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Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed. [ABSTRACT FROM AUTHOR]

Various conjugative plasmids were obtained by exogenous plasmid capture, biparental mating, and/or triparental mating methods from different environmental samples in Japan. Based on phylogenetic analyses of their whole-nucleotide sequences, new IncP/P-1 plasmids that could be classified into novel subgroups were obtained. Mini-replicons of the plasmids were constructed, and each of them was incompatible with at least one of the IncP/P-1 plasmids, although they showed diverse iteron sequences in their oriV regions. There were two large clades of IncP/P-1 plasmids, clade I and II. Plasmids in clade I and II included antibiotic resistance genes. Notably, nucleotide compositions of newly found plasmids exhibited different tendencies compared with those of the previously well-studied IncP/P-1 plasmids. Indeed, the host range of plasmids of clade II was different from that of clade I. Although few PromA plasmids have been reported, the number of plasmids belonging to PromAb, and -g subgroups detected in this study was close to that of IncP/P-1 plasmids. The host ranges of PromAγ and PromAδ plasmids were broad and transferred to different and distinct classes of Proteobacteria. Interestingly, PromA plasmids and many IncP/P-1 plasmids do not carry any accessory genes. These findings indicate the presence of "hitherto-unnoticed" conjugative plasmids, including IncP/P-1 or PromA derivative ones in nature. These plasmids would have important roles in the exchange of various genes, including antibiotic resistance genes, among different bacteria in nature. [ABSTRACT FROM AUTHOR]

Metal(loid) selection contributes to selection pressure on antibiotic resistance, but to our knowledge, evidence of the dissemination of antibiotic resistance genes (ARGs) induced by metal(loid)s in mine soil ecosystems is rare. In the current study, using a high-throughput sequencing (HTS)-based metagenomic approach, 819 ARG subtypes were identified in a mine soil ecosystem, indicating that these environmental habitats are important reservoirs of ARGs. The results showed that metal(loid)-induced coselection has an important role in the distribution of soil ARGs. Furthermore, metal(loid) selection-induced ARGs were mainly associated with resistance-nodulation-division (RND) antibiotic efflux, which is distinct from what is observed in agricultural soil ecosystems. By using independent genome binning, metal(loid)s were shown impose coselection pressure on multiple ARGs residing on mobile genetic elements (MGEs), which promotes the dissemination of the antibiotic resistome. Interestingly, the current results showed that the density of several MGEs conferring ARGs was considerably higher in organisms most closely related to the priority pathogens Pseudomonas aeruginosa and Escherichia coli. Together, the results of this study indicate that mine soil ecosystems are important reservoirs of ARGs and that metal(loid)-induced coselection plays critical roles in the dissemination of ARGs in this type of soil habitat. Key points: • Mining soil ecosystem is a reservoir of antibiotic resistance genes (ARGs). • ARGs distribute via bacterial resistance-nodulation-division efflux systems. • Metal(loid)s coselected ARGs residing on mobile genetic elements in P. aeruginosa and E. coli. [ABSTRACT FROM AUTHOR]

Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China. [ABSTRACT FROM AUTHOR]

This study investigated the effects of Bacillus licheniformis-fermented products (BLFPs) on the growth performance, faecal microbiota, and antibiotic resistance gene (ARG) expression in weaning piglets on a commercial farm. Ninety-six weaning piglets were randomly assigned to four treatments as follows: basal diet as control (C), basal diet plus 30 mg/kg of antibiotics (bacitracin methylene disalicylate) (A), basal diet plus 1 g/kg of BLFPs (F), and basal diet plus 15 mg/kg of antibiotics and 0.5 g/kg of BLFPs (AF), with six replicate pens per treatment and four pigs per pen. Results showed that, similar to antibiotics, replacing all or half the antibiotics with BLFPs improved the feed conversion ratio of weaning piglets from 15-28 d. Microbiota analysis showed that microbial community composition in the faeces showed a clear separation between groups. Replacing all the antibiotics with BLFPs increased the abundance of the genus, Streptococcus, in the faeces compared with the other groups. Half replacement of antibiotics with BLFPs increased the chloramphenicol resistance gene levels in the faeces compared with the C group, whereas full replacement of antibiotics with BLFPs reduced the streptomycin resistance gene levels compared with the C group. A trend of decreased levels of formic acid and acetic acid was observed in the group treated with BLFPs in combination with antibiotics compared with the C group. In conclusion, the field study demonstrates that replacing all or half the antibiotics with BLFPs can improve feed conversion ratio, modulate faecal microbiota, and alter ARG expression in weaning piglets. [ABSTRACT FROM AUTHOR]

The gut microbiota is closely linked to host nutrition, immunity, and health. Here, metagenomic analysis was conducted to elucidate the taxonomic and functional diversity of gut communities from hawksbills and green sea turtles. In terms of diversity and abundance, the gut microbiota of herbivorous green sea turtles showed a higher bacterial diversity and richness than that of hawksbills. Firmicutes dominated in all groups; however, the phylum Proteobacteria showed a higher relative abundance in hawksbills. Several metabolic pathways displayed broad prevalence and high relative abundances in the two sea turtle populations. Antibiotic resistance genes (ARGs) responsible for resistance to glycopeptide and tetracycline were the most abundant in all samples. In ARGs, the subtype macB was the most abundant in the two different sea turtle populations; however, evgS, bcrA, and efrA were more abundant in the green sea turtles, while in the hawksbills, tetT and tetB(P) were more abundant. Among mobile genetic elements (MGEs), the abundance of 16 MGE types showed a significant difference between the two sea turtle populations. MGE type transposase and plasmid were the most abundant in the two sea turtle populations. Additionally, gene functions were enriched in carbohydrate esterases, glycoside hydrolases, and polysaccharide lyases in the green sea turtles, whereas genes related to glycosyltransferases and auxiliary activities were highly abundant in hawksbills. These metagenomic profiles provide further insights into the microbial diversities of the two types of sea turtles and provide valuable information for future conservation efforts. [ABSTRACT FROM AUTHOR]

We present the complete genome sequence of Escherichia coli strain PEC1009 isolated from avian feces in Pakistan. The strain belongs to sequence type (ST) 10, a high-risk clone. The strain possesses two plasmids, and various plasmid-borne antibiotic resistance genes and chromosome-borne virulence factor genes were identified in its genome.

