Search

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95–7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance. [Display omitted] • The composition of phage communities varies in different habitats. • Terrestrial-inhabiting phage communities display complex and robust interactions. • Caudoviricetes have the capacity to carry specific antibiotic resistance genes. • Caudoviricetes display a high potential risk to human health. [ABSTRACT FROM AUTHOR]

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L. [Display omitted] • FMBO increased methane production and content during AD. • FMBO optimized the methanogenic performance of the AD process by enriching methanogens. • FMBO increased the gene's abundance of enzymes involved in the methanogenic pathways. • FMBO reduced ARGs and MGEs by affecting microorganisms. • The increase in methanogens did not result in an increased abundance of ARGs. [ABSTRACT FROM AUTHOR]

• Fe2+/Ca(ClO) 2 conditioning simultaneously promoted sludge dewatering and ARG removal. • Fe2+/Ca(ClO) 2 conditioning was even better than Fenton treatment to eliminate ARGs. • HOCl could penetrate the cell and induce direct oxidation of intracellular ARGs. • ARG removal was achieved by reducing potential hosts and related metabolic pathways. • Fe2+/Ca(ClO) 2 conditioning oxidized intracellular ARGs without bacterial cell lysis. Pre-acidification has been shown to be crucial in attenuating antibiotic resistance genes (ARGs) during the conditioning of sewage sludge. However, it is of great significance to develop alternative conditioning approaches that can effectively eliminate sludge-borne ARGs without relying on pre-acidification. This is due to the high investment costs and operational complexities associated with sludge pre-acidification. In this study, the effects of Fe2+/Ca(ClO) 2 conditioning treatment on the enhancement of sludge dewaterability and the removal of ARGs were compared with other conditioning technologies. The dose effect and the associated mechanisms were also investigated. The findings revealed that Fe2+/Ca(ClO) 2 conditioning treatment had the highest potential, even surpassing Fenton treatment with pre-acidification, in terms of eliminating the total ARGs. Moreover, the effectiveness of the treatment was found to be dose-dependent. This study also identified that the •OH radical reacted with extracellular polymeric substance (EPS) and extracellular ARGs, and the HOCl, the production of which was positively correlated with the dose of Fe2+/Ca(ClO) 2 , could infiltrate the EPS layer and diffuse into the cell of sludge flocs, inducing the oxidation of intracellular ARGs. Furthermore, this study observed a significant decrease in the predicted hosts of ARGs and MGEs in sludge conditioned with Fe2+/Ca(ClO) 2 , accompanied by a significant downregulation of metabolic pathways associated with ARG propagation, thereby contributing to the attenuation of sludge-borne ARGs. Based on these findings, it can be concluded that Fe2+/Ca(ClO) 2 conditioning treatment holds great potential for the removal of sludge-borne ARGs while also enhancing sludge dewaterability, which mainly relies on the intracellular oxidation by HOCl. [Display omitted] [ABSTRACT FROM AUTHOR]

Antibiotic resistance is a critical problem that results in a high morbidity and mortality rate. The process of discovering new chemotherapy and antibiotics is challenging, expensive, and time-consuming, with only a few getting approved for clinical use. Therefore, screening already-approved drugs to combat pathogens such as bacteria that cause serious infections in humans and animals is highly encouraged. In this work, we aim to identify approved antibiotics that can inhibit the mecA antibiotic resistance gene found in methicillin-resistant Staphylococcus aureus (MRSA) strains. The MecA protein sequence was utilized to perform a BLAST search against a drug database containing 4302 approved drugs. The results revealed that 50 medications, including known antibiotics for other bacterial strains, targeted the mecA antibiotic resistance gene. In addition, a structural similarity approach was employed to identify existing antibiotics for S. aureus, followed by molecular docking. The results of the docking experiment indicated that six drugs had a high binding affinity to the mecA antibiotic resistance gene. Furthermore, using the structural similarity strategy, it was discovered that afamelanotide, an approved drug with unclear antibiotic activity, had a strong binding affinity to the MRSA-MecA protein. These findings suggest that certain already-approved drugs have potential in chemotherapy against drug-resistant pathogenic bacteria, such as MRSA.

