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Environment International Feb 2022Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and...
Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.
Topics: Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial; RNA, Ribosomal, 16S
PubMed: 35016024
DOI: 10.1016/j.envint.2022.107077 -
BMC Bioinformatics Jan 2020Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species....
BACKGROUND
Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions.
RESULTS
We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26 Salmonella enterica isolates from Shanghai, China.
CONCLUSIONS
PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.
Topics: Alleles; China; Drug Resistance, Microbial; Salmonella enterica; Software; Whole Genome Sequencing
PubMed: 31941435
DOI: 10.1186/s12859-019-3335-y -
The Science of the Total Environment Jan 2023Antibiotic resistance is a major global public health concern. Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of its high... (Review)
Review
Antibiotic resistance is a major global public health concern. Acinetobacter baumannii is a nosocomial pathogen that has emerged as a global threat because of its high levels of resistance to many antibiotics, particularly those considered as last-resort antibiotics, such as carbapenems. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antibiotic resistance genes (ARGs), including the mobilization of ARGs within and between species. We conducted an in-depth, systematic investigation of the occurrence and dissemination of ARGs associated with MGEs in A. baumannii. We focused on a cross-sectoral approach that integrates humans, animals, and environments. Four strategies for the prevention of ARG dissemination through MGEs have been discussed: prevention of airborne transmission of ARGs using semi-permeable membrane-covered thermophilic composting; application of nanomaterials for the removal of emerging pollutants (antibiotics) and pathogens; tertiary treatment technologies for controlling ARGs and MGEs in wastewater treatment plants; and the removal of ARGs by advanced oxidation techniques. This review contemplates and evaluates the major drivers involved in the transmission of ARGs from the cross-sectoral perspective and ARG-transfer prevention processes.
Topics: Humans; Animals; Anti-Bacterial Agents; Acinetobacter baumannii; Genes, Bacterial; Drug Resistance, Microbial; Interspersed Repetitive Sequences
PubMed: 36257427
DOI: 10.1016/j.scitotenv.2022.159497 -
Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil.International Journal of Environmental... Jun 2022The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production...
The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that , , , , and were the dominant phyla, while , , , and were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Genes, Bacterial; Manure; Soil; Soil Microbiology; Vegetables
PubMed: 35805398
DOI: 10.3390/ijerph19137742 -
The Science of the Total Environment May 2023Aerosols are an important route for the transmission of antibiotic resistance genes (ARGs). Since the 2019 (COVID-19) pandemic, the large-scale use of disinfectants has...
Aerosols are an important route for the transmission of antibiotic resistance genes (ARGs). Since the 2019 (COVID-19) pandemic, the large-scale use of disinfectants has effectively prevented the spread of environmental microorganisms, but studies regarding the antibiotic resistance of airborne bacteria remain limited. This study focused on four functional urban areas (commercial areas, educational areas, residential areas and wastewater treatment plant) to study the variations in ARG abundances, bacterial community structures and risks to human health during the COVID-19 pandemic in aerosol. The results indicated the abundance of ARGs during the COVID-19 period were up to approximately 13-fold greater than before the COVID-19 period. Large-scale disinfection resulted in a decrease in total bacterial abundance. However, chlorine-resistant bacteria tended to be survived. Among the four functional areas, the diversity and abundance of aerosol bacteria were highest in commercial aera. Antibiotic susceptibility assays suggested elevated resistance of isolated bacteria to several tested antibiotics due to disinfection exposure. The potential exposure risks of ARGs to human health were 2 times higher than before the COVID-19 pandemic, and respiratory intake was the main exposure route. The results highlighted the elevated antibiotic resistance of bacteria in aerosols that were exposed to disinfectants after the COVID-19 pandemic. This study provides theoretical guidance for the rational use of disinfectants and control of antimicrobial resistance.
Topics: Humans; Pandemics; Genes, Bacterial; COVID-19; Respiratory Aerosols and Droplets; Drug Resistance, Microbial; Bacteria; Anti-Bacterial Agents; Disinfectants
PubMed: 36754321
DOI: 10.1016/j.scitotenv.2023.162035 -
Nature Reviews. Microbiology Jan 2021The rapid emergence of antibiotic resistance is recognized as a major public health threat. Nanomaterials have risen to tackle this problem through either improving the...
The rapid emergence of antibiotic resistance is recognized as a major public health threat. Nanomaterials have risen to tackle this problem through either improving the potency of existing antibiotics or generating entirely new antibacterial mechanisms.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Infections; Drug Resistance, Microbial; Humans; Nanostructures
PubMed: 33024312
DOI: 10.1038/s41579-020-00469-5 -
Journal of Dairy Science Jun 2022Antibiotic resistance genes, as newly emerging contaminants, have become a serious challenge to public health through the food chain. The gut of humans and animals is an...
