Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation

Fish are poor sentinels for surveillance of riverine antimicrobial resistance

Effective surveillance of antimicrobial resistance (AMR) in the environment is crucial for assessing the human and animal health risk of AMR pollution. Wastewater treatment plants (WWTPs) are one of the main sources of AMR pollutants discharged into water bodies. One important factor for assessing the risks associated with such pollution is the colonization potential of the resistant bacteria (ARB) and resistance genes (ARGs) from the environment into human or animal microbiomes upon exposure. This study explores whether fish can act as sentinels for surveillance of AMR pollution in general and specifically the human colonization potential of ARB in rivers impacted by WWTP effluents. Two riverine fish species, Brown trout, and European bullhead, were sampled up- and downstream a German WWTP. The two fish species were chosen due to their different lifestyles: Trout are mainly actively swimming in the water phase, while bullheads are sedentary and river sediment-associated. The bacterial microbiomes and resistomes of fish gills, skin, and feces were compared with those of the respective river water and sediment up- and downstream of the WWTP. Microbiomes of both fish mirrored the changes in river water and sediment downstream of the WWTP, with significant shifts in bacterial community composition, particularly an increase in Proteobacteria and Verrucomicrobia. However, increases in ARG abundances observed in water and sediment downstream of the WWTP were not reflected in any of the fish-associated resistomes. This indicates that while the fish microbiome is sensitive to environmental changes, resistomes of poikilothermic animals such as fish are less responsive to colonization by ARB originating from WWTPs and may not serve as effective sentinels for assessing AMR pollution and colonization risks in freshwater environments. This study highlights the complexity of using wildlife as indicators for environmental AMR pollution and suggests that other species are better suited for surveillance efforts.

Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto

This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.

Microplastics Pose an Elevated Antimicrobial Resistance Risk Than Natural Surfaces via a Systematic Comparative Study of Surface Biofilms in Rivers

The pervasive presence of antimicrobial resistance (AMR) in various ecosystems threatens global health, especially in persistent biofilm states. Both anthropogenic and natural surfaces in environments provide ideal habitats for biofilm development. Microplastics (MPs), as emerging and rapidly proliferating anthropogenic pollutants, are of particular concern due to their unique physicochemical properties and ubiquity across environments. However, it remains unclear whether biofilms on MPs pose a higher AMR risk compared with natural surfaces. Here, we employed an integrative approach combining phenotypic and genotypic AMR analysis via single-cell spectroscopy and high-throughput quantitative PCR to systematically compare AMR risks on 5 MPs (polyethylene, polystyrene, poly(vinyl chloride), polylactic acid, and Tetra Pak) and 3 natural surfaces (wood, rock, and glass) in an urban aquatic ecosystem. Our results revealed that MPs harbored a higher proportion of metabolically active antibiotic-resistant bacteria and more high-risk antibiotic resistance genes than natural surfaces. By incorporating phenotypic and genotypic AMR with three additional biofilm-related risk factors, including biofilm biomass, microbial activity, and pathogen abundance, the health risk of AMR was quantified and found to be highly dependent on surface types. MPs exhibited, on average, a 10-fold higher health risk than natural surfaces. A structural equation model further identified surface hydrophobicity and microbial diversity as pivotal factors determining AMR risks across different surfaces. This systematic comparison provides new insights into the real-world environmental impact of MPs pollution and underscores the necessity of integrating plastic pollution control into AMR management strategies.

Microbiome Diversity in Seafood Factories via Next-Generation Sequencing for Food Safety Management System (FSMS) Certifications in Malaysia

Next-Generation Sequencing (NGS) technology was applied to evaluate Food Safety Management System (FSMS) performance in seafood-processing factories by exploring microbiome diversity alongside traditional methods for detecting foodborne pathogens. A total of 210 environmental swabs collected from processing zones in six factories underwent 16S rRNA amplicon sequencing. FSMS-certified factories exhibited significantly higher species richness, with alpha diversity p-values of 0.0036 for observed ASVs, 0.0026 for Faith's PD and 0.032 for Shannon. Beta diversity analysis also revealed significant differences, with p-values of 0.001 for Bray-Curtis, unweighted UniFrac and Jaccard. Pathogens like Listeria monocytogenes, Salmonella spp. and Bacillus cereus were present in "uncertified" factories but absent in the "certified" factories. The "certified" factories had a significantly higher proportion of lactic acid bacteria (LAB) genera (70.22%) compared to "uncertified" factories (29.78%). The LAB genera included Streptococcus, Lactococcus, Lactobacillus and others. NGS has demonstrated superior capability by providing comprehensive microbiome detection, including the unculturable microorganisms and insights into microbial diversity, so it lacks the limitations that come with traditional culturing. These findings highlight the potential for leveraging beneficial microbes in bioremediation and pathogen control to enhance FSMS effectiveness in seafood-processing environments.

