Reservoir Of Antibiotic Resistance Genes Research Articles

Towards the definition of an antibiotic resistome signature in wastewater and downstream environments

Domestic wastewater is a significant reservoir of antibiotic resistance genes, which pose environmental and public health risks. We aimed to define an antibiotic resistome signature, represented by core genes, i.e., shared by ≥90% of the metagenomes of each of three conceptual environmental compartments – wastewater (influent, sludge, effluent), freshwater, and agricultural soil. The definition of resistome signatures would support the proposal of a framework for monitoring treatment efficacy and assessing the impact of treated wastewater discharge into the environment, such as freshwater and agricultural soil.Metagenomic data from 163 samples originating from wastewater (n=81), freshwater (n=58), and agricultural soils (n=24) across different regions (29 countries, 5 continents), were analysed regarding antibiotic resistance diversity, based on annotation against a database that merged CARD and ResFinder databases. The relative abundance of the total antibiotic resistance genes (corresponding to the ratio between the antibiotic resistance genes and total reads number) was not statistically different between raw and treated wastewater, being significantly higher than in freshwater or agricultural soils. The latter had the significantly lowest relative abundance of antibiotic resistance genes. Genes conferring resistance to aminoglycosides, beta-lactams, and tetracyclines were among the most abundant in wastewater environments, while multidrug resistance was equally distributed across all environments. The wastewater resistome signature included 27 antibiotic resistance genes that were detected in at least 90% of the wastewater resistomes, and that were not frequent in freshwater or agricultural soil resistomes. Among these were genes responsible for resistance to tetracyclines (n=8), macrolide-lincosamide-streptogramin B (n=7), aminoglycosides (n=4), beta-lactams (n=3), multidrug (n=2), sulphonamides (n=2), and polypeptides (n=1). This comprehensive assessment provides valuable insights into the dynamics of antibiotic resistance in urban wastewater systems and their potential ecological implications in diverse environmental settings. Furthermore, provides guidance for the implementation of One Health monitoring approaches.

Giant viruses as reservoirs of antibiotic resistance genes.

Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.

Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer

Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 108 to 1012 particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.

Distribution and community structure of antibiotic resistance genes in the Three Gorges Reservoir Area.

Antibiotic resistance genes (ARG) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes, and 6 resistance mechanisms were detected. The dominant ARG is the macB, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria. In this region, pH and NH4+ concentration were significantly negatively correlated with the relative abundance of most ARGs, while NO3- concentration and TN were significantly positively correlated with the relative abundance of most ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By studying the distribution of ARGs in the sediments of the Three Gorges Reservoir Area and the relationship between environmental factors and ARGs, we can more comprehensively understand the pollution status of ARGs in this area, and provide theoretical support for subsequent treatment.

Metagenomic insights into ecological risk of antibiotic resistome and mobilome in riverine plastisphere under impact of urbanization

Microplastics (MPs) are of increasing concern due to their role as reservoirs for antibiotic resistance genes (ARGs) and pathogens. To date, few studies have explored the influence of anthropogenic activities on ARGs and mobile genetic elements (MGEs) within various riverine MPs, in comparison to their natural counterparts. Here an in-situ incubation was conducted along heavily anthropogenically-impacted Houxi River to characterize the geographical pattern of antibiotic resistome, mobilome and pathogens inhabiting MPs- and leaf-biofilms. The metagenomics result showed a clear urbanization-driven profile in the distribution of ARGs, MGEs and pathogens, with their abundances sharply increasing 4.77 to 19.90 times from sparsely to densely populated regions. The significant correlation between human fecal marker crAssphage and ARG (R2 = 0.67, P=0.003) indicated the influence of anthropogenic activity on ARG proliferation in plastisphere and natural leaf surfaces. And mantel tests and random forest analysis revealed the impact of 17 socio-environmental factors, e.g., population density, antibiotic concentrations, and pore volume of materials, on the dissemination of ARGs. Partial least squares-path modeling further unveiled that intensifying human activities not only directly boosted ARGs abundance but also exerted a comparable indirect impact on ARGs propagation. Furthermore, the polyvinylchloride plastisphere created a pathogen-friendly habitat, harboring higher abundances of ARGs and MGEs, while polylactic acid are not likely to serve as vectors for pathogens in river, with a lower resistome risk score than that in leaf-biofilms. This study highlights the diverse ecological risks associated with the dissemination of ARGs and pathogens in varied MPs, offering insights for the policymaking of usage and control of plastics within urbanization.

Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China

Extraintestinal Pathogenic Escherichia coli (ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin E. coli strains. Additionally, 49 strains harbor toxins typical of enteric E. coli pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring fosA3, blaCTX-M-14, and mcr-1 genes between swine ExPEC and human-origin Salmonella enterica is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.

Research Progress of Antibiotic Resistance Genes Removal in Food Waste During Anaerobic Digestion

Food waste is one of the important reservoirs of antibiotic resistance genes （ARGs）, and its resource utilization has potential environmental risks. Anaerobic digestion （AD） technology can concurrently achieve resource recovery and ARGs removal, which is one of the popular resource technologies for food waste management. However, the removal efficiency of ARGs during the AD process is limited, and thus the safety of digestate for agricultural use is still questioned. Therefore, how to improve the performance of ARGs removal during the AD process is critical for efficient and environmentally friendly bioconversion of food waste. This study summarized the transmission pathways and mechanisms of ARGs in food waste； discussed the effects of different operation parameters on the transmission of ARGs in food waste during the AD process； described the research progress of exogenous addition of conductive materials, feedstock pretreatment, etc., strategies to enhance the removal of ARGs； and analyzed the migration regularity and removal mechanism of ARGs in food waste during the AD process, which mainly included microbial community structure evolution, mobile genetic element changes, and environmental factor changes. Finally, this study prospected the future improvement of methane yield and ARGs removal in the AD process of food waste based on the existing research.

Profiles of Antibiotic Resistance Genes in the Coastal Aquatic Environment of Xiamen City

The coastal areas and the adjacent islands are the hotspots of human economic and social activities, including urbanization, industrialization, and agricultural practices, which have profound impacts on the ecological environment of the coastal environment. Antibiotic resistance genes （ARGs）, as emerging contaminants, have become hot topics in water ecological security and public concern. However, the profiles of antibiotic resistome in the costal water remain largely unknown, impeding resistome risk assessment associated with coastal environments. In this study, the high-throughput quantitative PCR technique was used to investigate the abundance and distribution of ARGs in the coastal environment of Xiamen City. Combined with the 16S rDNA gene amplicon sequencing method, the structure and composition of the microbial community in a water environment were investigated, and the influencing factors and associated mechanism of ARGs in seawater were deeply explained. The results of this study showed that a total of 187 ARGs were detected in the coastal water environment, and the abundance level was up to 1.29×1010 copies·L-1. Multidrug resistance, aminoglycosides, and β lactamase resistance genes were the three main classes of antibiotic resistance genes in the water environment of the Xiamen coastal zone. On the whole, the profile of ARGs was of high abundance, great diversity, and common co-existence, and the coastal water environment was an important hot area and reservoir for antibiotic resistance genes. Twenty-two microbes, including Nautella, Candidatus, Tenacibaculum, Rubripirellula, and Woeseia, were potential carriers of the corresponding 16 antibiotic resistance genes. The mobile genetic elements （MGEs） and microbial community structure accounted for 93.9% of the variation in environmental resistance genes in water. Therefore, microbial community and its mobile genetic elements were the most important driving forces for the occurrence and evolution of ARGs in coastal waters. Based on the results, it is implied that the environmental antibiotic resistance genes in the waters near Xiamen Island have potential risks to water ecological security and human health and highlight the necessity for comprehensive surveillance of ARGs associated with microbial contamination in the coastal aquatic environment.

Decoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania

Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of blaOXA-23 and blaOXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.

