Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Molecular characteristics of chromosome-mediated colistin resistance in foodborne Salmonella isolates in China

OBJECTIVE

To determine the molecular characteristics and mechanisms of colistin-resistant (COLr) Salmonella isolates from 1224 chicken samples in Shanghai, China, between January 2021 and January 2022.

METHODS

Antimicrobial susceptibility testing, site-directed mutagenesis, RT-qPCR, and lipid A analysis was conducted to investigate the mechanisms of colistin resistance in Salmonella.

RESULTS

A total of 268 Salmonella isolates were obtained from chicken samples and 41 isolates were resistant to colistin. The uncommon extensively antimicrobial-resistant Salmonella Muenster was the predominant serotype, accounting for 87.8% (36/41) of the COLr isolates. Most (95.1%, 39/41) of the COLr isolates exhibited amino acid substitutions in the PmrAB. Ten different substitutions in PmrAB were identified, with Val161Gly (n = 14) and Gly206Glu (n = 10) in PmrB being the most prevalent. Four substitutions (Thr147Ser, Phe203Ser, Gly206Glu, and Asp250Tyr) in PmrB have not been reported before and were considered novel mutations. Additionally, it was demonstrated that these substitutions upregulated pmrE and pmrK expression, resulting in the production of L-Ara4N, which modified the lipid A and resulted in an 8-64-fold increase in the colistin MIC (2-8 mg/L). Finally, the deletion of pmrE or pmrK in mutants showed MIC values comparable to parental strains (0.25 mg/L), which suggested that colistin resistance may be conferred through the pmrE and pmrK pathways.

CONCLUSIONS

These findings illustrate the complex molecular mechanisms of colistin resistance in Salmonella, and the amino acid substitutions in PmrAB are the predominant molecular mechanisms. It is essential to implement monitoring and control measures for colistin resistance.

The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments

This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes (n = 10) than the pristine site (n = 4). Metal and multicompound resistance was more frequent in rural (14%) compared to urban samples (5%). Pristine samples lacked multidrug and multicompound resistance and had lower resistance to aminoglycosides and the MLS group. Multiresistance was evidenced by copper and aminocoumarin resistance in rural samples and aminoglycoside and mercury resistance in Pseudomonas in all environments. These findings highlight the impact of human activities on AMR and MR spread, emphasizing the need for environmental monitoring and management.

IMPORTANCE

Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.

Environmental fate of antibiotic resistance genes in livestock farming

As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.

A comprehensive One Health investigation of erythromycin and quinupristin/dalfopristin resistant Enterococcus spp. in Iran

Enterococci, flagged by the WHO as a rising cause of antibiotic-resistant infections, make surveillance crucial to control resistant strains. We investigated the resistance to linezolid, quinupristin/dalfopristin (Q/D), and erythromycin in Enterococcus faecalis (n = 251) and Enterococcus faecium (n = 434) isolates collected from patients, healthy carriers, hospitals, poultry, livestock, and municipal wastewater in Ardabil, Iran. The isolates were tested for resistance using phenotypic and genotypic methods. Although none of the isolates were resistant to linezolid, 24.9% of E. faecium isolates were resistant to Q/D, particularly those from patients and poultry slaughterhouse wastewater effluent (P < 0.05). The Q/D resistance genes msrC and ermB were detected in 76.85 and 20.37% of E. faecium isolates, respectively. Erythromycin resistance was common in E. faecalis (51.8%) and E. faecium (37.5%), with no significant difference between sources. However, isolates from patients and livestock wastewater had higher erythromycin MICs. Erythromycin resistance genes, such as ermB, ermC, ermTR, and ermA, were found in 80.7, 41.2, 26.5, and 19% of E. faecium and 80.3, 51.6, 22.4, and 25.8% of E. faecalis isolates, respectively. In conclusion, linezolid is a viable treatment for enterococcal infections in Ardabil, but widespread erythromycin- and Q/D-resistant enterococci pose a public health risk.

