The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria

Tracing antibiotics in sewers: Concentrations, measurement techniques, and mathematical approaches

Antibiotic contamination in sewer networks has significant environmental and health concerns worldwide, primarily due to its role in promoting bacterial resistance. In this literature review, antibiotic concentrations reported in urban sewers and hospital effluents, techniques for antimicrobial compound detection and quantification, and current modeling strategies are analyzed and discussed based on 91 papers published between 2014 and 2024. One-hundred and nine antibiotic compounds were reported across 80 studies, with sulfonamides, fluoroquinolones, and macrolides being the most frequently detected classes, while amphenicols and aminocyclitols were the least monitored. Advanced analytical techniques such as liquid chromatography and mass spectrometry are the most common approaches used for antibiotic quantification. Modeling efforts remain limited, with kinetic models, Risk Quotient (RQ) assessments, and Wastewater-Based Epidemiology (WBE) representing the main approaches identified. This review compiles 992 reports into a comprehensive dataset intended to support future research, especially for global monitoring, the development of predictive models, and the formulation of regulatory frameworks for managing antibiotic pollution in sewer systems.

Unravelling the advances of CRISPR-Cas9 as a precise antimicrobial therapy: A systematic review

Antimicrobial resistance is a critical public health threat, compromising treatment effectiveness. The spread of resistant pathogens, facilitated by genetic variability and horizontal gene transfer, primarily through plasmids, poses significant challenges to health systems.

OBJECTIVE

This review explores the potential of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology and Cas9 nucleases in combating antimicrobial resistance.

METHODS

The literature review followed the PRISMA guidelines using PubMed, Embase, and Scopus databases until July 2023.

RESULTS

The Enterobacterales family, particularly Escherichia coli, was the main focus. The resistance genes targeted were mainly associated with β-lactam antibiotics, specifically bla genes, and colistin resistance linked to the mcr-1 gene. Plasmid vectors have been the primary delivery method for the CRISPR-Cas9 system, with conjugative plasmids resensitizing bacterial strains to various antimicrobials. Other delivery methods included electroporation, phage-mediated delivery, and nanoparticles. The efficacy of the CRISPR-Cas9 system in resensitizing bacterial strains ranged from 4.7% to 100%.

CONCLUSIONS

Despite challenges in delivery strategies and clinical application, studies integrating nanotechnology present promising approaches to overcome these limitations. This review highlights new perspectives for the clinical use of CRISPR-Cas9 as a specific and efficient antimicrobial agent, potentially replacing traditional broad-spectrum antimicrobials in the future.

Genomic plasticity of extensively drug-resistant and multidrug-resistant Acinetobacter baumannii ST208 isolates from a fatal outbreak

BACKGROUND

The prevalence of multidrug-resistant Acinetobacter baumannii (MDRA) has rapidly increased and is linked to severe nosocomial infections. MDRA outbreaks in a Japanese hospital were analysed using whole-genome sequencing.

METHODS

Antibiotic susceptibility testing was performed on clinical isolates from hospitalised patients before and during the 2009 and 2010 outbreaks. Whole-genome sequencing was conducted to identify acquired antibiotic-resistance genes and genetic mutations.

RESULTS

Clinical A. baumannii isolates were resistant to β-lactams (broad-spectrum cephalosporins and carbapenems), aminoglycosides, chloramphenicol, fosfomycin, fluoroquinolones, tetracyclines, and trimethoprim-sulfamethoxazole. MDRA isolates harboured aac(6')-Ib-cr, abaF, armA, blaADC-30, blaTEM-1, and blaOXA-82, or both blaOXA-66 and blaOXA-23, catB8, mphE, msrE, and tet(B). blaOXA-82 genes were recombinationally multiplied. Quinolone resistance was also associated with gyrA S81L and parC S84L mutations. The MDRA isolates belonged to Oxford sequence type (ST) 208 and Pasteur ST2. Three of the 15 isolates developed an extensively drug-resistant (XDR) phenotype, and two isolates harboured an adeS mutation.

CONCLUSIONS

We identified molecular resistance markers in three XDR and one MDR isolate and provided a genomic description of resistance and virulence, as well as the origins of the isolates. The isolates are closely related to MDRA Oxford ST208 and Pasteur ST2, identified in Asia and Australia. MDRA isolates are of concern in both hospital and community settings in the Western Pacific region.

Hierarchical activation of resistance genes under tetracyclines selective pressure in complex microbial community

The pervasive use of antibiotics exerts selective pressure in both natural and anthropogenic environments, driving the propagation and evolution of antibiotic resistance genes (ARGs) in microbial communities. Understanding the succession of resistome under varying antibiotic stresses is crucial for mitigating the spread of ARGs. This study investigates the succession of resistome under exposure to four structurally different tetracyclines (TC) across concentrations ranging from environmental to clinical levels. A clear hierarchical activation of ARGs was observed, starting with the upregulation of multidrug and TC-specific efflux pump genes, followed by those involved in TC inactivation and ribosomal protection. By identifying the specific thresholds of transcriptional onset times and critical TC concentration ranges that triggered ARG abundance increases, it was found that all ARGs as a whole did not significantly increase when TC concentrations were maintained below 10-5 of the initial minimum inhibitory concentration (MIC0) within 2 h. Similarly, high-risk TC resistance genes do not proliferate when TC concentrations were kept below 10-3 × MIC0 within 24 h. These findings provide quantifiable benchmarks for concentration-time thresholds that can inform the establishment of environmental discharge limits and guide the implementation of targeted treatment technologies to mitigate ARG dissemination.

Bacterial abundance and antimicrobial resistance prevalence carried by adult house flies (Diptera: Muscidae) at Kansas dairy and beef cattle operations

House flies (Musca domestica L.) are filth-breeding pests of urban and rural environments around the world. Frequenting microbe-rich substrates for nutritional and reproductive needs, house flies pose a risk to human and animal health through their carriage and transmission of pathogenic and antimicrobial resistant bacteria (AMR). Adult house flies were collected from Kansas beef and dairy cattle operations to assess factors influencing bacterial abundance and AMR incidence flies. Aerobic culturable bacteria and suspected coliforms (SC) were enumerated from fly homogenate cultured on nonselective (tryptic soy agar) and selective (violet-red bile agar VRBA) media, respectively. Unique morphotypes of SC isolates were screened for tetracycline resistance and tested for resistance to 4 additional antibiotics to identify multi-drug resistant (MDR) isolates. Female house flies carried greater abundances of both culturable bacteria and SC than male flies. Abiotic factors such as ambient and soil temperatures correlated with culturable bacteria and SC abundances in flies, but farm type correlated only with SC abundance and trends of resistance phenotypes observed in SC isolates. Male and female flies from both farm types carried one or more AMR and MDR SC isolates (73.02% AMR and 31.09% MDR). The majority of AMR and MDR bacteria were Escherichia/Shigella sp., which possessed the widest range of phenotypic resistance variability found in our study. Our results further emphasize the role house flies play in harboring bacteria of risk to human and animal health and identified factors of potential use for the development of strategies to mitigate house fly transmission of bacterial pathogens and AMR within confined cattle operations.

Comprehensive Study of Antibiotics and Antibiotic Resistance Genes in Wastewater and Impacted Mediterranean Water Environments

Background: The spread of antimicrobial resistance is a central public health problem. Wastewater treatment plants and impacted environments are well-known hotspots for antibiotic resistance. However, there is still limited knowledge regarding where antibiotic resistance genes (ARGs) acquire mobility. Method: In this study, we aimed to gather evidence on the seasonal patterns of ARG spread in two Mediterranean areas from NE and E of Spain (Ebro River and Ebro Delta, and Xúquer River and Albufera de València), correlating ARG presence, with special focus on the faecal bacteria Escherichia coli, with antibiotic residues and environmental conditions. The analytical methodology employed was based on a suspect screening approach, while a novel prioritisation approach for antibiotics was proposed to identify those areas more susceptible to the spread of ARG. Results: Our findings demonstrate that ARG levels in wastewater were similar across different seasons, although a greater diversity of ARGs was recorded in summer. We hypothesise that horizontal gene transfer among aquatic bacterial populations during the northeastern Mediterranean summer, when temperatures reach approximately 35~40 °C, could be a key driver of ARG dissemination. By contrast, the highest concentrations of antibiotics in winter samples, with temperatures around 5~10 °C, may promote the spread of microbial resistance. Conclusions: Our key findings highlight that water temperature and sunlight irradiation are crucial factors influencing antibiotic levels and microbial abundance, requiring further investigation in future studies.