Chlorinated organophosphorus flame retardants induce the propagation of antibiotic resistance genes in sludge fermentation systems: Insight of chromosomal mutation and microbial traits

Waste activated sludge (WAS) is a critical reservoir for antibiotic resistance genes (ARGs) due to the prevalent misuse of antibiotics. Horizontal gene transfer (HGT) is the primary mechanism for ARGs spread through mobile genetic elements (MGEs). However, the role of non-antibiotic organophosphorus flame retardants (Cl-OFRs) in ARG transmission in the WAS fermentation system remains unclear. This study examines the effects of tris(2-chloroethyl) phosphate (TCEP), a representative Cl-OFR, on ARG dynamics in WAS fermentation using molecular docking and metagenomic analysis. The results showed a 33.4 % increase in ARG abundance in the presence of TCEP. Interestingly, HGT did not appear to be the primary mechanism of ARG dissemination under TCEP stress, as evidenced by a 2.51 % decrease in MGE abundance. TCEP binds to sludge through hydrogen bonds with a binding energy of − 3.6 kJ/mol, leading to microbial damage and an increase in the proportion of non-viable cells. This interaction prompts a microbial shift toward Firmicutes with thick cell walls, which are significant ARG carriers. Additionally, TCEP induces chromosomal mutations through oxidative stress and the SOS response, contributing to ARG formation. Microorganisms also develop multidrug resistance mechanisms to expel TCEP and mitigate its toxicity. This study provides a comprehensive understanding of Cl-OFRs effects on the ARGs fates in WAS fermentation system and offers guidance for the safe and efficient treatment of Cl-OFRs and WAS.

Sludge biolysis pretreatment to reduce antibiotic resistance genes (ARGs): Insight into the relationship between potential ARGs hosts and BALOs' preferred prey

As an important reservoir of antibiotic resistance genes (ARGs), the sludge discharged from wastewater treatment plants is the key intermediate for ARG transport into the environment. Bdellovibrio-and-like organisms (BALOs) are predatory bacteria that are expected to attack antibiotic-resistant bacteria (ARB). In this study, the screened BALOs (C3 & D15) were mixed with the sludge for biolysis to achieve the satisfying removal efficiencies of six tet genes, two sul genes, and one mobile genetic element (intl 1). Among them, tet(Q) demonstrated the highest reduction rate in relative abundance at 87.3 ± 1.0 %, while tet(X) displayed the lowest of 11.7 ± 0.2 %. The microorganisms, including Longilinea, Methanobacterium, Acetobacterium, Sulfurimonas, allobaculum, Gaiella, AAP99, Ellin6067, Rhodoferax, Ferruginibacter and Thermomonas, were expected to play a dual role in the reduction of ARGs by serving as ARB and BALOs’ preferred prey. Meanwhile, BALOs consortium improved ARGs reduction efficiency via the expansion of the prey profile. Additionally, BALOs decreased the relative abundance of not only pathogens (Shinella, Rickettsia, Burkholderia, Acinetobacter, Aeromonas, Clostridium, Klebsiella and Pseudomonas), but also the ARGs' host pathogens (Mycobacterium, Plesiocystis, Burkholderia, and Bacteroides). Therefore, the application of BALOs for sludge biolysis are promising to decrease the sludge's public health risks via limiting the spread of ARGs and pathogens into the environment.

Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem.

Xylem serves as a conduit linking soil to the aboveground plant parts and facilitating the upward movement of microbes into leaves and fruits. Despite this potential, the composition of the xylem microbiome and its associated risks, including antibiotic resistance, are understudied. Here, we cultivated tomatoes and analyzed their xylem sap to assess the microbiome and antibiotic resistance profiles following treatment with sewage sludge. Our findings show that xylem microbes primarily originate from soil, albeit with reduced diversity in comparison to those of their soil microbiomes. Using single-cell Raman spectroscopy coupled with D2O labeling, we detected significantly higher metabolic activity in xylem microbes than in rhizosphere soil, with 87% of xylem microbes active compared to just 36% in the soil. Additionally, xylem was pinpointed as a reservoir for antibiotic resistance genes (ARGs), with their abundance being 2.4-6.9 times higher than in rhizosphere soil. Sludge addition dramatically increased the abundance of ARGs in xylem and also increased their mobility and host pathogenicity. Xylem represents a distinct ecological niche for microbes and is a significant reservoir for ARGs. These results could be used to manage the resistome in crops and improve food safety.

