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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 -
Nature Communications Aug 2023Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic...
Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.
Topics: Animals; Anti-Bacterial Agents; Drug Resistance, Microbial; Genes, Bacterial; Microbiota; Respiratory System; Swine
PubMed: 37573429
DOI: 10.1038/s41467-023-40587-1 -
Nature Microbiology Mar 2024
Topics: Siderophores; Iron; Anti-Bacterial Agents; Drug Resistance, Microbial
PubMed: 38413833
DOI: 10.1038/s41564-024-01624-x -
Journal of Hazardous Materials Feb 2024Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review... (Review)
Review
Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.
Topics: Humans; Anti-Bacterial Agents; Genes, Bacterial; Metals, Heavy; Drug Resistance, Microbial; Waste Disposal Facilities
PubMed: 37976849
DOI: 10.1016/j.jhazmat.2023.132395 -
The Science of the Total Environment Dec 2023The atmosphere is an important reservoir and habitat for antibiotic resistance genes (ARGs) and is a main pathway to cause potential health risks through inhalation and...
The atmosphere is an important reservoir and habitat for antibiotic resistance genes (ARGs) and is a main pathway to cause potential health risks through inhalation and ingestion. However, the distribution characteristics of ARGs in the atmosphere and whether they were driven by atmospheric pollutants remain unclear. We annotated 392 public air metagenomic data worldwide and identified 1863 ARGs, mainly conferring to tetracycline, MLS, and multidrug resistance. We quantified these ARG's risk to human health and identified their principal pathogenic hosts, Burkholderia and Staphylococcus. Additionally, we found that bacteria in particulate contaminated air carry more ARGs than in chemically polluted air. This study revealed the influence of typical pollutants in the global atmosphere on the dissemination and risk of ARGs, providing a theoretical basis for the prevention and mitigation of the global risks associated with ARGs.
Topics: Humans; Anti-Bacterial Agents; Genes, Bacterial; Air Pollutants; Bacteria; Drug Resistance, Microbial
PubMed: 37543315
DOI: 10.1016/j.scitotenv.2023.165942 -
The Science of the Total Environment Aug 2023Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released... (Review)
Review
Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released into the environment, their fate will be subject to complex ecological processes. One of the processes prevalent in microbial communities - horizontal gene transfer - can largely facilitate the dissemination of antibiotic resistance genes (ARGs) across phylogenetic and ecological boundaries. Especially, plasmid transfer has aroused increasing concern as it has been proved a significant role in promoting ARG dissemination. As a multi-step process, plasmid transfer can be influenced by various factors, among which those stresses caused by environmental pollutants are important elements affecting the plasmid mediated ARG transfer in the environment. In fact, diverse traditional and emerging pollutants are continuously entering the environment nowadays, as evidenced by the global occurrence of pollutants like metals and pharmaceuticals in aquatic and terrestrial systems. It is therefore imperative to understand to what extent and in which way the plasmid mediated ARG dissemination can be influenced by these stresses. Over the past decades, numerous research endeavours have been made to understand the plasmid mediated ARG transfer under various environmental relevant pressures. In this review, progress and challenges of studies on environmental stress regulating plasmid mediated ARG dissemination will be discussed, with specific focus on emerging pollutants like antibiotics and non-antibiotic pharmaceuticals, metals and their nanoparticles, disinfectants and disinfection by-products, as well as the emerging particulate matter like microplastics. Despite the previous efforts, we are still lacking insights into the in situ plasmid transfer under environmental stresses, which can be addressed by future studies considering environmental relevant pollution status and multi-species microbial communities. We believe that future development of standardized high-throughput screening platforms will assist in rapidly identifying which pollutants enhance plasmid transfer and also which ones may block such gene transfer processes.
Topics: Phylogeny; Plastics; Drug Resistance, Microbial; Anti-Bacterial Agents; Genes, Bacterial; Environmental Pollutants; Plasmids; Gene Transfer, Horizontal; Pharmaceutical Preparations
PubMed: 37149187
DOI: 10.1016/j.scitotenv.2023.163870 -
The Science of the Total Environment Sep 2023The study assessed the occurrence and distribution of microbial community and antibiotic resistance genes (ARGs) in food waste, anaerobic digestate, and paddy soil...