Observed Prevalence and Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Bacteria in Loggerhead Sea Turtles (Caretta caretta) from the Adriatic Sea

Background/Objectives: Antimicrobial resistance (AMR) is a major global health concern with profound implications for human, animal, and environmental health. Marine ecosystems are emerging as reservoirs of resistant bacteria due to contamination from anthropogenic activities. This study aimed to investigate fluoroquinolone-resistant and multidrug-resistant bacteria in loggerhead sea turtles (Caretta caretta). Methods: Cloacal swabs were collected from 28 loggerhead sea turtles at a rescue center in southern Italy. Swabs were cultured in nutrient media supplemented with enrofloxacin. Bacterial isolates underwent identification by MALDI-TOF, antimicrobial susceptibility testing, and assessment for multidrug resistance. Conjugation experiments evaluated the transferability of enrofloxacin resistance. Results: Thirty-six enrofloxacin-resistant bacterial strains were isolated from 22 turtles. The identified species included Vagococcus fluvialis (13 strains), Citrobacter freundii (5), Escherichia coli (6), and Pseudomonas mendocina (4). Thirty-five isolates exhibited multidrug resistance, with resistance to critically important antibiotics such as imipenem observed in C. freundii and Enterobacter faecium. Conjugation experiments showed no transfer of resistance genes. Conclusions: The study highlights the prevalence of fluoroquinolone-resistant and multidrug-resistant bacteria in C. caretta, implicating marine environments as reservoirs of AMR. The findings underscore the need for stricter regulation of antimicrobial use and monitoring of resistance dissemination in marine ecosystems. These results contribute to understanding AMR dynamics within the One Health framework, emphasizing the interconnectedness of environmental, animal, and human health.

Measuring water pollution effects on antimicrobial resistance through explainable artificial intelligence

Antimicrobial resistance refers to the ability of pathogens to develop resistance to drugs designed to eliminate them, making the infections they cause more difficult to treat and increasing the likelihood of disease diffusion and mortality. As such, antimicrobial resistance is considered as one of the most significant and universal challenges to both health and society, as well as the environment. In our research, we employ the explainable artificial intelligence paradigm to identify the factors that most affect the onset of antimicrobial resistance in diversified territorial contexts, which can vary widely from each other in terms of climatic, economic and social conditions. Specifically, we employ a large set of indicators identified through the One Health framework to predict, at the country level, mortality resulting from antimicrobial resistance related to Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus pneumoniae. The analysis reveals the outstanding importance of indicators related to water accessibility and quality in determining mortality due to antimicrobial resistance to the considered pathogens across countries, providing perspective as a potential tool for decision support and monitoring.

Repurposing of paroxetine and fluoxetine for their antibacterial effects against clinical Pseudomonas aeruginosa isolates in Egypt

Background

Drug repositioning has emerged as a promising strategy for assessing its antimicrobial efficacy in treating infectious diseases.

Methods

Seventy-five samples were collected and investigated for the presence of Pseudomonas aeruginosa. Antibiotic resistance, hemolytic activity, twitching motility, and biofilm formation were assessed. lasI and lasR genes were detected using conventional PCR. Minimum inhibitory concentrations of paroxetine, fluoxetine, and levofloxacin were determined by broth micro-dilution. The fractional inhibitory concentration index was calculated to assess the interaction between fluoxetine/levofloxacin and paroxetine/levofloxacin combinations. Half the MIC values of the drugs were selected for inhibitory effect assessment for virulence factors. Antibacterial and healing effects of fluoxetine were investigated on 30 male albino rats using a digital camera, bacterial count, and histological examination.

Results

Our 25 P. aeruginosa isolates were highly drug-resistant. 80%, 92%, and 80% of isolates were positive for twitching motility, hemolysis, and biofilm formation, respectively. 92% of isolates were positive for lasI gene and 96% for lasR gene. MICs of fluoxetine and paroxetine ranged from 32 to 512 µg/mL and MICs of levofloxacin ranged from 1 to 256 µg/mL. A synergistic outcome was observed in both combinations. Biofilm formation, twitching motility, and hemolysis were inhibited by paroxetine and fluoxetine in the majority of isolates. Fluoxetine/levofloxacin and paroxetine/levofloxacin combinations inhibited twitching motility, hemolysis, and biofilm formation in all isolates. Enhanced wound healing was observed in rats treated with fluoxetine and levofloxacin, with the fluoxetine/levofloxacin combination group demonstrating the most significant wound-healing effect. Bacterial count decreased in rats treated with levofloxacin, fluoxetine, and the levofloxacin/fluoxetine combination. Histological examination revealed higher wound healing in the levofloxacin-treated group than the fluoxetine group, and the combination treatment group displayed the fastest rate of wound healing.

Conclusions

Paroxetine and fluoxetine showed considerable antibacterial inhibitory effects against multi-drug resistant P. aeruginosa isolates. Fluoxetine showed significant improvement in anti-inflammatory effects and wound healing. To the best of our knowledge, this is the first Egyptian study to investigate the repurposing of paroxetine and fluoxetine as antibacterial agents. Further studies are needed to investigate their applicability as antibacterial agents as single agents or in combination with other antibiotics.

Insights into the ecological and climate crisis: Emerging infections threatening human health

The Anthropocene era is marked by unprecedented human-induced alterations to the environment, resulting in a climate emergency and widespread ecological deterioration. A staggering number of up to one million species of plants and animals are in danger of becoming extinct, which includes over 10 % of insect species and 40 % of plant species. Unrestrained release of greenhouse gases, widespread deforestation, intense agricultural practices, excessive fishing, and alterations in land use have exceeded the ecological boundaries that were once responsible for humanity's wellbeing. As per the Intergovernmental Panel on Climate Change (IPCC), existing policies are expected to result in a minimum rise in global temperature of +2 °C, with more recent assessments indicating a potential increase of up to +2.9 °C. The effects of climate change and ecological degradation on the formation of diseases are complex and have multiple aspects. Deforestation diminishes biodiversity and compels wildlife to come into greater proximity with humans, hence promoting the transmission of zoonotic diseases. Climate change intensifies these impacts by modifying the habitats of disease carrying organisms, resulting in the expansion of vector-borne diseases such as malaria, dengue, and Zika virus into previously unaffected areas. Furthermore, climate change amplifies the occurrence and severity of extreme weather phenomena, which undermines water, sanitation, and hygiene (WASH) practices. This creates an environment conducive to the transmission of waterborne diseases such as cholera in densely populated resettlement camps. Climate-induced disasters contribute to the complexity of epidemiological landscapes, exacerbating antimicrobial resistance and posing a threat to modern medical advancements. This narrative review investigates the complex connections between the ecological-climatic crises and emerging illnesses, offering an overview on how environmental changes contribute to outbreaks that pose a substantial threat to public health.

Extended-spectrum β-lactamases genes in Gram-negative isolates from an urban river in Nicaragua

Limited resources and inadequate surveillance systems in developing countries have hindered research on antibiotic resistance gene transfer in aquatic environments. In this context, our study aimed to identify extended-spectrum beta-lactamase gene variants in Gram-negative isolates from the Tipitapa River-a significant Central America ecosystem. Samples were collected and assessed for key water parameters: dissolved oxygen, electrical conductivity, pH, and temperature. We employed a mix of microbiological, biochemical and molecular techniques, including multiplex PCR and sequencing, to characterize bacteria and determine the bla gene variants. Water quality parameters indicated areas impacted by human activities with high mineralization and eutrophication conditions. Among the bacteria analyzed, 48% belonged to the Enterobacteriaceae family, and a significant 88% displayed extended-spectrum beta-lactamases. Sequencing revealed four distinct bla gene variants in 84% of the isolates: bla-SHV-24, bla-SHV-13, bla-TEM-1, and bla-TEM-116, with bla-SHV-24 being the most common (47.62%). This is the first report of bla gene variants in the Tipitapa River, revealing their presence in globally concerning bacteria. The robust methodology enhances surveillance, enables geographic profiling of bla gene variants, and improves our understanding of biochemical patterns and gene transmission dynamics, providing essential insights into the global distribution of antibiotic resistance genes in Central America's natural waters.

Co-existence of a novel RND efflux pump tmexC6D6.2-toprJ1b and blaOXA-4 in the extensively drug-resistant Pseudomonas aeruginosa ST233 clone

The emergence of RND efflux pump gene cluster tmexCD-toprJ threats the clinical use of tigecycline as a last-resort antibiotic. Co-existence of extended spectrum β-lactamases and tmexCD-toprJ can accelerate the emergence of multidrug resistant or extensively drug-resistant Pseudomonas aeruginosa, leading to the production of high-risk clones. This study identified a novel gene cluster, tmexC6D6.2-toprJ1b, on the chromosome of a high-risk ST233 XDR P. aeruginosa from Chinese retail chicken samples. Genetic feature analysis revealed that a tnfxB6-tmexC6D6.2-toprJ1b-strBA-floR-tet(G)-IS6100-sul1-aadA2-int1-intA structure formed a putative transposition unit. tmexC6D6.2-toprJ1b shared high similarity at the nucleotide level with other tmexCD-toprJ gene clusters. tnfxB6 regulator was located downstream from the tmexC6D6.2-toprJ1b gene cluster and it did not affect bacterial resistance phenotype. The expression of tmexC6D6.2-toprJ1b could reduce the growth of E. coli and bring a moderate fitness cost. Further studies are needed to decipher the mechanism of the silencing of tnfxB6 in mediating the high-level resistance of tmexC6D6.2-torpJ1b and continuously monitor the coexistence of the novel tmexCD-toprJ gene cluster and the ESBLs-related resistance genes.

