Antimicrobial Resistance In Environment Research Articles

Dissemination and persistence of antimicrobial resistance (AMR) along the wastewater-river continuum

Antimicrobial resistance (AMR) is a global health hazard. Although clinical and agricultural environments are well-established contributors to the evolution and dissemination of AMR, research on wastewater treatment works (WwTWs) has highlighted their potential role as disseminators of AMR in freshwater environments. Using metagenomic sequencing and analysis, we investigated the changes in resistomes and associated mobile genetic elements within untreated wastewater influents and treated effluents of five WwTWs, and sediments collected from corresponding river environments in Oxfordshire, UK, across three seasonal periods within a year. Our analysis demonstrated a high diversity and abundance of antimicrobial resistance genes (ARGs) in untreated wastewater influents, reflecting the varied anthropogenic and environmental origins of wastewater. WwTWs effectively reduced AMR in the final effluent, with an average 87 % reduction in normalised ARG abundance and an average 63 % reduction in richness. However, wastewater effluents significantly impacted the antimicrobial resistome of the receiving rivers, with an average 543 % increase in ARG abundance and a 164 % increase in richness from upstream sediments to downstream sediments. The normalised abundance of the human gut-associated bacteriophage crAssphage was highly associated with both ARG abundance and richness. We observed seasonal variation in the resistome of raw influent which was not found in the effluent-receiving sediments. We illustrate the potential of WwTWs as focal points for disseminating ARGs and resistance-selecting chemicals, contributing to the elevation of environmental AMR. Our study emphasises the need for a comprehensive understanding of the anthropogenic impacts on AMR evolution and dissemination in wastewater and river environments, informing efforts to mitigate this growing public health crisis.

A Systematic Review on Antimicrobial Resistance in Ghana from a One Health Perspective.

Antimicrobial resistance (AMR) poses a global health threat, with lower-middle-income countries bearing a disproportionate burden. Surveillance of AMR under a One Health framework is needed to elucidate the associations among clinical, animal, and environmental AMR. This review aimed to describe the state of AMR in Ghana, focusing on One Health. This review utilized the PRISMA guidelines and major databases to systematically search and analyze AMR in Ghana published from 1 January 2014 to 1 May 2023. Out of the 48 articles that met the inclusion criteria, 28 studies were conducted on humans, 14 studies involved animals, and 6 studies focused on the environment. A total of 48 different pathogens were identified across the human, animal, and environmental sectors, with the most common being Escherichia coli (67%, n = 32), Klebsiella spp. (52%, n = 25), Pseudomonas spp. (40%, n = 19), and Salmonella spp. (38%, n = 18). Generally, a high prevalence of antibiotic resistance was observed among various bacterial species across the sectors. These bacteria exhibited resistance to commonly used antibiotics, with resistance to ampicillin and tetracycline exceeding 80%, and multidrug resistance (MDR) ranging from 17.6% in Shigella spp. to 100% in Acinetobacter spp. This review reaffirms the significant challenge of AMR in Ghana, with a high prevalence observed in the human, animal, and environmental sectors. Key pathogens (e.g., Staphylococcus aureus and Escherichia coli) found across the sectors emphasize the urgent need for a One Health approach to tackle AMR in Ghana.

Comparison of methods proposed for monitoring cefotaxime-resistant Escherichia coli in the water environment.

