Number Of Antibiotic Resistance Genes Research Articles

The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River

Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.

Prevalence, transmission and genomic epidemiology of mcr-1-positive colistin-resistant Escherichia coli strains isolated from international airplane waste, local resident fecal and wastewater treatment plants.

The emergence and dissemination of mcr-1-positive Escherichia coli (MCRPEC) represent a critical public health threat. Here, we conducted a prospective analysis of MCRPEC isolates from wastewater treatment plants (WWTPs), local residents' fecal (LRF), and international airplane waste (IAW) to investigate their genetic characteristics and transmission patterns circulating in human-environment domains. The MCRPEC prevalence was 2.43 % in WWTPs, 1.37 % in IAW and 0.69 % in LRF. MCRPEC showed substantial genetic diversity, encompassing 61 sequence types (primarily ST1011, ST101, and ST2705), 7 plasmid types (primarily IncI2), 8 phylogroups (primarily A and B1), 9 mcr-1-flanked lineages (primarily L5), 6 clusters (primarily C2 and C4), diverse serotypes, and 61.95 % transposon-containing strains. The mcr-1 gene co-existed with 46 antibiotic resistance genes (ARGs) and 19 virulence factor genes (VFGs). Notably, 6 IncI2 plasmids carried the blaCTX-M, IS1380, and mcr-1 genes. MCRPEC from WWTPs harbored a greater number of ARGs (56.95 ± 5.99) but fewer VFGs (15.03 ± 6.40) compared to those from human-associated sources (LRF and IAW). ST1011, ST2705, IncHI2, and L7 were prevalent in WWTP-derived MCRPEC, whereas IncX4 and L3 were more common in human-derived MCRPEC. Genetic features such as ST101, ST48, IncI2, L4, L5, C2, and C4 were simultaneously present in strains from LRF, IAW, and WWTPs. Core genetic analyses also showed genetically similar MCRPEC strains across various geographic locations. The findings underscore the extensive dissemination, strong environmental adaptation, and clonal transmission of MCRPEC across diverse reservoirs, reinforcing the urgent need for coordinated multisectoral surveillance of human and environment interfaces to effectively mitigate further transmission.

Effects of exogenous signaling molecules on anaerobic sludge digestion: Quorum sensing and antibiotic resistance genes

Regulating quorum sensing (QS) signaling molecules could improve wastewater treatment but might increase antibiotic resistance. This study investigated the effects of exogenous C6-HSL on anaerobic sludge under oxytetracycline stress, with a focus on antibiotic resistance genes (ARGs) and the QS response. The results revealed that exogenous oxytetracycline increased the copy number of ARGs by more than 68.8 %. It also facilitated a 3.04-fold increase in the concentration of signaling molecules and increased the abundance of QS genes. Further addition of the C6-HSL accelerated oxytetracycline degradation, and reduced its residual concentration by 70.9 %, alleviating oxytetracycline stress on microbial communities, and correspondingly reducing stress release from AHL by 75.4 %. Importantly, this did not exacerbate antibiotic resistance, with no significant difference (p > 0.05) in the ARG abundance. These findings may provide valuable insights into the relationship between QS process and antibiotic resistance.

The simultaneous addition of chitosan and peat enhanced the removals of antibiotics resistance genes during biogas residues composting

Direct reuse of biogas residue (BR) has the potential to contribute to the dissemination of antibiotic resistance genes (ARGs). Although high-temperature composting has been demonstrated as an effective method for the harmless treatment of organic waste, there is few researches on the fate of ARGs in high-temperature composting of BR. This research examined the impact of adding 5% chitosan and 15% peat on physicochemical characteristics, microbial communities, and removal of ARGs during BR-straw composting in 12 Biolan 220L composters for 48 days. Our results showed that the simultaneous addition of chitosan and peat extended the high-temperature period, and increased the highest temperature to 74 °C and germination index. These effects could be attributed to the presence of thermophilic cellulose-decomposing genera (Thermomyces and Thermobifida). Although the microbial communities differed compositionally among temperature stages, their dissimilarity drastically reduced at final stage, indicating that the impact of different treatments on microbial community composition decreases at the end of composting. Peat had a greater impact on aerobic genera capable of cellulose degradation at thermophilic stage than chitosan. Surprisingly, despite the total copy number of ARGs significantly decreased during composting, especially in the treatment with both chitosan and peat, intl1 gene abundance significantly increased 2 logs at thermophilic stage and maintained high level in the final compost, suggesting there is still a potential risk of transmission and proliferation of ARGs. Our work shed some lights on the development of waste resource utilization and emerging contaminants removal technology.