Bacterial antibiotic resistance has recently attracted increasing amounts of attention. Here, an artificially antibiotic-resistant bacterial community (ARBC) combined with five different constructed antibiotic-resistant bacteria (ARB) with single antibiotic resistance, namely, kanamycin (KAN), tetracycline (TET), cefotaxime (CTX), polymyxin B (PB), or gentamicin (GEM), was studied for the stress response to photocatalysis. With photocatalytic inactivation, the transfer and diffusion of antibiotic resistance genes (ARGs) in the ARBC decreased, and fewer multidrug-resistant bacteria (MDRB) emerged in aquatic environments. After several days of photocatalytic inactivation or Luria broth cultivation, >90% ARB were transformed to antibiotic-susceptible bacteria by discarding ARGs. Bacteria with double antibiotic resistance were the dominant species (99%) of residual ARB. The changes in ARG abundance varied, decreasing for the GEM and TET resistance genes and increasing for the KAN resistance genes. The change in the antibiotic resistance level was consistent with the change in ARG abundance. Correspondingly, point mutations occurred for the KAN, CTX and PB resistance genes after photocatalytic inactivation, which might be the reason why these genes persisted longer in the studied ARBC. In summary, photocatalytic inactivation could reduce the abundance of some ARGs and inhibit the emergence of MDRB as well as block ARG transfer in the bacterial community in aquatic environments. This work highlights the advantages of long-term photocatalytic inactivation for controlling antibiotic resistance and facilitates a better understanding of bacterial communities in real aquatic environments.

Aerobic composting technology is an efficient, safe and practical method to reduce the residues of antibiotics and antibiotic resistance genes (ARGs) due to unreasonable disposal of livestock manure. Nowadays, it remains unclear how aerobic composting works to minimize the level of remaining antibiotics and ARGs in manure. Moreover, aerobic composting techniques even have the potential to enhance ARGs level. Therefore, this study conducted a literature review on ARGs variation during the composting process to assess the fate, migration, and risk features of antibiotics and ARGs in different livestock manure and compost. The relationship between ARGs reduction and crucial factors (temperature, heavy metal, and microbial community structures) in the composting process was discussed. The merits and limitations of different technologies used in compost was summarized. The effects on ARGs reduction in the aerobic composting process with various strategies was examined. We attempt to provide a fresh and novel viewpoint on the advancement of global aerobic composting technology., Competing Interests: Declaration of competing interest 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., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Degradation of antibiotic resistance genes (ARGs) in water chlorination can be influenced by bromide (Br - ), a common component in water matrices; however, detailed kinetic information on this process is limited. This study investigated the degradation kinetics tetA and bla TEM-1 genes, contained within the plasmid pWH1266, when exposed to bromine, chlorine, and chlorine with varying concentrations of Br - across a pH range of 7.0-8.5. The degradation of four ARG amplicons, measured using quantitative polymerase chain reaction, was observed to pursue second-order kinetics with bromine, exhibiting k of 4.0 × 10 2 - 1.6 × 10 3  M -1  s -1 at pH 7.0 and 2.6 × 10 2 - 9.6 × 10 2  M -1  s -1 at pH 8.5. These k values increased linearly with the length of the ARG sequences (209-1136 bps), yielding sequence-independent k of 1.2 and 7.4 × 10 -1 (M AT + GC) -1  s -1  at pH 7.0 and 8.5, respectively. The degradation rate of ARGs during chlorination increased with rising Br - concentration due to the bromine formation through the reaction between chlorine with Br - , which subsequently degrades ARGs more rapidly than chlorine. This behavior was successfully simulated using a kinetic model derived from the reaction kinetics of bromine and chlorine reactions with ARGs. The existence of dissolved organic matter extracts only marginally decreased the enhanced degradation of ARGs with Br - , while ammonia significantly inhibited this process during chlorination, both with and without Br - , due to the low reactivity of NH 2 Cl and NH 2 Br toward ARGs. These findings highlight the importance of Br - in ARG degradation during water chlorination and the need for further studies in diverse water matrices., Competing Interests: Declaration of competing interest 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., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R 2 tra = 0.882, R 2 test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives., Competing Interests: Declaration of competing interest 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., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Aeromonas hydrophila, a prevalent pathogen in the aquaculture industry, poses significant challenges due to its drug-resistant strains. Moreover, residues of antibiotics like streptomycin, extensively employed in aquaculture settings, drive selective bacterial evolution, leading to the progressive development of resistance to this agent. However, the underlying mechanism of its intrinsic adaptation to antibiotics remains elusive. Here, we employed a quantitative proteomics approach to investigate the differences in protein expression between A. hydrophila under streptomycin (SM) stress and nonstress conditions. Notably, bioinformatics analysis unveiled the potential involvement of metal pathways, including metal cluster binding, iron-sulfur cluster binding, and transition metal ion binding, in influencing A. hydrophila's resistance to SM. Furthermore, we evaluated the sensitivity of eight gene deletion strains related to streptomycin and observed the potential roles of petA and AHA_4705 in SM resistance. Collectively, our findings enhance the understanding of A. hydrophila's response behavior to streptomycin stress and shed light on its intrinsic adaptation mechanism., (© 2024 Wiley‐VCH GmbH.)