Escherichia coli is a promising subject for globally coordinated surveillance of antimicrobial resistance (AMR) in water environments due to its clinical relevance and widespread use as an indicator of fecal contamination. Cefotaxime-resistant E. coli was recently evaluated favorably for this purpose by the World Health Organization TriCycle Protocol, which specifies tryptone bile x-glucuronide (TBX) medium and incubation at 35°C. We assessed comparability with the U.S. Environmental Protection Agency-approved method for E. coli quantification, which uses membrane-thermotolerant E. coli (mTEC) agar and incubation at 44.5°C, in terms of recovery of E. coli and cefotaxime-resistant E. coli from wastewater influent and surface waters. Total E. coli concentrations in wastewater influent were 106-108 CFU/100 mL, while cefotaxime-resistant E. coli were ~100-fold lower. Total E. coli in surface waters were ~102 CFU/100 mL, and cefotaxime-resistant isolates were near the limit of detection (0.4 CFU/100 mL). Total and putative cefotaxime-resistant E. coli concentrations did not differ significantly between media or by incubation method; however, colonies isolated on mTEC were more frequently confirmed to species (97.1%) compared to those from TBX (92.5%). Incubation in a water bath at 44.5°C significantly decreased non-specific background growth and improved confirmation frequency on both media (97.4%) compared to incubation at 35°C (92.3%). This study helps to advance globally coordinated AMR in water environments and suggests that the TriCycle Protocol is adaptable to other standard methods that may be required in different locales, while also offering a means to improve specificity by decreasing the frequency of false-positive identification of cefotaxime-resistant E. coli by modifying incubation conditions.IMPORTANCEAs antibiotic-resistant bacteria in water environments are increasingly recognized as contributors to the global antibiotic resistance crisis, the need for a monitoring subject that captures antibiotic resistance trends on a global scale increases. The World Health Organization TriCycle Protocol proposes the use of cefotaxime-resistant Escherichia coli isolated on tryptone bile x-glucuronide agar. The U.S. Environmental Protection Agency (USEPA) criteria for safe recreational waters also use E. coli as an indicator but specify the use of mTEC agar at a higher incubation temperature (44.5°C vs 35°C). We assessed the comparability of these methods for isolating total and cefotaxime-resistant E. coli, finding overall good agreement and performance, but significantly higher specificity toward E. coli selection with the use of the USEPA incubation protocol and mTEC agar. This study is the first to directly compare these methods and provides evidence that the methods may be used interchangeably for global surveillance of antibiotic resistance in the environment.

Towards monitoring the invisible threat: a global approach for tackling AMR in water resources and environment

The global threat of antimicrobial resistance (AMR) is now increasingly recognized for the danger posed by its environmental spread. Aquatic environments and wastewater represent a significant diffusion and selection pathway for antibiotic resistance genes and antibiotic resistant bacteria (ARGs and ARBs). During a collaborative hackathon event, the “Innovation Workshop on Water Quality Monitoring & Assessment,” held in September 2023, experts addressed four challenges related to water quality, including the challenge of globalization AMR surveillance in water. This paper, derived from the workshop findings, proposes a globally adaptable model for antimicrobial resistance surveillance intended as an advance to improve future monitoring systems. The new framework aims to address significant challenges, such as the lack of standardized methodological approaches or lack of funding, coordination, and awareness across a short-, medium- and long-term plan, integrating sustainability concepts, extending participation and monitoring capacity of countries, and offering efficient solutions. This vision is first articulated by creating a technical committee that promotes awareness of antimicrobial resistance and develops a single data management and communication platform. Subsequently, by developing local, national, and international policies, centralized laboratories will be established at the regional level, and built based on existing realities. These laboratories will include facilities to make the management of analyses more efficient, from sampling to reporting the final result. In the long term, activities that allow the maintenance of the created framework and continuous technological development and advancement will be promoted. All this will be achieved in collaboration with national and supranational bodies that are already addressing the issue at a global level.

Assessment of freshwater fish farms for the identification of the geographical areas harbouring antimicrobial resistance

Assessment of antimicrobial resistance (AMR) in freshwater fish farms has been rarely investigated. Aeromonas are considered as an indicator organism for monitoring AMR in aquatic environment. Identification of the geographical areas harbouring AMR have implications for developing AMR mitigation strategies. The present study investigated the prevalence of AMR in freshwater fish farms (n = 124) in four districts (A-D) of Uttar Pradesh, India. The study revealed significantly higher AMR in fish farms of district D for ceftazidime, cefotaxime and trimethoprim-sulfamethoxazole. Similarly, AMR to ciprofloxacin and tetracycline was significantly higher in district A, and cefoxitin (FOX) in district B. District D also showed the highest number of MDR strains, AmpC and ESBL producers. Overall, maximum AMR was seen to β-lactams (35.5%) and aminoglycosides (14.5%). Twenty-five AMR phenotypes and eighteen AMR genotypes were detected in the study. The farms of district D showed significantly higher number of resistant phenotypes (≥3 antimicrobials). Furthermore, the study identified the species of Aeromonas contributing to AMR. Two clusters were observed: cluster I- resistant to FOX only, and cluster II (comprising of A. caviae and A. veronii bv veronii)- resistant to multiple antimicrobials and included majority of AmpC producers. A. caviae had significantly higher MAR than other Aeromonas species. The ARGs shared among the cluster II species and its close relative A. veronii bv sobria were blaTEM,sul1, tet(E) and blaCIT. Overall, our study identified the geographical districts harbouring higher AMR in the freshwater fish farms. These findings suggest the need for spatial assessment of AMR in aquaculture.