Municipal-treated wastewater as a practical alternative to conventional rice irrigation: Effects on antibiotic resistance genes, virulence factors and human bacterial pathogens in soil, and responses of rice grain quality

Reuse of municipal-treated wastewater for agricultural irrigation is becoming increasingly prevalent due to growing demand and decline in freshwater supplies. However, the microbial contamination profile, including antibiotic resistance genes (ARGs), virulence factors (VFs), and human bacterial pathogens (HBPs) in agricultural soil irrigated with municipal-treated wastewater for paddy cultivation, was unknown. Here, metagenomic analysis was applied to provide a systematic insight into the resistome, VFs and HBPs in paddy soils irrigated with municipal-treated wastewater. The obtained results revealed that the residual antibiotics in municipal-treated wastewater has an impact on the antibiotic resistome by increasing both the total number and abundance of ARGs. Furthermore, it was found that sul1 could serve as a potential risk indicator for assessing ARG contamination. VFs, core HBP abundance, and dangerous pathogens remain unaffected by municipal-treated wastewater irrigation for paddy. The good coexistence patterns of ARGs-HBPs and ARGs-VFs demonstrated the presence of resistant pathogenic bacteria. The network analysis revealed that ARGs-bearing Legionella pneumophila, Mycobacterium marinum, Bordetella pertussis, Staphylococcus aureus, and Pseudomonas aeruginosa might be ranked as high-risk HBPs. Additionally, our investigation also demonstrated that reuse of municipal-treated wastewater for agricultural irrigation had no detrimental effects on rice plant growth and grain quality. This study was the first to investigate the response of VFs and HBPs in paddy soil under long-term municipal-treated wastewater irrigation. The obtained results provide a scientific basis for the safe application of municipal-treated wastewater.

Prevalence of antibiotic resistance genes, heavy metal, and bacterial community composition in sea sediments influenced by Eriocheir sinensis breeding aquaculture.

Eriocheir sinensis is the main aquaculture species in China. With the continuous expansion of the aquaculture scale, the demand for E. sinensis seedlings was also increased. The water used in breeding has well-nourished and its discharge into the sea posed significant risks. This study sampled the wastewater discharge points of the E. sinensis seedlings in Sheyang County, Jiangsu Province, and the areas far from the discharge points that were not affected in March and May 2023, respectively. A large number of antibiotic resistance genes (ARGs) were found in the sediment of the wastewater discharge area, and the highest ARG was sulfonamide ARG-sul1 using qPCR analysis, while ARGs were almost undetectable in the areas not affected by wastewater discharge. The 16S rRNA sequence analysis results showed that the main bacterial phyla at the wastewater discharge point were Bacteroidetes, Proteobacteria, and Thermodesulfobacteria. In the control point, the main bacterial phyla were Proteobacteria, Chlorobacterium, and Thermodesulfobacteria. There were significant differences in the composition of microbial communities between the two points, and the samples at the wastewater discharge point were more clustered and had higher similarity. The correlation network and redundancy analysis indicated that the phyla Bacteroidetes, Firmicutes, and Proteobacteria at the wastewater discharge points were positively correlated with most ARGs. The wastewater discharge had no effect on heavy metals from the two points. This study sets a foundation for future research by identifying key microbial taxa as potential ARG carriers and examining the interactions between microbial communities, ARGs, and heavy metals.

Whole-Genome Sequencing Reveals Temporal Trends in Antibiotic Resistance Genes in Escherichia coli Causing Pediatric Urinary Tract Infections in Central Vietnam.

(1) Background: Pediatric urinary tract infections (UTIs) pose significant challenges due to drug-resistant Escherichia coli (E. coli) strains. This study utilizes whole-genome sequencing to analyze temporal trends in antibiotic resistance genes (ARGs) in clinical E. coli isolates from pediatric UTI cases in central Vietnam. (2) Methods: We conducted whole-genome sequencing on 71 E. coli isolates collected from pediatric UTI patients between 2018 and 2020. ARGs were identified, and their prevalence over time was analyzed. Statistical tests were used to correlate ARG presence with antibiotic resistance. (3) Results: Of the 47 E. coli isolates with complete data, 40 distinct ARGs were identified, with a median of 10 resistance genes per isolate. A significant increase in the total number of ARGs per isolate was observed over time, from an average of 8.88 before June 2019 to 11.63 after. Notably, the prevalence of the aadA2 gene (aminoglycoside resistance) rose from 0% to 26.7%, and that of the blaNDM-5 gene (beta-lactam and carbapenem resistance) increased from 0% to 23.3%. Key correlations include blaEC with cephalosporin resistance, blaNDM-5 with carbapenem resistance, and sul2 with sulfamethoxazole/trimethoprim resistance. (4) Conclusions: Whole-genome sequencing reveals complex and evolving antibiotic resistance patterns in pediatric E. coli UTIs in central Vietnam, with a marked increase in ARG prevalence over time. Continuous surveillance and targeted treatments are essential to address these trends. Understanding genetic foundations is crucial for effective intervention strategies.

Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture.

There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.

Transfer of antibiotic resistance genes from soil to rice in paddy field

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

The distribution and key influential factors of antibiotic resistance genes in agricultural soils polluted by multiple heavy metals.

Due to anthropogenic activities such as mining, several agricultural soils are polluted by multiple heavy metals. However, it is still unclear whether multiple heavy metals could affect the distribution of antibiotic resistance genes (ARGs), and how metals affect ARGs. To understand ARGs' distribution in heavy metal-polluted soils, we chose soils contaminated by different types and contents of heavy metals to determine the ARGs' number and abundance through high-throughput quantitative real-time PCR (HT-qPCR) in this study. Additionally, the factors affecting ARGs' distribution, such as soil properties, mobile genetic genes (MGEs), and bacterial communities, were explored. The results demonstrated that the sampled soils were primarily contaminated by Cd, As, Pb, and Zn, and the pollution load index (PLI) values of these metals ranged from 1.3 to 2.7, indicating a low to moderate degree of heavy metal contamination. The number and abundance of ARGs ranged from 44 to 113 and from 2.74 × 107 copies/g to 1.07 × 108 copies/g, respectively. Besides, abundant MGEs in soils, ranging from 1.84 × 106 copies/g to 5.82 × 106 copies/g, were observed. The pathway analysis suggested that MGEs were the most important factor directly affecting ARG abundance (0.89). Notably, heavy metals also affected the ARG abundance. Proteobacteria and Actinobacteria, the main heavy metal tolerant bacteria, were found to be the main hosts of ARGs through network analysis. ARG-carrying pathogens (ACPs) in agricultural soils were found to carry MGEs, indicating a high risk of dissemination. This study provided important information for understanding the ARGs' fate and also the key factors affecting ARGs' spread in multiple heavy metal-contaminated soils.

Deeper Exploration of Gut Microbiome: Profile of Resistome, Virome and Viral Auxiliary Metabolic Genes of Three Ethnic Indian Groups.

The current study explored the resistomes and viromes of three Indian ethnic populations: Jaisalmer, Khargone, and Ladakh. These three groups had different dietary habits and antibiotic consumption rates. A resistome analysis indicated that compared to the Jaisalmer (n = 10) group, the burden of antibiotic resistance genes in the gut microbiome was higher in the Khargone (n = 12) and Ladakh (n = 9) groups. However, correlational analysis factoring in food habits, healthcare, and economic status was not statistically significant due to the limited number of samples. A considerable number of antibiotic resistance genes (ARGs) were present in well-known gut commensals such as Bifidobacteriaceae, Acidomonococcaceae, etc., as retrieved directly by mapping to the Resfinder database using the Groot tool. Further, the raw reads were assembled using MEGAHIT, and putative bacteriophages were retrieved using the VIBRANT tool. Many of the classified bacteriophages of the virome revealed that bacteria belonging to the families Bifidobacteriaceae and Enterocococcaceae were their hosts. The prophages identified in these groups primarily contained auxiliary metabolic genes (AMGs) for primary amino acid metabolism. However, there were significantly fewer AMGs in the Ladakh group than in the Jaisalmer group (p < 0.05). None of the classified bacteriophages or prophages contained ARGs. This indicates that phages do not normally carry antibiotic resistance genes.

The longitudinal trend and influential factors exploring of global antimicrobial resistance in Klebsiella pneumoniae

Klebsiella pneumoniae (Kp) is a human symbiotic opportunistic pathogen capable of causing severe hospital-based infections and community-acquired infections. The problem of antimicrobial resistance (AMR) has become increasing serious over time, posing a major threat to socio-economic and human development. In this study, we explored the global trend of AMR in 1786 strains of Kp isolated between 1982 and 2023. The number of antibiotic resistance genes (ARGs) in Kp increased significantly from 24.29 ± 5.44 to 32.42 ± 8.52 over time. Mobile genetic elements (MGEs) were responsible for the ARGs horizontal transfer of Kp strains. The results of structural equation modeling (SEM) indicated a strong association between the human development index and the increase of antibiotic consumption, which indirectly affected the occurrence and development of antibiotic resistance in Kp. The results of Generalized Linear Models (GLM) indicated that the influence of environmental factors such as temperature on the development of Kp resistance could not be ignored. Overall, this study monitored the longitudinal trend of antimicrobial resistance in Kp, explored the factors influencing antibiotic resistance, and provided insights for mitigating the threat of antimicrobial resistance.

