RESUMEN
Dissemination of antibiotic resistance genes (ARGs) has become a critical threat to public health. Activated sludge, rich in extracellular polymeric substances (EPS), is an important pool of ARGs. In this study, mechanisms of conjugation transfer of ARGs induced by EPS, including tightly bound EPS (TBEPS), soluble EPS (SEPS), and loosely bound EPS (LBEPS), were explored in terms of molecular diversities and electron transfer properties of EPS. Conjugation transfer frequency was increased by 9.98-folds (SEPS), 4.21-folds (LBEPS), and 15.75-folds (TBEPS) versus the control, respectively. Conjugation-related core genes involving SOS responses (9 genes), membrane permeability (18 genes), intercellular contact (17 genes), and energy metabolism pathways (13 genes) were all upregulated, especially in the presence of TBEPS. Carbohydrates and aliphatic substances in SEPS and LBEPS were contributors to ARG transfer, via influencing reactive oxygen species (ROS) formation (SEPS) and ROS and adenosine triphosphate (ATP) production (LBEPS). TBEPS had the highest redox potential and greatest lability and facilitated electron transfer and alternated respiration between cells, thus promoting ARG transfer by producing ATP. Generally, the chemical molecular characteristics and redox properties of EPS facilitated ARG transfer mainly by influencing lipid peroxidation and ATP, respectively.
Asunto(s)
Matriz Extracelular de Sustancias Poliméricas , Matriz Extracelular de Sustancias Poliméricas/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Transporte de Electrón/efectos de los fármacos , Aguas del Alcantarillado/microbiología , Conjugación Genética , Genes Bacterianos/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Adenosina Trifosfato/metabolismoRESUMEN
Benzylalkyldimethylethyl ammonium compounds (BAC) and polyvinyl chloride microplastics (PVC MPs), as the frequently detected pollutants in wastewater treatment plants (WWTPs), have attracted more concerns on their ecosystem risks. Therefore, this study investigated how the sulfur autotrophic denitrification (SAD) system responded to the single and joint stress of PVC MPs (1, 10 and 100 mg/L) and BAC (0.5, 5 and 10 mg/L). After 100 days of operation, the presence of 10 mg/L BAC led to obviously inhibitory effects on system performance and microbial metabolic activity. And the additions of PVC MPs or/and BAC stimulated the proliferation of intracellular resistance genes (RGs), whereas exposure to BAC increased the abundances of extracellular RGs and free RGs in water more significantly. Compared to the joint stress, BAC single stress resulted in higher abundances of free RGs in water, which further increased the risk of RGs propagation. Moreover, the interaction between mobile genetic elements and extracellular polymeric substances further increased the spread of RGs. Pathogens might be the potential hosts of RGs and enriched in SAD system and plastisphere, thereby leading to more serious ecological risks. This study will broaden the understanding of the environmental hazards posed by PVC MPs and BAC in WWTPs.
Asunto(s)
Procesos Autotróficos , Desnitrificación , Cloruro de Polivinilo , Contaminantes Químicos del Agua , Contaminantes Químicos del Agua/toxicidad , Azufre , Genes Bacterianos/efectos de los fármacos , Microbiota/efectos de los fármacos , Aguas ResidualesRESUMEN
Dialkyldimethyl ammonium compound (DADMAC) is widely used in daily life as a typical disinfectant and often co-exists with the heavy metal zinc in sewage environments. This study investigated the effects of co-exposure to zinc (1 mg/L) and DADMAC (0.2-5 mg/L) on the performance, bacterial community, and resistance genes (RGs) in a partial sulfur autotrophic denitrification coupled with anaerobic ammonium oxidation (PSAD-Anammox) system in a sequencing batch moving bed biofilm reactor for 150 days. Co-exposure to zinc and low concentration (0.2 mg/L) DADMAC did not affect the nitrogen removal ability of the PASD-Anammox system, but increased the abundance and transmission risk of free RGs in water. Co-exposure to zinc and medium-to-high (2-5 mg/L) DADMAC led to fluctuations in and inhibition of nitrogen removal, which might be related to the enrichment of heterotrophic denitrifying bacteria dominated by Denitratisoma. Co-exposure to zinc and high concentration DADMAC (5 mg/L) stimulated the secretion of extracellular polymeric substances and increased the proliferation risk of intracellular RGs in sludge. This study provided insights into the application of PSAD-Anammox system and the ecological risks of wastewater containing zinc and DADMAC.