Antibiotic Resistance Genes in Agricultural Soils: A Comprehensive Review of the Hidden Crisis and Exploring Control Strategies

This paper aims to review the sources, occurrence patterns, and potential risks of antibiotic resistance genes (ARGs) in agricultural soils and discuss strategies for their reduction. The pervasive utilization of antibiotics has led to the accumulation of ARGs in the soil. ARGs can be transferred among microorganisms via horizontal gene transfer, thereby increasing the likelihood of resistance dissemination and heightening the threat to public health. In this study, we propose that physical, chemical, and bioremediation approaches, namely electrokinetic remediation, advanced oxidation, and biochar application, can effectively decrease the abundance of ARGs in the soil. This study also highlights the significance of various control measures, such as establishing a strict regulatory mechanism for veterinary drugs, setting standards for the control of ARGs in organic fertilizers, and conducting technical guidance and on-farm soil monitoring to reduce the environmental spread of ARGs and protect public health.

Distribution and risk assessment of antibiotic resistance genes in swine farm wastewater and its surrounding environments: from soil to water

Livestock farms are important reservoirs of antibiotic resistance genes (ARGs). However, how wastewater irrigation from swine farms affects the surrounding environments, especially water bodies, is not fully understood. In this study, the occurrence pattern and potential risk of ARGs and mobile gene elements (MGEs) in a biogas slurry from a large-scale swine farm and its surrounding environments were investigated. Genes conferring resistance to tetracycline, sulfonamide, and multidrugs were found to be predominant in the biogas slurry, while sulfonamide and multidrug resistance genes exhibited the highest abundance in the surrounding environments. Overall, the total relative abundance of ARGs in the biogas slurry was 1.4-7 fold higher than that in the surrounding environments. PCA revealed the cluster pattern of samples based on sample types and a better correlation between swine farm wastewater and groundwater. A higher abundance of ARGs was found in groundwater farther away from the swine farm than that in nearby groundwater and surface water. Correlation analysis indicated that ARGs had a significant positive correlation with MGEs at each sampling site. The most abundant MGE IS6100 may mediate the horizontal transfer of lnuA from the swine farm to nearby groundwater. Considering the abundance, mobility, host pathogenicity, and the co-occurrence patterns with MGEs of ARGs, nine high-risk ARGs, namely, aadA2, aadA17, aac (6')-Ib, tetX, tetG, tetM, oprJ, sul1, and ermF, were screened in the environment. Our results indicated that the swine farm wastewater had long-term effects on the surrounding surface water and groundwater and that MGEs can serve as a medium that contributes to the widespread distribution of various ARGs. This study provides a theoretical basis for the risk assessment of ARGs in farms and the reuse of farm wastewater.

Vermicomposting significantly reduced antibiotic resistance genes in cow manure even under high tetracycline concentrations

Minimizing antibiotic resistance genes (ARGs) in livestock manure is crucial for curbing ARG dissemination. Vermicomposting can eliminate ARGs, but the effect of residual antibiotics on its reduction efficacy remains unclear. Herein, Eisenia foetida was employed to convert cow manure with varying concentrations of tetracycline (i.e., 0, 10, 100 mg/kg), aiming to explore the impact of tetracycline on ARG fate during vermicomposting for 35 days. Results showed that the total ARG abundance in vermicomposting (0.05 copies/16S rRNA copies) was significantly lower than that in natural composting (0.06 copies/16S rRNA copies) (p < 0.05). Notably, exposure to tetracycline increased total ARG abundance (p < 0.05) and stimulated microbial succession during vermicomposting, with some ARGs increasing and others decreasing. But ARGs removal in vermicomposting was still higher even under tetracycline stress than that in natural composting. Overall, vermicomposting is an effective method for reducing ARGs in cow manure even at high tetracycline levels.