Electrochemical and optical biosensors for the detection of E. Coli

E. coli is a common pathogenic microorganism responsible for numerous food and waterborne illnesses. Traditional detection methods often require long, multi-step processes and specialized equipment. Electrochemical and optical biosensors offer promising alternatives due to their high sensitivity, selectivity, and real-time monitoring capabilities. Recent advancements in sensor development focus on various techniques for detecting E. coli, including optical (fluorescence, colorimetric analysis, surface-enhanced Raman spectroscopy, surface plasmon resonance, localized surface plasmon resonance, chemiluminescence) and electrochemical (amperometric, voltammetry, impedance, potentiometric). Herein, the latest advancements in optical and electrochemical biosensors created for identifying E. coli with an emphasis on surface modifications employing nanomaterials and biomolecules are outlined in this review. Electrochemical biosensors exploit the unique electrochemical properties of E. coli or its specific biomolecules to generate a measurable signal. In contrast, optical biosensors rely on interactions between E. coli and optical elements to generate a detectable response. Moreover, optical detection has been exploited in portable devices such as smart phones and paper-based sensors. Different types of electrodes, nanoparticles, antibodies, aptamers, and fluorescence-based systems have been employed to enhance the sensitivity and specificity of these biosensors. Integrating nanotechnology and biorecognition (which bind to a specific region of the E. coli) elements has enabled the development of portable and miniaturized devices for on-site and point-of-care (POC) applications. These biosensors have demonstrated high sensitivity and offer low detection limits for E. coli detection. The convergence of electrochemical and optical technologies promises excellent opportunities to revolutionize E. coli detection, improving food safety and public health.

Water, sanitation, handwashing, and nutritional interventions can reduce child antibiotic use: evidence from Bangladesh and Kenya

Antibiotics can trigger antimicrobial resistance and microbiome alterations. Reducing pathogen exposure and undernutrition can reduce infections and antibiotic use. We assess effects of water, sanitation, handwashing (WSH) and nutrition interventions on caregiver-reported antibiotic use in Bangladesh and Kenya, longitudinally measured at three timepoints among birth cohorts (ages 3-28 months) in a cluster-randomized trial. Over 50% of children used antibiotics at least once in the 90 days preceding data collection. In Bangladesh, the prevalence of antibiotic use was 10-14% lower in groups receiving WSH (prevalence ratio [PR] = 0.90 (0.82-0.99)), nutrition (PR = 0.86 (0.78-0.94)), and nutrition+WSH (PR = 0.86 (0.79-0.93)) interventions. The prevalence of using antibiotics multiple times was 26-35% lower in intervention arms. Reductions were largest when the birth cohort was younger. In Kenya, interventions did not affect antibiotic use. In this work, we show that improving WSH and nutrition can reduce antibiotic use. Studies should assess whether such reductions translate to reduced antimicrobial resistance.

Making sense of sentinels: wildlife as the One Health bridge for environmental antimicrobial resistance surveillance

Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognized reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilized opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems.

Genetic Determinants and Biofilm Properties Useful in Estimation of UTI Pathogenicity of the Escherichia coli Strains Isolated from Free-Living Birds

Background/Objectives: According to the One Health concept, wild birds can be indicators of ecosystem pollution and disease incidence. Escherichia coli strains are widespread worldwide, but there are still few reports on the association of human infections with a potential reservoir of highly pathogenic human strains in wild birds. Fecal E. coli with uropathogenic potential (UPEC) can be transmitted between birds and humans and may be a risk factor for urinary tract infections (UTIs). Results: The results showed that above 50% of the isolates were grouped as highly pathogenic, according to Clermont phylogroup classification. Such strains were found to be stronger biofilm producers, with a higher adherence of monocytes than low pathogenic. However, the highest cytotoxicity was observed for strains described as aquatic environmental. Convergence of the results of the analysis of monocyte activation by E. coli strains and the ability to form biofilm by individual phylogroups of the strains tested was demonstrated. Genetic determinants of the uropathogenicity of E. coli (UPEC) correlate with the evidence of strain pathogenicity during monocyte activation in in vitro assays. Methods: In this study, we assessed the virulence potential of environmental strains isolated from wild waterfowl using genetic analysis (Clermont phylogroup classification) and phenotypic methods, including analysis of the human monocyte response to biofilm formation. The estimation of the ability to form biofilms was tested using crystal violet, and the pathogenic potential of strains by monocyte activation assay including changes in morphology, adhesion and cytotoxicity. Conclusions: In conclusion, the virulence of E. coli strains isolated from free-living birds is significant, and they can be considered environmental reservoirs of pathogenic strains. According to our observations, they can be responsible for the dissemination of uropathogenic strains among humans.

Investigating the occurrence of antimicrobial resistance in the environment in Canada: a scoping review

Antimicrobial resistance is an environmental, agricultural, and public health problem that is impacting the health of humans and animals. The role of the environment as a source of and transmission pathway for antibiotic resistant bacteria and antibiotic resistance genes is a topic of increasing interest that, to date, has received limited attention. This study aimed to describe the sources and possible pathways contributing to antimicrobial resistance dissemination through bioaerosols, water, and soil in Canada using a scoping review methodology and systems thinking approach. A systems map was created to describe the occurrence and relationships between sources and pathways for antimicrobial resistance dissemination through water, soil, and bioaerosols. The map guided the development of the scoping review protocol, specifically the keywords searched and what data were extracted from the included studies. In total, 103 studies of antimicrobial resistance in water, 67 in soil, and 12 in air were identified. Studies to detect the presence of antimicrobial resistance genes have mainly been conducted at wastewater treatment plants and commercial animal livestock facilities. We also identified elements in the systems map with little or no data available (e.g., retail) that need to be investigated further to have a better understanding of antimicrobial resistance dissemination through different Canadian environments.

Ethical bioprospecting and microbial assessments for sustainable solutions to the AMR crisis

Antimicrobial resistance (AMR) has been declared one of the top 10 global public health challenges of our age by the World Health Organization, and the World Bank describes AMR as a crisis affecting the finance, health, and agriculture sectors and a major threat to the attainment of Sustainable Development Goals. But what is AMR? It is a phenotype that evolves in microbes exposed to antimicrobial molecules and causes dangerous infections. This suggests that scientists and healthcare workers should be on the frontline in the search for sustainable solutions to AMR. Yet AMR is also a societal problem to be understood by everyone. This review aims to explore the need to address the problem of AMR through a coherent, international strategy with buy-in from all sectors of society. As reviewed here, the sustainable solutions to AMR will be driven by better understanding of AMR biology but will require more than this alone to succeed. Some advances on the horizon, such as the use of bacteriophage (phage) to treat AMR infections. However, many of the new technologies and new therapeutics to address AMR require access to biodiversity, where the custodians of that biodiversity-and the traditional knowledge required to access it-are needed as key partners in the scientific, clinical, biotechnological, and international ventures that would treat the problem of AMR and ultimately prevent its further evolution. Many of these advances will be built on microbial assessments to understand the extent of AMR in our environments and bioprospecting to identify microbes that may have beneficial uses. Genuine partnerships for access to this biodiversity and sharing of benefits accrued require a consideration of ethical practice and behavior. Behavior change is needed across all sectors of culturally diverse societies so that rapid deployment of solutions can be implemented for maximum effect against the impacts of AMR.

Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert

The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Still, microbial life has been reported in these environments, with limited information on their genetic properties and functional capabilities. Although diverse autochthonous multidrug-resistant bacteria were found in Antarctic Peninsula soils, posing whether these soils could act as a source of resistance determinants that could emerge among pathogens, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a cold desert in West Antarctica. Despite the extreme conditions, several bacterial phyla were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. Contrastive with Ecology Glacier soils from King George Island, the Union Glacier soil bacterial community is significantly less diverse, mainly attributed to scarce moisture. We recovered >80 species-level representative genomes (SRGs) of predominant bacteria and an ammonia-oxidating nitrogen- and carbon-fixing archaeon from a novel species of Nitrosocosmicus. Several resistance and virulence genes were found in Union Glacier soils, similar to those in other Antarctic cold desert areas but significantly distinct from those observed in maritime Antarctica and other non-cryosphere biomes. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarctica's soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in this continent.

