pore-water, while the bacterial load was maintained. The combined results from the real-scale agricultural field and the controlled lab microcosms indicate that the dissemination of ARGs in various subsurface environments needs to be taken into account during TWW irrigation scenarios.

Antibiotics in Food Chain: The Consequences for Antibiotic Resistance

Antibiotics have been used as essential therapeutics for nearly 100 years and, increasingly, as a preventive agent in the agricultural and animal industry. Continuous use and misuse of antibiotics have provoked the development of antibiotic resistant bacteria that progressively increased mortality from multidrug-resistant bacterial infections, thereby posing a tremendous threat to public health. The goal of our review is to advance the understanding of mechanisms of dissemination and the development of antibiotic resistance genes in the context of nutrition and related clinical, agricultural, veterinary, and environmental settings. We conclude with an overview of alternative strategies, including probiotics, essential oils, vaccines, and antibodies, as primary or adjunct preventive antimicrobial measures or therapies against multidrug-resistant bacterial infections. The solution for antibiotic resistance will require comprehensive and incessant efforts of policymakers in agriculture along with the development of alternative therapeutics by experts in diverse fields of microbiology, biochemistry, clinical research, genetic, and computational engineering.

An understated danger: Antimicrobial resistance in aquaculture and pet fish in Switzerland, a retrospective study from 2000 to 2017

Aquaculture is a rapidly growing field of food production. However, morbidity and mortality are higher in aquaculture species than in domestic animals. Bacterial diseases are a leading cause of farmed fish morbidity and are often treated with antimicrobials. Since most Swiss fish farms release effluents directly into surface water without treatment and since aquaculture fish are consumed by humans, antimicrobial resistance (AMR) and multi-resistance in aquaculture fish are important for environmental and public health. In this study, AMR tests for 14 antimicrobials were performed on 1,448 isolates from 1,134 diagnostic laboratory submissions from farmed and ornamental fish submissions for the period from 2000 to 2017. Amoxicillin, gentamycin and norfloxacin had the lowest proportion of resistant samples. However, AMR was highly variable over time. Resistance proportions were higher in: (a) ornamental fish compared with farmed fish, (b) fish from recirculation systems compared with those from other farming systems and (c) isolates originating from skin compared with those originating from inner organs. Multiple resistances were common. The results of this study provide useful data for Swiss fish veterinarians and some interesting hypotheses about risk factors for AMR in aquaculture and pet fish in Switzerland. However, further research is needed to define risk factors.

Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health

Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance-polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human-natural ecosystem interactions.

Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure

Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.

Antimicrobial resistance: A multifaceted problem with multipronged solutions

Infectious diseases still stand as a major cause of morbidity and mortality, and this problem can be worsened with the current antimicrobial resistance crisis. To tackle this crisis more studies analyzing the causes, routes, and reservoirs where antimicrobial resistance can emerge and expand, together with new antimicrobials and strategies for fighting antimicrobial resistance are needed. In the current special issue of MicrobiologyOpen, a set of articles dealing with the multiple faces of antimicrobial resistance are presented. These articles provide new information for understanding and addressing this problem.

Metagenomic analysis of an urban resistome before and after wastewater treatment

Determining the effect of wastewater treatment in water resistome is a topic of interest for water quality, mainly under re-use and One-Health perspectives. The resistome, the plasmidome, and the bacterial community composition of samples from influents and treated effluents from a wastewater treatment plant located in Northern Portugal were studied using metagenomic techniques. Wastewater treatment contributed to reduce the abundance of resistance genes and of plasmid replicons, coinciding with a decline in the number of intrinsic resistance genes from Enterobacteriaceae, as well as with a reduction in the relative abundance of Firmicutes and Proteobacteria after treatment. These taxons comprise bacterial pathogens, including those belonging to the ESKAPE group, which encompasses bacteria with the highest risk of acquiring antibiotic resistance, being the most relevant hosts of resistance genes acquired through horizontal gene transfer. Our results support that wastewater treatment efficiently removes the hosts of antibiotic resistance genes and, consequently, the harboured antibiotic resistance genes. Principal component analysis indicates that the resistome and the bacterial composition clustered together in influent samples, while did not cluster in final effluent samples. Our results suggest that wastewater treatment mitigates the environmental dissemination of urban resistome, through the removal of the hosts harbouring mobile resistance genes.

Transfer potentials of antibiotic resistance genes in Escherichia spp. strains from different sources

Multidrug-resistant Escherichia coli and antibiotic-resistance genes (ARGs) present a danger to public health. However, information on the dissemination potentials of antibiotic resistance among bacteria from different environments is lacking. We isolated multiple antibiotic-resistant Escherichia spp. from animal farms, hospitals, and municipal wastewater-treatment plants (MWWTPs) using culture-based methods, and carried out resistance phenotype and gene analyses. Thirty-five isolates of multiple antibiotic-resistant Escherichia spp. were further screened to detect 61 ARGs, 18 mobile genetic elements (MGEs), and gene cassettes. The isolates from livestock manure and MWWTPs showed greater diversity in plasmid profiling than hospital wastewater. Each Escherichia sp. carried 21-26 ARGs and 8-12 MGEs. In addition, 11 gene cassettes were detected in 34 Escherichia isolates, with greater diversity in livestock manure and MWWTPs than in hospital wastewater. The results indicated that the potential for ARG transfer was higher in livestock manure and MWWTPs compared with human clinical sources, possibly related to the high occurrence of both residual antibiotics and heavy metals in these environments.

Diversity analysis and metagenomic insights into antibiotic and metal resistance among Himalayan hot spring bacteriobiome insinuating inherent environmental baseline levels of antibiotic and metal tolerance

OBJECTIVES

Mechanisms of occurrence and expression of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. In this research, comparative profiling of ARGs and metal tolerance genes among thermophilic bacteria has been done by functional metagenomic methods.

METHODS

Shotgun metagenomic sequence data were generated using Illumina HiSeq 4000. Putative ARGs from the PROKKA predicted genes were identified with the ardbAnno V.1.0 script available from the ARDB (Antibiotic Resistance Genes Database) consortium using the non-redundant resistance genes as a reference. Putative metal resistance genes (MRGs) were identified by using BacMetScan V.1.0. The whole-genome sequencing for bacterial isolates was performed using Illumina HiSeq 4000 sequencing technology with a paired-end sequencing module.

RESULTS

Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes in two hot springs of Sikkim. ARG analysis through shotgun gene sequencing was found to be negative in the case of thermophilic bacteria. However, few genes were detected but they showed maximum similarity with mesophilic bacteria. Concurrently, MRGs were also detected in the metagenome sequence of isolates from hot springs. Detection of MRGs and absence of ARGs investigated by whole-genome sequencing in the reference genome sequence of thermophilic Geobacillus also conveyed the same message.

CONCLUSION

The study of ARGs and MRGs (Heavy metal resistance gene) among culturable and non-culturable bacteria from the hot springs of Sikkim via metagenomics showed a preferential selection of MRGs over ARGs. The absence of ARGs also does not support the co-selection of ARGs and MRGs in these environments. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which have an abundance of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARGs in a thermophilic environments as it reduces the chances of horizontal gene transfer.