RESISTÊNCIA A ANTIMICROBIANOS EM ESCHERICHIA COLI EM AMOSTRAS AMBIENTAIS: UMA BREVE REVISÃO

The antimicrobial resistance of environmental strains has a serious impact on the aquatic ecosystem, as well as on human and veterinary medicine. One way to verify problems related to the presence of drugs in the environment is to carry out monitoring using bacteria that are bioindicators of contamination, such as Escherichia coli. Given this scenario, the objective of this study was to carry out a short review on antimicrobial resistance in pediatric Escherichia coli from environmental samples. Thus, this study constitutes a bibliographic review of an analytical nature, dealing with the theme of antimicrobial resistance in environments; topic that has been much discussed in the academic community. It was defined as inclusion of inclusion: articles published between the years 2016 and 2022, in the PubMed database. As a result, it was found that in the analyzed years, there was an oscillation of publications on themes related to resistance, plasmids and integrons. Thus, we conclude that research on antimicrobial resistance in environmental strains should be increasingly carried out, with the objective of monitoring and verifying which drugs are more present in the environment as the consequences generated are still unknown.

Impact of low-dose ozone nanobubble treatments on antimicrobial resistance genes in pond water.

Antimicrobial resistance (AMR) poses a significant global health threat as the silent pandemic. Because of the use of antimicrobials in aquaculture systems, fish farms may be potential reservoirs for the dissemination of antimicrobial resistance genes (ARGs). Treatments with disinfectants have been promoted to reduce the use of antibiotics; however, the effect of these types of treatments on AMR or ARGs is not well known. This study aimed to evaluate the effects of low dose ozone treatments (0.15 mg/L) on ARG dynamics in pond water using metagenomic shotgun sequencing analysis. The results suggested that ozone disinfection can increase the relative abundance of acquired ARGs and intrinsic efflux mediated ARGs found in the resistance nodulation cell division (RND) family. Notably, a co-occurrence of efflux and non-efflux ARGs within the same bacterial genera was also observed, with most of these genera dominating the bacterial population following ozone treatments. These findings suggest that ozone treatments may selectively favor the survival of bacterial genera harboring efflux ARGs, which may also have non-efflux ARGs. This study underscores the importance of considering the potential impacts of disinfection practices on AMR gene dissemination particularly in aquaculture settings where disinfectants are frequently used at low levels. Future endeavors should prioritize the evaluation of these strategies, as they may be associated with an increased risk of AMR in aquatic environments.

One Health Determinants of Escherichia coli Antimicrobial Resistance in Humans in the Community: An Umbrella Review.

To date, the scientific literature on health variables for Escherichia coli antimicrobial resistance (AMR) has been investigated throughout several systematic reviews, often with a focus on only one aspect of the One Health variables: human, animal, or environment. The aim of this umbrella review is to conduct a systematic synthesis of existing evidence on Escherichia coli AMR in humans in the community from a One Health perspective. PubMed, EMBASE, and CINAHL were searched on "antibiotic resistance" and "systematic review" from inception until 25 March 2022 (PROSPERO: CRD42022316431). The methodological quality was assessed, and the importance of identified variables was tabulated across all included reviews. Twenty-three reviews were included in this study, covering 860 primary studies. All reviews were of (critically) low quality. Most reviews focused on humans (20), 3 on animals, and 1 on both human and environmental variables. Antibiotic use, urinary tract infections, diabetes, and international travel were identified as the most important human variables. Poultry farms and swimming in freshwater were identified as potential sources for AMR transmission from the animal and environmental perspectives. This umbrella review highlights a gap in high-quality literature investigating the time between variable exposure, AMR testing, and animal and environmental AMR variables.

Unveiling antimicrobial resistance in Chilean fertilized soils: a One Health perspective on environmental AMR surveillance.