Bacterial mercury (Hg) methylation is critical for bioremediating Hg pollution, but the impact of emerging antibiotics on this process has rarely been reported. This study innovatively investigated the interactions between Hg-methylating bacteria of Geobacter metallireducens GS-15 and two quinolone antibiotics: lomefloxacin (LOM) and ciprofloxacin (CIP) at 5 μg/L. Short-term LOM exposure increased methylmercury (MeHg) yield by 36 % compared to antibiotic-free conditions, caused by hormesis to alter bioactivities of single GS-15 cells. Long-term CIP exposure led to more antibiotic resistance and mercury tolerance in GS-15 cells, doubling MeHg productivity and significantly increasing expression of Hg methylation (hgcA by 95 folds) and antibiotic resistance (gyrA by 54 folds) genes, while mercury resistance gene merA only increased by 2.5 folds than without selective pressure. These results suggest quinolone antibiotics at environmentally contaminated concentrations stimulate bacterial Hg methylation to form highly toxic MeHg, raising considerable concern for the Hg-antibiotic complex in contaminated environments., Competing Interests: Declaration of competing interest 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., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Many multidrug-resistant (MDR) bacteria have evolved through the accumulation of antibiotic resistance genes (ARGs). Although the potential risk of probiotics as reservoirs of ARGs has been recognized, strategies for blocking the transfer of ARGs while using probiotics have rarely been explored. The probiotic Escherichia coli Nissle 1917 (EcN) has long been used for treating intestinal diseases. Here, we demonstrate frequent transfer of ARGs into EcN both in vitro and in vivo , raising concerns about its potential risk of accumulating antibiotic resistance. Given that no CRISPR-Cas system was found in natural EcN, we integrated the type I-E CRISPR-Cas3 system derived from E. coli BW25113 into EcN. The engineered EcN was able to efficiently cleave multiple ARGs [i.e., mcr-1 , bla NDM-1 , and tet (X)] encoding enzymes for degrading last-resort antibiotics. Through co-incubation of EcN expressing Cas3-Cascade and that expressing Cas9, we showed that the growth of the former strain outcompeted the latter strain, demonstrating a better clinical application prospect of EcN expressing the type I-E CRISPR-Cas3 system. In the intestine of a model animal (i.e., zebrafish), the engineered EcN exhibited immunity against the transfer of CRISPR-targeted ARGs. Our work equips EcN with immunity against the transfer of multiple ARGs by exploiting the exogenous type I-E CRISPR-Cas3 system, thereby reducing the risk of the spread of ARGs while using it as a probiotic chassis for generating living therapeutics., Importance: To reduce the development of antibiotic resistance, probiotics have been considered as a substitute for antibiotics. However, probiotics themselves are reservoirs of antibiotic resistance genes (ARGs). This study introduces a new strategy for limiting the spread of ARGs by engineering the typical probiotic strain Escherichia coli Nissle 1917 (EcN), which has been used for treating intestinal diseases and developed as living therapeutics. We also demonstrate that the type I CRISPR-Cas system imposes a lower growth burden than the type II CRISPR-Cas system, highlighting its promising clinical application potential. Our work not only provides a new strategy for restricting the transfer of ARGs while using probiotics but also enriches the genetic engineering toolbox of EcN, paving the way for the safe use and development of probiotics as living therapeutics.

Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10 -2 -1.5 × 10 -1 copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas., Competing Interests: Declaration of competing interest 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., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.

Wastewater-based surveillance (WBS) of multidrug-resistant bacteria could complement clinical data, serving as a population-level early warning tool. This study evaluated WBS as a pandemic preparedness tool, by selectively isolating and culturing methicillin-resistant Staphylococcus aureus (MRSA) with CHROMagar MRSA. Some 24-h composite wastewater samples ( n  = 80) were collected from ten treatment plants across Finland between February 2021 and January 2022. MRSA prevalence in wastewater samples was 27.5% ( n  = 22/80), showing seasonal and temporal variations. Phenotypic antimicrobial susceptibility testing (AST) with microdilution showed that over 80% of isolates were drug-resistant to clindamycin, sulfamethoxazole/trimethoprim, tetracycline, fusidic acid, and erythromycin. Four isolates (18.2%) were vancomycin-resistant. WGS revealed that 31.8% ( n  = 7) of the isolates belonged to the ST8- t 008 and ST6- t 304 spa types, respectively. In addition, two spa types ( t 011 and t 034) belong to the CC398 complex. The mec A gene was found in all isolates ( n  = 22) and three tetracycline resistance determinants ( tet 38, tet K, and tet M) were detected with tet 38 being the most abundant (81.8%, n  = 18/22). Three isolates harboured the plasmid-mediated sat 4 gene that confers resistance to Streptothricin. In addition, resistance determinants to macrolide antibiotics ( mph (C)/ msr (A) and fosfomycin ( fos B) were detected in the seven isolates that belonged to spa type t 008. All isolates except one harboured the SCC mec&#95; type&#95;IVa(2B). Six ST8 isolates harboured the LukS/F-PV genes encoding the Panton-Valentine leukocidin (PVL) and were also positive for the Arginine Catabolic Mobile Element (ACME), suggesting they belong to the USA300 clone. The Inc18 plasmid was the most abundant as it was detected in 72.7% ( n  = 16/22) of the isolates. Other plasmid replicons detected were the rep&#95;trans and repA&#95;N which were detected in 45.4% ( n  = 10/22) and 40.9% ( n  = 9/22) of the isolates respectively. Ten isolates harboured at least three plasmid replicons and no plasmid replicons were detected in four isolates (ST6/ t 304). The cgMLST revealed that some isolates aggregated into two genomically indistinguishable clusters: ST6/ t 304 belonging to cluster type CT12405 (≤20 allelic differences) and ST8/ t 008 belonging to cluster type CT1925 (<8 allelic differences). Overall, we found a high genotypic concordance with the national clinical bacterial resistance data. Our study demonstrates the sensitivity of culture-based wastewater surveillance for MRSA using clinical media following pre-enrichment, reliably predicting pathogen occurrence at the population level., 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. Kirsi-Maarit Lehto and Sami Oikarinen are the stakeholders of GreenSeq Ltd. Finland. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations or those of the publisher, the editors, or the reviewers., (© 2024 The Authors. Published by Elsevier B.V.)