Oxygen vacancy-dependent synergistic disinfection of antibiotic-resistant bacteria by BiOBr nanoflower induced H2O2 activation

Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) pose a significant threat to both ecosystems and human health. Owing to the excellent catalytic activity, eco-safety, and convenience for defect engineering, BiOBr with oxygen vacancies (OVs) of different density thus were fabricated and employed to activate H2O2 for ARB disinfection/ARGs degradation in present study. We found that BiOBr with OVs of appropriate density induced via ethanol reduction (BOB-E) could effectively activate H2O2, achieving excellent ARB disinfection and ARGs degradation efficiency. Moreover, this disinfection system exhibited remarkable tolerance to complex water environments and actual water conditions. In-situ characterization and theoretical calculations revealed that OVs in BOB-E could effectively capture and activate aqueous H2O2 into HO· and O2·-. The generated reactive oxygen species combined with electron transfer could damage the cell membrane system and degrade genetic materials of ARB, leading to effective disinfection. The impressive reusability, high performance achieved in two immobilized reaction systems (packed column and baffled ditch reactor), excellent degradation of emerging organic pollutants supported the feasibility of BOB-E/H2O2 system towards practical water decontamination. Overall, this study not only provides insights into fabrication of bismuth-based catalysts for efficient ARB disinfection/ARGs degradation via OVs regulation, but also paves the way for their practical applications.

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.

Effects of sulfamethoxazole and copper on the natural microbial community from a fertilized soil

Cattle manure or its digestate, which often contains antibiotic residues, can be used as an organic fertilizer and copper (Cu) as a fungicide in agriculture. Consequently, both antibiotics and Cu are considered soil contaminants. In this work, microcosms were performed with soil amended with either manure or digestate with Cu and an antibiotic (sulfamethoxazole, SMX) co-presence and the planting of Lactuca sativa. After the addition of the organic amendments, a prompt increase in the microbial activity and at the same time of the sul1 and intI1 genes was observed, although ARGs generally decreased over time. In the amended and spiked microcosms, the microbial community was able to remove more than 99% of SMX in 36 days and the antibiotic did not bioaccumulate in the lettuce. Interestingly, where Cu and SMX were co-present, ARGs (particularly sul2) increased, showing how copper had a strong effect on resistance persistence in the soil. Copper also had a detrimental effect on the plant-microbiome system, affecting plant biomass and microbial activity in all conditions except in a digestate presence. When adding digestate microbial activity, biodiversity and lettuce biomass increased, with or without copper present. Not only did the microbial community favour plant growth, but lettuce also positively influenced its composition by increasing bacterial diversity and classes (e.g., Alphaproteobacteria) and genera (e.g., Bacillus), thus indicating a good-quality soil. KEY POINTS: • Cattle digestate promoted the highest microbial activity, diversity, and plant growth • Cattle digestate counteracted detrimental contaminant effects • Cu presence promoted antibiotic cross-resistance in soil.

Evaluation of virulence determinants and cell surface properties associated with biofilm formation in methicillin-resistant Staphylococcus aureus (MRSA) and extended spectrum beta-lactamase (ESBL) Escherichia coli from livestock and poultry origin

Antibiotic resistance poses a persistent threat to modern medicine due to the emergence of novel antibiotic-resistant strains. Therefore, a timely understanding of antibiotic resistance and the virulence biology of pathogenic bacteria, particularly those of public health significance, is crucial for implementing effective mitigation strategies. This study aimed to investigate the virulence profiles of ten S. aureus isolates (NDa to NDj) and ten E. coli isolates (ND1 to ND10) originating from livestock and poultry, and to assess how various cell surface properties and biofilm formation abilities influence antibiotic resistance phenotypes. Antibiotic resistance profiling through phenotypic (AST) and genotypic methods (PCR) confirmed that NDa to NDe were methicillin-resistant S. aureus (MRSA) and ND1 to ND5 were extended-spectrum β-lactamase (ESBL) producing E. coli isolates. Virulence properties such as hemolytic activity, coagulase activity, and nuclease activity were found to be independent of the antibiotic resistance phenotype in S. aureus. In contrast, biofilm formation phenotype was observed to influence antibiotic resistance phenotypes, with MRSA and ESBL E. coli isolates demonstrating higher biofilm formation potency. Chemical and enzymatic analysis of S. aureus and E. coli biofilms revealed proteins and polysaccharides as major components, followed by nucleic acids. Furthermore, cell surface properties such as auto-aggregation and hydrophobicity were notably higher in isolates with strong to medium biofilm-forming capabilities (ESBL and MRSA isolates), corroborated by genomic confirmation of various genes associated with biofilm, adhesion, and colonization. In conclusion, this study highlights that surface hydrophobicity and biofilm formation ability of MRSA (NDa to NDe) and ESBL E. coli (ND1 to ND5) isolates may influence antibiotic resistance phenotypes.