Environmental Applications of GM Microorganisms: Tiny Critters Posing Huge Challenges for Risk Assessment and Governance

In recent years, the interest in developing genetically modified microorganisms (GMMs), including GMMs developed by genome editing, for use in the environment has significantly increased. However, the scientific knowledge on the ecology of such GMMs is severely limited. There is also little experience at the hands of regulators on how to evaluate the environmental safety of GMMs and on how to assess whether they provide sustainable alternatives to current (agricultural) production systems. This review analyzes two different GMM applications, GM microalgae for biofuel production and nitrogen-fixing GM soil bacteria for use as biofertilizers. We assess the challenges posed by such GMMs for regulatory environmental risk assessment (ERA) against the background of the GMO legislation existing in the European Union (EU). Based on our analysis, we present recommendations for ERA and the monitoring of GMM applications, and in particular for the improvement of the existing EU guidance. We also explore whether existing approaches for technology assessment can provide a framework for the broader assessment of GMM applications. To this end, we recommend developing and implementing an evidence-based sustainability analysis and other methods of technology assessment to support decision making and to address broader societal concerns linked to the use of GMM applications in the environment.

Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo

Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.

An eco-evolutionary perspective on antimicrobial resistance in the context of One Health

The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.

Assessment of viable Enterobacteriaceae and Enterococcus spp. across the agro-ecosystem of an antibiotic-free swine farm

Agricultural practices, specifically the use of antibiotics and other biocides, have repercussions on human, animal, and plant health. The aim of this study was to evaluate the levels of Enterobacteriaceae and Enterococcus, as antibiotic-resistant marker bacteria, in various matrices across the agro-ecosystem of an antibiotic-free swine farm in Quebec (Canada), namely pig feed, feces, manure, agricultural soil, water and sediment from a crossing stream, and soil from nearby forests. Samples were collected in fall 2022, spring and fall 2023, and spring 2024. All samples were subjected to counts of total, cefotaxime-, and ciprofloxacin-resistant Enterobacteriaceae as well as total and vancomycin-resistant Enterococcus spp. The frequency of total and cefotaxime-resistant Enterobacteriaceae along with the vancomycin-resistant Enterococcus decreased with age in pig feces, from weaning to the end of the fattening period. High proportions of the Enterobacteriaceae recovered from feces and environmental samples were resistant to cefotaxime. Application of manure on fields contributed a significant input of Enterococcus, but those resistant to vancomycin were under the detection limit. This study shows the prevalence of antibiotic-resistant bacteria in a farm agro-ecosystem even without the administration of antibiotics to the animals and highlights the complexity of components influencing antimicrobial resistance in the environment.

Determinants of antimicrobial resistance in biosolids: A systematic review, database, and meta-analysis

Biosolids can provide a nutrient rich soil amendment, particularly for poor soils and semi-arid or drought-prone areas. However, there are concerns that sludge and biosolids could be a source of propagation and exposure to AMR determinants such as antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). To inform risk assessment efforts, a systematic literature review was performed to build a comprehensive spreadsheet database of ARB and ARG concentrations in biosolids (and some sludges specified as intended for land application), along with 69 other quantitative and qualitative meta-data fields from 68 published studies describing sampling information and processing methods that can be used for modeling purposes. Mean ARG concentrations per gram in positive samples of biosolids ranged from -5.7 log10(gene copies [gc]/g) to 12.92 log10(gc/g) (with these range values reported per dry weight), and aqueous concentrations ranged from 0.9 log10(gc/L) to 14.6 log10(gc/L). Mean ARB concentrations per gram of biosolids ranged from 2.02 log10 (colony forming units [CFU]/g) to 9.00 log10 (CFU/g) (dry weight), and aqueous concentrations ranged from 3.23 log10 (CFU/L) to 12.0 log10 (CFU/L). ARG log removal values (LRVs) during sewage sludge stabilization were calculated from a meta-analysis of mean concentrations before and after stabilization from 31 studies, ranging from -2.05 to 5.52 logs. The classes of resistance most relevant for a risk assessment corresponded to sulfonamide (sul1 and sul2), tetracycline (tetZ, tetX, tetA and tetG), beta-lactam (blaTEM), macrolide (ermB and ermF), aminoglycoside (strA and aac(6')-Ib-cr), and integron-associated (intI1). The resistance classes most relevant for ARB risk assessment included sulfonamides (sulfamethoxazole and sulfamethazine), cephalosporin (cephalothin and cefoxitin), penicillin (ampicillin), and ciprofloxin (ciprofloxacin). Considerations for exposure assessment are discussed to highlight risk assessment needs relating to antimicrobial resistance (AMR) associated with biosolids application. This study aids in prioritization of resources for reducing the spread of AMR within a One Health framework.

Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus

INTRODUCTION

Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies. Here we used genomic analysis to track the movement and transmission of CREs within clinical and environmental samples.

METHODS

25 isolates were cultured from clinical patient samples or swabs, that tested positive for OXA-48-like variants using the NG-Test® CARBA-5 test and whole genome sequenced (WGS) using Oxford Nanopore Technologies (ONT). 158 swabs and 52 wastewater samples were collected from the ward environment. 60 isolates (matching clinical isolate genera; Klebsiella, Enterobacter, Citrobacter and Escherichia) were isolated from the environmental samples using selective agar. Metagenomic sequencing was undertaken on 36 environmental wastewater and swab samples.

RESULTS

21/25 (84%) clinical isolates had > 1 blaOXA gene and 19/25 (76%) harboured > 1 blaNDM gene. Enterobacterales were most commonly isolated from environmental wastewater samples 27/52 (51.9%), then stick swabs 5/43 (11.6%) and sponge swabs 5/115 (4.3%). 11/60 (18%) environmental isolates harboured > 1 blaOXA gene and 1.9% (1/60) harboured blaNDM-1. blaOXA genes were found in 2/36 (5.5%) metagenomic environmental samples.

CONCLUSIONS

Potential for putative patient-patient and patient-ward transmission was shown. Metagenomic sampling needs optimization to improve sensitivity.

Captivity increased the abundance of high-risk antibiotic resistance genes in the giant panda gut microbiome

Captivity is a key strategy for protecting endangered species, but research has primarily focused on artificial breeding and reintroduction to bolster wild populations, often overlooking the environmental and health risks associated with antibiotic resistance genes (ARGs). Here, we conducted a comprehensive analysis of the microbiome and ARG profiles in the gut of wild giant pandas across five representative populations, as well as one captive population, utilizing 16S rRNA gene sequencing and High-Throughput Quantitative PCR. Our findings revealed that both geographic location and captivity significantly influenced the gut microbial community and ARG composition in the gut of giant pandas. Additionally, we identified core microbiomes with essential ecological functions, particularly those related to food utilization, were identified in the giant panda gut across different regions. The gut ARGs in giant pandas exhibited a broad range of subtypes, with multidrug resistance genes being the most prevalent. Notably, the captive population harbored the highest abundance of high-risk ARGs, especially those conferring tetracycline resistance. High-risk multidrug ARGs (e.g., tolC, mepA, and mdtA) were found to be strongly correlated with the potential pathogens, such as Escherichia_Shigellina and Pseudomonas. Furthermore, bamboo-associated ARGs and mobile genetic elements (MGEs) contributed significantly to the ARG abundance in the giant panda gut, indicating that diet plays a crucial role in shaping gut resistome. Collectively, our study provides a detailed mapping of giant panda gut microbiomes and ARG distribution, offering valuable insights for conservation efforts and advancing our understanding of ARG dynamics in giant panda populations.

Occurrence and human exposure risk of antibiotic resistance genes in tillage soils of dryland regions: A case study of northern Ningxia Plain, China

Agricultural soils are important source and sink of antibiotic resistance genes (ARGs). However, little is known about the fate of ARGs in dryland soils, while its human exposure risks were seriously overlooked. Taking the northern Ningxia Plain as a case, this study explored the occurrence of ARGs and its relationship with mobile genetic elements (MGEs), pathogens, and environmental factors. Furthermore, the concentrations of airborne ARGs by soil wind erosion and the human exposure doses of soil ARGs were evaluated. The results showed the abundances of different regions ranged from 4.0 × 105 to 1.6 × 106 copies/g. Soil ARGs are driven by MGEs, but multiply impacted by soil properties, nutrition, and bacterial community. Vibrio metschnikovii, Acinetobacter schindleri, and Serratia marcescens are potential pathogenic hosts for ARGs. Further exploration revealed the concentration of ARGs loaded in dust by soil wind erosion reached more than 105 copies/m3, which were even higher than those found in sewage treatment plants and hospitals. Skin contact is the primary route of ARGs exposure, with a maximum dose of 24071.33 copies/kg/d, which is largely attributed to ARGs loaded in dust. This study bridged the gap on ARGs in dryland soils, and provided reference for human exposure risk assessment of soil ARGs.