Carbapenem-Resistant E. coli Adherence to Magnetic Nanoparticles

Carbapenem-resistant Enterobacterales (CRE) is an emerging global concern. Specifically, carbapenemase-producing (CP) E. coli strains in CRE have recently been found in clinical, environmental, and food samples worldwide, causing many hospitalizations and deaths. Their rapid identification and characterization are paramount in control, management options, and treatment choices. Thus, this study aimed to characterize the cell surface properties of carbapenem-resistant (R) E. coli isolates and their interaction with glycan-coated magnetic nanoparticles (gMNPs) compared with carbapenem-susceptible (S) E coli. This study used two groups of bacteria: The first group included E. coli (R) isolates harboring carbapenemases and had no antibiotic exposure. Their initial gMNP-cell binding capacity, with cell surface characteristics, was assessed. In the second group, one of the E. coli (R) isolates and E. coli (S) had long-term serial antibiotic exposure, which we used to observe their cell surface characteristics and gMNP interactions. Initially, cell surface characteristics (cell morphology and cell surface charge) of the E. coli isolates were evaluated using confocal laser scanning microscope (LSCM) and a Zetasizer, respectively. The interaction of gMNPs with the E. coli isolates was assessed through LSCM and transmission electron microscope (TEM). Further, the gMNP-cell attachment was quantified as a concentration factor (CF) through the standard plating method. The results showed that the CF values of all E. coli (R) were significantly different from those of E. coli (S), which could be due to the differences in cell characteristics. The E. coli (R) isolates displayed heterogeneous cell shapes (rod and round cells) and lower negative zeta potential (cell surface charge) values compared to E. coli (S). Further, this research identified the differences in the cell surface characteristics of E. coli (S) under carbapenem exposure, compared to unexposed E. coli (S) that impact their attachment capacity. The gMNPs captured more E. coli (S) cells compared to carbapenem-exposed E. coli (S) and all E. coli (R) isolates. This study clearly found that differences in cell surface characteristics impact their interaction with magnetic nanoparticles. The gained insights aid in further understanding adhesion mechanisms to develop or improve bacterial isolation techniques and diagnostic and treatment methods for CRE.

Fate of fluoroquinolones associated with antimicrobial resistance in circular periurban agriculture

Animal antibiotic use contributes to antimicrobial resistance (AMR) in humans. While animal manure benefits soil fertility, it also acts as hotspot for antibiotic residues, antibiotic-resistant bacteria, and their genes. Amending soils with poultry litter is recognized as "magic" among horticulture farmers and it remains a common practice globally. However, this poses a risk especially in countries where prophylactic use of antibiotics is allowed. In Argentina, fluoroquinolones are used in this way besides being listed as essential medicines and classified as "watch" by the World Health Organization. Antibiotic selective pressure can favour AMR in the environment but the fate of antibiotic residues and AMR dissemination from these practices remains poorly understood. Our research addresses this gap with a biological model tracing fluoroquinolones from poultry to soil to lettuce and tracking anthropogenic AMR with the proposed biomarker genes sul1 and intI1. Fresh poultry litter was stored for six months before application in a horticulture field experiment. The experiment included control and manured plots where lettuce was cultivated till harvest. Enrofloxacin concentration was 7.3 μg/kg in fresh poultry litter, while its metabolite ciprofloxacin was 39.22 μg/kg after storage. Although no fluoroquinolones were detected in soils, lettuce from manured plots contained enrofloxacin and ciprofloxacin at 14.97 and 9.77 μg/kg, respectively, providing evidence of fluoroquinolone bioaccumulation in plants. Abundance of sul1 and intI1 in poultry litter was not affected by storage. Manured soils showed better soil quality than controls, but sul1 gene abundance was 1.6 times higher, reaching 7.61 Log sul1/g soil. A less sensitive, but significant effect was registered for intI1. These findings show that static storage is insufficient to stop the transmission of antibiotics and AMR biomarkers from poultry to horticulture. Amending soil with industrial poultry litter contributes to pollution with these emergent contaminants and risks human antibiotic exposure through fresh vegetables.

Tetracycline resistance gene transfer from Escherichia coli donors to Salmonella Heidelberg in chickens is impacted by the genetic context of donors

Chicken ceca are a rich source of bacteria, including zoonotic pathogens such as Salmonella enterica. The microbiota includes strains/species carrying antimicrobial resistance genes and horizontal transfer of resistance determinants between species may increase the risk to public health and farming systems. Possible sources of these antimicrobial resistance donors - the eggshell carrying bacteria from the hen vertically transmitted to the offspring, or the barn environment where chicks are hatched and raised - has been little explored. In this study, we used Salmonella enterica serovar Heidelberg to evaluate if layer chicks raised in different environments (using combinations of sterilized or non-sterile eggs placed in sterilized isolation chambers or non-sterile rooms) acquired transferable tetracycline resistance genes from surrounding bacteria, especially Escherichia coli. Two-day old chicks were challenged with an antibiotic-susceptible S. Heidelberg strain SH2813nalR and Salmonella recovered from the cecum of birds at different timepoints to test the in vivo acquisition of tetracycline resistance. Tetracycline-resistant E. coli isolates recovered from birds from the in vivo experiment were used to test the in vitro transfer of tetracycline resistance genes from E. coli to Salmonella. Even though Salmonella SH2813nalR colonized the 2-day old chicks after oral challenge, tetracycline-resistant Salmonella transconjugants were not recovered, as previously observed. In vitro experiments provided similar results. We discuss several hypotheses that might explain the absence of transconjugants in vitro and in vivo, despite the presence of diverse plasmids in the recovered E. coli. The factors that can inhibit/promote antimicrobial resistance transfers to Salmonella for different plasmid types need further exploration.

Identification and characterisation of colistin-resistant Acinetobacter colistiniresistens co-producing IMP-1 and OXA-58 carbapenemases

Background

Carbapenem-resistant Acinetobacter is of increasing global concern because infections are challenging to treat with standard antibiotics. Here, we identified a previously uncharacterised Acinetobacter sp. clinical isolate as Acinetobacter colistiniresistens co-producing IMP-1 and OXA-58. We also examined expression of genes related to antibiotic susceptibility and drug resistance, including bla IMP.

Methods

The isolate was deposited at the National Institute of Technology and Evaluation (NITE) as Acinetobacter sp. NBRC 110496. Susceptibility was defined according to the Clinical and Laboratory Standards Institute (CLSI) breakpoints. Genomic and clonal analyses were performed to identify species and resistance genes.

Results

The isolate was resistant to β-lactams, including broad-spectrum cephalosporins and carbapenems, polymyxins, and trimethoprim/sulfamethoxazole. Genomic analysis identified the isolate as A. colistiniresistens harbouring bla IMP-1, bla OXA-58, bla OXA-670, aac(6')-Ib, aac(6')-Ij, ant(3")-I I, aph(3')-VI, msrE, mphE, and sul1. Colistin resistance was associated with the eptA-like gene, which encodes a lipid A-modifying enzyme. SNP-based phylogenetic analysis revealed that the strain clustered with other strains isolated in Japan. The IMP-1/OXA-58-producing strain described in this study has a novel integron structure surrounding bla IMP-1, aacA and sul1.

Conclusions

Colistin-resistant IMP-1/OXA-58-co-producing A. colistiniresistens was identified in a patient. This isolate could serve as a reservoir for carbapenemase-producing organisms. This study suggests that screening for colistin-resistant isolates is crucial to preserve colistin as a therapeutic agent for multidrug-resistant bacteria. Identification of this MDR isolate in Asia, and the danger of it spreading worldwide, should raise serious concerns.

Comparative metagenomics of microbial communities and resistome in southern farming systems: implications for antimicrobial stewardship and public health

Agricultural practices significantly influence microbial diversity and the distribution of virulence and antimicrobial resistance (AMR) genes, with implications for ecosystem health and food safety. This study used metagenomic sequencing to analyze 60 samples (30 per state) including water, soil, and manure (10 each) from Alabama (a mix of cattle and poultry sources) and Tennessee (primarily from cattle). The results highlighted a rich microbial diversity, predominantly comprising Bacteria (67%) and Viruses (33%), with a total of over 1,950 microbial species identified. The dominant bacterial phyla were Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, with the viral communities primarily represented by Phixviricota and Uroviricota. Distinct state-specific microbial profiles were evident, with Alabama demonstrating a higher prevalence of viral populations and unique bacterial phyla compared to Tennessee. The influence of environmental and agricultural practices was reflected in the microbial compositions: soil samples were notably rich in Actinobacteria, water samples were dominated by Proteobacteria and Cyanobacteria, and manure samples from Alabama showed a predominance of Actinobacteria. Further analyses, including diversity assessment and enterotype clustering, revealed complex microbial structures. Tennessee showed higher microbial diversity and phylogenetic complexity across most sample types compared to Alabama, with poultry-related samples displaying distinct diversity trends. Principal Coordinate Analysis (PCoA) highlighted notable state-specific variations, particularly in manure samples. Differential abundance analysis demonstrated elevated levels of Deinococcus and Ligilactobacillus in Alabama, indicating regional effects on microbial distributions. The virulome analysis revealed a significant presence of virulence genes in samples from Alabama. The community resistome was extensive, encompassing 109 AMR genes across 18 antibiotic classes, with manure samples displaying considerable diversity. Ecological analysis of the interactions between AMR gene subtypes and microbial taxa revealed a sophisticated network, often facilitated by bacteriophages. These findings underscore the critical role of agricultural practices in shaping microbial diversity and resistance patterns, highlighting the need for targeted AMR mitigation strategies in agricultural ecosystems to protect both public health and environmental integrity.

Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines

Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.

Molecular epidemiological investigation of Salmonella isolated from the environment, animals, foods and patients in China

Salmonella as a foodborne pathogen, has a very important impact on human health. This study characterized the serotype, plasmid replicon, MLST typing, resistance phenotype and resistance gene of 282 strains of Salmonella isolated from the environment, animals, foods, and patients in China. These strains are classified into four sources: poultry farms (39/282), animals (30/282), foods (164/282), and hospitals (49/282) their resistance to ciprofloxacin, levofloxacin and ceftazidime is gradually increasing. Among them, ST11, ST19 and ST314 are dominant ST types; Salmonella enteritidis, Salmonella typhimurium and Kentucky Salmonella enteritidis serotypes are the dominant serotypes. This study conducted a comprehensive molecular epidemiological investigation of Salmonella from the unique perspective of Onehealth. It was revealed that the mcr-1 carried by Salmonella mainly relies on the horizontal transfer of Inc I2 and Inc Q plasmids. And a novel integron variable region cassette arrangement pattern aadA2-aadA23-catB3-tet(B)-dfrA12-eptB has emerged in Salmonella strains. More noteworthy is the outbreak of blaTEM-148 subtype in Salmonella from food sources, in which the Inc HI plasmid played an important role.

Prevalence of Antimicrobial Resistant Escherichia coli from Sinking Creek in Northeast Tennessee

Antibiotic resistance (AR) is a critical global health threat exacerbated by complex human-animal-environment interactions. Aquatic environments, particularly surface water systems, can serve as reservoirs and transmission routes for AR bacteria. This study investigated the prevalence of AR E. coli in Sinking Creek, a pathogen-impacted creek in Northeast Tennessee. Water samples were collected monthly from four sites along the creek over a 6-month period. E. coli isolates were cultured, identified, and tested for susceptibility to eight antibiotics using the Kirby-Bauer disk diffusion method and broth disk elution method for colistin. Data were analyzed to determine the prevalence of AR and multidrug resistance (MDR) among isolates. Of the 122 water samples, 89.3% contained E. coli. Among the 177 isolates tested, resistance was highest to ciprofloxacin (64.2%) and nitrofurantoin (62.7%), and lowest to fosfomycin (14.1%) and colistin (6.0%). Significant differences in resistance to ceftriaxone and amoxicillin/clavulanic acid were observed between sampling sites. MDR was prevalent in 47.5% of isolates, with 5.1% resistant to seven antibiotics. The most frequent MDR patterns (6.8%) included three antibiotics: ceftriaxone, ciprofloxacin, and nitrofurantoin. The high prevalence of AR E. coli in Sinking Creek poses a significant public health risk, highlighting the need for ongoing surveillance and intervention strategies to prevent the spread of AR bacteria.

Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system

Introduction. Salmonella enterica is a significant enteric pathogen affecting human and livestock health. Pork production is a common source of Salmonella contamination, with emerging multidrug resistance (MDR) posing a global health threat.Gap statement. Salmonella contamination and antimicrobial resistance (AMR) profiles in the pig production chain are underreported.Aim. To investigate the prevalence of S. enterica in the pig production chain and characterise their AMR profiles.Methodology. We collected 485 samples from pig farms, a standard pig abattoir and retail markets in Patthalung and Songkhla provinces in southern Thailand. Antimicrobial susceptibility testing was performed on these samples, and AMR profiles were determined.Results. S. enterica was detected in 68.67% of farm samples, 45.95% of abattoir samples and 50.67% of retail market samples. Analysis of 264 isolates, representing 18 serotypes, identified S. enterica serotype Rissen as the most prevalent. The predominant resistance phenotypes included ampicillin (AMP, 91.29%), tetracycline (TET, 88.26%) and streptomycin (STR, 84.47%). Over 80% of isolates showed resistance to three or more antimicrobial classes, indicating MDR. The AMP-STR-TET resistance pattern was found in nearly 70% of all MDR isolates across the production chain.Conclusions. The high prevalence of MDR is consistent with extensive antimicrobial use in the livestock sector. The presence of extensively resistant S. enterica highlights the urgent need for antimicrobial stewardship. Strengthening preventive strategies and control measures is crucial to mitigate the risk of MDR Salmonella spreading from farm to fork.

Chemical fertilizers promote dissemination of ARGs in maize rhizosphere: An overlooked risk revealed after 37-year traditional agriculture practice

Bacterial communities in soil and rhizosphere maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs and antibiotic resistant bacteria (ARB) are well-characterized under traditional farming practices. Here we compared the ARG profiles of maize rhizosphere and their bulk soils using metagenomic analysis to identify the ARG dissemination and explored the potential impact of chemical fertilization on ARB. Results showed a relatively lower abundance but higher diversity of ARGs under fertilization than straw-return. Moreover, the abundance and diversity of MGEs were significantly promoted by chemical fertilizer inputs in the rhizosphere compared to bulk soil. Machine learning and bipartite networks identified three bacterial genera (Pseudomonas, Bacillus and Streptomyces) as biomarkers for ARG accumulation. Thus we cultured 509 isolates belonging to these three genera from the rhizosphere and tested their antimicrobial susceptibility, and found that multi-resistance was frequently observed among Pseudomonas isolates. Assembly-based tracking explained that ARGs and four class I integrons (LR134330, LS998783, CP065848, LT883143) were co-occurred among contigs from Pseudomonas sp. Chemical fertilizers may shape the resistomes of maize rhizosphere, highlighting that rhizosphere carried multidrug-resistant Pseudomonas isolates, which may pose a risk to animal and human health. This study adds knowledge of long-term chemical fertilization on ARG dissemination in farmland systems and provides information for decision-making in agricultural production and monitoring.

Cell morphology as biomarker of carbapenem exposure

Characterizing the physiological response of bacterial cells to antibiotics is crucial for designing diagnostic techniques, treatment choices, and drug development. While bacterial cells at sublethal doses of antibiotics are commonly characterized, the impact of exposure to high concentrations of antibiotics on bacteria after long-term serial exposure and their effect on withdrawal need attention for further characterization. This study investigated the effect of increasing imipenem concentrations on carbapenem-susceptible (S) and carbapenem-resistant (R) E. coli on their growth adaptation and cell surface structure. We exposed the bacterial population to increasing imipenem concentrations through 30 exposure cycles. Cell morphology was observed using a 3D laser scanning confocal microscope (LSCM) and transmission electron microscope (TEM). Results showed that the exposure resulted in significant morphological changes in E. coli (S) cells, while minor changes were seen in E. coli (R) cells. The rod-shaped E. coli (S) gradually transformed into round shapes. Further, the exposed E. coli (S) cells' surface area-to-volume ratio (SA/V) was also significantly different from the control, which is non-exposed E. coli (S). Then, the exposed E. coli (S) cells were re-grown in antibiotic-free environment for 100 growth cycles to determine if the changes in cells were reversible. The results showed that their cell morphology remained round, showing that the cell morphology was not reversible. The morphological response of these cells to imipenem can assist in understanding the resistance mechanism in the context of diagnostics and antibacterial therapies.