Asunto(s)
Procesos Autotróficos , Reactores Biológicos , Desnitrificación , Zinc , Zinc/química , Desnitrificación/efectos de los fármacos , Bacterias/efectos de los fármacos , Bacterias/genética , Bacterias/metabolismo , Compuestos de Amonio Cuaternario/farmacología , Compuestos de Amonio Cuaternario/química , Azufre/química , Biopelículas/efectos de los fármacos , Oxidación-Reducción , Genes Bacterianos/efectos de los fármacos , Compuestos de Amonio/química , Contaminantes Químicos del Agua/toxicidad , Nitrógeno/metabolismo , Anaerobiosis , Farmacorresistencia Bacteriana/genética , Farmacorresistencia Bacteriana/efectos de los fármacosRESUMEN
Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.
Asunto(s)
Aguas Residuales , Aguas Residuales/microbiología , Farmacorresistencia Microbiana/genética , Lagos/microbiología , Genes Bacterianos/efectos de los fármacos , Contaminación del Agua , Microbiología del Agua , Microbiota/efectos de los fármacos , Antibacterianos/farmacología , Plásmidos/genética , Farmacorresistencia Bacteriana/genética , Bacterias/efectos de los fármacos , Bacterias/genética , Bacterias/clasificaciónRESUMEN
Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.
Asunto(s)
Antibacterianos , Carpas , Microplásticos , Oxitetraciclina , Cloruro de Polivinilo , Contaminantes Químicos del Agua , Animales , Microplásticos/toxicidad , Contaminantes Químicos del Agua/toxicidad , Oxitetraciclina/toxicidad , Carpas/microbiología , Antibacterianos/farmacología , Antibacterianos/toxicidad , Microbioma Gastrointestinal/efectos de los fármacos , Bacterias/efectos de los fármacos , Bacterias/genética , Sulfametazina/toxicidad , Genes Bacterianos/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Farmacorresistencia Bacteriana/genética , Farmacorresistencia Bacteriana/efectos de los fármacosRESUMEN
In this study, oversized microplastics (OMPs) were intentionally introduced into soil containing manure-borne doxycycline (DOX). This strategic approach was used to systematically examine the effects of combined OMP and DOX pollution on the growth of pak choi, analyze alterations in soil environmental metabolites, and explore the potential migration of antibiotic resistance genes (ARGs). The results revealed a more pronounced impact of DOX than of OMPs. Slender-fiber OMPs (SF OMPs) had a more substantial influence on the growth of pak choi than did coarse-fiber OMPs (CF OMPs). Conversely, CF OMPs had a more significant effect on the migration of ARGs within the system. When DOX was combined with OMPs, the negative effects of DOX on pak choi growth were mitigated through the synthesis of indole through the adjustment of carbon metabolism and amino acid metabolism in pak choi roots. In this process, Pseudohongiellaceae and Xanthomonadaceae were key bacteria. During the migration of ARGs, the potential host bacterium Limnobacter should be considered. Additionally, the majority of potential host bacteria in the pak choi endophytic environment were associated with tetG. This study provides insights into the intricate interplay among DOX, OMPs, ARGs, plant growth, soil metabolism, and the microbiome.