Spatial and Temporal Distribution of Antibiotic Resistance Genes in Different River Sediments in Typical Cities: A Case Study of Shijiazhuang

Rivers are important reservoirs of antibiotic resistance genes (ARGs). However, most current studies have focused on the temporal and spatial distribution, and data on the differences in the species and abundance of ARGs between urban and rural rivers is still lacking for certain areas. In view of this, two rural rivers and three urban rivers were selected in Shijiazhuang City. In both December 2020 and April 2021, sediments were collected at 15 sampling sites. Metagenomic sequencing technology was used to compare the differences in temporal-spatial variation for ARGs in sediments. The results showed that:① 162 and 79 ARGs were detected in urban (4 776 ±4 452) and rural rivers (1 043 ±632), respectively. The abundance and species of ARGs in urban rivers were higher than those in rural rivers. ② The relative abundances of sulfonamide (SAs,27 %), aminoglycoside (AGs,26 %), and multidrug (MDs,15 %) ARGs had the highest abundance in urban rivers, whereas the relative abundance of MDs ARGs was highest in rural rivers (65 %). On the whole, the complexity of ARGs in urban rivers was higher than that in rural rivers. ③ There was a significant positive correlation between SAs, AGs, MDs, tetracycline, phenicol, macrolides-lincosamids-streptogramins (MLS), β-lactams, and diaminopyrimidine ARGs in urban rivers (P < 0.01); however, there was a significant negative correlation between glycopeptide ARGs and all types of ARGs (P < 0.05 and P < 0.01). There was a significant positive correlation between MDs and SAs ARGs in rural rivers (P < 0.05), but there was a significant negative correlation between amino aminocoumarin, peptide, rifamycin, and fosfomycin ARGs (P < 0.05 and P < 0.01). ④ For the temporal variation in urban rivers, 162 ARGs (4 776 ±4 452) and 148 ARGs (5 673 ±5 626) were detected in December and April, respectively. For the temporal variation in rural rivers, 79 species (1 043 ±632) and 46 species (467 ±183) were detected in December and April, respectively. ⑤ RDA analysis results showed that the spatial-temporal distributions of ARGs in urban and rural rivers were different. Correlation analysis showed that the ARGs in urban rivers were significantly correlated with the number of industrial enterprises, whereas the ARGs in rural rivers were significantly correlated with the output value of animal husbandry. In general, this study identified the main influencing factors for ARGs in different rivers and provided data support for ARGs risk management in different rivers.

Multidrug resistance profile in Lactobacillus delbrueckii: a food industry species with probiotic properties.

Lactobacillus delbrueckii, a widely used lactic acid bacterium in the food industry, has been studied for its probiotic properties and reservoir of antibiotic-resistant genes, raising safety concerns for probiotic formulations and fermented products. This review consolidates findings from 60 articles published between 2012 and 2023, focusing on the global antibiotic resistance profile and associated genetic factors in L. delbrueckii strains. Resistance to aminoglycosides, particularly streptomycin, kanamycin, and gentamicin, as well as resistance to glycopeptides (vancomycin), fluoroquinolones (ciprofloxacin), and tetracyclines was predominant. Notably, although resistance genes have been identified, they have not been linked to mobile genetic elements, reducing the risk of dissemination. However, a significant limitation is the insufficient exploration of responsible genes or mobile elements in 80% of studies, hindering safety assessments. Additionally, most articles originated from Asian and Middle Eastern countries, with strains often isolated from fermented dairy foods. Therefore, these findings underscore the necessity for comprehensive analyses of new strains of L. delbrueckii for potential industrial and biotherapeutic applications and in combating the rise of antibiotic-resistant pathogens.