Research is lacking on the health risks of antibiotics and antibiotic resistance genes (ARGs) in water dropwort grown in livestock wastewater. Our results showed that antibiotics from livestock wastewater were absorbed and bioaccumulated by water dropwort. The concentration of antibiotics was higher in the roots than in the stems and leaves. The health-risk coefficients of antibiotics in water dropwort were below the threshold (<0.1), indicating that in this case study, the consumption of water dropwort used to purify livestock wastewater was safe for humans considering accumulated antibiotics. ARGs were closely correlated between livestock wastewater and water dropwort, with the results showing that all 13 ARGs detected in the livestock wastewater were also found in the water dropwort. Tetracycline resistance genes were more abundant than the other ARGs in both the livestock wastewater and water dropwort. The estimated daily intake of ARGs in water dropwort for humans ranged from 2.06 × 106 to 7.75 × 1012 copies g−1, suggesting the potential risk of intaking ARGs in water dropwort cannot be ignored. Although the safety of consuming water dropwort used to purify livestock wastewater, considering accumulated antibiotics and ARGs, was assessed in this study, more studies should be conducted to ensure we fully understand the health risks. [ABSTRACT FROM AUTHOR]

To date, probiotic bacteria are used in the diet and have various clinical applications. There are reports of antibiotic resistance genes in these bacteria that can transfer to other commensal and pathogenic bacteria. The aim of this study was to use whole-genome sequence analysis to identify antibiotic resistance genes in a group of bacterial with probiotic properties. Also, this study followed existing issues about the importance and presence of antibiotic resistance genes in these bacteria and the dangers that may affect human health in the future. In the current study, a collection of 126 complete probiotic bacterial genomes was analyzed for antibiotic resistance genes. The results of the current study showed that there are various resistance genes in these bacteria that some of them are transferable to other bacteria. The tet(W) tetracycline resistance gene was more than other antibiotic resistance genes in these bacteria and this gene was found in Bifidobacterium and Lactobacillus. In our study, the most numbers of antibiotic resistance genes were transferred with mobile genetic elements. We propose that probiotic companies before the use of a micro-organism as a probiotic, perform an antibiotic susceptibility testing for a large number of antibiotics. Also, they perform analysis of complete genome sequence for prediction of antibiotic resistance genes. [ABSTRACT FROM AUTHOR]

Abuse of heavy metals and antibiotics results in the dissemination of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Ditch wetlands are important sinks for heavy metals and antibiotics. The relationships between bacterial communities and MRG/ARG dissemination under dual stresses of heavy metals and antibiotics remain unclear. The responses of MRGs and ARGs to the co-selective pressure of cadmium (Cd) and doxycycline (DC) in ditch wetlands were investigated after 7-day and 84-day exposures. In ecological ditches, residual rates of Cd and DC varied from 0.4 to –5.73% and 0 to –0.61%, respectively. The greatest total relative abundance of ARGs was observed in the Cd 5 mg L–1 + DC 50 mg L–1 group. A significant level of DC (50 mg L–1) significantly reduced the total relative abundances of MRGs at a concentration of 5 mg L–1 Cd stress. Redundancy analysis indicated that Cd and DC had strong positive effects on most ARGs and MRGs after a 7-day exposure. Meanwhile, the class 1 integron gene (intI1) exhibited strong positive correlations with most ARGs and cadmium resistance genes (czcA) after an 84-day exposure. Network analysis showed that Acinetobacter and Pseudomonas were the potential dominant host genera for ARGs and MRGs, and tetracycline resistance genes (tetA), czcA , and intI1 shared the same potential host bacteria Trichococcus after an 84-day exposure. [ABSTRACT FROM AUTHOR]

Copyright of Asian Journals of Ecotoxicology is the property of Gai Kan Bian Wei Hui and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

ABSTRACT: Objectives: Bacillus toyonensis is widespread in nature. Multidrug-resistant B. toyonensis strain 4HC1 was isolated from polyethylene submerged in the water column near a beach in Øygarden, Norway. We analysed the whole genome sequence of strain 4HC1 in order to understand the genetic basis of the observed phenotypic antibiotic resistance. Methods: Whole-genome sequencing of B. toyonensis strain 4HC1 was performed on Illumina MiSeq platform using 2 × 300 bp chemistry. The genome sequence was assembled using SPAdes v.3.13.0 and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Results: The draft genome of strain 4HC1 is 6 156 259 bp (133 contigs) in size with a GC content of 34.95%. The genome comprises 6089 protein-coding genes, 86 tRNAs and 24 rRNAs. Strain 4HC1 is resistant to cefotaxime, trimethoprim and ampicillin and carries various antibiotic resistance genes (ARGs), including several β-lactamases, aminoglycoside 6-adenylyltransferase, a TetM family tetracycline resistance gene, two different tetracycline efflux pumps, and a bleomycin resistance gene. Several virulence genes including genes involved in immune evasion, iron acquisition and toxins were also detected in strain 4HC1. Conclusion: The draft genome sequence of B. toyonensis strain 4HC1 released here shows the presence of various ARGs and virulence genes in a multidrug-resistant strain isolated from marine plastic.