Antimicrobial resistance (AMR) poses a global health threat to aquatic environments and its propagation is a hot topic. Therefore, deactivating antibiotic-resistant bacteria (ARB) and removing antibiotic resistance genes (ARGs) from water is crucial for controlling AMR transmission. Peracetic acid (PAA), which is known for its potent oxidizing properties and limited by-product formation, is emerging as a favorable disinfectant for water treatment. In this study, we aimed to assess the efficacy of pre-exposure to PAA followed by UV treatment (PAA-UV/PAA) compared with the simultaneous application of UV and PAA (UV/PAA). The focus was on deactivating vancomycin-resistant Enterococcus faecalis (VREfs), a typical ARB in water. Pre-exposure to PAA significantly enhanced the efficacy of subsequent UV/PAA treatment. At a UV fluence of 7.2 mJ cm -2 , the PAA-UV/PAA method achieved a 6.21 log reduction in VREfs, surpassing the 1.29 log reduction observed with UV/PAA. Moreover, compared to UV/PAA, PAA-UV/PAA showed increased efficacy with longer pre-exposure times and higher PAA concentrations, maintaining superior performance across a broad pH range and in the presence of humic acid. Flow cytometry analysis indicated minimal cellular membrane damage using both methods. However, the assessments of superoxide dismutase (SOD) activity and adenosine triphosphate content revealed that PAA-UV/PAA induced greater oxidative stress under similar UV irradiation conditions, leading to slower bacterial regrowth. Specifically, SOD activity in PAA-UV/PAA surged to 3.06 times its baseline, exceeding the 1.73-fold increase under UV/PAA conditions. Additionally, pre-exposure to PAA amplified ARGs degradation and reduced resistance gene leakage, effectively mitigating the spread of AMR. Pre-exposure to 200 μM PAA for 10 and 20 min enhanced vanB gene removal efficiency by 0.14 log and 1.29 log, respectively. Our study provides a feasible approach for optimizing UV/PAA disinfection for efficient removal of ARB and ARGs., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Minghao Sui reports financial support was provided by Ministry of Science and Technology of the People's Republic of China. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

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

Abstract 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 Avibacterium paragallinarum is the etiological agent of infectious coryza, an acute respiratory disease of chickens that is globally distributed and causes serious economic losses for chicken production. A. paragallinarum is a Gram-negative bacterium that releases outer membrane vesicles (OMVs). In this study, a comparative genomic analysis of A. paragallinarum isolate P4chr1 and its OMVs was carried out, and the ability to transfer antibiotic resistance genes (ARGs) via the OMVs was studied. Sequencing and data analyses demonstrated that the genomic size of A. paragallinarum P4chr1 was approximately 2.77 Mb with a 25 kb tolerance island that covered six types of antibiotics and 11 ARGs. The genomic size of its OMVs was approximately 2.69 Mb, covering 97% of the genomic length and almost all the gene sequences of P4chr1. Purified and DNase-treated A. paragallinarum P4chr1 OMVs were cocultured with the antibiotic-sensitive A. paragallinarum Modesto strain on an antibiotic (chloramphenicol, erythromycin, tetracycline, or streptomycin)-containing plate, and the corresponding ARGs were detected in the colonies grown on the plates. However, using an antimicrobial susceptibility test, we found that ARGs delivered by OMVs were not persistent but only appeared transiently on the antibiotic-containing plates. Antibiotic resistance and ARGs were lost by the second bacterial passage. IMPORTANCE The functions and roles of OMVs on ARG and virulent gene transfer and dissemination have been reported in numerous Gram-negative bacteria. However, the role of OMVs in mediating antibiotic resistance in A. paragallinarum has not been reported. This study is the first report to compare the genomic characteristics of OMVs with its parent A. paragallinarum strain and to study A. paragallinarum ARG transfer via OMVs. This work has provided useful data for further studies focusing on nonplasmid ARG transfer mediated by A. paragallinarum OMVs.

ABSTRACT: Since antibiotic resistance is a global health issues, the use of antibiotics in animal feed for growth promotion has been restricted in many countries. Bacillus licheniformis probiotic is a potential alternative to antibiotics for increasing poultry performance. Through metagenomic sequencing, this study investigated the effects of B. licheniformis–fermented products (BLFPs) and enramycin on the microbial community composition and antibiotic resistance gene (ARG) distribution in the cecal digesta of broilers at the age of 35 d. In total, 144 one-day-old male broiler chicks (Ross 308) were randomly assigned to 4 dietary treatments as follows: basal diet (control [C] group), basal diet plus 10 mg/kg enramycin (E group), basal diet plus 1 g/kg BLFPs (L group), and basal diet plus 3 g/kg BLFPs (H group), with 6 replicate cages per treatment group and 6 birds per cage. The results indicated that the cecal alpha diversity (richness and evenness) of bacterial species was higher in the H group than in the C group. Principal coordinate analysis of microbiota and the ARG composition indicated clear differences among the cecal samples of the groups. In the cecal digesta, the abundance of active bacteria associated with probiotic properties, such as Lactobacillus crispatus and Akkermansia muciniphila, was higher in the H group than in the other groups. Enramycin treatment promoted the expression of peptide (bcrA), glycopeptide (vanRI), and lincosamide (lsaE) resistance genes but inhibited the expression of aminocoumarin (parY) and pleuromutilin (TaeA) resistance genes. BLFP (1 and 3 g/kg) treatment suppressed the expression of aminoglycoside (ANT(6)-Ib), streptogramin (vatB), and peptide (ugd) resistance genes but enhanced the expression of macrolide (efrA) and aminocoumarin (novA) resistance genes. The abundance of peptide resistance genes in Bacteroides spp. was lower in the H group than in the C group. The abundance of lincosamide resistance genes in Lactobacillus spp. was higher in the E group than in the other groups. These results demonstrated that differential changes in the structure of 3 g/kg BLFPs and enramycin-induced cecal microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the cecal microbiota of broilers.