The study assessed the occurrence and distribution of microbial community and antibiotic resistance genes (ARGs) in food waste, anaerobic digestate, and paddy soil samples, and revealed the potential hosts of ARGs and factors influencing their distribution. A total of 24 bacterial phyla were identified, of which 16 were shared by all samples, with Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria accounting for 65.9-92.3 % of the total bacterial community. Firmicutes was the most abundant bacteria in food waste and digestate samples, accounting for 33-83 % of the total microbial community. However, in paddy soil samples with digestate, Proteobacteria had the highest relative abundance of 38-60 %. Further, 22 ARGs were detected in food waste and digestate samples, with multidrug, macrolide-lincosamide-streptogramin (MLS), bacitracin, aminoglycoside, tetracycline, vancomycin, sulfonamide, and rifamycin resistance genes being the most abundant and shared by all samples. The highest total relative abundance of ARGs in food waste, digestate, and soil without and with digestate was detected in samples from January 2020, May 2020, October 2019, and May 2020, respectively. The MLS, vancomycin, tetracycline, aminoglycoside, and sulfonamide resistance genes had higher relative abundance in food waste and anaerobic digestate samples, whereas multidrug, bacteriocin, quinolone, and rifampin resistance genes were more abundant in paddy soil samples. Redundancy analysis demonstrated that aminoglycoside, tetracycline, sulfonamide, and rifamycin resistance genes were positively correlated with total ammonia nitrogen and pH of food waste and digestate samples. Vancomycin, multidrug, bacitracin, and fosmidomycin resistance genes had positive correlations with potassium, moisture, and organic matter in soil samples. The co-occurrence of ARG subtypes with bacterial genera was investigated using network analysis. Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were identified as potential hosts of multidrug resistance genes.
Topics: Anti-Bacterial Agents; Food; Genes, Bacterial; Vancomycin; Bacitracin; Soil; Anaerobiosis; Refuse Disposal; Bacteria; Drug Resistance, Microbial; Microbiota; Rifamycins; Aminoglycosides; Tetracyclines
PubMed: 37196953
DOI: 10.1016/j.scitotenv.2023.164192 -
Microbial Genomics May 2024The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact... (Review)
Review
The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.
Topics: Humans; Microbiota; Mouth; Anti-Bacterial Agents; History, Ancient; Diet; Bacteria; Drug Resistance, Microbial; Drug Resistance, Bacterial; History, Medieval; History, 17th Century; History, 18th Century; History, 16th Century
PubMed: 38739117
DOI: 10.1099/mgen.0.001251 -
Journal of Environmental Management Sep 2023The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in...
The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10 to 1.90 × 10 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.
Topics: Oxytetracycline; Genes, Bacterial; RNA, Ribosomal, 16S; Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Drug Resistance, Microbial; Bacteria; Anti-Bacterial Agents; Aquaculture; Microbiota; Nitrogen; Geologic Sediments
PubMed: 37141714
DOI: 10.1016/j.jenvman.2023.118052 -
Environmental Science and Pollution... Nov 2023Engine oil spills have been associated with a wide range of human health problems. However, little is known about the effects of petroleum hydrocarbon pollution on soil...
Engine oil spills have been associated with a wide range of human health problems. However, little is known about the effects of petroleum hydrocarbon pollution on soil microbial communities. In this study, three samples were collected from oil-polluted soils (OPS), and one control soil (CS) from Taolin town, China, near the old engine's scrapes was used. The aims of this study were to conduct metagenomic sequencing and subsequently perform resistome and virulome analysis. We also aimed to validate anti-microbial resistance and virulence genes and anti-bacterial sensitivity profiles among the isolates from oil-polluted soils. The OPS microbial community was dominated by bacterial species compared to the control samples which were dominated by metazoans and other organisms. Secondly, the resistosome and virulome analysis showed that ARGs and virulence factors were higher among OPS microbial communities. Antibiotic susceptibility assay and qPCR analysis for ARGs and virulence factors showed that the oil-polluted soil samples had remarkably enhanced expression of these ARGs and some virulence genes. Our study suggests that oil pollution contributes to shifting microbial communities to more resilient types that could survive the toxicity of oil pollution and subsequently become more resilient in terms of higher resistance and virulence potential.
Topics: Humans; Virulence; Bacteria; Genes, Bacterial; Soil; Drug Resistance, Microbial; China; Virulence Factors; Soil Microbiology; Anti-Bacterial Agents
PubMed: 37792198
DOI: 10.1007/s11356-023-30137-z