Antimicrobial use in laboratory rodent facilities in Australia and New Zealand- a cross-sectional survey of veterinarians and facility managers

This cross-sectional study surveyed veterinarians and facility managers to characterise the use of antimicrobials in laboratory rodent facilities within Australia and New Zealand. Most facilities (71%) reported routine administration of antimicrobials. The indications for antibiotic use reflected those described in publications and differed significantly to reasons for use in non-laboratory animals. Antimicrobials used include those of critical importance to human health, and access to these drugs is unregulated, as prescription-only classes are ordered through research catalogues, without human or veterinary physician prescriptions. The ways in which antimicrobials are used in Australian and New Zealand rodent facilities are likely contributing to antimicrobial resistance within rodent populations, particularly as they are largely administered in drinking water, risking subtherapeutic dosing. Much antimicrobial use reported is unnecessary and could be replaced with changes to husbandry and handling. The generation of resistance in both pathogenic and commensal microbes may also represent a work health and safety issue for humans working with these animals. Reported disposal of antimicrobials included discharge into wastewater, without inactivation, and some respondents reported disposal of substrate, or soiled bedding, nesting material, and disposable enrichment items, from treated animals and medicated feed into landfill, without prior inactivation. Environmental contamination with resistant microbes and antimicrobials is a significant driver of antimicrobial resistance. As such, significant opportunities exist to implement judicious and responsible use of antimicrobials within research rodent facilities in Australia and New Zealand, with a particular focus on instituting aseptic surgery, optimising dosing regimens, and inactivation of medicated water and substrate before disposal.

Regulation of Antibiotic Resistance Genes on Agricultural Land Is Dependent on Both Choice of Organic Amendment and Prevalence of Predatory Bacteria

Antibiotic resistance genes (ARGs) are widespread in the environment, and soils, specifically, are hotspots for microorganisms with inherent antibiotic resistance. Manure and sludge used as fertilizers in agricultural production have been shown to contain vast amounts of ARGs, and due to continued applications, ARGs accumulate in agricultural soils. Some soils, however, harbor a resilience capacity that could depend on specific soil properties, as well as the presence of predatory bacteria that are able to hydrolyse living bacteria, including bacteria of clinical importance. The objectives of this study were to (i) investigate if the antibiotic resistance profile of the soil microbiota could be differently affected by the addition of cow manure, chicken manure, and sludge, and (ii) investigate if the amendments had an effect on the presence of predatory bacteria. The three organic amendments were mixed separately with a field soil, divided into pots, and incubated in a greenhouse for 28 days. Droplet digital PCR (ddPCR) was used to quantify three ARGs, two predatory bacteria, and total number of bacteria. In this study, we demonstrated that the choice of organic amendment significantly affected the antibiotic resistance profile of soil, and promoted the growth of predatory bacteria, while the total number of bacteria was unaffected.

Incidence, identification and antibiotic resistance of Salmonella spp. in the well waters of Tadla Plain, Morocco

Concerns about challenges with water availability in the Tadla Plain region of Morocco have grown as a result of groundwater contamination brought on by human activity, climate change, and insufficient groundwater management. The objective of the study is to measure the number of resistant bacteria in the groundwater of Beni Moussa and Beni Aamir, as well as to evaluate the level of water pollution in this area. 200 samples were therefore gathered from 43 wells over the course of four seasonal campaigns in 2017 and 2018. Additionally, the samples were examined to determine whether Salmonella species were present and if they were resistant to the 16 antibiotics that were tested. Salmonella spp. have been identified in 31 isolated strains in total, accounting for 18.02% of all isolated strains. Data on antibiotic resistance show that 58.1% of Salmonella spp. strains are multidrug-resistant (MDR); 38.7% of Salmonella strains are tolerant to at least six antibiotics, 19.4% to at least nine antibiotics, 9.7% to four to seven antibiotics, 6.5% to at least eleven antibiotics, and the remaining 3.2% to up to twelve antibiotics. A considerable level of resistance to cefepime (61.29%), imipenem (54.84%), ceftazidime (45.16%), ofloxacin (70.97%), and ertapenem (74.19%) was found in the data. Consequently, it is important to monitor and regulate the growth of MDR in order to prevent the groundwater's quality from declining.

High frequency of multidrug-resistant Escherichia coli from cattle in the Cerrado and Pantanal biomes of Brazil

The indiscriminate use of antimicrobials has led to the emergence of resistant bacteria, especially pathogenic strains of Escherichia coli, which are associated with diseases in animals and humans. The aim of the present study was to characterize E. coli isolates in calves with regards to the presence of virulence genes and investigate the resistance of the isolates to different antimicrobials. Between 2021 and 2023, 456 fecal samples were collected from calves in the Pantanal and Cerrado biomes of the state of Mato Grosso do Sul, Brazil. All samples were subjected to microbiological analysis and disc diffusion antibiogram testing. The polymerase chain reaction method was used to detect virulence genes. Bacterial growth was found in 451 of the 456 samples and biochemically identified as Escherichia coli. All 451 isolates (100 %) exhibited some phenotypic resistance to antimicrobials and 67.62 % exhibited multidrug resistance. The frequency of multidrug-resistant isolates in the Cerrado biome was significantly higher than that in the Pantanal biome (p = 0.0001). In the Cerrado, the most common pathotype was Shiga toxin-producing Escherichia coli (STEC) (28 %), followed by toxigenic Escherichia coli (ETEC) (11 %), enterohemorrhagic Escherichia coli (EHEC) (8 %) and enteropathogenic Escherichia coli (EPEC) (2 %). In most cases, the concomitant occurrence of pathotypes was more common, the most frequent of which were ETEC + STEC (33 %), ETEC + EHEC (15 %) and ETEC + EPEC (3 %). The STEC pathotype (30 %) was also found more frequently in the Pantanal, followed by EHEC (12 %), ETEC (9 %) and EPEC (6 %). The STEC pathotype had a significantly higher frequency of multidrug resistance (p = 0.0486) compared to the other pathotypes identified. The frequency of resistance was lower in strains from the Pantanal biome compared to those from the Cerrado biome. Although some factors are discussed in this paper, it is necessary to clarify the reasons for this difference and the possible impacts of these findings on both animal and human health in the region.

Characteristics and health impacts of bioaerosols in animal barns: A comprehensive study

Bioaerosols produced during animal production have potential adverse effects on the health of workers and animals. Our objective was to investigate characteristics, antibiotic-resistance genes (ARGs), and health risks of bioaerosols in various animal barns. Poultry and swine barns had high concentrations of airborne bacteria (11156 and 10917 CFU/m3, respectively). Acinetobacter, Clostridium sensu stricto, Corynebacterium, Pseudomonas, Psychrobacter, Streptococcus, and Staphylococcus were dominant pathogenic bacteria in animal barns, with Firmicutes being the most abundant bacterial phylum. Based on linear discriminant analysis effect size (LEfSe), there were more discriminative biomarkers in cattle barns than in poultry or swine barns, although the latter had the highest abundance of bacterial pathogens and high abundances of ARGs (including tetM, tetO, tetQ, tetW sul1, sul2, ermA, ermB) and intI1). Based on network analyses, there were higher co-occurrence patterns between bacteria and ARGs in bioaerosol from swine barns. Furthermore, in these barns, relative abundance of bacteria in bioaerosol samples was greatly affected by environmental factors, mainly temperature, relative humidity, and concentrations of CO2, NH3, and PM2.5. This study provided novel data regarding airborne bio-contaminants in animal enclosures and an impetus to improve management to reduce potential health impacts on humans and animals.

Transmission of antibiotic resistance through organic amendments in arable land: A 3-year field study with pigeonpea-wheat cropping system

The worldwide emergence of antimicrobial resistance (AMR) poses a substantial risk to human health and environmental stability. In agriculture, organic amendments (derived from organic sources such as manure, and plant residues) are beneficial in restoring soil properties and providing essential nutrients to crops but raise concerns about harboring antibiotic resistance, which emphasizes the need for vigilant monitoring and strategic interventions in their application. The current study assessed the impact of farming practices (organic and conventional) in a three-year field experiment with pigeonpea-wheat cropping system, focusing on the transmission of AMR using culture-dependent and -independent approaches, and soil nutrient content. Markers for antibiotic resistance genes (ARGs) (aminoglycoside-aacA, β-lactam-blaTEM, chloramphenicol-cmlA1, macrolide-ermB, sulfonamides-sul1, sul2, and tetracycline-tetO) and integrons (intl1 and intl2) were targeted using qPCR. Manure amendments, particularly FYM1, exhibited a higher abundance of copies of ARGs compared to the rhizospheric soil. Organic farming was associated with higher copies of intl2, sul1, blaTEM, and tetO genes, while conventional farming showed increased copies of sul2 and ermB genes in the rhizosphere. Significant positive correlations were observed among soil nutrient contents, ARGs, and MGEs. The notable prevalence of ARGs linked to manure amendments serves as a cautionary note, demanding responsible management practices.