The wide presence of antibiotics and minerals warrants their combined effects on the denitrification in natural aquatic environment. Herein, we investigated the effects of two antibiotics, sulfamethazine (SMZ) and chlortetracycline (CTC), on the reduction of NO3--N and accumulation of NO2--N in the absence and presence of engineered nanoparticles (NPs) (Al2O3, SiO2, and geothite) using 16 S rRNA sequencing and high-throughput quantitative PCR. The results showed that the addition of antibiotics inhibited the reduction of NO3--N by changing the bacterial community structure and reducing the abundance of denitrification genes, while engineered NPs promoted the denitrification by increasing the abundance of denitrification genes. In the binary systems, engineered NPs alleviated the inhibitory effect of antibiotics through enriching the denitrification genes and adsorbing antibiotics. Antibiotics and its combination with engineered NPs changed the composition of functional genes related to C, N, P, S metabolisms (p

Antibiotics are administered to livestock at subtherapeutic levels to promote growth, and their degradation in manure is slow. High antibiotic concentrations can inhibit bacterial activity. Livestock excretes antibiotics via feces and urine, leading to their accumulation in manure. This can result in the propagation of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Anaerobic digestion (AD) manure treatment technologies are gaining popularity due to their ability to mitigate organic matter pollution and pathogens, and produce methane-rich biogas as renewable energy. AD is influenced by multiple factors, including temperature, pH, total solids (TS), substrate type, organic loading rate (OLR), hydraulic retention time (HRT), intermediate substrates, and pre-treatments. Temperature plays a critical role, and thermophilic AD has been found to be more effective in reducing ARGs in manure compared to mesophilic AD, as evidenced by numerous studies. This review paper investigates the fundamental principles of process parameters affecting the degradation of ARGs in anaerobic digestion. The management of waste to mitigate antibiotic resistance in microorganisms presents a significant challenge, highlighting the need for effective waste management technologies. As the prevalence of antibiotic resistance continues to rise, urgent implementation of effective treatment strategies is necessary.

Aiming at the pollution of antibiotic resistance genes (ARGs) in solid wastes such as antibiotic residues, livestock and poultry manure, sludge, etc., this article discussed the effects of traditional aerobic composting technology and enhanced composting technology with external additives on ARGs. The influence of heavy metals and bacterial commun让ies in the oxygen composting system on the growth and decline of ARGs and the horizontal transmission of ARGs between different microorganisms by microorganisms through movable genetic elements within the molecules were analyzed・ The study found that different heavy metals have different effects on multiple ARGs at different concentrations; the positive correlation between different ARGs and the same host bacteria indicates the coexistence of different ARGs, and further concluded that the bacterial community succession may be all mixed the main driving force for the different fates of ARGs under composting conditions. [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored. [ABSTRACT FROM AUTHOR]

Copyright of Iranian Journal of Veterinary Science & Technology is the property of Ferdowsi University of Mashhad Press 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.)

Biochar has been used to alleviate the contamination of antibiotic resistance genes (ARGs) in soil and to inhibit ARGs transfer from soil to plants. However, the effect of aged biochar on ARGs abundance in soil and ARGs enrichment in plants are scarcely investigated. In this study, a pot experiment was conducted to compare the effects of fresh and aged biochars on the accumulation of five typical ARGs including tetX, tetW, sul2, ermB, and intI1 in a chicken manure-fertilized soil and in pakchoi (Brassica chinensis L.). Results showed that both biochars significantly decreased the abundance of tetW, sul2, and ermB and increased the abundance of tetX and intI1 in soil. However, the accumulation of all tested ARGs in pakchoi were significantly decreased by both biochars. At the lower addition rate (1%), the fresh biochar was superior to the aged biochar in decreasing the accumulation of some genes (tetW, tetX, and sul2) in pakchoi, whereas an opposite tendency was observed for other genes (ermB and intI1). As the addition rate increased to 2%, the difference between the two biochars diminished, and a similar capacity of decreasing ARGs transfer was observed. The reduction in ARGs accumulation in pakchoi was highly related to the type of ARGs, the biochar addition level, and the aging of biochar. Our results provide insights into the naturally aged biochar on the fate of ARGs in a soil–plant system. [ABSTRACT FROM AUTHOR]

Microbial electrolysis cells (MECs) have been applied for antibiotic degradation but simultaneously induced antibiotic resistance genes (ARGs), thus representing a risk to disseminate antibiotic resistance. However, few studies were on the potential and risk of ARGs transmission in the MECs. This work assessed conjugative transfer of ARGs under three tested conditions (voltages, cell concentration, and donor/recipient ratio) in both single- and two-chamber MECs. The results indicated that voltages (> 0.9 V) facilitated the horizontal frequency of ARGs in the single-chamber MECs and anode chamber of two-chamber MECs. The donor cell number (donor/recipient ratio was 2:1) increased the transfer frequency of ARGs. Furthermore, voltages ranged from 0.9 to 2.5 V increased reactive oxygen species (ROS) production and cell membrane permeability in MECs. These findings offer new insights into the roles of ARG transfer under different applied voltages in the MECs, which should not be ignored for horizontal transfer of antibiotic resistance. [ABSTRACT FROM AUTHOR]

[Display omitted] • Multiple factors co-shaped the profile of antibiotics and ARGs in landfill leachate. • Leachate age was crucial to the profile of antibiotics and ARGs. • Extreme abundance of the same category of ARGs occurs in the same period. • Antibiotic concentrations vary by 1–2 orders of magnitude in dry and rainy seasons. • Most of ARGs had a higher detection level in rainy season. Landfill leachate is an important source and sink of antibiotics and antibiotic resistance genes (ARGs), which poses a potential threat to human health and ecological environment. Ten antibiotics and 8 ARGs in leachates collected from Zhejiang Province, China, were systematically investigated. The effects of multiple factors were considered: leachate age, season when the leachate was sampled (dry or rainy), heavy metal concentrations, and leachate quality parameters. Leachate age was crucial to the profile of the detectable antibiotics and ARGs. The total concentration of antibiotics were in the order of macrolides > sulfonamides > tetracyclines and they decreased significantly with leachate age. Similarly, fewer ARGs were harbored in aged leachate; the order of abundance of the ARGs was mexF (11.92 ± 0.22 log 10 gene copies/L) > sul2 > Intl1 > sul1 > ermB > mefA > tetM > tetQ (9.57 ± 1.32 log 10 gene copies/L). The extreme abundances (i.e., the maxima and minima) of ARGs relating to the same class of antibiotic were always surprisingly similar and appeared in leachate of the same age. Seasonal variation greatly affected the concentrations of antibiotics in the leachate—the concentration difference between the dry and rainy seasons could reach two orders of magnitude. Heavy metal concentrations and leachate quality parameters also had important effects on the distribution of antibiotics and ARGs. Overall, the profile of antibiotics and ARGs in leachates was influenced by numerous factors, and the pollution of antibiotics and ARGs may be reduced and controlled by adjusting the environmental factors. [ABSTRACT FROM AUTHOR]

