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The Science of the Total Environment Sep 2023Antibiotic resistant bacteria (ARB) are a major health risk caused particularly by anthropogenic activities. Acquisition of antibiotic resistances by bacteria is known...
Antibiotic resistant bacteria (ARB) are a major health risk caused particularly by anthropogenic activities. Acquisition of antibiotic resistances by bacteria is known to have happened before the discovery of antibiotics and can occur through different routes. Bacteriophages are thought to have an important contribution to the dissemination of antibiotic resistance genes (ARGs) in the environment. In this study, seven ARGs (bla, bla, bla, bla, mecA, vanA, and mcr-1) were investigated, in the bacteriophage fraction, in raw urban and hospital wastewaters. The genes were quantified in 58 raw wastewater samples collected at five WWTPs (n = 38) and hospitals (n = 20). All genes were detected in the phage DNA fraction, with the bla genes found in higher frequency. On the other hand, mecA and mcr-1 were the least frequently detected genes. Concentrations varied between 10 copies/L and 10 copies/L. The gene coding for the resistance to colistin (mcr-1), a last-resort antibiotic for the treatment of multidrug-resistant Gram-negative infections, was identified in raw urban and hospital wastewaters with positivity rates of 19 % and 10 %, respectively. ARGs patterns varied between hospital and raw urban wastewaters, and within hospitals and WWTP. This study suggests that phages are reservoirs of ARGs, and that ARGs (with particularly emphasis on resistance to colistin and vancomycin) in the phage fraction are already widely widespread in the environment with potential large implications for public health.
Topics: Wastewater; Anti-Bacterial Agents; Genes, Bacterial; Colistin; Bacteriophages; Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Drug Resistance, Microbial; Bacteria; Hospitals
PubMed: 37315610
DOI: 10.1016/j.scitotenv.2023.164708 -
Science Advances Nov 2022Although edaphic antibiotic resistance genes (ARGs) pose serious threats to human well-being, their spatially explicit patterns and responses to environmental...
Although edaphic antibiotic resistance genes (ARGs) pose serious threats to human well-being, their spatially explicit patterns and responses to environmental constraints at the global scale are not well understood. This knowledge gap is hindering the global action plan on antibiotic resistance launched by the World Health Organization. Here, a global analysis of 1088 soil metagenomic samples detected 558 ARGs in soils, where ARG abundance in agricultural habitats was higher than that in nonagricultural habitats. Soil ARGs were mostly carried by clinical pathogens and gut microbes that mediated the control of climatic and anthropogenic factors to ARGs. We generated a global map of soil ARG abundance, where the identified microbial hosts, agricultural activities, and anthropogenic factors explained ARG hot spots in India, East Asia, Western Europe, and the United States. Our results highlight health threats from soil clinical pathogens carrying ARGs and determine regions prioritized to control soil antibiotic resistance worldwide.
Topics: Humans; Soil; Anti-Bacterial Agents; Soil Microbiology; Genes, Bacterial; Drug Resistance, Microbial
PubMed: 36383677
DOI: 10.1126/sciadv.abq8015 -
Proceedings of the National Academy of... Nov 2020Antibiotic use is a key driver of antibiotic resistance. Understanding the quantitative association between antibiotic use and resulting resistance is important for...
Antibiotic use is a key driver of antibiotic resistance. Understanding the quantitative association between antibiotic use and resulting resistance is important for predicting future rates of antibiotic resistance and for designing antibiotic stewardship policy. However, the use-resistance association is complicated by "spillover," in which one population's level of antibiotic use affects another population's level of resistance via the transmission of bacteria between those populations. Spillover is known to have effects at the level of families and hospitals, but it is unclear if spillover is relevant at larger scales. We used mathematical modeling and analysis of observational data to address this question. First, we used dynamical models of antibiotic resistance to predict the effects of spillover. Whereas populations completely isolated from one another do not experience any spillover, we found that if even 1% of interactions are between populations, then spillover may have large consequences: The effect of a change in antibiotic use in one population on antibiotic resistance in that population could be reduced by as much as 50%. Then, we quantified spillover in observational antibiotic use and resistance data from US states and European countries for three pathogen-antibiotic combinations, finding that increased interactions between populations were associated with smaller differences in antibiotic resistance between those populations. Thus, spillover may have an important impact at the level of states and countries, which has ramifications for predicting the future of antibiotic resistance, designing antibiotic resistance stewardship policy, and interpreting stewardship interventions.