Asunto(s)
Antibacterianos , Doxiciclina , Estiércol , Microplásticos , Contaminantes del Suelo , Doxiciclina/farmacología , Doxiciclina/toxicidad , Antibacterianos/toxicidad , Antibacterianos/farmacología , Estiércol/microbiología , Contaminantes del Suelo/toxicidad , Microplásticos/toxicidad , Farmacorresistencia Microbiana/genética , Microbiología del Suelo , Bacterias/efectos de los fármacos , Bacterias/genética , Bacterias/metabolismo , Genes Bacterianos/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , MultiómicaRESUMEN
Nanoscale zero-valent iron (ZVI) and the oxides have been documented as an effective approach for mitigating the dissemination of antibiotic resistance genes (ARGs) during anaerobic digestion (AD). However, the mechanism of ARGs dissemination mitigated by nanoscale ZVI and iron oxides remain unclear. Here, we investigated the influencing mechanisms of nanoscale ZVI and iron oxides on ARGs dissemination during AD. qPCR results indicated that nanoscale ZVI and iron oxides significantly declined the total ARGs abundances, and the strongest inhibiting effect was observed by 10 g/L nanoscale ZVI. Mantel test showed ARGs distribution was positively correlated with physiochemical properties, integrons and microbial community, among which microbial community primarily contributed to ARGs dissemination (39.74%). Furthermore, redundancy and null model analyses suggested the dominant and potential ARGs host was Fastidiosipila, and homogeneous selection in the determinism factors was the largest factor for driving Fastidiosipila variation, confirming the inhibition of Fastidiosipila was primary reason for mitigating ARGs dissemination by nanoscale ZVI and iron oxides. These results were related to the inhibition of ARGs transfer related functions. This work provides novel evidence for mitigating ARGs dissemination through regulating microbial succession and regulation induced by ZVI and iron oxides.
Asunto(s)
Farmacorresistencia Microbiana , Compuestos Férricos , Hierro , Hierro/química , Hierro/metabolismo , Compuestos Férricos/química , Farmacorresistencia Microbiana/genética , Anaerobiosis , Microbiota/efectos de los fármacos , Genes Bacterianos/efectos de los fármacos , Bacterias/efectos de los fármacos , Bacterias/genética , Bacterias/metabolismo , Farmacorresistencia Bacteriana/genética , Antibacterianos/farmacología , Antibacterianos/químicaRESUMEN
Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1-5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks.
Asunto(s)
Farmacorresistencia Microbiana , Ipomoea , Microplásticos , Microbiología del Suelo , Contaminantes del Suelo , Contaminantes del Suelo/toxicidad , Microplásticos/toxicidad , Ipomoea/genética , Ipomoea/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Rizosfera , Polietileno , Genes Bacterianos/efectos de los fármacos , Brassica/genética , Brassica/efectos de los fármacos , Brassica/microbiología , Bacterias/efectos de los fármacos , Bacterias/genética , Bacterias/clasificación , Suelo/química , Metales Pesados/toxicidad , Microbiota/efectos de los fármacosRESUMEN
Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.
Asunto(s)
Farmacorresistencia Microbiana , Hormesis , Salinidad , Microbiología del Suelo , Farmacorresistencia Microbiana/genética , Hormesis/efectos de los fármacos , Antibacterianos/farmacología , Genes Bacterianos/efectos de los fármacos , Suelo/química , Bacterias/efectos de los fármacos , Bacterias/genéticaRESUMEN
UV/peracetic acid (PAA) treatment presents a promising approach for antibiotic removal, but its effects on microbial community and proliferation of antibiotic resistance genes (ARGs) during the subsequent bio-treatment remain unclear. Thus, we evaluated the effects of the UV/PAA on tetracycline (TTC) degradation, followed by introduction of the treated wastewater into the bio-treatment system to monitor changes in ARG expression and biodegradability. Results demonstrated effective TTC elimination by the UV/PAA system, with carbon-centered radicals playing a significant role. Crucially, the UV/PAA system not only eliminated antibacterial activity but also inhibited potential ARG host growth, thereby minimizing the emergence and dissemination of ARGs during subsequent bio-treatment. Additionally, the UV/PAA system efficiently removed multi-antibiotic resistant bacteria and ARGs from the bio-treatment effluent, preventing ARGs from being released into the environment. Hence, we propose a multi-barrier strategy for treating antibiotic-containing wastewater, integrating UV/PAA pre-treatment and post-disinfection with bio-treatment. The inhibition of ARGs transmission by the integrated system was verified through actual soil testing, confirming its effectiveness in preventing ARGs dissemination in the surrounding natural ecosystem. Overall, the UV/PAA treatment system offers a promising solution for tackling ARGs challenges by controlling ARGs proliferation at the source and minimizing their release at the end of the treatment process.