Modulatory Effect of Competitive Exclusion on the Transmission of ESBL E. coli in Chickens

The extensive use of antimicrobial agents in broiler farms causes the emergence of antimicrobial resistance of E. coli producing severe economic losses to the poultry industry; therefore, monitoring the transmission of ESBL E. coli is of great significance throughout broiler farms. For this reason, we investigated the efficiency of competitive exclusion (CE) products to control the excretion and transmission of ESBL-producing E. coli in broiler chickens. Three hundred samples from 100 broiler chickens were screened for the incidence of E. coli by standard microbiological techniques. The overall isolation percentage was 39% and differentiated serologically into ten different serotypes: O158, O128, O125, O124, O91, O78, O55, O44, O2, and O1. The isolates represented absolute resistance to ampicillin, cefotaxime, and cephalexin. The effectiveness of CE (commercial probiotic product; Gro2MAX) on ESBL-producing E. coli (O78) isolate transmission and excretion was studied in vivo. The results showed that the CE product has interesting properties, making it an excellent candidate for targeted drug delivery by inhibiting bacterial growth and downregulating biofilm, adhesins, and toxin-associated genes loci. The histopathological findings demonstrated the capability of CE in repairing internal organ tissues. Our outcomes suggested that the administration of CE (probiotic products) in broiler farms could be a safe and alternative approach to control the transmission of ESBL-producing virulent E. coli in broiler chickens.

Antimicrobial resistance in the wild: Insights from epigenetics

Spreading of bacterial and fungal strains that are resistant to antimicrobials poses a serious threat to the well-being of humans, animals, and plants. Antimicrobial resistance has been mainly investigated in clinical settings. However, throughout their evolutionary history microorganisms in the wild have encountered antimicrobial substances, forcing them to evolve strategies to combat antimicrobial action. It is well known that many of these strategies are based on genetic mechanisms, but these do not fully explain important aspects of the antimicrobial response such as the rapid development of resistance, reversible phenotypes, and hetero-resistance. Consequently, attention has turned toward epigenetic pathways that may offer additional insights into antimicrobial mechanisms. The aim of this review is to explore the epigenetic mechanisms that confer antimicrobial resistance, focusing on those that might be relevant for resistance in the wild. First, we examine the presence of antimicrobials in natural settings. Then we describe the documented epigenetic mechanisms in bacteria and fungi associated with antimicrobial resistance and discuss innovative epigenetic editing techniques to establish causality in this context. Finally, we discuss the relevance of these epigenetic mechanisms on the evolutionary dynamics of antimicrobial resistance in the wild, emphasizing the critical role of priming in the adaptation process. We underscore the necessity of incorporating non-genetic mechanisms into our understanding of antimicrobial resistance evolution. These mechanisms offer invaluable insights into the dynamics of antimicrobial adaptation within natural ecosystems.

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution

BACKGROUND

Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk to human health. However, little is known about the interaction of these pollutants at environmental concentrations and the response of the microbial communities in the plastisphere to sub-lethal antibiotic pollution. Here, we describe the bacterial dynamics underlying this response in surface water bacteria at the community, resistome and mobilome level using a combination of methods (next-generation sequencing and qPCR), sequencing targets (16S rRNA gene, pre-clinical and clinical class 1 integron cassettes and metagenomes), technologies (short and long read sequencing), and assembly approaches (non-assembled reads, genome assembly, bacteriophage and plasmid assembly).

RESULTS

Our results show a shift in the microbial community response to antibiotics in the plastisphere microbiome compared to surface water communities and describe the bacterial subpopulations that respond differently to antibiotic and microplastic pollution. The plastisphere showed an increased tolerance to antibiotics and selected different antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs). Several metagenome assembled genomes (MAGs) derived from the antibiotic-exposed plastisphere contained ARGs, virulence factors, and genes involved in plasmid conjugation. These include Comamonas, Chryseobacterium, the opportunistic pathogen Stenotrophomonas maltophilia, and other MAGs belonging to genera that have been associated to human infections, such as Achromobacter. The abundance of the integron-associated ciprofloxacin resistance gene aac(6')-Ib-cr increased under ciprofloxacin exposure in both freshwater microbial communities and in the plastisphere. Regarding the antibiotic mobilome, although no significant changes in ARG load in class 1 integrons and plasmids were observed in polluted samples, we identified three ARG-containing viral contigs that were integrated into MAGs as prophages.

CONCLUSIONS

This study illustrates how the selective nature of the plastisphere influences bacterial response to antibiotics at sub-lethal selective pressure. The microbial changes identified here help define the selective role of the plastisphere and its impact on the maintenance of environmental antibiotic resistance in combination with other anthropogenic pollutants. This research highlights the need to evaluate the impact of aquatic pollutants in environmental microbial communities using complex scenarios with combined stresses. Video Abstract.

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition

BACKGROUND

In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age.

RESULTS

We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs.

CONCLUSIONS

We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.

Screening Key Sites of Class 2 Integron Integrase that Impact Recombination Efficiency

By capturing and expressing exogenous resistance gene cassettes through site-specific recombination, integrons play important roles in the horizontal transfer of antimicrobial resistant genes among bacteria. The characteristics of integron integrase make it to be a potential gene editing tool enzyme. In this study, a random mutation library using error-prone PCR was constructed, and amino acid residues mutants that impact on attI2 × attC or attC × attC recombination efficiency were screened and analyzed. Thirteen amino acid mutations were identified to be critical impacted on site-specific recombination of IntI2, including the predicted catalyzed site Y301. Nine of 13 mutated amino acid residues that have critically impacted on IntI2 activity were relative concentrated and near the predicted catalyzed site Y301 in the predicted three-dimensional structure indicated the importance of this area in maintain the activity of IntI2. No mutant with obviously increased recombination activity (more than four-fold as high as that of wild IntI2) was found in library screening, except P95S, R100K slightly increased (within two-fold) the excision activity of IntI2, and S243T slightly increased (within two-fold) both excision and integration activity of IntI2. These findings will provide clues for further specific modification of integron integrase to be a tool enzyme as well as establishing a new gene editing system and applied practically.

Detection and genomic characterization of Klebsiella pneumoniae and Escherichia coli harboring tet(X4) in black kites (Milvus migrans) in Pakistan

The emergence of plasmid-mediated tigecycline resistance gene tet(X4) among clinically relevant bacteria has promoted significant concerns, as tigecycline is considered a last-resort drug against serious infections caused by multidrug-resistant bacteria. We herein focused on the isolation and molecular characterization of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) in wild bird populations with anthropogenic interaction in Faisalabad, Pakistan. A total of 150 birds including black kites (Milvus migrans) and house crows (Corvus splendens) were screened for the presence of tigecycline resistance K. pneumoniae and E. coli. We found two K. pneumoniae and one E. coli isolate carrying tet(X4) originating from black kites. A combination of short- and long-read sequencing strategies showed that tet(X4) was located on a broad host range IncFII plasmid family in K. pneumoniae isolates whereas on an IncFII-IncFIB hybrid plasmid in E. coli. We also found an integrative and conjugative element ICEKp2 in K. pneumoniae isolate KP8336. We demonstrate the first description of tet(X4) gene in the WHO critical-priority pathogen K. pneumoniae among wild birds. The convergence of tet(X4) and virulence associated ICEKp2 in a wild bird with known anthropogenic contact should be further investigated to evaluate the potential epidemiological implications. The potential risk of global transmission of tet(X4)-positive K. pneumoniae and E. coli warrant comprehensive evaluation and emphasizes the need for effective mitigation strategies to reduce anthropogenic-driven dissemination of AMR in the environment.

Diarrheagenic Escherichia coli with Multidrug Resistance in Cattle from Mexico

Mexico is an important producer/exporter of cattle and cattle products. In the last decade, an increase in antibiotic resistance in E. coli pathotype strains from livestock environments has been reported. This study aimed to determine the prevalence and antibiotic resistance profiles of E. coli pathotype strains from the feces of beef or dairy cattle reared in the states of Aguascalientes (AG, central) and Nuevo Leon (NL, northeastern) in Mexico. One hundred and ten fecal samples were collected (beef cattle-AG = 30; dairy cattle-AG = 20; beef cattle-NL = 30; dairy cattle-NL = 30). From these, E. coli was isolated using selective/differential media and confirmed on chromogenic media. Multiplex PCR was used to identify diarrheagenic E. coli, and the Kirby-Bauer technique was used to determine the antimicrobial susceptibilities. All the animals harbored E. coli, and pathotypes were found in 34 animals from both, beef and dairy cattle, mainly from Aguascalientes. Of the positive samples, 31 harbored a single E. coli pathotype, whereas three samples harbored two different pathotypes; EHEC was the most prevalent, followed by EPEC, ETEC, and EIEC or the combination of two of them in some samples. Most pathotype strains (19/37) were isolated from beef cattle. Neither the animals' productive purpose (beef or dairy cattle) (r = 0.155) nor the geographic regions (Aguascalientes or Nuevo Leon) (r = -0.066) had a strong positive correlation with the number of E. coli pathotype strains. However, animals reared in Aguascalientes had up to 8.5-fold higher risk of harboring E. coli pathotype strains than those reared in Nuevo Leon. All pathotype strains were resistant to erythromycin, tetracycline, and trimethoprim/sulfamethoxazole, and all dairy cattle pathotype strains were further resistant to five β-lactams (χ2, P = 0.017). The existence of these pathotypes and multidrug-resistant pathogens in the food chain is a risk to public health.