The long-term use of veterinary antibiotics has led to increasing contamination of antibiotic resistance genes（ARGs）in livestock and poultry farming environments, and the risks and negative effects of ARGs in the environment have garnered research attention. In this study, we review the pollution and diffusion of ARGs in livestock and poultry farming environments. We analyzed the differences in the concentration of ARGs in manure between different livestock species and different countries and regions. We elaborate the changes in ARGs during manure composting and the growth pattern of ARGs during wastewater treatments. In addition, we discuss the effects of ARG input to the surrounding soil and atmosphere via manure application and airflow on the natural resistance levels in the surrounding environment media. Finally, based on the pollution status of ARGs in livestock and poultry manure, we summarize and propose measures to reduce the discharge and diffusion of ARGs from livestock farms in the future. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Applied Ecology / Yingyong Shengtai Xuebao is the property of Chinese Journal of Applied Ecology 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.)

[Display omitted] • 5% biochar addition enhanced SMFC power and reduced ARG risks efficiently. • Excessive (10%) biochar addition would increase the abundance of ARGs. • Biochar impacted ARG spread via insertion sequences, transposases and prophages. • Biological factors showed a greater impact on ARGs than electrochemical effects. • Genetic material and amino acid synthesis controlled ARGs by influencing metabolism. This study is the first to explore the performance and mechanism of biochar-impacted sediment microbial fuel cell for removing antibiotic resistance genes (ARGs), and examines the effects of different biochar contents. The addition of 5% biochar produced the highest output voltage and power density, which increased by 100% and 219%, respectively, while simultaneously reducing the abundance and risk of ARGs. Comparatively, the addition of moderate amount of biochar (1–5%) promoted the removal of ARGs, while the opposite was true for excessive (10%) biochar. Biochar affected ARGs through prophages, insertion sequence, and transposons. Biological factors and voltage jointly influenced ARGs variation, with the former accounting for 56%. Further analysis of functional genes indicated that biochar controlled ARGs by regulating the synthesis of genetic material and amino acids to influence metabolism. Overall, findings of this study shed light on the potential removal of ARGs in microbial electrochemical systems. [ABSTRACT FROM AUTHOR]

• ARB can achieve >5-log reduction in the E-UV/Cl 2 process. • No photoreactivation of ARB occurred after the E-UV/Cl 2 treatment. • Intracellular ARGs can achieve >4-log reduction in the E-UV/Cl 2 process. • AFM analysis shows low risk of horizontal gene transfer after the E-UV/Cl 2 treatment. • ARG removal was associated to •OH, Cl 2 ‒•, and ClO• exposures. The UV/chlorine (UV/Cl 2) process is a developing advanced oxidation process and can efficiently remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the transportation and storage of chlorine solutions limit the application of the UV/Cl 2 process, especially for decentralized water treatment. To overcome the limitation, an electrochemically driven UV/Cl 2 process (E-UV/Cl 2) where Cl 2 can be electrochemically produced in situ from anodic oxidation of chloride (Cl−) ubiquitously present in various water matrices was evaluated in this study. >5-log inactivation of the ARB (E. coli) was achieved within 5 s of the E-UV/Cl 2 process, and no photoreactivation of the ARB was observed after the treatment. In addition to the ARB, intracellular and extracellular ARGs (tet A, sul 1, sul 2, and erm B) could be effectively degraded (e.g., log(C 0 /C) > 4 for i-ARGs) within 5 min of the E-UV/Cl 2 process. Atomic force microscopy showed that the most of the i-ARGs were interrupted into short fragments (< 30 nm) during the E-UV/Cl 2 process, which can thus effectively prevent the self-repair of i-ARGs and the horizontal gene transfer. Modelling results showed that the abatement efficiencies of i-ARG correlated positively with the exposures of •OH, Cl 2 −•, and ClO• during the E-UV/Cl 2 process. Due to the short treatment time (5 min) required for ARB and ARG removal, insignificant concentrations of trihalomethanes (THMs) were generated during of the E-UV/Cl 2 process, and the energy consumption (E EO) of ARG removal was ∼0.20‒0.27 kWh/m3-log, which is generally comparable to that of the UV/Cl 2 process (0.18–0.23 kWh/m3-log). These results demonstrate that the E-UV/Cl 2 process can provide a feasible and attractive alternative to the UV/Cl 2 process for ARB and ARG removal in decentralized water treatment system. [Display omitted] [ABSTRACT FROM AUTHOR]

• The virome in activated sludge treating antibiotic production wastewater were revealed. • The contribution of transduction to the HGT of ARGs appears to be relatively limited. • Folate-related AMGs were the most prevalent AMGs. • Some new potential virus-host assignments were discovered. • Antibiotics has not driven viral communities into either lytic or lysogenic cycles. Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like , increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress. [ABSTRACT FROM AUTHOR]

Antibiotic resistance is a continually rising threat to global health. A primary driver of the evolution of new strains of resistant pathogens is the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). However, identifying and quantifying ARGs subject to HGT remains a significant challenge. Here, we introduce HT-ARGfinder (horizontally transferred ARG finder), a pipeline that detects and enumerates horizontally transferred ARGs in metagenomic data while also estimating the directionality of transfer. To demonstrate the pipeline, we applied it to an array of publicly-available wastewater metagenomes, including hospital sewage. We compare the horizontally transferred ARGs detected across various sample types and estimate their directionality of transfer among donors and recipients. This study introduces a comprehensive tool to track mobile ARGs in wastewater and other aquatic environments.