River waters in Greece: A reservoir for clinically relevant extended-spectrum-β-lactamases-producing Escherichia coli

In the current study, the genotypic characteristics such as antimicrobial resistance and virulence genes, and plasmid replicons and phenotypic characteristics such as biofilm formation and antimicrobial resistance of 87 extended-spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-Ec) isolated from 7 water bodies in northern Greece were investigated. Our data show a high prevalence (60.0 %) of ESBL-Ec in surface waters that exhibit high genetic diversity, suggesting multiple sources of their transmission into the aquatic environment. When evaluating the antimicrobial resistance of isolates, wide variation in their resistance profiles has been detected, with all isolates being multi-drug resistant (MDR). Regarding biofilm formation capacity and phylogenetic groups, the majority (54.0 %, 47/87) of ESBL-Ec were classified as no biofilm producers mainly assigned to phylogroup A (35.6 %; 31/87), followed by B2 (26.5 %; 23/87). PCR screening showed that a high proportion of the isolates tested positive for the blaCTX-M-1 group genes (69 %, 60/87), followed by blaTEM (55.2 %, 48/87), blaOXA (25.3 %, 22/87) and blaCTX-M-9 (17.2 %, 15/87). A subset of 28 ESBL-Ec strains was further investigated by applying whole genome sequencing (WGS), and among them, certain clinically significant sequence types were identified, such as ST131 and ST10. The corresponding in silico analysis predicted all these isolates as human pathogens, while a significant proportion of WGS-ESBL-Ec were assigned to extraintestinal pathogenic E. coli (ExPEC; 32.1 %), and urinary pathogenic E. coli (UPEC; 28.6 %) pathotypes. Comparative phylogenetic analysis, showed that the genomes of the ST131-O25:H4-H30 isolates are genetically linked to the human clinical strains. Here, we report for the first time the detection of a plasmid-mediated mobile colistin resistance gene in ESBL-Ec in Greece isolated from an environmental source. Overall, this study underlines the role of surface waters as a reservoir for antibiotic resistance genes and for presumptive pathogenic ESBL-Ec.

Antibiotic resistance of Escherichia coli isolated from food and clinical environment in China from 2001 to 2020

Antibiotics are widely used in China's aquaculture, agricultural, and clinical settings and can lead to antibiotic resistance in various pathogens. Although the pooled prevalence estimate (PPE) and antibiotic resistance of Escherichia coli (E. coli) in food and clinical settings has been extensively studied, a comprehensive analysis of the published literature is lacking. We conducted a comprehensive search for research indicators for 2001–2020 in eight major Chinese and English literature databases. Antibiotic PPE and resistance trends of 5933 and 29,451 E. coli isolates were screened and analysed in 35 food studies (total 1821) and 62 clinical studies (total 5159). E. coli strains derived from food had the highest antibiotic resistance rate to tetracycline (TET, 71.3 %), followed by trimethoprim-sulfamethoxazole (SXT, 62.5 %) and cefazolin (CFZ, 36.2 %). E. coli strains isolated from clinical environments were highly resistant to piperacillin (PIP, 71.7 %), TET (68.3 %) and CFZ (60.9 %), consistent with foodborne E. coli drug resistance patterns. E. coli strains isolated from food and clinical samples collected in laboratories carry multiple antibiotic resistance genes (ARGs), such as blaTEM, gryA, gryB, sul1, and tetA, making E. coli a reservoir of ARGs. This study highlights the presence of drug-resistant E. coli pathogens and ARGs in food and clinical environments.

Deciphering the pathogenic risks of microplastics as emerging particulate organic matter in aquatic ecosystem

Microplastics are accumulating rapidly in aquatic ecosystems, providing habitats for pathogens and vectors for antibiotic resistance genes (ARGs), potentially increasing pathogenic risks. However, few studies have considered microplastics as particulate organic matter (POM) to elucidate their pathogenic risks and underlying mechanisms. Here, we performed microcosm experiments with microplastics and natural POM (leaves, algae, soil), thoroughly investigating their distinct effects on the community compositions, functional profiles, opportunistic pathogens, and ARGs in Particle-Associated (PA) and Free-Living (FL) bacterial communities. We found that both microplastics and leaves have comparable impacts on microbial community structures and functions, enriching opportunistic pathogens and ARGs, which may pose potential environmental risks. These effects are likely driven by their influences on water properties, including dissolved organic carbon, nitrate, DO, and pH. However, microplastics uniquely promoted pathogens as keystone species and further amplified their capacity as hosts for ARGs, potentially posing a higher pathogenic risk than natural POM. Our research also emphasized the importance of considering both PA and FL bacteria when assessing microplastic impacts, as they exhibited different responses. Overall, our study elucidates the role and underlying mechanism of microplastics as an emerging POM in intensifying pathogenic risks of aquatic ecosystems in comparison with conventional natural POM.