Antimicrobial resistance (AMR) poses a significant threat to humans and animals as well as the environment. Within agricultural settings, the utilization of antimicrobial agents in animal husbandry can lead to the emergence of antimicrobial resistance. In Chile, the widespread use of animal-derived organic amendments, including manure and compost, requires an examination of the potential emergence of AMR resulting from their application. The aim of this research was to identify and compare AMR genes found in fertilized soils and manure in Los Andes city, Chile. Soil samples were collected from an agricultural field, comprising unamended soils, amended soils, and manure used for crop fertilization. The selected genes (n = 28) included genes associated with resistance to beta-lactams, tetracyclines, sulfonamides, polymyxins, macrolides, quinolones, aminoglycosides, as well as mobile genetic elements and multidrug resistance genes. Twenty genes were successfully identified in the samples. Tetracycline resistance genes displayed the highest prevalence, followed by MGE and sulfonamides, while quinolone resistance genes were comparatively less abundant. Notably, blaOXA, sulA, tetO, tetW, tetM, aac (6) ib., and intI1, exhibited higher frequencies in unamended soils, indicating their potential persistence within the soil microbiome and contribution to the perpetuation of AMR over time. Given the complex nature of AMR, it is crucial to adopt an integrated surveillance framework that embraces the One Health approach, involving multiple sectors, to effectively address this challenge. This study represents the first investigation of antimicrobial resistance genes in agricultural soils in Chile, shedding light on the presence and dynamics of AMR in this context.

Relating Antimicrobial Resistance and Virulence in Surface-Water E. coli.

The role of the environment in the emergence and spread of antimicrobial resistance (AMR) is being increasingly recognized, raising questions about the public health risks associated with environmental AMR. Yet, little is known about pathogenicity among resistant bacteria in environmental systems. Existing studies on the association between AMR and virulence are contradictory, as fitness costs and genetic co-occurrence can be opposing influences. Using Escherichia coli isolated from surface waters in eastern North Carolina, we compared virulence gene prevalence between isolates resistant and susceptible to antibiotics. We also compared the prevalence of isolates from sub-watersheds with or without commercial hog operations (CHOs). Isolates that had previously been evaluated for phenotypic AMR were paired by matching isolates resistant to any tested antibiotic with fully susceptible isolates from the same sample date and site, forming 87 pairs. These 174 isolates were evaluated by conventional PCR for seven virulence genes (bfp, fimH, cnf-1, STa (estA), EAST-1 (astA), eae, and hlyA). One gene, fimH, was found in 93.1% of isolates. Excluding fimH, at least one virulence gene was detected in 24.7% of isolates. Significant negative associations were found between resistance to at least one antibiotic and presence of at least one virulence gene, tetracycline resistance and presence of a virulence gene, resistance and STa presence, and tetracycline resistance and STa presence. No significant associations were found between CHO presence and virulence, though some sub-significant associations merit further study. This work builds our understanding of factors controlling AMR dissemination through the environment and potential health risks.

Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework.

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined. To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region. A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km. Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

Assessment of the stability of antimicrobials and resistance genes during short- and long-term storage condition: accounting for uncertainties in bioanalytical workflows

Unravelling complexities in antimicrobial agent–microbe interactions in the context of antimicrobial resistance (AMR) requires robust analytical workflows accounting for all uncertainties. Temporal storage of wastewater samples under refrigerated or frozen conditions prior to chemical and biological analysis is widely used to facilitate laboratory routine but may affect stability of analytes over time. Yet, little knowledge exists regarding stability of biological and chemical determinants in environmental samples, which hampers validity of research outputs. This study examines, for the first time, the stability of 32 antimicrobials (AAs) including commonly used classes of antibiotics and their representative metabolites and variation of 5 antibiotic resistance genes (ARGs) (ermB, sul1, tetW, blaCTX-M, qnrS), as well as intI1 and 16S rRNA genes in a reference wastewater sample stored under freezing condition for up to 1 year. Ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) and quantitative PCR (qPCR) techniques were adopted to measure concentration of AAs and ARGs, respectively. Results suggested that parent compounds are less affected by freezing storage compared to the metabolites. β-Lactams, clindamycin, and N-desmethyl clindamycin are the most-affected compounds which were poorly recovered (34–67%) from the starting concentration. By contrast, sulfonamides, macrolides, quinolones, and azoles are generally stable under freezing condition. No consistent differences were observed in gene copies between fresh and frozen samples, and ermB and tetW showed the highest variabilities at 30% under freezing condition. Overall, this study adds to the current knowledge on environmental AMR monitoring and emphasises the need for standardised protocols for AMR monitoring in the wastewater samples.Graphical

