Majority Of Antibiotic Resistance Genes Research Articles

Prevalence of antibiotics, antibiotic resistance genes, and their associations in municipal wastewater treatment plants along the Yangtze River basin, China

The overuse and misuse of antibiotics have resulted in the pollution of antibiotics and antibiotic resistance genes (ARGs) in municipal wastewater treatment plants (WWTPs), posing threats to ecological security and human health. Thus, a comprehensive investigation was conducted to assess the occurrence, removal efficiency, and ecological risk of antibiotics, along with the diversity, abundance, and co-occurrence of ARGs, and their correlations in 13 WWTPs along the Yangtze River Basin. Among 35 target antibiotics, 23 antibiotics within 6 categories were detected in all the samples. Amoxicillin (AMO), ofloxacin (OFL), and pefloxacin (PEF) were predominant in influents, while AMO exhibited dominance with the highest concentration of 1409 ng/L in effluents. Although antibiotic removal performance varied among different WWTPs, a significant decrease in each antibiotic category and overall antibiotics was observed in effluents compared with that in influents (p < 0.05). Remarkably, ecological risk assessment revealed high risks associated with AMO and ciprofloxacin (CIP) and medium risks linked to several antibiotics, notably including OFL, roxithromycin (ROX), clarithromycin (CLA), and tetracycline (TC). Furthermore, 96 ARG subtypes within 12 resistance types were detected in this study, and the total absolute abundance and diversity of ARGs were significantly decreased from influents to effluents (p < 0.05). Enrichment of 38 ARGs (e.g., blaNDM, ermA, vatA, mexA, and dfrA25) in effluents indicated potential health risks. Various mobile genetic elements (MGEs), exhibited significant correlations with a majority of ARGs in both influents and effluents, such as intⅠ1, tnpA1, tnpA5, and tp614, underscoring the important role of MGEs in contributing to the ARG dissemination. Many antibiotics displayed lower correlations with corresponding ARGs, but exhibited higher correlations with other ARGs, suggesting complex selective pressures influencing ARG propagation. Overall, the incomplete elimination of antibiotics and ARGs in WWTPs is likely to pose adverse impacts on aquatic ecosystems in the Yangtze River Basin.

Genomic revisitation and reclassification of the genus Providencia.

The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.

Antimicrobial resistance in E. Coli of animal origin and discovery of a novel ICE mobile element in Northeast China

BackgroundMultidrug resistance in Enterobacteriaceae including resistance to quinolones is rising worldwide. The development of resistance may lead to the emergence of new transmission mechanisms. In this study, the collection of different E. coli was performed from animals and subjected to subsequent procedures including pulsed-field gel electrophoresis, micro-broth dilution method, polymerase chain reaction. Whole genome sequencing of E. coli C3 was performed to detect the affinity, antimicrobial resistance and major carriers of the isolates.ResultsA total of 66 E. coli were isolated and their antibiotic resistance genes, frequency of horizontal transfer and genetic environment of E. coli C3 were determined. The results showed there were both different and same types in PFGE typing, indicating clonal transmission of E. coli among different animals. The detection of antimicrobial resistance and major antibiotic resistance genes and the plasmid transfer results showed that strains from different sources had high levels of resistance to commonly used clinical antibiotics and could be spread horizontally. Whole-genome sequencing discovered a novel ICE mobile element.ConclusionIn summary, the antimicrobial resistance of E. coli in northeast China is a serious issue and there is a risk of antimicrobial resistance transmission. Meanwhile, a novel ICE mobile element appeared in the process of antimicrobial resistance formation.