Asunto(s)
Antibacterianos , Ácido Peracético , Rayos Ultravioleta , Aguas Residuales , Antibacterianos/farmacología , Antibacterianos/química , Ácido Peracético/farmacología , Tetraciclina/farmacología , Farmacorresistencia Microbiana/genética , Genes Bacterianos/efectos de los fármacos , Purificación del Agua/métodos , Eliminación de Residuos Líquidos/métodos , Contaminantes Químicos del Agua/toxicidad , Bacterias/efectos de los fármacos , Bacterias/genética , Bacterias/efectos de la radiación , Desinfección/métodos , Biodegradación AmbientalRESUMEN
The proliferation of antibiotic resistant genes (ARGs) and antibiotic resistant bacteria (ARB) caused by antibiotic abuse has raised concerns about the global infectious-disease crisis. This study employed periodate (PI)/ferrate (VI) (Fe (VI)) system to disinfect Gram-negative ARB (Escherichia coli DH5α) and Gram-positive bacteria (Bacillus subtilis ATCC6633). The PI/Fe (VI) system could inactivate 1 × 108 CFU/mL of Gram-negative ARB and Gram-positive bacteria by 4.0 and 2.8 log in 30 min. Neutral and acidic pH, increase of PI dosage and Fe (VI) dosage had positive impacts on the inactivation efficiency of ARB, while alkaline solution and the coexistence of 10 mM Cl-, NO3-, SO42- and 20 mg/L humic acid had slightly negative impacts. The reactive species generated by PI/Fe (VI) system could disrupt the integrity of cell membrane and wall, leading to oxidative stress and lipid peroxidation. Intracellular hereditary substance, including DNA and ARGs (tetA), would leak into the external environment through damaged cells and be degraded. The electron spin resonance analysis and quenching experiments indicated that Fe (IV)/Fe (V) played a leading role in disinfection. Meanwhile, PI/Fe (VI) system also had an efficient removal effect on sulfadiazine, which was expected to inhibit the ARGs transmission from the source.
Asunto(s)
Bacillus subtilis , Desinfección , Hierro , Hierro/química , Desinfección/métodos , Bacillus subtilis/efectos de los fármacos , Bacillus subtilis/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Farmacorresistencia Bacteriana/genética , Desinfectantes/farmacología , Antibacterianos/farmacología , Genes Bacterianos/efectos de los fármacosRESUMEN
The use of livestock manure is an important way for antibiotic resistance genes (ARGs) to enter the environment, and composting is an effective method for removing ARGs from livestock manure. In this study, different volume ratios of Chinese medicinal herbal residues (CMHRs) were added to laboratory-scale chicken manure composting to evaluate their effects, if any, on the behavior of ARGs, mobile genetic elements (MGEs), and the bacterial community. At the end of the composting period, the composition of the microbial community changed. Firmicutes decreased and Bacteroidetes increased. The most striking effect was that the relative abundance of the 21 ARGs and 5 MGEs detected decreased by varying degrees in the different treatments (except for sulI and intI1). The removal rate of the ARGs increased with the increased addition of CMHRs. The correlations between transferase genes (tnpA and tnpA-02) and ARGs were significant (p < 0.05); therefore, transposons play an important role in the horizontal gene transfer of ARGs in chicken manure. The results imply that CMHRs would be an effective bulking agent for the removal of ARGs from chicken manure composting.