Bacteriophages from faecal contamination are an important reservoir for AMR in aquatic environments

Bacteriophages have been shown to play an important role in harbouring and propagating antibiotic resistance genes (ARGs). Faecal matter contains high levels of phages, suggesting that faecal contamination of water bodies may lead to increased antimicrobial resistance (AMR) levels due to increased phage loading in aquatic environments. In this study, we assessed whether faecal pollution of three rivers (Rivers Liffey, Tolka, and Dodder) was responsible for increased levels of ARGs in phage particles using established phage-faecal markers, focusing on four ARGs (blaTEM, tet(O), qnrS, and sul1). We observed all four ARGs in phage fractions in all three rivers, with ARGs more frequently observed in agricultural and urban sampling sites compared to their source. These findings highlight the role of faecal pollution in environmental AMR and the impact of agricultural and urban activities on water quality. Furthermore, our results suggest the importance of including phages as indicators when assessing environmental AMR, as they serve as significant reservoirs of resistance genes in aquatic environments. This study provides important insights into the role of faecal pollution and phages in the prevalence of AMR in the environment and the need for their inclusion in future studies to provide a comprehensive understanding of environmental AMR.

A Scoping Review of Antimicrobial Usage and Antimicrobial Resistance in Beef Cow-Calf Herds in the United States and Canada.

The magnitude and knowledge gaps regarding antimicrobial use (AMU) and antimicrobial resistance (AMR) have not been summarized for the North American cow-calf production sector, although estimates of AMU and AMR are essential to AMR risk analysis. The objectives of this scoping review were to map AMU and AMR in the beef cow-calf sector in Canada and the United States, summarize published AMU/AMR predictors, and identify research gaps. An electronic search was conducted of four bibliographic databases and Google Scholar, augmented by a hand-search of captured studies. Twenty-three of three-hundred and forty-three publications screened advanced to data extraction. Of these, 10 were conducted in the USA and 13 in Canada. Thirteen studied AMR and twelve studied AMU, with two reporting both. Of twelve captured AMU studies, nine presented counts of herd AMU by antimicrobial class or specific antimicrobial. Antimicrobial resistance in Escherichia coli (E. coli) was reported in nine studies. Risk factors for AMU include herd size, vaccine use, and start date of calving season. Overall, a small number of AMR studies were available for synthesis in primarily one population (cows) reporting E. coli AMR. Additional studies targeting reasons for AMU in calves, the impact of management procedures on AMU, potential environmental AMR sources, and AMR in respiratory pathogens and enteric organisms other than E. coli for pre-weaning calves are required to inform AMR risk mitigation strategies.

Excessive disinfection aggravated the environmental prevalence of antimicrobial resistance during COVID-19 pandemic

During COVID-19 pandemic, chemicals from excessive consumption of pharmaceuticals and disinfectants i.e., antibiotics, quaternary ammonium compounds (QACs), and trihalomethanes (THMs), flowed into the urban environment, imposing unprecedented selective pressure to antimicrobial resistance (AMR). To decipher the obscure character pandemic-related chemicals portrayed in altering environmental AMR, 40 environmental samples covering water and soil matrix from surroundings of Wuhan designated hospitals were collected on March 2020 and June 2020. Chemical concentrations and antibiotic resistance gene (ARG) profiles were revealed by ultra-high-performance liquid chromatography-tandem mass spectrometry and metagenomics. Selective pressure from pandemic-related chemicals ascended by 1.4–5.8 times in March 2020 and then declined to normal level of pre-pandemic period in June 2020. Correspondingly, the relative abundance of ARGs under increasing selective pressure was 20.1 times that under normal selective pressure. Moreover, effect from QACs and THMs in aggravating the prevalence of AMR was elaborated by null model, variation partition and co-occurrence network analyses. Pandemic-related chemicals, of which QACs and THMs respectively displayed close interaction with efflux pump genes and mobile genetic elements, contributed >50 % in shaping ARG profile. QACs bolstered the cross resistance effectuated by qacEΔ1 and cmeB to 3.0 times higher while THMs boosted horizon ARG transfer by 7.9 times for initiating microbial response to oxidative stress. Under ascending selective pressure, qepA encoding quinolone efflux pump and oxa-20 encoding β-lactamases were identified as priority ARGs with potential human health risk. Collectively, this research validated the synergistic effect of QACs and THMs in exacerbating environmental AMR, appealing for the rational usage of disinfectants and the attention for environmental microbes in one-health perspective.

Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters.

Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.

Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?

The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2024;43:623-636. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Can Stray Cats Be Reservoirs of Antimicrobial Resistance?

The emergence and spread of antimicrobial resistance (AMR) is a global problem that requires a One Health approach. Despite several studies have reported the role of companion animals as reservoirs of AMR, limited information is available regarding the role of cats in the circulation of AMR. In this study, we evaluated the phenotypic and genotypic profile of 75 Escherichia coli isolated from rectal swabs and fecal samples of 75 stray cats (living in solitary or in a colony) sampled in Palermo (Sicily, Italy), to determine whether these animals may participate in the spread of AMR. Susceptibility to 8 antibiotics was tested using Minimum Inhibitory Concentration assays, while the presence of the common antibiotic resistance genes blaTEM, blaCTX-M, tet(A), and tet(B) was investigated by PCR. From the 75 E. coli isolates analyzed, 43% were resistant to at least one of the eight antibiotics tested, with 31% of the isolates resistant to ampicillin, 23% to cefotaxime, 21% to tetracycline, 20% to cefazolin, and 17% to amoxicillin/clavulanic acid. Most isolates harbored the blaTEM gene (29%), followed by blaCTX-M (23%), tet(A) (21%), and tet(B) (20%). Our results confirm the fecal carriage of antibiotic-resistant E. coli and clinically relevant resistance genes in stray cats. This study highlights the potential role of stray cats in the spread of AMR in urban environments, emphasising the need to better understand their role in AMR circulation when planning strategies to combat it.

Probiotics beyond the farm: Benefits, costs, and considerations of using antibiotic alternatives in livestock

The increasing global expansion of antimicrobial resistant infections warrants the development of effective antibiotic alternative therapies, particularly for use in livestock production, an agricultural sector that is perceived to disproportionately contribute to the antimicrobial resistance (AMR) crisis by consuming nearly two-thirds of the global antibiotic supply. Probiotics and probiotic derived compounds are promising alternative therapies, and their successful use in disease prevention, treatment, and animal performance commands attention. However, insufficient or outdated probiotic screening techniques may unintentionally contribute to this crisis, and few longitudinal studies have been conducted to determine what role probiotics play in AMR dissemination in animal hosts and the surrounding environment. In this review, we briefly summarize the current literature regarding the efficacy, feasibility, and limitations of probiotics, including an evaluation of their impact on the animal microbiome and resistome and their potential to influence AMR in the environment. Probiotic application for livestock is often touted as an ideal alternative therapy that might reduce the need for antibiotic use in agriculture and the negative downstream impacts. However, as detailed in this review, limited research has been conducted linking probiotic usage with reductions in AMR in agricultural or natural environments. Additionally, we discuss the methods, including limitations, of current probiotic screening techniques across the globe, highlighting approaches aimed at reducing antibiotic usage and ensuring safe and effective probiotic mediated health outcomes. Based on this information, we propose economic and logistical considerations for bringing probiotic therapies to market including regulatory roadblocks, future innovations, and the significant gaps in knowledge requiring additional research to ensure probiotics are suitable long-term options for livestock producers as an antibiotic alternative therapy.

Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics

Antimicrobial resistance (AMR) in soils represents a serious risk to human health through the food chain and human-nature contact. However, the active antibiotic-resistant bacteria (ARB) residing in soils that primarily drive AMR dissemination are poorly explored. Here, single-cell Raman-D2O coupled with targeted metagenomics is developed as a culture-independent approach to phenotypically and genotypically profiling active ARB against clinical antibiotics in a wide range of soils. This method quantifies the prevalence (contamination degree) and activity (spread potential) of soil ARB and reveals a clear elevation with increasing anthropogenic activities such as farming and the creation of pollution, thereby constituting a factor that is critical for the assessment of AMR risks. Further targeted sorting and metagenomic sequencing of the most active soil ARB uncover several uncultured genera and a pathogenic strain. Furthermore, the underlying resistance genes, virulence factor genes, and associated mobile genetic elements (including plasmids, insertion sequences, and prophages) are fully deciphered at the single-cell level. This study advances our understanding of the soil active AMR repertoire by linking the resistant phenome to the genome. It will aid in the risk assessment of environmental AMR and guide the combat under the One Health framework.