Abstract Background The gut microbiome is essential for the host’s health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda’s gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis. Results Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways. Conclusion Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome’s functional characteristics; however, it needs further studies to ascertain the study outcomes.

Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.

Abuse of heavy metals and antibiotics results in the dissemination of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Ditch wetlands are important sinks for heavy metals and antibiotics. The relationships between bacterial communities and MRG/ARG dissemination under dual stresses of heavy metals and antibiotics remain unclear. The responses of MRGs and ARGs to the co-selective pressure of cadmium (Cd) and doxycycline (DC) in ditch wetlands were investigated after 7-day and 84-day exposures. In ecological ditches, residual rates of Cd and DC varied from 0.4 to –5.73% and 0 to –0.61%, respectively. The greatest total relative abundance of ARGs was observed in the Cd 5 mg L–1 + DC 50 mg L–1 group. A significant level of DC (50 mg L–1) significantly reduced the total relative abundances of MRGs at a concentration of 5 mg L–1 Cd stress. Redundancy analysis indicated that Cd and DC had strong positive effects on most ARGs and MRGs after a 7-day exposure. Meanwhile, the class 1 integron gene (intI1) exhibited strong positive correlations with most ARGs and cadmium resistance genes (czcA) after an 84-day exposure. Network analysis showed that Acinetobacter and Pseudomonas were the potential dominant host genera for ARGs and MRGs, and tetracycline resistance genes (tetA), czcA, and intI1 shared the same potential host bacteria Trichococcus after an 84-day exposure.

Background: Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database. Results: Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes. Conclusions: Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes. [ABSTRACT FROM AUTHOR]

With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments. [Display omitted] [ABSTRACT FROM AUTHOR]

Various members of the enteric bacteria in recent times are evolving diverse survival mechanisms for antibiotic therapy resulting in failure of treatment in infection and disease cases. The Enterococcus species are potential strains implicated in gastrointestinal tract infection and are recently evolving in the resistance mechanism. The study evaluates the occurrence of New Delhi Metallo-beta-lactamase 1 (NDM-1) amongst Enterococcus species using the phenotypic and genomic characterization of environmental strains in the Oghara water nexus. Presumptive isolates of Enterococcus species were retrieved from various sampled water sources and confirmed using polymerase chain reaction (PCR). Antibiotic susceptibility testing was conducted on confirmed isolates using Kirby-Bauer disk diffusion methods. The result reveals 63 genus isolates confirmed Enterococcus species, of which 42 (67%) were Enterococcus faecium, 15 (23%) were Enterococcus faecalis, and 6 (10%) were other Enterococcus species. Fourteen among the E. faecalis isolates show resistance to Ertapenem-EDTA, while 17 (44.8%) of the E. faecium show resistance to Ertapenem-EDTA to presumptively reveal their NDM-1 phenotype. The PCR detection of the NDM-1 gene further confirmed 23 (36.5%) isolates as positive genotypes amongst the isolates that previously showed presumptive NDM-1 phenotype. It was also observed that 10 (15.9%) of Enterococcus faecium members harbored the NDM-1 genotype, whereas 8 (12.7%) members of the Enterococcus faecalis harbored the NDM-1 genotype. The observation of such resistance determinants necessitates a call for the adroit application of relevant therapeutics in the management of related infections and an environmental health caution to prevent the spread of such resistance potential enteric bacteria pathogens. [ABSTRACT FROM AUTHOR]