The presence of antibiotic resistance genes (ARGs) in soils has received extensive attention regarding its impacts on environmental, animal, and human systems under One Health. However, the health risks of soil ARGs and microbial determinants of soil resistomes remain poorly understood. Here, a nationwide metagenomic investigation of ARGs in cropland and forest soils in China was conducted. The findings indicated that the abundance and richness of high-risk (i.e., mobilizable, pathogen-carriable and clinically relevant) ARGs in cropland soils were 25.7 times and 8.4 times higher, respectively, compared to those identified in forest soils, suggesting the contribution of agricultural practices to the elevated risk level of soil resistomes. The biosynthetic potential of antibacterials best explained the total ARG abundance (Mantel's r = 0.52, p < 0.001) when compared with environmental variables and anthropogenic disturbance. Both microbial producers' self-resistance and antagonistic interactions contributed to the ARG abundance, of which self-resistance ARGs account for 14.1 %− 35.1 % in abundance. With the increased biosynthetic potential of antibacterials, the antagonistic interactions within the microbial community were greatly enhanced, leading to a significant increase in ARG abundance. Overall, these findings advance our understanding of the emergence and dissemination of soil ARGs and provide critical implications for the risk control of soil resistomes. [Display omitted] • Agricultural activities increase the risk level of soil resistome. • The soil ARGs are influenced by the biosynthetic potential of antibacterials. • Producers' self-resistance and microbial antagonisms contribute to ARG prevalence. [ABSTRACT FROM AUTHOR]

[Display omitted] • CTC achieved a maximum of 97.8% removal in the MMT-CS bio-enhanced process. • MMT-CS promoted EPS secretion and electron transfer in the system. • The mechanism of bio-enhanced degradation of CTC by MMT-CS was revealed. • Paracoccus and Terrimonas were the key bacteria gene in MMT-CS bio-enhanced process. • The biological metabolic pathways of CTC were clarified. The efficient degradation of antibiotics holds significant implications for mitigating environmental pollution. This study synthesized a montmorillonite chitosan composite material (MMT-CS) using the gel template method. Subsequently, a bio-enhanced reactor was constructed to facilitate the degradation of chlorotetracycline (CTC). The addition of MMT-CS composite material enables the degradation of different concentrations of CTC. MMT-CS, a conductive carrier, effectively promotes microbial adhesion and boosts the metabolic activity of functional microorganisms. Additionally, it facilitates the maintenance of microbial activity under CTC pressure by promoting the secretion of extracellular polymeric substances, increasing critical enzyme activity, and enhancing the electron transfer capacity within the system. In this MMT-CS bio-enhanced process, Paracoccus (11.4%) and Bacillus (3.9%) are utilized as essential bacteria genes. The results of metabolic pathways prediction indicated significant enhancements in membrane-transport, nucleotide-metabolism, replication-repair, and lipid-metabolism. Thus, the developed self-supporting MMT-CS bio-enhanced process ensured the stability of the system during the removal of antibiotics. [ABSTRACT FROM AUTHOR]

The significant threat of antibiotic resistance genes (ARGs) to aquatic environments health has been widely acknowledged. To date, several studies have focused on the distribution and diversity of ARGs in a single river while their profiles in complex river networks are largely known. Here, the spatiotemporal dynamics of ARG profiles in a canal network were examined using high-throughput quantitative PCR, and the underlying assembly processes and its main environmental influencing factors were elucidated using multiple statistical analyses. The results demonstrated significant seasonal dynamics with greater richness and relative abundance of ARGs observed during the dry season compared to the wet season. ARG profiles exhibited a pronounced distance-decay pattern in the dry season, whereas no such pattern was evident in the wet season. Null model analysis indicated that deterministic processes, in contrast to stochastic processes, had a significant impact on shaping the ARG profiles. Furthermore, it was found that Firmicutes and pH emerged as the foremost factors influencing these profiles. This study enhanced our comprehension of the variations in ARG profiles within canal networks, which may contribute to the design of efficient management approaches aimed at restraining the propagation of ARGs. [Display omitted] • 131 ARGs were detected with higher abundances in the dry season than wet season. • Deterministic processes dominated assembly of ARGs communities in river networks. • Firmicutes and pH mainly shaped ARGs communities in river networks (p < 0.01). [ABSTRACT FROM AUTHOR]

• SPMs are hotspots for ARGs and the HGB act as supercarriers of ARGs. • Anoxic microenvironments on SPMs provide ideal habitats for HGB and other anaerobes. • SPMs facilitate synergy between HGB and denitrifiers for propagation of ARGs. Human gut antibiotic resistome widely occur in anoxic environments characterized by high density of bacterial cells and frequent transmission of antibiotic resistance genes (ARGs). Such resistome is greatly diluted, degraded, and restrained in the aerobic habitats within most natural rivers (regarded as "terrestrial guts") connecting continents and the oceans. Here we implemented a large-scale monitoring campaign extending 5,200 km along the Yellow River, and provide the first integral biogeographic pattern for both ARGs and their hosts. We identified plentiful ARGs (24 types and 809 subtypes) and their hosts (24 phyla and 757 MAGs) in three media (water, suspended particulate matter (SPM), and sediment). Unexpectedly, we found diverse human gut bacteria (HGB) acting as supercarriers of ARGs in this oxygen-rich river. We further discovered that numerous microhabitats were created within stratified biofilms that surround SPMs, particularly regarding the aggregation of anaerobic HGB. These microhabitats provide numerous ideal sinks for anaerobic bacteria and facilitate horizontal transfer of ARGs within the stratified biofilms, Furthermore, the stratification of biofilms surrounding SPMs has facilitated synergy between human gut flora and denitrifiers for propagation of ARGs in the anoxic atmospheres, leading to high occurrence of human gut antibiotic resistome. SPMs play active roles in the dynamic interactions of river water and sediment, thus accelerating the evolution of riverine resistome and transmission of human gut antibiotic resistome. This study revealed the special contribution of SPMs to the propagation of ARGs, and highlighted the necessity of making alternative strategies for sustainable management of large rivers with hyper-concentrated sediment-laden flows. [Display omitted] [ABSTRACT FROM AUTHOR]