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.

Dissemination of antimicrobial resistance in agricultural ecosystems following irrigation with treated municipal wastewater

The spread of antimicrobial resistance (AMR) in agricultural systems via irrigation water is a serious public health issue as it can be transmitted to humans through the food chain. Therefore, understanding the dissemination routes of antibiotic resistance genes (ARGs) in agricultural systems is crucial for the assessment of health risks associated with eating fresh vegetables such as spinach and radish irrigated with treated municipal wastewater (TMW). In this study, we investigated the bacterial community structure and resistome in the soil-plant-earthworm continuum after irrigation of spinach and radish with TMW containing the antibiotics trimethoprim (TMP), sulfamethoxazole (SMZ), and sulfapyridine (SPD) using 16S rRNA gene sequencing and high throughput quantitative PCR (HT-qPCR). The study was conducted in two phases: Phase I involved eight weeks of spinach and radish production using TMW for irrigation, whereas Phase II entailed three weeks of earthworm exposure to contaminated plant material obtained in Phase I. The 16S data indicated that the rhizosphere bacterial community composition and structure were more resilient to antibiotic residuals in the irrigated water, with radish showing less susceptibility than spinach than those of bulk soils. The HT-qPCR analysis revealed that a total of 271 ARGs (out of 285) and 9 mobile genetic elements (MGEs) (out of 10) were detected in all samples. Higher diversity and abundance of ARGs were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. However, compared to spinach, radish ARG dynamics in the soil biome were more stable due to the change of antibiotic introduction to the soil. At the class level, multi-drug resistance (MDR) class was altered significantly by the presence of antibiotics in irrigation water. Compared to earthworm fecal samples, their corresponding soil environments showed a higher number of detected ARGs, suggesting that earthworms could play a role in reducing ARG dissemination in the soil environments. These findings will not only provide insight into the dissemination of ARGs in agricultural environments due to antibiotic residuals in irrigated water but could help understand the potential human health risks associated with ARGs.

From Herd Health to Public Health: Digital Tools for Combating Antibiotic Resistance in Dairy Farms

The emergence of antimicrobial resistance (AMR) is a significant threat to global food security, human health, and the future of livestock production. Higher rates of antimicrobial use in dairy farming and the sheer lack of new antimicrobials available for use focused attention on the question of how the dairy production sector contributed to the development of AMR and paved the path toward taking action to curtail it on the targeted type of farms. This paper aims to provide an introduction to a phenomenon that has gained considerable attention in the recent past due to its ever-increasing impact, the use of antimicrobial drugs, the emergence of antimicrobial resistance (AMR) on dairy farms, and seeks to discuss the possibilities of approaches such as digital health monitoring and precision livestock farming. Using sensors, data, knowledge, automation, etc., digital health monitoring, as well as Precision Livestock Farming (PLF), is expected to enhance health control and minimize disease and antimicrobial usage. The work presents a literature review on the current status and trends of AMR in dairy farms, an understanding of the concept of digital health monitoring and PLF, and the presentation and usefulness of digital health monitoring and PLF in preventing AMR. The study also analyses the strengths and weaknesses of adopting and incorporating digital technologies and artificial intelligence for dairy farming and presents areas for further study and level of use.

The impacts of animal agriculture on One Health-Bacterial zoonosis, antimicrobial resistance, and beyond