Aims: To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions. Methods and Results: Gut microbes, antibiotic resistance genes (ARGs) and virulence factors genes (VFGs) were analysed using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients, whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug‐related resistance genes and Capsule and LOS‐related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs. Conclusions: Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, E. coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and E. hallii may be beneficial for IBD patients and could serve as potential probiotics for IBD treatment. Significance and Impact of the Study: This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome‐based therapies. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Agro-Environment Science is the property of Journal of Agro-Environment Science Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective Understanding of bacterial antibiotic resistance is the basis for guiding clinical anti-infective therapy and monitoring antimicrobial resistance trends. The study was aimed to investigate the antibiotic resistance characteristics of nontyphoidal Salmonella isolates from foodborne disease cases in Jiangxi Province in 2018, study the correlations between resistance phenotypes and genotypes, and evaluate the application prospects of whole genome sequencing (WGS) in antimicrobial resistance surveillance. Methods In this study, 58 nontyphoidal Salmonella strains were isolated from foodborne disease patients in Jiangxi Province in 2018 and were tested for susceptibility to 14 antimicrobials using broth microdilution. The 58 isolates were subjected to WGS, and resistance genes were identified from assembled sequences that compared with ResFinder database. Results 77.59% (45/58) of isolates were resistant to tetracycline, and 72.41% (42/58) were resistant to ampicillin. 100.00% of isolates were susceptible to imipenem. 56.90% (33/58) of isolates displayed resistance to at least 3 classes of antibiotics, and 3.45% (2/58) of isolates had resistance to at least 6 of 8 classes tested. A total of 47 unique resistance genes referred to 11 classes of antibiotics, plus mutations in gyrA, gyrB and parC structural of quinolone resistance-determining region (QRDR), were identified. 100.00% (58/58) of isolates had aminoglycoside resistance genes, and 72.41% (42/58) of isolates harboured tetracycline resistance genes. Macrolide resistance genes were presented in 3.45% (2/58) of isolates. 77.59% (45/58) of isolates were contained at least 3 classes of antibiotics resistance genes, and 1.72% (1/58) of isolates harboured at least 9 classes of resistance genes. The overall resistance genotypes and phenotypes were consistent in 93.43% (611/654) of cases. Except quinolones, the correlations were above 91% for tested antibiotics. Correlations were 100% for some classes of antibiotics. Conclusion The antibiotic resistance phenomenon of these isolates was serious. The resistance phenotypes were in good accordance with genotypes, and WGS can be used as an effective tool to predict the antibiotic resistance of nontyphoidal Salmonella. As more new antibiotic resistance genes were discovered, the consistency of resistance genotypes and phenotypes will be further improved.

Abstract Background Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect diverse bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate. Results We evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, when a lenient threshold of e value of ≤ 1 × e−5 and query coverage of ≥ 60% were employed in the Resfams database, the novel β-lactamases bla HRV-1 and bla HRVM-1 were found. These genes had unique sequences, forming distinct clades of class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring bla HRV-1 and bla HRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages. Conclusion Our results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions. Video abstract.

Abstract Background The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. Results The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. Conclusions Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.

Plasmids that carry antibiotic resistance genes occur frequently in Aeromonas salmonicida subsp. salmonicida, an aquatic pathogen with severe consequences in salmonid farming. Here, we describe a 67 kb plasmid found in the A. salmonicida subsp. salmonicida Strain SHY15-2939 from Quebec, Canada. This new plasmid, named pAsa-2939 and identified by high throughput sequencing, displays features never found before in this bacterial species. It contains a transposon related to the Tn21 family, but with an unusual organization. This transposon bears a catB3 gene (chloramphenicol resistance) that has not been detected yet in A. salmonicida subsp. salmonicida. The plasmid is transferable by conjugation into Aeromonas hydrophila, but not into Escherichia coli. Based on PCR analysis and genomic sequencing (Illumina and PacBio), we determined that the transposon is unstable in A. salmonicida subsp. salmonicida Strain SHY15-2939, but it is stable in A. hydrophila trans-conjugants, which explains the chloramphenicol resistance variability observed in SHY15-2939. These results suggest that this bacterium is likely not the most appropriate host for this plasmid. The presence of pAsa-2939 in A. salmonicida subsp. salmonicida also strengthens the reservoir role of this bacterium for antibiotic resistance genes, even those that resist antibiotics not used in aquaculture in Québec, such as chloramphenicol.

Abstract Background Identification of antibiotic resistance genes from environmental samples has been a critical sub-domain of gene discovery which is directly connected to human health. However, it is drawing extraordinary attention in recent years and regarded as a severe threat to human health by many institutions around the world. To satisfy the needs for efficient ARG discovery, a series of online antibiotic resistance gene databases have been published. This article will conduct an in-depth analysis of CARD, one of the most widely used ARG databases. Results The decision model of CARD is based the alignment score with a single ARG type. We discover the occasions where the model is likely to make false prediction, and then propose an optimization method on top of the current CARD model. The optimization is expected to raise the coherence with BLAST homology relationships and improve the confidence for identification of ARGs using the database. Conclusions The absence of public recognized benchmark makes it challenging to evaluate the performance of ARG identification. However, possible wrong predictions and methods for resolving the problem can be inferred by computational analysis of the identification method and the underlying reference sequences. We hope our work can bring insight to the mission of precise ARG type classifications.