Antibiotic resistance genes, as newly emerging contaminants, have become a serious challenge to public health through the food chain. The gut of humans and animals is an important reservoir for the development and dissemination of antibiotic resistance genes because of the great abundance and diversity of intestinal microbiota. In the present study, we evaluated the influence of goat milk on the diversity and abundance of antibiotic resistance genes and gut microbial communities, especially pathogenic bacteria. Male mice were used, 12 for each of the 2 groups: a control group that received sterile distilled water and a treated group that received goat milk, and gut microbiota and antibiotic resistance genes were compared in these groups using metagenomic analysis. The results revealed that ingestion of goat milk decreased the diversity and abundance of antibiotic resistance genes in the mice gut. The relative abundance of fluoroquinolone, peptide, macrolide, and β-lactam resistance genes in the total microbial genes significantly decreased after the intervention. Goat milk intake also significantly reduced the abundance of pathogenic bacteria, such as Clostridium bolteae, Clostridium symbiosum, Helicobacter cinaedi, and Helicobacter bilis. Therefore, goat milk intake might decrease the transfer potential of antibiotic resistance gene to pathogenic bacteria in the gut. In addition, bacteria with multiple resistance mechanisms accounted for approximately 4.5% of total microbial communities in the control group, whereas it was not detectable in the goat milk group, indicating the total inhibition by goat milk intake. This study highlights the influence of goat milk on antibiotic resistome and microbial communities in the gut, and provides a new insight into the function of goat milk for further study.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Eating; Feces; Gastrointestinal Microbiome; Goats; Male; Mice; Milk
PubMed: 35346469
DOI: 10.3168/jds.2021-21325 -
Nature Ecology & Evolution Sep 2021During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs....
During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. Bottlenecks-that is, reductions in bacterial population size-lead to an increased influence of random effects (genetic drift) during bacterial evolution, and varying antibiotic concentrations during treatment may favour distinct resistance variants. Both aspects influence the process of bacterial evolution during antibiotic therapy and thereby treatment outcome. Surprisingly, the joint influence of these interconnected factors on the evolution of antibiotic resistance remains largely unexplored. Here we combine evolution experiments with genomic and genetic analyses to demonstrate that bottleneck size and antibiotic-induced selection reproducibly impact the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Resistance is favoured-expectedly-under high antibiotic selection and weak bottlenecks, but-unexpectedly-also under low antibiotic selection and severe bottlenecks. The latter is likely to result from a reduced probability of losing favourable variants through drift under weak selection. Moreover, the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks, in combination with drug-induced selection, are currently neglected key determinants of pathogen evolution and outcome of antibiotic treatment.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Humans; Pseudomonas aeruginosa
PubMed: 34312522
DOI: 10.1038/s41559-021-01511-2 -
The Lancet. Global Health Jul 2021Although the individual and societal consequences of antibiotic resistance spiral upwards, coordinated action has not kept pace on a global scale. The COVID-19 pandemic... (Review)
Review
Although the individual and societal consequences of antibiotic resistance spiral upwards, coordinated action has not kept pace on a global scale. The COVID-19 pandemic has highlighted the need for resilient health systems and has resulted in an unprecedented rate of collaboration in scientific, medical, social, and political dimensions. The pandemic has also created a renewed awareness of the importance of infectious diseases and is a substantial entry point for reigniting the momentum towards containing the silent pandemic of antibiotic resistance. In this Viewpoint, we discuss the limitations in the current narrative on antibiotic resistance and how it could be improved, including concerted efforts to close essential data gaps. We discuss the need for capacity building and coordination at the national and global levels to strengthen the understanding of the importance of sustainable access to effective antibiotics for all health systems that could generate tangible links to current processes for global health and development.
Topics: COVID-19; Delivery of Health Care; Drug Resistance, Microbial; Global Health; Humans
PubMed: 34143980
DOI: 10.1016/S2214-109X(21)00163-7 -
Mathematical Biosciences and... Aug 2019Antibiotic resistance is a growing threat to human health and is caused by mainly the overuse of antibiotics in clinical medicine. Clinically, drug resistance emerges...
Antibiotic resistance is a growing threat to human health and is caused by mainly the overuse of antibiotics in clinical medicine. Clinically, drug resistance emerges after a series of antibiotic treatments, implying that each treatment changes the intestinal flora composition and the accumulations of these changes induce the resistance. But mathematically, this cumulative effect cannot be achieved by a general population model, because the system will return to its pre-treatment state (an isolated steady state) after each cure. Based on the fact that sensitive bacteria and resistant bacteria are similar in most respects except their reactions to antibiotics, we developed a mathematical model with a specific phase-space structure: instead of isolated points, the steady states of this system compose one-dimensional manifolds (line segments). This structure explains the fundamental mechanism of antibiotic resistance: after antibiotic treatment, the system cannot return to the pretreatment healthy steady state but rather slightly moves along the manifold to a different steady state. Each use of antibiotics can change the ratio of resistant to susceptible pathogens in the host. The change the ratio can persist and accumulate, and finally promotes the emergence of antimicrobial resistance. We also assessed key factors (such as pathogen composition, the amount and composition of beneficial bacteria, medication duration and bactericidal rates of drugs) influencing the development of drug resistance. In addition, we clarified how fecal microbiota transplantation affects the treatment of antibiotic-resistant infections. The effect is essentially a transfer towards the healthy state in the phase space. Finally, based on the mechanisms revealed by the mathematical models, we suggested some strategies to delay or prevent the emergence of drug resistance. These findings not only provide a solid theoretical basis for the treatment of antimicrobial resistance, but also inspire clues to the phenomenon of drug resistance.
Topics: Anti-Bacterial Agents; Bacterial Infections; Computer Simulation; Drug Resistance, Bacterial; Drug Resistance, Microbial; Fecal Microbiota Transplantation; Feces; Humans; Intestines; Methicillin-Resistant Staphylococcus aureus; Models, Theoretical; Probiotics; Risk
PubMed: 31698603
DOI: 10.3934/mbe.2019354