Tetracycline and Phenicol Resistance Genes and Mechanisms: Importance for Agriculture, the Environment, and Humans. - Related Documents




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389201.0000Tetracycline and Phenicol Resistance Genes and Mechanisms: Importance for Agriculture, the Environment, and Humans. Recent reports have speculated on the future impact that antibiotic-resistant bacteria will have on food production, human health, and global economics. This review examines microbial resistance to tetracyclines and phenicols, antibiotics that are widely used in global food production. The mechanisms of resistance, mode of spread between agriculturally and human-impacted environments and ecosystems, distribution among bacteria, and the genes most likely to be associated with agricultural and environmental settings are included. Forty-six different tetracycline resistance () genes have been identified in 126 genera, with (M) having the broadest taxonomic distribution among all bacteria and (B) having the broadest coverage among the Gram-negative genera. Phenicol resistance genes are organized into 37 groups and have been identified in 70 bacterial genera. The review provides the latest information on tetracycline and phenicol resistance genes, including their association with mobile genetic elements in bacteria of environmental, medical, and veterinary relevance. Knowing what specific antibiotic-resistance genes (ARGs) are found in specific bacterial species and/or genera is critical when using a selective suite of ARGs for detection or surveillance studies. As detection methods move to molecular techniques, our knowledge about which type of bacteria carry which resistance gene(s) will become more important to ensure that the whole spectrum of bacteria are included in future surveillance studies. This review provides information needed to integrate the biology, taxonomy, and ecology of tetracycline- and phenicol-resistant bacteria and their resistance genes so that informative surveillance strategies can be developed and the correct genes selected.201627065405
432210.9999Multi-Drug Resistance in Bacterial Genomes-A Comprehensive Bioinformatic Analysis. Antimicrobial resistance is presently one of the greatest threats to public health. The excessive and indiscriminate use of antibiotics imposes a continuous selective pressure that triggers the emergence of multi-drug resistance. We performed a large-scale analysis of closed bacterial genomes to identify multi-drug resistance considering the ResFinder antimicrobial classes. We found that more than 95% of the genomes harbor genes associated with resistance to disinfectants, glycopeptides, macrolides, and tetracyclines. On average, each genome encodes resistance to more than nine different classes of antimicrobial drugs. We found higher-than-expected co-occurrences of resistance genes in both plasmids and chromosomes for several classes of antibiotic resistance, including classes categorized as critical according to the World Health Organization (WHO). As a result of antibiotic-resistant priority pathogens, higher-than-expected co-occurrences appear in plasmids, increasing the potential for resistance dissemination. For the first time, co-occurrences of antibiotic resistance have been investigated for priority pathogens as defined by the WHO. For critically important pathogens, co-occurrences appear in plasmids, not in chromosomes, suggesting that the resistances may be epidemic and probably recent. These results hint at the need for new approaches to treating infections caused by critically important bacteria.202337511196
390220.9999Integrons and antibiotic resistance genes in water-borne pathogens: threat detection and risk assessment. Antibiotic-resistant genes (ARGs) are regarded as emerging environmental pollutants and pose a serious health risk to the human population. Integrons are genetic elements that are involved in the spread of ARGs amongst bacterial species. They also act as reservoirs of these resistance traits, further contributing to the development of multi-drug resistance in several water-borne pathogens. Due to inter- and intra-species transfer, integrons are now commonly reported in important water-borne pathogens such as Vibrio, Campylobacter, Salmonella, Shigella, Escherichia coli and other opportunistic pathogens. These pathogens exhibit immense diversity in their resistance gene cassettes. The evolution of multiple novel and complex gene cassettes in integrons further suggests the selection and horizontal transfer of ARGs in multi-drug resistant bacteria. Thus, the detection and characterization of these integrons in water-borne pathogens, especially in epidemic and pandemic strains, is of the utmost importance. It will provide a framework in which health authorities can conduct improved surveillance of antibiotic resistance in our natural water bodies. Such a study will also be helpful in developing better strategies for the containment and cure of infections caused by these bacteria.201930990401
389830.9999Enterococci as a One Health indicator of antimicrobial resistance. The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.202438696839