Impact of Combined Pollution of Ciprofloxacin and Copper on the Diversity of Archaeal Communities and Antibiotic-Resistance Genes.

This study aimed to explore the response of archaeal communities and antibiotic-resistance genes (ARGs) to ciprofloxacin (CIP, 0.05-40 mg/L) and copper (Cu, 3 mg/L) combined pollution during stress- and post-effect periods in an activated sludge system. With the increase in the CIP concentration, the diversity of archaea decreased, but the richness increased under the stress of 10 mg/L CIP. Under stress and post effects, the change in unknown archaeal community structure was more significant than that of the known archaea. The relative abundance of unknown archaea was significantly reduced with the increase in CIP concentration. Meanwhile, there were certain archaea that belonged to abundant and rare taxa with different resistance and recovery characteristics. Among them, Methanosaeta (49.15-83.66%), Methanoculleus (0.11-0.45%), and Nitrososphaera (0.03-0.36%) were the typical resistant archaea to combined pollution. And the resistance of the abundant taxa to combined pollution was significantly higher than that of the rare taxa. Symbiotic and competitive relationships were observed between the known and the unknown archaea. The interactions of abundant known taxa were mainly symbiotic relationships. While the rare unknown taxa were mainly competitive relationships in the post-effect period. Rare archaea showed an important ecological niche under the stress-effect. Some archaea displayed positive correlation with ARGs and played important roles as potential hosts of ARGs during stress- and post-periods. Methanospirillum, Methanosphaerula, Nitrososphaera and some rare unknown archaea also significantly co-occurred with a large number of ARGs. Overall, this study points out the importance of interactions among known and unknown archaeal communities and ARGs in a wastewater treatment system under the stress of antibiotics and heavy metal combined pollution.

Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort

IntroductionOur understanding of particular gut microbiota members such as Bifidobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level beneficial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; comparing their genomic characteristics with strains isolated from infants across North America, Europe, and other regions of Africa.Materials and methodFrom 110 infant stool samples collected in Harare, Zimbabwe, 20 randomly selected samples were used to isolate dominant early-life gut microbiota members Bifidobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbohydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibiotic resistance genes (ARGs).ResultsThe study observed some location-based clustering within the main five identified taxonomic groups. Furthermore, there were varying and overall species-specific numbers of genes belonging to different GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specific variances were identified in the potential of Bifidobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifidobacterium, while Enterococcus genomes exhibited a high abundance of aspartyl peptidases. Both genera harboured resistance genes against multiple classes of antimicrobial drugs, with Enterococcus genomes containing a higher number of ARGs compared to Bifidobacterium, on average.ConclusionThis study identified promising probiotic strains within Zimbabwean isolates, offering the potential for early-life diet and microbial therapies. However, the presence of antibiotic resistance genes in infant-associated microbes raises concerns for infection risk and next-stage probiotic development. Further investigation in larger cohorts, particularly in regions with limited existing data on antibiotic and probiotic use, is crucial to validate these initial insights.Impact statementThis research represents the first investigation of its kind in the Zimbabwean context, focusing on potential probiotic strains within the early-life gut microbiota. By identifying local probiotic strains, this research can contribute to the development of probiotic interventions that are tailored to the Zimbabwean population, which can help address local health challenges and promote better health outcomes for infants. Another essential aspect of the study is the investigation of antimicrobial resistance genes present in Zimbabwean bacterial strains. Antimicrobial resistance is a significant global health concern, and understanding the prevalence and distribution of resistance genes in different regions can help inform public health policies and interventions.

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.

Effects of antibiotic resistance genes on health risks of rivers in habitat of wild animals under human disturbance - based on analysis of antibiotic resistance genes and virulence factors in microbes of river sediments.