The industrialization of animal agriculture has undoubtedly contributed to the improvement of human well-being by increasing the efficiency of food animal production. At the same time, it has also drastically impacted the natural environment and human society. The One Health initiative emphasizes the interdependency of the health of ecosystems, animals, and humans. In this paper, we discuss some of the most profound consequences of animal agriculture practices from a One Health perspective. More specifically, we focus on impacts to host-microbe interactions by elaborating on how modern animal agriculture affects zoonotic infections, specifically those of bacterial origin, and the concomitant emergence of antimicrobial resistance (AMR). A key question underlying these deeply interconnected issues is how to better prevent, monitor, and manage infections in animal agriculture. To address this, we outline approaches to mitigate the impacts of agricultural bacterial zoonoses and AMR, including the development of novel treatments as well as non-drug approaches comprising integrated surveillance programs and policy and education regarding agricultural practices and antimicrobial stewardship. Finally, we touch upon additional major environmental and health factors impacted by animal agriculture within the One Health context, including animal welfare, food security, food safety, and climate change. Charting how these issues are interwoven to comprise the complex web of animal agriculture's broad impacts on One Health will allow for the development of concerted, multidisciplinary interventions which are truly necessary to tackle these issues from a One Health perspective.

Multidrug-resistant Escherichia coli strains isolated from swine manure biofertilizer in Brazil

Escherichia coli is one of the key bacteria responsible for a variety of diseases in humans and livestock-associated infections around the globe. It is the leading cause of mortality in neonatal and weaned piglets in pig husbandry, causing diarrhea and significant harm to the industry. Furthermore, the frequent and intensive use of antimicrobials for the prevention of diseases, particularly gastrointestinal diseases, may promote the selection of multidrug-resistant (MDR) strains. These resistant genotypes can be transmitted through the excrement of animals, including swine. It is common practice to use porcine manure processed by biodigesters as fertilizer. This study aimed to examine the antimicrobial susceptibility, the presence of virulence genes frequently associated with pathotypes of intestinal pathogenic E. coli (InPEC), and antimicrobial resistance genes (ARGs) of 28 E. coli isolates collected from swine manure fertilizers. In addition, the enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) technique was used to investigate the genetic relationship among the strains. Using disk diffusion, the antimicrobial susceptibility profiles of the strains were determined. Using polymerase chain reaction (PCR), 14 distinct virulence genes associated with the most prevalent diarrhea and intestinal pathogenic E. coli (DEC/InPEC) and five ARGs were analyzed. All isolates tested positive for multidrug resistance. There was no detection of any of the 14 virulence genes associated with InPECs, indicating the presence of an avirulent commensal microbiota. Molecular classification by ERIC-PCR revealed that the majority of isolates (27 isolates) coalesced into a larger cluster with a genetic similarity of 47.7%; only one strain did not cluster in this cluster, indicating a high level of genetic diversity among the analyzed isolates. Thus, it is of the utmost importance to conduct epidemiological surveillance of animal breeding facilities in order to determine their microbiota and formulate plans to reduce the use of antimicrobials and improve animal welfare.

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Other Antimicrobial-Resistant Gram-Negative Pathogens Isolated from Bovine Mastitis: A One Health Perspective

Antimicrobial resistance (AMR) poses an imminent threat to global public health, driven in part by the widespread use of antimicrobials in both humans and animals. Within the dairy cattle industry, Gram-negative coliforms such as Escherichia coli and Klebsiella pneumoniae stand out as major causative agents of clinical mastitis. These same bacterial species are frequently associated with severe infections in humans, including bloodstream and urinary tract infections, and contribute significantly to the alarming surge in antimicrobial-resistant bacterial infections worldwide. Additionally, mastitis-causing coliforms often carry AMR genes akin to those found in hospital-acquired strains, notably the extended-spectrum beta-lactamase genes. This raises concerns regarding the potential transmission of resistant bacteria and AMR from mastitis cases in dairy cattle to humans. In this narrative review, we explore the distinctive characteristics of antimicrobial-resistant E. coli and Klebsiella spp. strains implicated in clinical mastitis and human infections. We focus on the molecular mechanisms underlying AMR in these bacterial populations and critically evaluate the potential for interspecies transmission. Despite some degree of similarity observed in sequence types and mobile genetic elements between strains found in humans and cows, the existing literature does not provide conclusive evidence to assert that coliforms responsible for mastitis in cows pose a direct threat to human health. Finally, we also scrutinize the existing literature, identifying gaps and limitations, and propose avenues for future research to address these pressing challenges comprehensively.