Commensal bacteria in raw milk, the reservoirs for antibiotic resistance genes during cold chain transportation

The emergence and prevalence of antibiotic resistance genes (ARGs) in food pose a great threat to public health and have attracted globally attention. Shotgun metagenomics sequencing is widely used to characterize ARGs in the environment. However, the distribution, co-occurrence patterns, and host information of ARGs in raw milk to the cold chain transportation duration with shotgun metagenomics sequencing, are not fully understood in China. In this study, species annotation and ARG annotation were performed on 40 raw milk samples collected from Beijing (BJ), Hebei (HB), Inner Mongolia (NMG), Shanghai (SH), and Guangdong (GD) using shotgun sequencing based on the Illumina platform. A total of 4731 bacterial species were annotated, of which 37 were dominant (relative abundance >1%). And also, 259 ARGs were annotated, corresponding to 69 kinds of antibiotic resistance. The NMG samples, which had the lowest bacterial community richness and bacterial diversity, were annotated with the highest number of ARGs, revealing the potential risk of bacterial resistance in NMG samples. Spearman correlation analysis and network analysis were showed that the probable bacterial hosts of multiple highly abundant ARGs (MacB and VanRC) in samples from provinces except for the BJ samples were Pseudomonas and Serratia, rather than conventionally known foodborne pathogens. It is noteworthy that the relative abundance of Pseudomonas fluorescens conformed to the Allometricl function with the cold chain transportation duration, the finding that could provide a reference for assessing the freshness and the risk assessment of antibiotic resistance genes of raw milk. In addition, the dairy industry should be aware of the risk of ARGs transferring from highly abundant commensal bacteria. Raw milk for transportation by cold chain, higher abundance of Pseudomonas in some samples should be kept in mind, and the roles of ARGs carried by these bacteria should be further investigated.

Critical insights into the Hormesis of antibiotic resistome in saline soil: Implications from salinity regulation

Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.

Metagenomic profiles of the antimicrobial resistance in traditional Chinese fermented meat products: Core resistome and co-occurrence patterns

Antimicrobial resistance (AMR) poses a significant challenge to global health, and the presence of antibiotic resistance genes (ARGs) in food poses a potential threat to public health. Traditional Chinese fermented meat products (FMPs) are highly favored because of their unique flavors and cultural value. However, microbial safety and the potential distribution and composition of AMR in these products remain unclear. In this study, a comprehensive analysis of bacterial composition and antibiotic-resistant populations in 216 samples of traditional fermented meat products from different regions of China was conducted using a metagenomic approach. Staphylococcus was the most abundant genus in the samples, accounting for an average abundance of 29.9 %, followed by Tetragenococcus (17.1 %), and Latilactobacillus (3.6 %). A core resistome of FMP samples was constructed for the first time using co-occurrence network analysis, which revealed the distribution and interrelationships of ARGs and bio/metal-resistant genes (BMRGs). Random forest analysis identified the lincosamide nucleotidyltransferase lnuA and the multidrug and toxic compound extrusion (MATE) transporter abeM as potential indicators for assessing the overall abundance of the core resistome. Additionally, Staphylococcus, Acinetobacter, and Pseudomonas were identified as hosts constituting the core resistome. Despite their low abundance, the latter two still serve as major reservoirs of antibiotic resistance genes. Notably, Lactococcus cremoris was identified as the key host for tetracycline resistance genes in the samples, highlighting the need for enhanced resistance monitoring in lactic acid bacteria. Based on our findings, in the microbial safety assessment of fermented meat products, beyond common foodborne pathogens, attention should be focused on detecting and controlling coagulase-negative Staphylococcus, Acinetobacter, and Pseudomonas, and addressing bacterial resistance. The quantitative detection of lnuA and abeM could provide a convenient and rapid method for assessing the overall abundance of the core resistome. Our findings have important implications for the control of bacterial resistance and prevention of pathogenic bacteria in fermented meat products.