Asunto(s)
Antibacterianos/efectos adversos , Compostaje/métodos , Farmacorresistencia Microbiana/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Medicamentos Herbarios Chinos/farmacología , Genes Bacterianos/efectos de los fármacos , Estiércol/microbiología , Microbiota/efectos de los fármacos , Animales , Bacterias/genética , Pollos , Transferencia de Gen Horizontal/genética , Genes Bacterianos/genética , Ganado/microbiología , Medicina Tradicional China/métodos , Microbiota/genéticaRESUMEN
The use of phenicol antibiotics in animals has increased. In recent years, it has been reported that the transferable gene mediates phenicol-oxazolidinone resistance. This study analyzed the prevalence and characteristics of phenicol-oxazolidinone resistance genes in Enterococcus faecalis and Enterococcus faecium isolated from food-producing animals and meat in Korea in 2018. Furthermore, for the first time, we reported the genome sequence of E. faecalis strain, which possesses the phenicol-oxazolidinone resistance gene on both the chromosome and plasmid. Among the 327 isolates, optrA, poxtA, and fexA genes were found in 15 (4.6%), 8 (2.5%), and 17 isolates (5.2%), respectively. Twenty E. faecalis strains carrying resistance genes belonged to eight sequence types (STs), and transferability was found in 17 isolates. The genome sequences revealed that resistant genes were present in the chromosome or plasmid, or both. In strains EFS17 and EFS108, optrA was located downstream of the ermA and ant(9)-1 genes. The strains EFS36 and EFS108 harboring poxtA-encoding plasmid cocarried fexA and cfr(D). These islands also contained IS1216E or the transposon Tn554, enabling the horizontal transfer of the phenicol-oxazolidinone resistance with other antimicrobial-resistant genes. Our results suggest that it is necessary to promote the prudent use of antibiotics through continuous monitoring and reevaluation.
Asunto(s)
Antiinfecciosos/farmacología , Cloranfenicol/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Enterococcus faecalis/genética , Enterococcus faecium/genética , Carne/microbiología , Oxazolidinonas/farmacología , Animales , Bovinos/microbiología , Biología Computacional , Enterococcus faecalis/efectos de los fármacos , Enterococcus faecalis/aislamiento & purificación , Enterococcus faecium/efectos de los fármacos , Enterococcus faecium/aislamiento & purificación , Análisis de los Alimentos , Transferencia de Gen Horizontal , Genes Bacterianos/efectos de los fármacos , Genoma Bacteriano , Tipificación de Secuencias Multilocus , Plásmidos , República de Corea , Porcinos/microbiología , Secuenciación Completa del GenomaRESUMEN
Chemical-genetics (C-G) experiments can be used to identify interactions between inhibitory compounds and bacterial genes, potentially revealing the targets of drugs, or other functionally interacting genes and pathways. C-G experiments involve constructing a library of hypomorphic strains with essential genes that can be knocked-down, treating it with an inhibitory compound, and using high-throughput sequencing to quantify changes in relative abundance of individual mutants. The hypothesis is that, if the target of a drug or other genes in the same pathway are present in the library, such genes will display an excessive fitness defect due to the synergy between the dual stresses of protein depletion and antibiotic exposure. While assays at a single drug concentration are susceptible to noise and can yield false-positive interactions, improved detection can be achieved by requiring that the synergy between gene and drug be concentration-dependent. We present a novel statistical method based on Linear Mixed Models, called CGA-LMM, for analyzing C-G data. The approach is designed to capture the dependence of the abundance of each gene in the hypomorph library on increasing concentrations of drug through slope coefficients. To determine which genes represent candidate interactions, CGA-LMM uses a conservative population-based approach in which genes with negative slopes are considered significant only if they are outliers with respect to the rest of the population (assuming that most genes in the library do not interact with a given inhibitor). We applied the method to analyze 3 independent hypomorph libraries of M. tuberculosis for interactions with antibiotics with anti-tubercular activity, and we identify known target genes or expected interactions for 7 out of 9 drugs where relevant interacting genes are known.