Studying the ecological risk of antibiotic resistance genes (ARGs) to wild animals from human disturbance (HD) is an important aspect of "One Health". The highest risk level of ARGs is reflected in pathogenic antibiotic-resistant bacteria (PARBs). Metagenomics was used to analyze the characteristics of PARBs in river sediments. Then, the total contribution of ARGs and virulence factors (VFs) were assessed to determine the health risk of PARBs to the rivers. Results showed that HD increased the diversity and total relative abundance of ARG groups, as well as increased the kinds of PARBs, their total relative abundance, and their gene numbers of ARGs and VFs. The total health risks of PARBs in wild habitat group (CK group), agriculture group (WA group), grazing group (WG group), and domestic sewage group (WS group) were 0.067 × 10-3, -1.55 × 10-3, 87.93 × 10-3, and 153.53 × 10-3, respectively. Grazing and domestic sewage increased the health risk of PARBs. However, agriculture did not increase the total health risk of the rivers, but agriculture also introduced new pathogenic mechanisms and increased the range of drug resistance. More serious was the increased transfer risk of ARGs in the PARBs from the rivers to wild animals under agriculture and grazing. If the ARGs in the PARBs are transferred from the rivers under HD to wild animals, then wild animals may face severe challenges of acquiring new pathogenic mechanisms and developing resistance to antibiotics. Further analysis showed that the total phosphorus (TP) and dissolved organic nitrogen (DON) were related to the risk of ARGs. Therefore, controlling human emissions of TP and DON could reduce the health risk of rivers.

Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria.

Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.

Field-based investigation reveals selective enrichment of companion microbes in vegetables leading to specific accumulation of antibiotic resistance genes

Vegetables capture antibiotic resistance genes (ARGs) from the soil and then pass them on to consumers through the delivery chain and food chain, and are therefore the key node that may increase the risk of human exposure to ARGs. This study investigates the patterns and driving forces behind the transmission of ARGs from soil to vegetables by the commonly planted cash crops in the coastal region of southern China, i.e. broccoli, pumpkin, and broad bean, to investigate. The study used metagenomic data to reveal the microbial and ARGs profiles of various vegetables and the soil they are grown. The results indicate significant differences in the accumulation of ARGs among different vegetables harvested in the same area at the same time frame, and the ARGs accumulation ability of the three vegetables was in the order of broccoli, broad bean, and pumpkin. In addition, broccoli collected the highest number of ARGs in types (n = 14), while pumpkin (n = 13) does not obtain trimethoprim resistance genes and broad beans (n = 10) do not obtain chloramphenicol, fosmidomycin, quinolone, rifamycin, or trimethoprim resistance genes. Host tracking analysis shows a strong positive correlation (|rho| > 0.8, p < 0.05) between enriched ARGs and plant companion microbes. Enrichment analysis of metabolic pathways of companion microbes shows that vegetables exhibit a discernible enrichment of companion microbes, with significant differences among vegetables. This phenomenon is primarily due to the screening of carbohydrate metabolism capabilities among companion microbes and leads varied patterns of ARGs that spread from the soil to vegetables. This offers a novel insight into the intervention of foodborne transmission of ARGs.

Metagenomic and transcriptomic analysis revealing the impact of oxytetracycline and ciprofloxacin on gut microbiota and gene expression in the Chinese giant salamander (Andrias davidianus)

Excessive antibiotic use has led to the spread of antibiotic resistance genes (ARGs), impacting gut microbiota and host health. However, the effects of antibiotics on amphibian populations remain unclear. We investigated the impact of oxytetracycline (OTC) and ciprofloxacin (CIP) on Chinese giant salamanders (Andrias davidianus), focusing on gut microbiota, ARGs, and gene expression by performing metagenome and transcriptome sequencing. A. davidianus were given OTC (20 or 40 mg/kg) or CIP (50 or 100 mg/kg) orally for 7 days. The results revealed that oral administration of OTC and CIP led to distinct changes in microbial composition and functional potential, with CIP treatment having a greater impact than OTC. Antibiotic treatment also influenced the abundance of ARGs, with an increase in fluoroquinolone and multi-drug resistance genes observed post-treatment. The construction of metagenome-assembled genomes (MAGs) accurately validated that CIP intervention enriched fish-associated potential pathogens Aeromonas hydrophila carrying an increased number of ARGs. Additionally, mobile genetic elements (MGEs), such as phages and plasmids, were implicated in the dissemination of ARGs. Transcriptomic analysis of the gut revealed significant alterations in gene expression, particularly in immune-related pathways, with differential effects observed between OTC and CIP treatments. Integration of metagenomic and transcriptomic data highlighted potential correlations between gut gene expression and microbial composition, suggesting complex interactions between the host gut and its gut microbiota in response to antibiotic exposure. These findings underscore the importance of understanding the impact of antibiotic intervention on the gut microbiome and host health in amphibians, particularly in the context of antibiotic resistance and immune function.