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Nature Reviews. Microbiology May 2022Antibiotic resistance is a global health challenge, involving the transfer of bacteria and genes between humans, animals and the environment. Although multiple barriers... (Review)
Review
Antibiotic resistance is a global health challenge, involving the transfer of bacteria and genes between humans, animals and the environment. Although multiple barriers restrict the flow of both bacteria and genes, pathogens recurrently acquire new resistance factors from other species, thereby reducing our ability to prevent and treat bacterial infections. Evolutionary events that lead to the emergence of new resistance factors in pathogens are rare and challenging to predict, but may be associated with vast ramifications. Transmission events of already widespread resistant strains are, on the other hand, common, quantifiable and more predictable, but the consequences of each event are limited. Quantifying the pathways and identifying the drivers of and bottlenecks for environmental evolution and transmission of antibiotic resistance are key components to understand and manage the resistance crisis as a whole. In this Review, we present our current understanding of the roles of the environment, including antibiotic pollution, in resistance evolution, in transmission and as a mere reflection of the regional antibiotic resistance situation in the clinic. We provide a perspective on current evidence, describe risk scenarios, discuss methods for surveillance and the assessment of potential drivers, and finally identify some actions to mitigate risks.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Bacterial Infections; Drug Resistance, Bacterial; Drug Resistance, Microbial
PubMed: 34737424
DOI: 10.1038/s41579-021-00649-x -
EMBO Reports Dec 2020Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of... (Review)
Review
Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.
Topics: Anti-Bacterial Agents; Bacteria; Drug Resistance, Bacterial; Drug Resistance, Microbial; Humans
PubMed: 33400359
DOI: 10.15252/embr.202051034 -
Brazilian Journal of Microbiology :... Dec 2021The assembly of microorganisms over a surface and their ability to develop resistance against available antibiotics are major concerns of interest. To survive against... (Review)
Review
The assembly of microorganisms over a surface and their ability to develop resistance against available antibiotics are major concerns of interest. To survive against harsh environmental conditions including known antibiotics, the microorganisms form a unique structure, referred to as biofilm. The mechanism of biofilm formation is triggered and regulated by quorum sensing, hostile environmental conditions, nutrient availability, hydrodynamic conditions, cell-to-cell communication, signaling cascades, and secondary messengers. Antibiotic resistance, escape of microbes from the body's immune system, recalcitrant infections, biofilm-associated deaths, and food spoilage are some of the problems associated with microbial biofilms which pose a threat to humans, veterinary, and food processing sectors. In this review, we focus in detail on biofilm formation, its architecture, composition, genes and signaling cascades involved, and multifold antibiotic resistance exhibited by microorganisms dwelling within biofilms. We also highlight different physical, chemical, and biological biofilm control strategies including those based on plant products. So, this review aims at providing researchers the knowledge regarding recent advances on the mechanisms involved in biofilm formation at the molecular level as well as the emergent method used to get rid of antibiotic-resistant and life-threatening biofilms.
Topics: Anti-Bacterial Agents; Bacterial Physiological Phenomena; Biofilms; Drug Resistance, Microbial; Quorum Sensing
PubMed: 34558029
DOI: 10.1007/s42770-021-00624-x -
Journal of Molecular Biology Aug 2019The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The... (Review)
Review
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Biological Evolution; Biological Products; Carrier Proteins; Drug Combinations; Drug Discovery; Drug Resistance, Microbial; Drug Synergism; Environment; Humans; Kinetics; Metagenomics; Thermodynamics
PubMed: 31288031
DOI: 10.1016/j.jmb.2019.06.033 -
Antimicrobial Agents and Chemotherapy Jan 2020The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly... (Review)
Review
The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Infections; Drug Resistance, Microbial; Epigenesis, Genetic; Humans
PubMed: 31740560
DOI: 10.1128/AAC.02225-19 -
The Journal of Infectious Diseases Jun 2021This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by... (Review)
Review
This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid-mediated quinolone resistance. Finally, the role of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome is discussed, along with the potential for future microbiome-directed methods to detect and prevent infection.
Topics: Anti-Infective Agents; Bacterial Infections; Drug Resistance, Microbial; Gastrointestinal Microbiome; Gastrointestinal Tract; Genes, Microbial; Humans; Metagenomics; Plasmids
PubMed: 33326581
DOI: 10.1093/infdis/jiaa497 -
Nature Communications Feb 2021Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes...
Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.
Topics: Animals; Bacteria; Female; Gastrointestinal Microbiome; Genes, Microbial; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; Phylogeny; Species Specificity; Swine
PubMed: 33597514
DOI: 10.1038/s41467-021-21295-0 -
Biochemical Society Transactions Apr 2021Determining pattern in the dynamics of population evolution is a long-standing focus of evolutionary biology. Complementing the study of natural populations, microbial... (Review)
Review
Determining pattern in the dynamics of population evolution is a long-standing focus of evolutionary biology. Complementing the study of natural populations, microbial laboratory evolution experiments have become an important tool for addressing these dynamics because they allow detailed and replicated analysis of evolution in response to controlled environmental and genetic conditions. Key findings include a tendency for smoothly declining rates of adaptation during selection in constant environments, at least in part a reflection of antagonism between accumulating beneficial mutations, and a large number of beneficial mutations available to replicate populations leading to significant, but relatively low genetic parallelism, even as phenotypic characteristics show high similarity. Together, there is a picture of adaptation as a process with a varied and largely unpredictable genetic basis leading to much more similar phenotypic outcomes. Increasing sophistication of sequencing and genetic tools will allow insight into mechanisms behind these and other patterns.
Topics: Adaptation, Physiological; Bacteria; Evolution, Molecular; Genetic Fitness; Genetic Variation; Genotype; Mutation; Plasmids; Population Dynamics; Selection, Genetic
PubMed: 33843990
DOI: 10.1042/BST20200885 -
Metabolites Nov 2022In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant... (Review)
Review
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus . Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
PubMed: 36422239
DOI: 10.3390/metabo12111100