Topics: Anti-Bacterial Agents; Antimicrobial Stewardship; Bacteria; Cross-Sectional Studies; Drug Resistance, Bacterial; Drug Resistance, Microbial; Europe; Hospitals; Humans; Streptococcus pneumoniae; United States
PubMed: 33139558
DOI: 10.1073/pnas.2013694117 -
Journal of Exposure Science &... Jan 2020The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built... (Review)
Review
The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Ecology; Gene Transfer, Horizontal; Humans
PubMed: 31591493
DOI: 10.1038/s41370-019-0171-0 -
Poultry Science Dec 2021Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their...
Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34-11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45-9.80 log copies/g) and soil (0-7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 10- 6.82 × 10 copies/g. The average abundances of 5 antibiotic resistance genes were above 10 copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.
Topics: Animals; Anti-Bacterial Agents; Chickens; Drug Resistance, Microbial; Farms; Female; Genes, Bacterial; Manure; Soil Microbiology
PubMed: 34695626
DOI: 10.1016/j.psj.2021.101485 -
Clinical Microbiology and Infection :... Sep 2022The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available... (Review)
Review
BACKGROUND
The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available to clinicians 48 hours after sampling, at best. Recently, clinical metagenomics, the metagenomic sequencing of samples with the purpose of identifying microorganisms and determining their susceptibility to antimicrobials, has emerged as a potential diagnostic tool that could prove faster than culture. Clinical metagenomics indeed has the potential to detect antibiotic resistance genes (ARGs) and mutations associated with resistance. Nevertheless, many challenges have yet to be overcome in order to make rapid phenotypic inference of antibiotic susceptibility from metagenomic data a reality.
OBJECTIVES
The objective of this narrative review is to discuss the challenges underlying the phenotypic inference of antibiotic susceptibility from metagenomic data.
SOURCES
We conducted a narrative review using published articles available in the National Center for Biotechnology Information PubMed database.
CONTENT
We review the current ARG databases with a specific emphasis on those which now provide associations with phenotypic data. Next, we discuss the bioinformatic tools designed to identify ARGs in metagenomes. We then report on the performance of phenotypic inference from genomic data and the issue predicting the expression of ARGs. Finally, we address the challenge of linking an ARG to this host.
IMPLICATIONS
Significant improvements have recently been made in associating ARG and phenotype, and the inference of susceptibility from genomic data has been demonstrated in pathogenic bacteria such as Staphylococci and Enterobacterales. Resistance involving gene expression is more challenging however, and inferring susceptibility from species such as Pseudomonas aeruginosa remains difficult. Future research directions include the consideration of gene expression via RNA sequencing and machine learning.
Topics: Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial; Metagenome; Metagenomics
PubMed: 35551982
DOI: 10.1016/j.cmi.2022.04.017 -
Microbiological Research Jan 2022The emergence and spread of drug-resistant microorganisms that have acquired new resistance mechanisms, leading to antibiotic resistance, continue to threaten the health... (Review)
Review
The emergence and spread of drug-resistant microorganisms that have acquired new resistance mechanisms, leading to antibiotic resistance, continue to threaten the health of humans and animals worldwide. Non-human primates (NHPs), as close living relatives of human beings in the world, have a high degree of genetic and physiological similarity to humans. However, despite its importance, we lack a comprehensive characterization or understanding of the similarities and differences of the antibiotic resistance genes of the gut microbiome carried by non-human primates and humans. In the present study, the diversity and abundance of antibiotic resistance genes carried by the gut microbiota of cynomolgus monkeys (Macaca fascicularis) were investigated by metagenomic analysis. In total, 60 resistance types conferring resistance to 11 categories of antibiotics were identified in the gut microbiome of cynomolgus monkeys. Interestingly, the composition and abundance of ARGs carried by the gut microbiota of cynomolgus monkeys can be significantly affected by dietary changes. Moreover, we found that all ARG types carried by humans are also present in cynomolgus monkeys. The tetracycline resistance gene tet(37) is evolutionarily conserved and highly homologous. Taken together, our study provides a comprehensive overview of the diversity and richness of ARGs in the gut microbiota of cynomolgus monkeys and underlines the potentially crucial role of diet in the gut health of monkeys and humans.
Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Microbial; Gastrointestinal Microbiome; Haplorhini; Metagenomics
PubMed: 34742104
DOI: 10.1016/j.micres.2021.126895 -
Journal of Global Antimicrobial... Sep 2020The aim of this study was to evaluate antibiotic susceptibility patterns in commercially available dietary and probiotic supplements.
OBJECTIVES
The aim of this study was to evaluate antibiotic susceptibility patterns in commercially available dietary and probiotic supplements.
METHODS
Probiotic strains were isolated from the dietary supplements (designated as sample B, D and V), and multidrug resistance profiles were tested using the Kirby-Bauer test. Minimum inhibitory concentrations and double-disk synergy tests were performed to detect the mechanism of action of the resistance, and the presence of extended spectrum β-lactamase activity (ESBL) was confirmed.
RESULTS
The isolates Streptococcus faecalis and Bacillus mesentericus (both from sample B) were found to be resistant to penicillin G, Lactobacillus acidophilus (sample D) was resistant to ampicillin, and all the isolates from samples B, D and V were resistant to ceftazidime. The isolates Lactobacillus sporogenes, S. faecalis, B. mesentericus from sample B, Lactobacillus. rhamnosus, Saccharomyces boulardii from sample D, and L. sporogenes (sample V) were resistant to erythromycin.
CONCLUSIONS
The findings showed the presence of antibiotic resistance in probiotic bacteria isolated from commercially available dietary supplements. Because multidrug resistance is a serious emerging issue, and the risk of drug-resistant gene transfer to commensals or pathogens of the gut is inevitable, the safety of probiotics has become a major criterion of interest. The findings of this study would serve as a platform for further screening and characterization of the determinants of antibiotic resistance and the genetic mechanisms of resistance.
Topics: Dietary Supplements; Disk Diffusion Antimicrobial Tests; Drug Resistance, Microbial; Microbial Sensitivity Tests; Probiotics
PubMed: 32084605
DOI: 10.1016/j.jgar.2020.02.007 -
Nature Communications Jul 2023Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be...
Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen P. aeruginosa. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.
Topics: Humans; Drug Resistance, Microbial; Patients
PubMed: 37438338
DOI: 10.1038/s41467-023-39416-2 -
Journal of Microbiology and... Nov 2019The rise of antimicrobial resistance (AR) is a major threat to global health. The food animal industry contributes to the increasing occurrence of AR. Multiple factors... (Review)
Review
The rise of antimicrobial resistance (AR) is a major threat to global health. The food animal industry contributes to the increasing occurrence of AR. Multiple factors can affect the occurrence and dissemination of AR in the animal industry, including antibiotic use and farm management. Many studies have focused on how the use of antibiotics in food-producing animals has led to the development of AR. However, a few effective mitigating strategies for AR have been developed in food-producing animals, especially those exposed to the environment. The aim of this review is to summarize potential strategies applicable for mitigating AR at the environment-livestock interface.
Topics: Animals; Animals, Wild; Anti-Bacterial Agents; Bacterial Infections; Drug Resistance, Microbial; Environmental Microbiology; Farms; Livestock; Manure; Water Purification
PubMed: 31693837
DOI: 10.4014/jmb.1909.09030