A systematic review of antibiotic resistance driven by metal-based nanoparticles: Mechanisms and a call for risk mitigation

Elevations in antibiotic resistance genes (ARGs) are due not only to the antibiotic burden, but also to numerous environmental pressures (e.g., pesticides, metal ions, or psychotropic pharmaceuticals), which have led to an international public health emergency. Metal-based nanoparticles (MNPs) poison bacteria while propelling nanoresistance at ambient or sub-lethal concentrations, acting as a wide spectrum germicidal agent. Awareness of MNPs driven antibiotic resistance has created a surge of investigation into the molecule mechanisms of evolving and spreading environmental antibiotic resistome. Co-occurrence of MNPs resistance and antibiotic resistance emerge in environmental pathogens and benign microbes may entail a crucial outcome for human health. In this review we expound on the systematic mechanism of ARGs proliferation under the stress of MNPs, including reactive oxygen species (ROS) induced mutation, horizontal gene transfer (HGT) relevant genes regulation, nano-property, quorum sensing, and biofilm formation and highlighting on the momentous contribution of nanoparticle released ion. As antibiotic resistance pattern alteration is closely knit with the mediate activation of nanoparticle in water, soil, manure, or sludge habitats, we have proposed a virulence and evolution based antibiotic resistance risk assessment strategy for MNP contaminated areas and discussed practicable approaches that call for risk management in critical environmental compartments.

Advanced treatment of antibiotic-polluted wastewater by a consortium composed of bacteria and mixed cyanobacteria

This study constructed a cyanobacteria-bacteria consortium using a mixture of non-toxic cyanobacteria (Synechococcus sp. and Chroococcus sp.) immobilized in calcium alginate and native bacteria in wastewater. The consortium was used for the advanced treatment of sulfamethoxazole-polluted wastewater and the production of cyanobacterial lipid. Mixed cyanobacteria increased the abundances of denitrifying bacteria and phosphorus-accumulating bacteria as well as stimulated various functional enzymes in the wastewater bacterial community, which efficiently removed 70.01-71.86% of TN, 91.45-97.04% of TP and 70.72-76.85% of COD from the wastewater. The removal efficiency of 55.29-69.90% for sulfamethoxazole was mainly attributed to the upregulation of genes encoding oxidases, reductases, oxidoreductases and transferases in two cyanobacterial species as well as the increased abundances of Stenotrophomonas, Sediminibacterium, Arenimonas, Novosphingobium, Flavobacterium and Hydrogenophaga in wastewater bacterial community. Transcriptomic responses proved that mixed cyanobacteria presented an elevated lipid productivity of 33.90 mg/L/day as an adaptive stress response to sulfamethoxazole. Sediminibacterium, Flavobacterium and Exiguobacterium in the wastewater bacterial community may also promote cyanobacterial lipid synthesis through symbiosis. Results of this study proved that the mixed cyanobacteria-bacteria consortium was a promising approach for advanced wastewater treatment coupled to cyanobacterial lipid production.

The bacterial and archaeal communities of flies, manure, lagoons, and troughs at a working dairy

Background

Fundamental investigations into the location, load, and persistence of microbes, whether beneficial or detrimental, are scarce. Many questions about the retention and survival of microbes on various surfaces, as well as the load necessary for spread, exist. To answer these questions, we must know more about where to find various microbes and in what concentrations, the composition of the microbial communities, and the extent of dissemination between various elements. This study investigated the diversity, composition, and relative abundance of the communities associated with manure, lagoons, troughs, house flies, and stable flies present at a dairy, implementing two different free-stall management systems: flow-through and cross-vent. Shotgun metagenomics at the community level was used to compare the microbiomes within the dairy, allowing confident interpretation at the species level.

Results

The results showed that there were significant difference in microbial composition between not only each of the dairy elements but also management styles. The primary exceptions were the microbiomes of the house fly and the stable fly. Their compositions heavily overlapped with one another, but interestingly, not with the other components sampled. Additionally, both species of flies carried more pathogens than the other elements of the dairy, indicating that they may not share these organisms with the other components, or that the environments offered by the other components are unsatisfactory for the survival of some pathogens..