Microplastics (MPs) are emerging ubiquitous pollutants in aquatic environment and have received extensive global attention. In addition to the traditional studies related to the toxicity of MPs and their carrier effects, their unique surface-induced biofilm formation also increases the ecotoxicity potential of MPs from multiple perspectives. In this review, the ecological risks of MPs biofilms were summarized and assessed in detail from several aspects, including the formation and factors affecting the development of MPs biofilms, the selective enrichment and propagation mechanisms of current pollution status of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in MPs biofilms, the dominant bacterial communities in MPs biofilms, as well as the potential risks of ARGs and MGEs transferring from MPs biofilms to aquatic organisms. On this basis, this paper also put forward the inadequacy and prospects of the current research and revealed that the MGEs-mediated ARG propagation on MPs under actual environmental conditions and the ecological risk of the transmission of ARGs and MGEs to aquatic organisms and human beings are hot spots for future research. Relevant research from the perspective of MPs biofilm should be carried out as soon as possible to provide support for the ecological pollution prevention and control of MPs. [Display omitted] [ABSTRACT FROM AUTHOR]

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

The widespread use of disinfectants during the global response to the 2019 coronavirus pandemic has increased the co-occurrence of disinfection byproducts (DBPs) and antibiotic resistance genes (ARGs). Although DBPs pose major threats to public health globally, there is limited knowledge regarding their biological effects on ARGs. This study aimed to investigate the effects of two inorganic DBPs (chlorite and bromate) on the conjugative transfer of RP4 plasmid among Escherichia coli strains at environmentally relevant concentrations. Interestingly, the frequency of conjugative transfer was initially inhibited when the exposure time to chlorite or bromate was less than 24 h. However, this inhibition transformed into promotion when the exposure time was extended to 36 h. Short exposures to chlorite or bromate were shown to impede the electron transport chain, resulting in an ATP shortage and subsequently inhibiting conjugative transfer. Consequently, this stimulates the overproduction of reactive oxygen species (ROS) and activation of the SOS response. Upon prolonged exposure, the resurgent energy supply promoted conjugative transfer. These findings offer novel and valuable insights into the effects of environmentally relevant concentrations of inorganic DBPs on the conjugative transfer of ARGs, thereby providing a theoretical basis for the management of DBPs. [Display omitted] • Exposure to chlorite/bromate first suppresses and then promotes the HGT of ARGs. • Disruption of the electron transport chain contributed to the inhibited conjugation. • Restoration of energy supply and increased ROS production facilitated conjugation. [ABSTRACT FROM AUTHOR]

The toxic effects of antibiotics on anammox bacteria (AnAOB) draw much attention. Zero valent iron (ZVI) can improve anammox performance, but whether ZVI promotes resistance to antibiotics stress is unknown. In this study, the effect of tetracycline hydrochloride (TCH) on anammox in the 10 wt% ZVI modified carrier filled system (R1) was investigated. Results showed that semi-inhibitory concentration (IC 50) of TCH in R1 was 30.93 mg/L. In comparison, IC 50 of TCH in R0 filled with conventional carriers was only 18.87 mg/L. Long-term effects showed that the inhibition of anammox biofilm by low concentration of TCH (≤ 50 μg/L) was not significant, whereas R1 exhibited better anammox performance than R0 when TCH was 100–200 μg/L. More extracellular polymeric substances (EPS) on the modified carriers was beneficial to trap TCH to mitigate toxicity. In addition, the heme-c contents and the enzymatic activities of NIR, HZS, HDH of R1 were higher than those of R0 regardless of the TCH dosing. The synergistic TCH degradation bacterium Ignavibacterium was enriched in R1, which might further mitigate the toxic effect of TCH. qPCR results of antibiotic resistance genes (ARGs) showed tetX , tetA and tetG were up-regulated on ZVI modified carrier, implying more enzymes were produced to inactivate and pump out TCH to resist the stress. [Display omitted] • ZVI-10 carriers promoted AnAOB resistance to TCH stress with IC 50 of 30.93 mg/L. • ZVI-10 carriers induced more EPS to trap TCH to attenuate the toxicity to AnAOB. • Activities of NIR, HZS and HDH, as well as heme-c contents were enhanced. • The synergistic TCH degradation bacterium Ignavibacterium was enriched. • Enzymatic TCH inactivation and efflux pumping were the main mechanisms to resist TCH. [ABSTRACT FROM AUTHOR]

Antibiotic resistance genes (ARGs) have been steadily increasing due to the extensive overuse of antibiotics in the marine environment. Currently, the research considering ARGs distribution in marine ecosystems gains more interest. As the coastal sea has been regarded as one of the most polluted areas by antibiotic contaminants in China. However, no comprehensive review of the spatial distribution of ARGs in marine environment surrounding China. The main objective of this review is to investigate the level, characteristic, and spatial distribution of ARGs in the marine environment (seawater and sediments) surrounding China. Key sea areas, such as Bohai Sea, Yellow Sea, East China Sea, and South China Sea were selected in this review. The marine environment was the reservoir of ARGs, and ARGs in seawater were generally 1 to 2 orders of magnitude higher than that in sediments. Total ARGs were more abundant in the Yellow Sea, followed by the Bohai Sea, the East China Sea, and the South China Sea. This study raises questions regarding the spread and distribution for antibiotic resistance in marine environments. [Display omitted] • Qnr A was the predominant ARG in the marine areas surrounding China. • The relative abundances of ARGs in seawater were higher than that in sediments. • The Yellow Sea held the highest relative abundance of ARGs. • Human activities have impacts on the abundance of ARGs in the marine environment. [ABSTRACT FROM AUTHOR]