Distinct climatic regions drive antibiotic resistance genes dynamics across public parks and pristine soil ecosystems

To address the global concern of antibiotic resistance, a one-health concept is considered necessary that recognizes the interdependency between humans, animals and the environment, and acknowledges that each of these factors contributes to the evolution and rapid bloom of antibiotic resistance genes (ARGs). We implemented a GeoChip 5.0 strategy to examine the wide-spectrum profile of ARGs in the soil of urban parks and reference forests across three distinct climatic regions: Boreal (Lathi, Finland), Temperate (Baltimore, USA), and Tropical (Singapore). ARGs encoding multidrug resistance (MRGs) were among the most abundant, accounting for 90% of all ARGs detected. MRGs include MFS, MATE, Mex, SMR and ABC, which are involved in the transportation/efflux of multiple antibiotics. Multivariate analysis revealed that the ARG profile tends to be partitioned separately in urban parks and climatic regions. In addition, we opted to examine the impact of plant functional type (recalcitrant and labile tree litter, lawn) on ARGs. There was no significant influence of vegetation type on ARGs except in the tropical region, where its impact was evident as compared with boreal and temperate regions. More interestingly, the majority of ARGs were detected to have a higher relative abundance in the tropical region as compared to the boreal and temperate regions. Regional characteristics of the tropical area likely affects ARGs and the ARG-host profile, thereby boosting soil microbial abundances. Additionally, MFS, Mex, B_lactamase_A, vgb, ABC, Van, fosb, ABC_ multi, Tet and Mate_antibiotic were considerably more abundant in old parks as compared with young parks across the three climatic regions. Nevertheless, urban parks harboured a significantly higher abundance of ARGs than forests. Our study presents evidence of ARGs in varied climatic regions and provides valuable new insights in our understanding of ARGs in human-dominated environments as well as their prevalence in pristine ecosystems.

Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter.

The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.

Insight into using a novel ultraviolet/peracetic acid combination disinfection process to simultaneously remove antibiotics and antibiotic resistance genes in wastewater: Mechanism and comparison with conventional processes

In this study, the simultaneous removal mechanism of antibiotics and antibiotic resistance genes (ARGs) was investigated using the novel ultraviolet/peracetic acid (UV/PAA) combination disinfection process and conventional disinfection processes were also applied for comparison. The results showed that UV/PAA disinfection with a high UV dosage (UV/PAA-H) was most effective for the removal of tetracyclines, quinolones, macrolides and β-lactams; their average removal efficiencies ranged from 25.7% to 100%, while NaClO disinfection was effective for the removal of sulfonamides (∼81.6%). The majority of ARGs were well removed after the UV/PAA-H disinfection, while specific genes including tetB, tetC, ermA and blaTEM significantly increased after NaClO disinfection. In addition, β-lactam resistance genes (-35.9%) and macrolides resistance genes (-12.0%) remarkably augmented after UV/NaClO disinfection. The highly reactive oxidation species generated from UV/PAA process including hydroxyl radicals (•OH) and carbon-centered organic radicals (R-C•), were responsible for the elimination of antibiotics and ARGs. Correlation analysis showed that tetracycline, sulfonamide and macrolide antibiotics removal showed a positive correlation with the corresponding ARGs, and a low dose of antibiotic residues played an important role in the distribution of ARGs. Metagenomic sequencing analysis showed that UV/PAA disinfection could not only greatly decrease the abundance of resistant bacteria but also downregulate the expression of key functional genes involved in ARGs propagation and inhibit the signal transduction of the host bacteria, underlying that its removal mechanism was quite different from that of NaClO-based disinfection processes. Our study provides valuable information for understanding the simultaneous removal mechanism of antibiotics and ARGs in wastewater during the disinfection processes, especially for the novel UV/PAA combination process.

Occurrence of the colistin resistance mcr‐1 gene in soils from intensive vegetable production and native vegetation

AbstractColistin, currently regarded as the last‐resort antibiotic for the treatment of infections caused by multidrug‐resistant bacteria, is used in poultry production to treat and prevent infection, and as a growth promoter. Poultry litter is commonly used as organic fertilizer; however, there are no reports on the effect of its application regarding colistin resistance in soils. Thus, the objective of the present study was to compare the abundance of the colistin resistance gene (mcr‐1) in soils from vegetable production areas that received non‐composted poultry litter as organic fertilizer and native vegetation areas. The mcr‐1 gene was detected in all soil samples from both areas. A significant difference (p &lt; 0.05) was observed in the relative abundance of the mcr‐1 gene between soils pertaining to the vegetable production area and the native vegetation area in six of those 10 properties. This is the first report of the presence of the colistin resistance gene in soils from Brazil. The vast majority of antibiotic resistance genes acquired by human pathogens originated in natural environments. Thus, the presence of the mcr‐1 gene in soils treated with poultry litter and from native vegetation areas reinforces the need for studies that minimize potential risks of the development of colistin resistance.Highlights Poultry litter usually is employed as fertilizer; however, there are no reports of its impact in colistin resistance in soils. The mcr‐1 gene was detected in soils from both native vegetation and vegetable production. This is the first report of the presence of colistin resistance gene in soils from Brazil. The presence of mcr‐1 gene in soils can increase risks of the development and spread of colistin resistance.