Conclusion

The lack of overlapping pathogen profiles suggests a lack of transfer from flies to other dairy elements. Dairy health data, showing a low incidence of disease, suggests minimal sharing of bacteria by the flies at a level required for infection, given the health program of this dairy. While flies did carry a multitude of pathogenic bacteria, the mere presence of the bacteria associated with the flies did not necessarily translate into high risk leading to morbidity and mortality at this dairy. Thus, using flies as the sole sentinel of dairy health may not be appropriate for all bacterial pathogens or dairies.

Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment

Treated municipal wastewater (TMW) can provide a reliable source of irrigation water for crops, which is especially important in arid areas where water resources are limited or prone to drought. Nonetheless, TMW may contain residual antibiotics, potentially exposing the crops to these substances. The goal of this study was to investigate the dissemination of antibiotics resistance genes (ARGs) in the soil-plant-earthworm continuum after irrigation of spinach and radish plants with TMW containing trimethoprim, sulfamethoxazole, and sulfapyridine in a greenhouse experiment, followed by feeding of earthworms with harvested plant materials. Our results showed that antibiotic resistance genes (ARGs) were enriched in the soil-plant-earthworm microbiomes irrigated with TMW and TMW spiked with higher concentrations of antibiotics. The number of ARGs and antibiotic-resistant bacteria (ARB) enrichment varied with plant type, with spinach harboring a significantly higher amount of ARGs and ARB compared to radish. Our data showed that bulk and rhizosphere soils of spinach and radish plants irrigated with MilliQ water, TMW, TMW10, or TMW100 had significant differences in bacterial community (p < 0.001), ARG (p < 0.001), and virulence factor gene (VFG) (p < 0.001) diversities. The abundance of ARGs significantly decreased from bulk soil to rhizosphere to phyllosphere and endosphere. Using metagenome assembled genomes (MAGs), we recovered many bacterial MAGs and a near complete genome (>90 %) of bacterial MAG of genus Leclercia adecarboxylata B from the fecal microbiome of earthworm that was fed harvested radish tubers and spinach leaves grown on TMW10 irrigated waters, and this bacterium has been shown to be an emerging pathogen causing infection in immunocompromised patients that may lead to health complications and death. Therefore, crops irrigated with TMW containing residual antibiotics and ARGs may lead to increased incidences of enrichment of ARB in the soil-plant-earthworm continuum.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Efficient and effective immobilization of tetracycline and copper from wastewater by zero-valent iron fabricated hydrochar derived from walnut peel

Antibiotics and heavy metals often coexist as non-point-source contaminants in wastewater and their quite contrary physiochemical properties make their co-removal processes challenging. In this work, a bifunctional zero-valent iron-modified hydrochar derived from walnut peel (MWPHC) was synthesized, which was then applied for the simultaneous removal of tetracycline (TC) and Cu(II) from wastewater. Based on the characterizations, Fe0 species were successfully distributed on the surface of the walnut peel substrates. The TC and Cu(II) could be synergistically immobilized, and bridging effects were observed between them, and MWPHC exhibited excellent ability on the simultaneous removal of TC (qmax = 433.59 mg/g) and Cu(II) (qmax = 586.25 mg/g). Furthermore, the engineering feasibility of the MWPHC was evaluated using column and regeneration experiments. These results shed light on the tailored MWPHC as an environmental functional material for pollution control of co-existing antibiotic and heavy metal contaminants in agro-industrial wastewater.

Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary

To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.

A Comprehensive Study of Historical Detection Data for Pathogen Isolates from U.S. Cattle