389340.9999Diverse antibiotic resistance genes in dairy cow manure. Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings. IMPORTANCE The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.201424757214
390050.9999Antimicrobial resistance pattern in domestic animal - wildlife - environmental niche via the food chain to humans with a Bangladesh perspective; a systematic review. BACKGROUND: Antimicrobial resistance (AMR) is a growing concern globally, but the impact is very deleterious in the context of Bangladesh. Recent review article on the AMR issue demonstrates the scenario in human medicine; unfortunately, no attempt was taken to address this as One Health issue. The antimicrobial resistance bacteria or genes are circulating in the fragile ecosystems and disseminate into human food chain through direct or indirect ways. In this systematic review we are exploring the mechanism or the process of development of resistance pathogen into human food chain via the domestic animal, wildlife and environmental sources in the context of One Health and future recommendation to mitigate this issue in Bangladesh. RESULTS: Tetracycline resistance genes were presenting in almost all sample sources in higher concentrations against enteric pathogen Escherichia coli. The second most significant antibiotics are amino-penicillin that showed resistant pattern across different source of samples. It is a matter of concerns that cephalosporin tends to acquire resistance in wildlife species that might be an indication of this antibiotic resistance gene or the pathogen been circulating in our surrounding environment though the mechanism is still unclear. CONCLUSIONS: Steps to control antibiotic release and environmental disposal from all uses should be immediate and obligatory. There is a need for detailed system biology analysis of resistance development in-situ.202032838793
670760.9999Investigating the occurrence of antimicrobial resistance in the environment in Canada: a scoping review. Antimicrobial resistance is an environmental, agricultural, and public health problem that is impacting the health of humans and animals. The role of the environment as a source of and transmission pathway for antibiotic resistant bacteria and antibiotic resistance genes is a topic of increasing interest that, to date, has received limited attention. This study aimed to describe the sources and possible pathways contributing to antimicrobial resistance dissemination through bioaerosols, water, and soil in Canada using a scoping review methodology and systems thinking approach. A systems map was created to describe the occurrence and relationships between sources and pathways for antimicrobial resistance dissemination through water, soil, and bioaerosols. The map guided the development of the scoping review protocol, specifically the keywords searched and what data were extracted from the included studies. In total, 103 studies of antimicrobial resistance in water, 67 in soil, and 12 in air were identified. Studies to detect the presence of antimicrobial resistance genes have mainly been conducted at wastewater treatment plants and commercial animal livestock facilities. We also identified elements in the systems map with little or no data available (e.g., retail) that need to be investigated further to have a better understanding of antimicrobial resistance dissemination through different Canadian environments.202540279669
408370.9999Antibiotic resistance gene discovery in food-producing animals. Numerous environmental reservoirs contribute to the widespread antibiotic resistance problem in human pathogens. One environmental reservoir of particular importance is the intestinal bacteria of food-producing animals. In this review I examine recent discoveries of antibiotic resistance genes in agricultural animals. Two types of antibiotic resistance gene discoveries will be discussed: the use of classic microbiological and molecular techniques, such as culturing and PCR, to identify known genes not previously reported in animals; and the application of high-throughput technologies, such as metagenomics, to identify novel genes and gene transfer mechanisms. These discoveries confirm that antibiotics should be limited to prudent uses.201424994584
389480.9999Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics. Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.202133916668
389690.9999Antimicrobial resistance genes in bacteria from animal-based foods. Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.202032762867