Partitioning of Antibiotic Resistance Genes and Fecal Indicators Varies Intra and Inter-Storm during Combined Sewer Overflows.

Combined sewer overflows (CSOs) degrade water quality through the release of microbial contaminants in CSO effluent. Improved understanding of the partitioning of microbial contaminants onto settleable particles can provide insight into their fate in end-of-pipe treatment systems or following release during CSO events. Sampling was performed across the hydrograph for three storm events as well as during baseflow and wet weather in three surface waters impacted by CSO. qPCR was performed for select antibiotic resistance genes (ARG) and a marker gene for human fecal indicator organisms (BacHum) in samples processed the partitioning of microbial contaminants on settleable particles versus suspended in the aqueous phase. Amplicon sequencing was performed on both fractions of storm samples to further define the timing and partitioning of microbial contaminants released during CSO events. Samples collected at the CSO outfall exhibited microbial community signatures of wastewater at select time points early or late in the storm events. CSOs were found to be a source of ARG. In surrounding surface waters, sul1 was higher in samples from select locations during wet weather compared to baseflow. Otherwise, ARG concentrations were variable with no differences between baseflow and wet weather conditions. The majority of ARG at the CSO outfall were observed on the attached fraction of samples: 64–79% of sul1 and 59–88% of tet(G). However, the timing of peak ARG and human fecal indicator marker gene BacHum did not necessarily coincide with observation of the microbial signature of wastewater in CSO effluent. Therefore, unit processes that remove settleable particles (e.g., hydrodynamic separators) operated throughout a CSO event would achieve up to (0.5–0.9)-log removal of ARG and fecal indicators by removing the attached fraction of measured genes. Secondary treatment would be required if greater removal of these targets is needed.

Accumulation and expression of multiple antibiotic resistance genes in Arcobacter cryaerophilus that thrives in sewage.

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also determined that a majority of ARGs was being expressed in sewage, suggestive of trace levels of antibiotics or other stresses that could act as a selective force that amplifies multidrug resistant bacteria in municipal sewage. Because all bacteria are not eliminated even after several rounds of wastewater treatment, ARGs in sewage could affect public health due to their potential to contaminate environmental water.

Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes.

Background Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system was developed for M. haemolytica from the genome sequences of 1133 North American isolates, and used to identify genetic differences between isolates from the lungs and upper respiratory tract of cattle with and without clinical signs of respiratory disease.ResultsA total of 26,081 nucleotide polymorphisms were characterized after quality control filtering of 48,403 putative polymorphisms. Phylogenetic analyses of nucleotide polymorphism genotypes split M. haemolytica into two major genotypes (1 and 2) that each were further divided into multiple subtypes. Multiple polymorphisms were identified with alleles that tagged genotypes 1 or 2, and their respective subtypes. Only genotype 2 M. haemolytica associated with the lungs of diseased cattle and the sequence of a particular integrative and conjugative element (ICE). Additionally, isolates belonging to one subtype of genotype 2 (2b), had the majority of antibiotic resistance genes detected in this study, which were assorted into seven combinations that ranged from 1 to 12 resistance genes.ConclusionsTyping of diverse M. haemolytica by nucleotide polymorphism genotypes successfully identified associations with diseased cattle lungs, ICE sequence, and antibiotic resistance genes. Management of cattle by their carriage of M. haemolytica could be an effective intervention strategy to reduce the prevalence of respiratory disease and supplemental needs for antibiotic treatments in North American herds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3316-8) contains supplementary material, which is available to authorized users.