Foodborne pathogens pose substantial health hazards and result in considerable economic losses in the U.S. Fortunately, the National Center for Biotechnology Information Pathogen Detection Isolates Browser (NPDIB) provides valuable access to antimicrobial resistance (AMR) genes and antimicrobial assay data. This study aimed to conduct the first comprehensive investigation of AMR genes in pathogens isolated from U.S. cattle over the past decade, driven by the urgent need to address the dangers of AMR specifically originating in pathogens isolated from U.S. cattle. In this study, around 28,000 pathogen isolate samples were extracted from the NPDIB and then analyzed using multivariate statistical methods, mainly principal component analysis (PCA) and hierarchical clustering (H-clustering). These approaches were necessary due to the high dimensions of the raw data. Specifically, PCA was utilized to reduce the dimensions of the data, converting it to a two-dimensional space, and H-clustering was used to better identify the differences among data points. The findings from this work highlighted Salmonella enterica and Escherichia coli as the predominant pathogens among the isolates, with E. coli being the more concerning pathogen due to its increasing prevalence in recent years. Moreover, tetracycline was observed as the most commonly resistant antimicrobial, with the resistance genes mdsA, mdsB, mdtM, blaEC, and acrF being the most prevalent in pathogen isolates from U.S. cattle. The occurrence of mdtM, blaEC, acrF, and glpT_E448k showed an increase in pathogens isolated from U.S. cattle in recent years. Furthermore, based on the data collected for the locations of AMR cases, Texas, California, and Nebraska were the major areas carrying major AMR genes or antimicrobials with detected resistance. The results from this study provide potential directions for targeted interventions to mitigate pathogens' antimicrobial resistance in U.S. cattle.

MXene@Au based electrochemical biosensor with pretreatment by magnetic nanoparticles for determination of MRSA from clinical samples

Pathogenic bacteria are associated with high morbidity rates and present significant diagnostic challenges in terms of rapid detection. This study introduces a magnetic separation-based electrochemical biosensor for the detection of Methicillin-resistant Staphylococcus aureus (MRSA). Vancomycin (Van) was used to modify on the surface of polyethyleneimine (PEI) mediated MBs (MBs-PEI-Van) for separation and enrichment of MRSA. The MBs-PEI-Van shown a satisfactory stability and applicability with capture effective (CE) > 85% in both PBS and cerebrospinal fluid (CSF) samples. MXene@Au with controllable size of AuNPs was synthesized by a self-reduction method and employed to modify the glassy carbon electrode (GCE). Immunoglobulin G (IgG) was loaded onto the modified electrode to immobilize MRSA, and ferroceneboronic acid (Fc-BA) was used as a probe for quantitative determination. The differential pulse voltammetry (DPV) current was plotted against the concentration of MRSA from 3.8 × 101 to 3.8 × 107 CFU/mL with a limit of detection (LOD) of 3.8 × 101 CFU/mL. In addition, MRSA was successfully detected in spiked CSF samples with satisfactory recoveries (94.35-107.81 %) and validation results (RSD < 11 %). Overall, this study presents a promising method for the detection of MRSA, with the potential to be further developed into a universal pathogen detection method.

Antimicrobial activity of α-mangostin against Staphylococcus species from companion animals in vitro and therapeutic potential of α-mangostin in skin diseases caused by S. pseudintermedius

Antimicrobial resistance in Staphylococcus species from companion animals is becoming increasingly prevalent worldwide. S. pseudintermedius is a leading cause of skin infections in companion animals. α-mangostin (α-MG) exhibits various pharmacological activities, including antimicrobial activity against G (+) bacteria. This study investigated the antimicrobial activity of α-MG against clinical isolates of Staphylococcus species from companion animals and assessed the therapeutic potential of α-MG in skin diseases induced by S. pseudintermedius in a murine model. Furthermore, the action mechanisms of α-MG against S. pseudintermedius were investigated. α-MG exhibited antimicrobial activity against clinical isolates of five different Staphylococcus species from skin diseases of companion animals in vitro, but not G (-) bacteria. α-MG specifically interacted with the major histocompatibility complex II analogous protein (MAP) domain-containing protein located in the cytoplasmic membrane of S. pseudintermedius via hydroxyl groups at C-3 and C-6. Pretreatment of S. pseudintermedius with anti-MAP domain-containing protein polyclonal serum significantly reduced the antimicrobial activity of α-MG. The sub-minimum inhibitory concentration of α-MG differentially regulated 194 genes, especially metabolic pathway and virulence determinants, in S. pseudintermedius. α-MG in pluronic lecithin organogel significantly reduced the bacterial number, partially restored the epidermal barrier, and suppressed the expression of cytokine genes associated with pro-inflammatory, Th1, Th2, and Th17 in skin lesions induced by S. pseudintermedius in a murine model. Thus, α-MG is a potential therapeutic candidate for treating skin diseases caused by Staphylococcus species in companion animals.