Development of an in vitro biofilm model for the study of the impact of fluoroquinolones on sewer biofilm microbiota

Sewer biofilms are likely to constitute hotspots for selecting and accumulating antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study aimed to optimize culture conditions to obtain in vitro biofilms, mimicking the biofilm collected in sewers, to study the impact of fluoroquinolones (FQs) on sewer biofilm microbiota. Biofilms were grown on coupons in CDC Biofilm Reactors®, continuously fed with nutrients and inoculum (1/100 diluted wastewater). Different culture conditions were tested: (i) initial inoculum: diluted wastewater with or without sewer biofilm, (ii) coupon material: concrete vs. polycarbonate, and (iii) time of culture: 7 versus 14 days. This study found that the biomass was highest when in vitro biofilms were formed on concrete coupons. The biofilm taxonomic diversity was not affected by adding sewer biofilm to the initial inoculum nor by the coupon material. Pseudomonadales, Burkholderiales and Enterobacterales dominated in the sewer biofilm composition, whereas in vitro biofilms were mainly composed of Enterobacterales. The relative abundance of qnrA, B, D and S genes was higher in in vitro biofilms than sewer biofilm. The resistome of sewer biofilm showed the highest Shannon diversity index compared to wastewater and in vitro biofilms. A PCoA analysis showed differentiation of samples according to the nature of the sample, and a Procrustes analysis showed that the ARG changes observed were linked to changes in the microbial community. The following growing conditions were selected for in vitro biofilms: concrete coupons, initial inoculation with sewer biofilm, and a culture duration of 14 days. Then, biofilms were established under high and low concentrations of FQs to validate our in vitro biofilm model. Fluoroquinolone exposure had no significant impact on the abundance of qnr genes, but high concentration exposure increased the proportion of mutations in gyrA (codons S83L and D87N) and parC (codon S80I). In conclusion, this study allowed the determination of the culture conditions to develop an in vitro model of sewer biofilm; and was successfully used to investigate the impact of FQs on sewer microbiota. In the future, this setup could be used to clarify the role of sewer biofilms in disseminating resistance to FQs in the environment.

Sanitation in urban areas may limit the spread of antimicrobial resistance via flies

Synanthropic filth flies are common where sanitation is poor and fecal wastes are accessible to them. These flies have been proposed as mechanical vectors for the localized transport of fecal microbes including antimicrobial resistant (AMR) organisms and associated antimicrobial resistance genes (ARGs), increasing exposure risks. We evaluated whether an onsite sanitation intervention in Maputo, Mozambique reduced the concentration of enteric bacteria and the frequency of detection of ARGs carried by flies collected in household compounds of low-income neighborhoods. Additionally, we assessed the phenotypic resistance profile of Enterobacteriaceae isolates recovered from flies during the pre-intervention phase. After fly enumeration at study compounds, quantitative polymerase chain reaction was used to quantify an enteric 16S rRNA gene (i.e., specific to a cluster of phylotypes corresponding to 5% of the human fecal microflora), 28 ARGs, and Kirby Bauer Disk Diffusion of Enterobacteriaceae isolates was utilized to assess resistance to eleven clinically relevant antibiotics. The intervention was associated with a 1.5 log10 reduction (95% confidence interval: -0.73, -2.3) in the concentration of the enteric 16S gene and a 31% reduction (adjusted prevalence ratio = 0.69, [0.52, 0.92]) in the mean number of ARGs per fly compared to a control group with poor sanitation. This protective effect was consistent across the six ARG classes that we detected. Enterobacteriaceae isolates-only from the pre-intervention phase-were resistant to a mean of 3.4 antibiotics out of the eleven assessed. Improving onsite sanitation infrastructure in low-income informal settlements may help reduce fly-mediated transmission of enteric bacteria and the ARGs carried by them.

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.

Intramuscular therapeutic doses of enrofloxacin affect microbial community structure but not the relative abundance of fluoroquinolones resistance genes in swine manure

Livestock manure is a major source of veterinary antibiotics and antibiotic resistance genes (ARGs). Elucidation of the residual characteristics of ARGs in livestock manure following the administration of veterinary antibiotics is critical to assess their ecotoxicological effects and environmental contamination risks. Here, we investigated the effects of enrofloxacin (ENR), a fluoroquinolone antibiotic commonly used as a therapeutic drug in animal husbandry, on the characteristics of ARGs, mobile genetic elements, and microbial community structure in swine manure following its intramuscular administration for 3 days and a withdrawal period of 10 days. The results revealed the highest concentrations of ENR and ciprofloxacin (CIP) in swine manure at the end of the administration period, ENR concentrations in swine manure in groups L and H were 88.67 ± 45.46 and 219.75 ± 88.05 mg/kg DM, respectively. Approximately 15 fluoroquinolone resistance genes (FRGs) and 48 fluoroquinolone-related multidrug resistance genes (F-MRGs) were detected in swine manure; the relative abundance of the F-MRGs was considerably higher than that of the FRGs. On day 3, the relative abundance of qacA was significantly higher in group H than in group CK, and no significant differences in the relative abundance of other FRGs, F-MRGs, or MGEs were observed between the three groups on day 3 and day 13. The microbial community structure in swine manure was significantly altered on day 3, and the altered community structure was restored on day 13. The FRGs and F-MRGs with the highest relative abundance were qacA and adeF, respectively, and Clostridium and Lactobacillus were the dominant bacterial genera carrying these genes in swine manure. In summary, a single treatment of intramuscular ENR transiently increased antibiotic concentrations and altered the microbial community structure in swine manure; however, this treatment did not significantly affect the abundance of FRGs and F-MRGs.

Do contaminants compromise the use of recycled nutrients in organic agriculture? A review and synthesis of current knowledge on contaminant concentrations, fate in the environment and risk assessment

Use of nutrients recycled from societal waste streams in agriculture is part of the circular economy, and in line with organic farming principles. Nevertheless, diverse contaminants in waste streams create doubts among organic farmers about potential risks for soil health. Here, we gather the current knowledge on contaminant levels in waste streams and recycled nutrient sources, and discuss associated risks. For potentially toxic elements (PTEs), the input of zinc (Zn) and copper (Cu) from mineral feed supplements remains of concern, while concentrations of PTEs in many waste streams have decreased substantially in Europe. The same applies to organic contaminants, although new chemical groups such as flame retardants are of emerging concern and globally contamination levels differ strongly. Compared to inorganic fertilizers, application of organic fertilizers derived from human or animal feces is associated with an increased risk for environmental dissemination of antibiotic resistance. The risk depends on the quality of the organic fertilizers, which varies between geographical regions, but farmland application of sewage sludge appears to be a safe practice as shown by some studies (e.g. from Sweden). Microplastic concentrations in agricultural soils show a wide spread and our understanding of its toxicity is limited, hampering a sound risk assessment. Methods for assessing public health risks for organic contaminants must include emerging contaminants and potential interactions of multiple compounds. Evidence from long-term field experiments suggests that soils may be more resilient and capable to degrade or stabilize pollutants than often assumed. In view of the need to source nutrients for expanding areas under organic farming, we discuss inputs originating from conventional farms vs. non-agricultural (i.e. societal) inputs. Closing nutrient cycles between agriculture and society is feasible in many cases, without being compromised by contaminants, and should be enhanced, aided by improved source control, waste treatment and sound risk assessments.

Differences in Relevant Physicochemical Properties Correlate with Synergistic Activity of Antimicrobial Peptides

With the urgent need for new medical approaches due to increased bacterial resistance to antibiotics, antimicrobial peptides (AMPs) have been considered as potential treatments for infections. Experiments indicate that combinations of several types of AMPs might be even more effective at inhibiting bacterial growth with reduced toxicity and a lower likelihood of inducing bacterial resistance. The molecular mechanisms of AMP-AMP synergistic antimicrobial activity, however, remain not well understood. Here, we present a theoretical approach that allows us to relate the physicochemical properties of AMPs and their antimicrobial cooperativity. It utilizes correlation and bioinformatics analysis. A concept of physicochemical similarity is introduced, and it is found that less similar AMPs with respect to certain physicochemical properties lead to greater synergy because of their complementary antibacterial actions. The analysis of correlations between the similarity and the antimicrobial properties allows us to effectively separate synergistic from nonsynergistic AMP pairs. Our theoretical approach can be used for the rational design of more effective AMP combinations for specific bacterial targets, for clarifying the mechanisms of bacterial elimination, and for a better understanding of cooperativity phenomena in biological systems.