The ocean as a global reservoir of antibiotic resistance genes.

Recent studies of natural environments have revealed vast genetic reservoirs of antibiotic resistance (AR) genes. Soil bacteria and human pathogens share AR genes, and AR genes have been discovered in a variety of habitats. However, there is little knowledge about the presence and diversity of AR genes in marine environments and which organisms host AR genes. To address this, we identified the diversity of genes conferring resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine in diverse marine environments using functional metagenomics (the cloning and screening of random DNA fragments). Marine environments were host to a diversity of AR-conferring genes. Antibiotic-resistant clones were found at all sites, with 28% of the genes identified as known AR genes (encoding beta-lactamases, bicyclomycin resistance pumps, etc.). However, the majority of AR genes were not previously classified as such but had products similar to proteins such as transport pumps, oxidoreductases, and hydrolases. Furthermore, 44% of the genes conferring antibiotic resistance were found in abundant marine taxa (e.g., Pelagibacter, Prochlorococcus, and Vibrio). Therefore, we uncovered a previously unknown diversity of genes that conferred an AR phenotype among marine environments, which makes the ocean a global reservoir of both clinically relevant and potentially novel AR genes.

Seasonal variations in antibiotic resistance gene transport in the almendares river, havana, cuba.

Numerous studies have quantified antibiotic resistance genes (ARG) in rivers and streams around the world, and significant relationships have been shown that relate different pollutant outputs and increased local ARG levels. However, most studies have not considered ambient flow conditions, which can vary dramatically especially in tropical countries. Here, ARG were quantified in water column and sediment samples during the dry- and wet-seasons to assess how seasonal and other factors influence ARG transport down the Almendares River (Havana, Cuba). Eight locations were sampled and stream flow estimated during both seasons; qPCR was used to quantify four tetracycline, two erythromycin, and three beta-lactam resistance genes. ARG concentrations were higher in wet-season versus dry-season samples, which combined with higher flows, indicated much greater ARG transport downstream during the wet-season. However, water column ARG levels were more spatially variable in the dry-season than the wet-season, with the proximity of waste outfalls strongly influencing local ARG levels. Results confirm that dry-season sampling provides a useful picture of the impact of individual waste inputs on local stream ARG levels, whereas the majority of ARGs in this tropical river were transported downstream during the wet-season, possibly due to re-entrainment of ARG from sediments.

In situ detection of antibiotic-resistance elements in single Bacillus cereus spores

Rapid detection of Bacillus spores is a challenging task in food and defense industries. In situ labeling of spores would be advantageous for detection by automated systems based on single-cell analysis. Determination of antibiotic-resistance genes in bacterial spores using in situ labeling has never been developed. Most of the in situ detection schemes employ techniques such as fluorescence in situ hybridization (FISH) that target the naturally amplified ribosomal RNA (rRNA). However, the majority of antibiotic-resistance genes has a plasmidic or chromosomal origin and is present in low copy numbers in the cell. The main challenge in the development of low-target in situ detection in spores is the permeabilization procedure and the signal amplification required for detection. This study presents permeabilization and in situ signal amplification protocols, using Bacillus cereus spores as a model, in order to detect antibiotic-resistance genes. The permeabilization protocol was designed based on the different layers of the Bacillus spore. Catalyzed reporter deposition (CARD)–FISH and in situ polymerase chain reaction (PCR) were used as signal amplification techniques. B. cereus was transformed with the high copy number pC194 and low copy number pMTL500Eres plasmids in order to induce resistance to chloramphenicol and erythromycin, respectively. In addition, a rifampicin-resistant B. cereus strain, conferred by a single-nucleotide polymorphism (SNP) in the chromosome, was used. Using CARD–FISH, only the high copy number plasmid pC194 was detected. On the other hand, in situ PCR gave positive results in all tested instances. This study demonstrated that it was feasible to detect antibiotic-resistance genes in Bacillus spores using in situ techniques. In addition, in situ PCR has been shown to be more sensitive and more applicable than CARD–FISH in detecting low copy targets.