Resistome in the indoor dust samples from workplaces and households: a pilot study

The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored. This pilot study aimed to analyze resistome in indoor dust samples from participants' workplaces (a pediatric hospital, a maternity hospital, and a research center) and households and compare two different approaches to the ARGs analysis; high-throughput quantitative PCR (HT-qPCR) and whole metagenome shotgun sequencing (WMGS). In total, 143 ARGs were detected using HT-qPCR, with ARGs associated with the macrolides, lincosamides, and streptogramin B (MLSB) phenotype being the most abundant, followed by MDR (multi-drug resistance) genes, and genes conferring resistance to aminoglycosides. A higher overall relative quantity of ARGs was observed in indoor dust samples from workplaces than from households, with the pediatric hospital being associated with the highest relative quantity of ARGs. WMGS analysis revealed 36 ARGs, of which five were detected by both HT-qPCR and WMGS techniques. Accordingly, the efficacy of the WMGS approach to detect ARGs was lower than that of HT-qPCR. In summary, our pilot data revealed that indoor dust in buildings where people spend most of their time (workplaces, households) can be a significant source of antimicrobial-resistant microorganisms, which may potentially pose a health risk to both humans and animals.

MetaCompare 2.0: differential ranking of ecological and human health resistome risks

While numerous environmental factors contribute to the spread of antibiotic resistance genes (ARGs), quantifying their relative contributions remains a fundamental challenge. Similarly, it is important to differentiate acute human health risks from environmental exposure, versus broader ecological risk of ARG evolution and spread across microbial taxa. Recent studies have proposed various methods for achieving such aims. Here, we introduce MetaCompare 2.0, which improves upon original MetaCompare pipeline by differentiating indicators of human health resistome risk (potential for human pathogens of acute resistance concern to acquire ARGs) from ecological resistome risk (overall mobility of ARGs and potential for pathogen acquisition). The updated pipeline's sensitivity was demonstrated by analyzing diverse publicly-available metagenomes from wastewater, surface water, soil, sediment, human gut, and synthetic microbial communities. MetaCompare 2.0 provided distinct rankings of the metagenomes according to both human health resistome risk and ecological resistome risk, with both scores trending higher when influenced by anthropogenic impact or other stress. We evaluated the robustness of the pipeline to sequence assembly methods, sequencing depth, contig count, and metagenomic library coverage bias. The risk scores were remarkably consistent despite variations in these technological aspects. We packaged the improved pipeline into a publicly-available web service (http://metacompare.cs.vt.edu/) that provides an easy-to-use interface for computing resistome risk scores and visualizing results.

Environmental Antimicrobial Resistance: Implications for Food Safety and Public Health

Antimicrobial resistance (AMR) is a serious global health issue, aggravated by antibiotic overuse and misuse in human medicine, animal care, and agriculture. This study looks at the different mechanisms that drive AMR, such as environmental contamination, horizontal gene transfer, and selective pressure, as well as the severe implications of AMR for human and animal health. This study demonstrates the need for concerted efforts across the scientific, healthcare, agricultural, and policy sectors to control the emergence of AMR. Some crucial strategies discussed include developing antimicrobial stewardship (AMS) programs, encouraging targeted narrow-spectrum antibiotic use, and emphasizing the significance of strict regulatory frameworks and surveillance systems, like the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the Access, Watch, and Reserve (AWaRe) classification. This study also emphasizes the need for national and international action plans in combating AMR and promotes the One Health strategy, which unifies environmental, animal, and human health. This study concludes that preventing the spread of AMR and maintaining the effectiveness of antibiotics for future generations requires a comprehensive, multidisciplinary, and internationally coordinated strategy.

Aged Microplastics and Antibiotic Resistance Genes: A Review of Aging Effects on Their Interactions

Background: Microplastic aging affects the dynamics of antibiotic resistance genes (ARGs) on microplastics, yet no review presents the effects of microplastic aging on the associated ARGs. Objectives: This review, therefore, aims to discuss the effects of different types of microplastic aging, as well as the other pollutants on or around microplastics and the chemicals leached from microplastics, on the associated ARGs. Results: It highlights that microplastic photoaging generally results in higher sorption of antibiotics and ARGs due to increased microplastic surface area and functional group changes. Photoaging produces reactive oxygen species, facilitating ARG transfer by increasing bacterial cell membrane permeability. Reactive oxygen species can interact with biofilms, suggesting combined effects of microplastic aging on ARGs. The effects of mechanical aging were deduced from studies showing larger microplastics anchoring more ARGs due to rough surfaces. Smaller microplastics from aging penetrate deeper and smaller places and transport ARGs to these places. High temperatures are likely to reduce biofilm mass and ARGs, but the variation of ARGs on microplastics subjected to thermal aging remains unknown due to limited studies. Biotic aging results in biofilm formation on microplastics, and biofilms, often with unique microbial structures, invariably enrich ARGs. Higher oxidative stress promotes ARG transfer in the biofilms due to higher cell membrane permeability. Other environmental pollutants, particularly heavy metals, antibacterial, chlorination by-products, and other functional genes, could increase microplastic-associated ARGs, as do microplastic additives like phthalates and bisphenols. Conclusions: This review provides insights into the environmental fate of co-existing microplastics and ARGs under the influences of aging. Further studies could examine the effects of mechanical and thermal MP aging on their interactions with ARGs.

The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland

The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.