The effect of manure application on the distribution and accumulation of antibiotic resistance genes (ARGs) in tissue of root vegetables remains unclear, which poses a bottleneck in assessing the health risks from root vegetables due to application of manure. Towards this goal, experiments were conducted in pots to investigate the distribution and bioaccumulation of ARGs in carrot tissues due to application of pig manure. The 144 ARGs targeting nine types of antibiotics were quantified by high throughput qPCR in the soil and plant samples. The rhizosphere was a hot spot for ARGs enrichment in the manured soil. The abundance, diversity, and bioaccumulation factors of ARGs in the phyllosphere were significantly higher than those of carrot root skin and tuber. Manure application increased bioaccumulation of 12 ARGs and 2 MGEs in carrot tuber with 124 the highest factor. The application of manure increased transfer of 10 ARGs and 3 MGEs from carrot skin to inner tuber by factors of 0.1–11.8. The average gene copy number of ARGs of per gram carrot root was about 4.8 × 104 and 1.1 × 106 in the control and the manured treatment, respectively. Children and adults may co-ingest 2.7 × 107 and 3.2 × 107 of ARGs copies/d from carrots grown with pig manure, using estimated human intake values. However, peeling may reduce the intake of ARGs by 28–91% and of MGEs by 46–59%. In conclusion, the application of pig manure increased the accumulation of ARGs in the skin of carrots, whereas peeling was an effective strategy to reduce the risk.

ABSTRACT: Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34–11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45–9.80 log copies/g) and soil (0–7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 109– 6.82 × 1011 copies/g. The average abundances of 5 antibiotic resistance genes were above 1010 copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) is regarded as one of the most important priority pathogens within the One Health interface. However, few studies have investigated the occurrence of ESBL-EC in giant pandas, along with their antibiotic-resistant characteristics and horizontal gene transfer abilities. In this study, we successfully identified 12 ESBL-EC strains (8.33%, 12/144) out of 144 E. coli strains which isolated from giant pandas. We further detected antibiotic resistance genes (ARGs), virulence-associated genes (VAGs) and mobile genetic elements (MGEs) among the 12 ESBL-EC strains, and the results showed that 13 ARGs and 11 VAGs were detected, of which bla CTX-M (100.00%, 12/12, with 5 variants observed) and papA (83.33%, 10/12) were the most prevalent, respectively. And ISEcp1 (66.67%, 8/12) and IS26 (66.67%, 8/12) were the predominant MGEs. Furthermore, horizontal gene transfer ability analysis of the 12 ESBL-EC showed that all bla CTX-M genes could be transferred by conjugative plasmids, indicating high horizontal gene transfer ability. In addition, ARGs of rmtB and sul2 , VAGs of papA , fimC and ompT , MGEs of ISEcp1 and IS26 were all found to be co-transferred with bla CTX-M . Phylogenetic analysis clustered these ESBL-EC strains into group B2 (75.00%, 9/12), D (16.67%, 2/12), and B1 (8.33%, 1/12), and 10 sequence types (STs) were identified among 12 ESBL-EC (including ST48, ST127, ST206, ST354, ST648, ST1706, and four new STs). Our present study showed that ESBL-EC strains from captive giant pandas are reservoirs of ARGs, VAGs and MGEs that can co-transfer with bla CTX-M via plasmids. Transmissible ESBL-EC strains with high diversity of resistance and virulence elements are a potential threat to humans, animals and surrounding environment., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Liu, Fan, Zhang, Yuan, Zhong, Wang, Wang, Zhou, Zhang, Geng, Peng, Wang, Zhang, Yan, Luo, Shi and Zhong.)

In recent years, aerosols have been recognized as a prominent medium for the transmission of antibiotic-resistant bacteria and genes. Among these, particles with a particle size of 2 μm (PM 2.5 ) can directly penetrate the alveoli. However, the presence of antibiotic-resistant genes in aerosols from pet hospitals and the potential risks posed by antibiotic-resistant bacteria in these aerosols to humans and animals need to be investigated. In this study, cefotaxime-resistant bacteria were collected from 5 representative pet hospitals in Changchun using a Six-Stage Andersen Cascade Impactor. The distribution of bacteria in each stage was analyzed, and bacteria from stage 5 and 6 were isolated and identified. Minimal inhibitory concentrations of isolates against 12 antimicrobials were determined using broth microdilution method. Quantitative Polymerase Chain Reaction was employed to detect resistance genes and mobile genetic elements that could facilitate resistance spread. The results indicated that ARBs were enriched in stage 5 (1.1-2.1 μm) and stage 3 (3.3-4.7 μm) of the sampler. A total of 159 isolates were collected from stage 5 and 6. Among these isolates, the genera Enterococcus spp. (51%), Staphylococcus spp. (19%), and Bacillus spp. (14%) were the most prevalent. The isolates exhibited the highest resistance to tetracycline and the lowest resistance to cefquinome. Furthermore, 56 (73%) isolates were multidrug-resistant. Quantitative PCR revealed the expression of 165 genes in these isolates, with mobile genetic elements showing the highest expression levels. In conclusion, PM 2.5 from pet hospitals harbor a significant number of antibiotic-resistant bacteria and carry mobile genetic elements, posing a potential risk for alveolar infections and the dissemination of antibiotic resistance genes., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier B.V.)

Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Antibiotics can disturb the gut microbial community and host metabolism. However, their recovery after antibiotics exposure needs to be characterized, and the correlation between gut microbiota and host metabolism remains unclear. In this study, mice were exposed to 0.5, 1.5 and 10 g/L tetracycline hydrochloride (TET) for 2 weeks, then recovered without TET for another 2 weeks. The results showed that 2-week TET exposure changed microbial community and functions in the mouse gut, and increased abundance of antibiotic resistance genes (ARGs), especially in the 10 g/L TET group. After a 2-week recovery, these changes could only be recovered to the control level in the 0.5 g/L TET exposure group, except for ARGs. Besides gut microbiota, TET exposure also changed metabolic profiles in mouse urine. The 2-week recovery significantly reduced changes in metabolic profiles. Some altered metabolites were found to have a very high correlation with gut microbial community and functions, indicating that TET exposure might induce certain changes in urinary metabolic profiles by altering the gut microbiota. The results from this study suggest that the influences of low-level TET exposure are reversible, except for ARGs, which should be paid more attention. During the application of TET, their dosage should be effectively considered and controlled. [ABSTRACT FROM AUTHOR]

Background: Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results: Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion: In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea. [ABSTRACT FROM AUTHOR]

Copyright of SDU Journal of Engineering Sciences & Design / Mühendislik Bilimleri ve Tasarım Dergisi is the property of Journal of Engineering Sciences & Design and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Agro-Environment Science is the property of Journal of Agro-Environment Science Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Manure storage methods can affect the concentration and prevalence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in cattle manure prior to land application. The objective of this study was to compare stockpiling and composting with respect to their effectiveness in reducing ARB and ARGs in beef cattle manure in a field-scale study. Field experiments were conducted in different seasons with different bulking agents for composting. For both the winter-spring cycle and the summer-fall cycle, ARB concentrations declined below the limit of quantification rapidly in both composting piles and stockpiles; however, ARB prevalence was significantly greater in the composting piles than in the stockpiles. This was likely due to the introduction of ARB from bulking agents. There was no significant change in ARG concentrations between initial and final concentrations for either manure storage treatment during the winter-spring cycle, but a significant reduction of the ARGs erm(B), tet(O), and tet(Q) over time was observed for both the composting pile and stockpile during the summer-fall cycle. Results from this study suggest that (i) bulking agent may be an important source of ARB and ARGs for composting; (ii) during cold months, the heterogeneity of the temperature profile in composting piles could result in poor ARG reduction; and (iii) during warm months, both stockpiling and composting can be effective in reducing ARG abundance. [ABSTRACT FROM AUTHOR]

Faecal microbiota transplantation (FMT) has received considerable attention in recent years due to its remarkable efficacy in restoring a normal gut microbiome. Here, we established the groups of post‐FMT recipient piglets using germ‐free piglets during early life to characterize the colonization of gut microbiota composition and the enrichment of resistance gene acquisition. By metagenomic analysis, we identified 115 bacterial phyla and 2111 bacterial genera that were acquired by the FMT recipients. We found that early‐life microbial colonization and the spread of resistomes in recipient piglets were age dependent. A total of 425, 425 and 358 AR genes primarily belonging to 114, 114 and 102 different types were detected in the donors, post‐FMT recipients in the FMT‐3D group and post‐FMT recipients in the FMT‐15D group respectively. Genes that encoded tetracycline, macrolide and chloramphenicol resistance proteins were the most dominant AR genes, and the results corresponded with the exposure of antibiotic consumption at farm. Bacteroides, Escherichia, Clostridium, Parabacteroides, Treponema, Lactobacillus and Enterococcus were significantly correlated with the distribution of AR genes. More importantly, the relative abundance of AR genes was positively correlated with the levels of mobile genetic elements. Our results indicate that early‐life microbial colonization can persistently shape the gut microbiota and antibiotic resistome. [ABSTRACT FROM AUTHOR]