Asunto(s)
Antibacterianos , Descubrimiento de Drogas , Genes Bacterianos , Mycobacterium tuberculosis , Antibacterianos/farmacología , Genes Bacterianos/efectos de los fármacos , Mycobacterium tuberculosis/metabolismoRESUMEN
Bacteriophages are the most abundant biological entities on earth and may play an important role in the transmission of antibiotic resistance genes (ARG) from host bacteria. Although the specialized transduction mediated by the temperate phage targeting a specific insertion site is widely explored, the carrying characteristics of "transducing particles" for different ARG subtypes in the process of generalized transduction remains largely unclear. Here, we isolated a new T4-like lytic phage targeting transconjugant Escherichia coli C600 that contained plasmid pHNAH67 (KX246266) and encoded 11 different ARG subtypes. We found that phage AH67C600_Q9 can misload plasmid-borne ARGs and package host DNA randomly. Moreover, for any specific ARG subtype, the carrying frequency was negatively correlated with the multiplicity of infection (MOI). Further, whole genome sequencing (WGS) identified that only 0.338% (4/1183) of the contigs of an entire purified phage population contained ARG sequences; these were floR, sul2, aph(4)-Ia, and fosA. The low coverage indicated that long-read sequencing methods are needed to explore the mechanism of ARG transmission during generalized transduction.
Asunto(s)
Antibacterianos/farmacología , Bacteriófagos/genética , Farmacorresistencia Microbiana/genética , Plásmidos , Bacterias/efectos de los fármacos , Bacteriófagos/aislamiento & purificación , Empaquetamiento del ADN/efectos de los fármacos , Escherichia coli/genética , Genes Bacterianos/efectos de los fármacos , Genoma Viral , Alineación de SecuenciaRESUMEN
Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with periprosthetic tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known periprosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209 ×. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis approach clearly influenced the results, i.e. read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.
Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana , Infecciones Estafilocócicas/microbiología , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/genética , Cultivo de Sangre , Farmacorresistencia Bacteriana/efectos de los fármacos , Genes Bacterianos/efectos de los fármacos , Humanos , Metagenómica , Infecciones Estafilocócicas/tratamiento farmacológico , Staphylococcus aureus/patogenicidad , Virulencia/efectos de los fármacos , Factores de Virulencia/genéticaRESUMEN
Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an 'omics-based' framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as 'current threats' (Rank I; 3%) - already present among pathogens - and 'future threats' (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 'current threat' ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II ('future threats'). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.
Asunto(s)
Antibacterianos/farmacología , Farmacorresistencia Bacteriana/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , Bacterias/efectos de los fármacos , Bacterias/genética , Bases de Datos Factuales , Microbioma Gastrointestinal/efectos de los fármacos , Genes Bacterianos/efectos de los fármacos , Genoma , Humanos , Metagenoma , PlásmidosRESUMEN
The complex reservoir of metabolite-producing bacteria in the gastrointestinal tract contributes tremendously to human health and disease. Bacterial composition, and by extension gut metabolomic composition, is undoubtably influenced by the use of modern antibiotics. Herein, we demonstrate that polymyxin B, a last resort antibiotic, influences the production of the genotoxic metabolite colibactin from adherent-invasive Escherichia coli (AIEC) NC101. Colibactin can promote colorectal cancer through DNA double stranded breaks and interstrand cross-links. While the structure and biosynthesis of colibactin have been elucidated, chemical-induced regulation of its biosynthetic gene cluster and subsequent production of the genotoxin by E. coli are largely unexplored. Using a multiomic approach, we identified that polymyxin B stress enhances the abundance of colibactin biosynthesis proteins (Clb's) in multiple pks+ E. coli strains, including pro-carcinogenic AIEC, NC101; the probiotic strain, Nissle 1917; and the antibiotic testing strain, ATCC 25922. Expression analysis via qPCR revealed that increased transcription of clb genes likely contributes to elevated Clb protein levels in NC101. Enhanced production of Clb's by NC101 under polymyxin stress matched an increased production of the colibactin prodrug motif, a proxy for the mature genotoxic metabolite. Furthermore, E. coli with a heightened tolerance for polymyxin induced greater mammalian DNA damage, assessed by quantification of γH2AX staining in cultured intestinal epithelial cells. This study establishes a key link between the polymyxin B stress response and colibactin production in pks+ E. coli. Ultimately, our findings will inform future studies investigating colibactin regulation and the ability of seemingly innocuous commensal microbes to induce host disease.