Purpose: Sewage sludge land application is strongly recommended to improve soil quality and fertility despite the presence of pollutants, pathogens and antibiotic resistance genes. This study aimed to assess the fertilization value of low and recommended by law sewage sludge dose (15 t ha−1). Materials and methods: In a 540-day field study, the effect of sewage sludge on the soil physicochemical and microbial parameters, emphasising antibiotic and metal resistance spread, was investigated. Results: In contrast to expectations, sewage sludge did not improve the organic matter, nutrient content and microbial activity in the soil; therefore, the fertilization effect was not achieved. Moreover, an increase in the bioavailable Cd, Ni and Cu content was observed. Canonical correspondence analysis revealed that these increases mainly explain the changes in the soil microbial community. Sixteen resistance genes and four integron classes were detected in both the total DNA and on plasmids isolated from sewage sludge. Obtained plasmids confer β-lactam resistance or extreme resistance to tetracycline (> 256 μg mL−1). Two antibiotic resistance genes (blaNPS-2, tetA) were transferred into the fertilized soil and detected up to 6 months after the fertilization. Conclusion: Our results provide evidence that the regulated dose of sewage sludge, even when characterized by low total metal content, may affect soil microbial microbiome and resistome. Therefore, these findings provide critical data that have public health implications, which may raise concerns about the suitability of applying sewage sludge to the soil even at the low regulated dose. [ABSTRACT FROM AUTHOR]

Fresh vegetables play a significant role in the human diet. However, ready-to-eat (RTE) vegetables have been associated with increasing foodborne outbreaks including L. monocytogenes, which is a common human pathogen associated with foodborne infections resulting in listeriosis. This study aims to assess the resistance of vegetable-borne L. monocytogenes to antibiotics. L. monocytogenes was isolated and molecularly characterized using polymerase chain reaction (PCR) from 17 RTE vegetable samples. The confirmed L. monocytogenes was further assessed for phenotypic and genotypic antibiotic resistance using the disc diffusion test and PCR primers targeting six antibiotic classes and thirty-one related antibiotic resistance genes (ARGs), respectively. The results revealed that Listeria counts ranged from 1.60 to 3.44 log10 CFU/g in the samples. The isolates exhibited high resistance against penicillin G, erythromycin, vancomycin, tetracycline, trimethoprim-sulfamethoxazole, and nitrofurantoin among the 108 isolates tested. A total of 71 multiple antibiotic resistance (MAR) phenotypes were observed in the isolates, which ranged from resistance to 3 to 13 antibiotics. The MAR index was ˃0.2 in 97% of the isolates. Some of the highly detected ARG subtypes included SulI (100%), TEM (76.9%), tetA (59%), and tetM (54.7%). The findings show a high occurrence of multidrug-resistant L. monocytogenes and clinical ARGs in fresh vegetables, which constitutes an immediate danger for the health security of the public.

Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net.

Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net. Overall BacAnt's service workflow. The figure is adapted with permissions from IntegronFinder (Cury et al., 2016). [ABSTRACT FROM AUTHOR]

Dairy cows with mastitis are frequently treated with antibiotics. The potential effect of antibiotics on the milk microbiome is still not clear. Therefore, the objective of this research was to investigate the effect of 2 commonly used cephalosporins on the milk microbiota of dairy cows and the antibiotic resistance genes in the milk. The milk samples were collected from 7 dairy cows at the period before medication (d 0), medication (d 1, 2, 3), withdrawal period (d 4, 6, 8), and the period after withdrawal (d 9, 11, 13, 15). We applied 16S rRNA sequencing to explore the microbiota changes, and antibiotic resistance patterns were investigated by quantitative PCR. The microbiota richness and diversity in each sample were calculated using the Chao 1 (richness), Shannon (diversity), and Simpson (diversity) indices. The cephalosporins treatment lowered the Simpson diversity value at the period of withdrawal. Members of the Enterobacter genera were the most affected bacteria associated with mastitis. Meanwhile, antibiotic resistance genes in the milk were also influenced by antibiotic treatment. The cephalosporins treatment raised the proportion of bla TEM in milk samples at the period of withdrawal. Therefore, the treatment of cephalosporins led to change in the milk microbiota and increase of β-lactam resistance gene in the milk at the time of withdrawal period. [ABSTRACT FROM AUTHOR]

In this study, it was aimed to investigate the prevalence of Staphylococcus aureus in poultry meats (32 chickens, 9 turkeys, 9 quails) sold in Isparta and Antalya provinces, and to determine the presence of enterotoxin genes as well as antibiotic resistance profiles and resistance genes. Baird Parker agar medium was used to isolate presumptive S. aureus from poultry meats. The species-level identification of isolates was done by polymerase chain reaction (PCR) using primer pair specific to the thermostable nuclease gene (nuc) in S. aureus. As a result of the PCR analysis, amplicons of 458 bp specific to the nuc gene were obtained in 16 of 130 presumptive S. aureus isolates. The frequency of S. aureus in poultry meat samples was found to be 20% (10/50). Coagulase test showed that all the S. aureus isolates were coagulase positive. Disk diffusion test showed that all of the isolates (100 %) were susceptible to chloramphenicol and teicoplanin and resistant to penicillin G. It was determined that 81.25 % (13/16) of the isolates were methicillin resistant S. aureus (MRSA). The most common antibiotic resistance gene in S. aureus strains was found to be blaZ (62.5 %, 10/16) as a result of PCR. The presence of sea, seb, sec, sed and see genes was not detected in any of the S. aureus strains. [ABSTRACT FROM AUTHOR]

Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately. [ABSTRACT FROM AUTHOR]

Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG). [Display omitted] • The abundance of ARGs in phages is low relative to bacteria. • The virome could extract more phage sequences than the metagenome. • Aiphoviridae is the phage that co-occurs with the most ARGs. • The risk of phage-mediated horizontal transfer of ARGs cannot be neglected. [ABSTRACT FROM AUTHOR]

Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere. [Display omitted] • N or P limitation increased bacterial richness and diversity in the phycosphere. • N or P limitation promoted the bacterial nitrate metabolism in the phycosphere. • P limitation promoted the ARGs proliferation more significantly than N limitation. • MGEs were the predominant contributing factor to the proliferation of ARGs. • Algal physiology played a key role in the distribution of ARGs in the phycosphere. [ABSTRACT FROM AUTHOR]

[Display omitted] • Environmental factors affected the spread of phage-borne ARGs mediated by nTiO 2. • HA impaired the membrane stability and induced the formation of biogenesis OMVs. • nTiO 2 mitigated HA-boosted ARGs transfer by inhibiting membrane instability in dark. • Photoexcited HA-nTiO 2 generated massive O 2 −, exacerbating ARGs transduction. • Environmental factors play vital role in nanomaterials' impact on ARGs spread. Bacteriophages are key reservoirs of antibiotic resistance genes (ARGs) and are pivotal for their acquisition, maintenance, and dissemination. As extensively distributed contaminants, nanomaterials can interfere with the horizontal transfer of phage-borne ARGs. However, the effects of environmental factors on this process remain unclear. Therefore, the effect of nanoscale titanium dioxide (nTiO 2) on the dissemination of ARGs via bacteriophage transduction under humic acid (HA) and Ultraviolet A illumination was investigated in this study. In the dark, 20 mg/L nTiO 2 did not promote the propagation of ARGs and attenuated the positive effect of HA on the transductive transfer of ARGs. Further evidence revealed that nTiO 2 can absorb HA on its surface and decrease the free HA content, thereby mitigating the instability of the outer membrane and leading to diminished transductant formation. Conversely, coexposure to HA and nTiO 2 synergistically promoted transduction under Ultraviolet A illumination. Massive superoxide radicals produced by photoexcitation of the HA-nTiO 2 complex elevated the membrane permeability and boosted intracellular oxidative stress, resulting in the enhanced dissemination of ARGs through phage transduction. The results of this study provide insights into the roles of environmental factors in transductive ARGs dissemination mediated by nTiO 2 and are beneficial for the risk assessment of nanomaterials. [ABSTRACT FROM AUTHOR]

[Display omitted] • Co-exposure to high copper and tetracycline increased the abundance of ARGs in the mouse guts. • Abnormal copper and/or tetracycline exposure significantly affected the community structure of the mouse gut microbiota. • Abnormal intake of copper and/or tetracyclines increased the enrichment of potential pathogens in the mouse guts and the pathogenic risk to public health. The widespread use of copper and tetracycline as growth promoters in the breeding industry poses a potential threat to environmental health. Nevertheless, to the best of our knowledge, the potential adverse effects of copper and tetracycline on the gut microbiota remain unknown. Herein, mice were fed different concentrations of copper and/or tetracycline for 6 weeks to simulate real life–like exposure in the breeding industry. Following the exposure, antibiotic resistance genes (ARGs), potential pathogens, and other pathogenic factors were analyzed in mouse feces. The co-exposure of copper with tetracycline significantly increased the abundance of ARGs and enriched more potential pathogens in the gut of the co-treated mice. Copper and/or tetracycline exposure increased the abundance of bacteria carrying either ARGs, metal resistance genes, or virulence factors, contributing to the widespread dissemination of potentially harmful genes posing a severe risk to public health. Our study provides insights into the effects of copper and tetracycline exposure on the gut resistome and potential pathogens, and our findings can help reduce the risks associated with antibiotic resistance under the One Health framework. [ABSTRACT FROM AUTHOR]