Asunto(s)
Farmacorresistencia Bacteriana/efectos de los fármacos , Escherichia coli/efectos de los fármacos , Péptidos/efectos de los fármacos , Polimixinas/farmacología , Animales , Evolución Biológica , Línea Celular , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Genes Bacterianos/efectos de los fármacos , Familia de Multigenes/efectos de los fármacos , Mutágenos/metabolismo , Péptido Sintasas/genética , Péptidos/metabolismo , Sintasas Poliquetidas/genética , Policétidos/metabolismo , Ratas , Regulación hacia Arriba/efectos de los fármacosRESUMEN
Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different quality substrates on the fate of ARGs were assessed during manure composting. Results showed that the total relative abundances of ARGs and intI1 in additive treatments were lower than that in control, and high quality treatment with low C/N ratio and lignin significantly decreased the relative abundance of tetW, ermB, ermC, sul1 and sul2 at the end of composting. Additionally, higher quality treatment reduced the relative abundances of some pathogens such as Actinomadura and Pusillimonas, and some thermotolerant degrading-related bacteria comprising Pseudogracilibacillus and Sinibacillus on day 42, probably owing to the change of composting properties in piles. Structural equation models (SEMs) further verified that the physiochemical properties of composting were the dominant contributor to the variations in ARGs and they could also indirectly impact ARGs by influencing bacterial community and the abundance of intI1. Overall, these findings indicated that additives with high quality reduced the reservoir of antibiotic resistance genes of livestock manure compost.
Asunto(s)
Compostaje/métodos , Farmacorresistencia Microbiana/genética , Genes Bacterianos/efectos de los fármacos , Estiércol/análisis , Estiércol/microbiología , Animales , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Carbono/análisis , Carbono/farmacología , Pollos/microbiología , Lignina/análisis , Lignina/farmacología , Microbiota/efectos de los fármacos , Nitrógeno/análisis , Nitrógeno/farmacologíaRESUMEN
Antibiotic resistance genes (ARGs) in livestock farms have attracted a growing attention with potential effects on human health. As one of the most important organic fertilizer, swine waste provided an ideal environment for understanding the dissemination and accumulation of ARGs in agricultural ecosystems. Here we conducted a year-round follow-up trace from swine waste to receiving environments, with the purpose of revealing the contamination profiles and ecological risks of ARGs at different seasons. Results indicated that a variety of common ARGs and even high-risk ARGs (i.e., blaampC, blaOXA-1, blaTEM-1 and mcr-1) were prevalent from swine waste to farmland soil, with changing in various degrees from season to season. Regarding the occurrence pattern of ARGs, tetracycline resistance genes (tet-ARGs) were predominant genes at four seasons in all fresh pig feces, swine manure, manured soil and wastewater. The levels of most ARGs in solid waste were reduced at a different degree via natural composting, and the removal effect was best in summer, while ARGs decreased poorly after wastewater treatment, especially in winter (up to 10-1 copies/16S copies in the residual level), which increased the possibility of propagation to receiving environment. This concern was also validated by the investigation on farmland environment with long-term application of manure, where causing an increase in ARG abundances in soils (approximately 0.9-32.7 times). To our knowledge, this study is the first to demonstrate the distribution pattern of ARGs from swine waste to its receiving farmland environment at all seasons on this integrity chain.