3901100.9999Antimicrobial resistance in Chile and The One Health paradigm: Dealing with threats to human and veterinary health resulting from antimicrobial use in salmon aquaculture and the clinic. The emergence and dissemination of antimicrobial-resistant bacteria (ARB) is currently seen as one of the major threats to human and animal public health. Veterinary use of antimicrobials in both developing and developed countries is many-fold greater than their use in human medicine and is an important determinant in selection of ARB. In light of the recently outlined National Plan Against Antimicrobial Resistance in Chile, our findings on antimicrobial use in salmon aquaculture and their impact on the environment and human health are highly relevant. Ninety-five percent of tetracyclines, phenicols and quinolones imported into Chile between 1998 and 2015 were for veterinary use, mostly in salmon aquaculture. Excessive use of antimicrobials at aquaculture sites was associated with antimicrobial residues in marine sediments 8 km distant and the presence of resistant marine bacteria harboring easily transmissible resistance genes, in mobile genetic elements, to these same antimicrobials. Moreover, quinolone and integron resistance genes in human pathogens isolated from patients in coastal regions adjacent to aquaculture sites were identical to genes isolated from regional marine bacteria, consistent with genetic communication between bacteria in these different environments. Passage of antimicrobials into the marine environment can potentially diminish environmental diversity, contaminate wild fish for human consumption, and facilitate the appearance of harmful algal blooms and resistant zoonotic and human pathogens. Our findings suggest that changes in aquaculture in Chile that prevent fish infections and decrease antimicrobial usage will prove a determining factor in preventing human and animal infections with multiply-resistant ARB in accord with the modern paradigm of One Health.201830534910
3884110.9999Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non-agricultural metagenomes. There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.201223133629
3897120.9999The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review. Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.201931002332
4321130.9999The prevalence and distribution of aminoglycoside resistance genes. Choosing the appropriate antibiotics to treat bacterial infections has grown more challenging as a result of the emergence of antibiotic-resistant bacteria. Aminoglycosides, as broad-spectrum antibiotics, are increasingly being used clinically; however, for most effective employment of aminoglycosides, a comprehensive understanding of aminoglycoside resistance genes' prevalence and dissemination is required. Therefore, to better understand the global resistance status of aminoglycoside antibiotics and the prevalence of antibiotic-resistance genes (ARGs) in various bacterial species, this systematic review gathered relevant data from multiple studies. Two primary resistance mechanisms-aminoglycoside enzymatic modification and 16S rRNA methylation-were assessed, and the prevalence of the corresponding ARGs was described. The coexistence of aminoglycoside ARGs with other ARGs was also demonstrated, as was the relationship between aminoglycoside ARGs and resistant phenotypes. The lack of effective therapeutic agents to combat resistant pathogens presents a real threat to public health. The combination of aminoglycosides with other antibiotics may provide a novel treatment strategy.202340078603
4042140.9999Integrons in the intestinal microbiota as reservoirs for transmission of antibiotic resistance genes. The human intestinal microbiota plays a major beneficial role in immune development and resistance to pathogens. The use of antibiotics, however, can cause the spread of antibiotic resistance genes within the resident intestinal microbiota. Important vectors for this are integrons. This review therefore focuses on the integrons in non-pathogenic bacteria as a potential source for the development and persistence of multidrug resistance. Integrons are a group of genetic elements which are assembly platforms that can capture specific gene cassettes and express them. Integrons in pathogenic bacteria have been extensively investigated, while integrons in the intestinal microbiota have not yet gained much attention. Knowledge of the integrons residing in the microbiota, however, can potentially aid in controlling the spread of antibiotic resistance genes to pathogens.201425437798
4154150.9999Resistance to the tetracyclines and macrolide-lincosamide-streptogramin group of antibiotics and its genetic linkage - a review. An excessive use of antimicrobial agents poses a risk for the selection of resistant bacteria. Of particular interest are antibiotics that have large consumption rates in both veterinary and human medicine, such as the tetracyclines and macrolide-lincosamide-streptogramin (MLS) group of antibiotics. A high load of these agents increases the risk of transmission of resistant bacteria and/or resistance determinants to humans, leading to a subsequent therapeutic failure. An increasing incidence of bacteria resistant to both tetracyclines and MLS antibiotics has been recently observed. This review summarizes the current knowledge on different tetracycline and MLS resistance genes that can be linked together on transposable elements.201728664720
3889160.9999Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems. The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.202540298543
4323170.9999Current trends of human infections and antibiotic resistance of the genus Shewanella. Shewanella spp. are commonly known as environmental bacteria and are most frequently isolated from aquatic areas. Currently, diseases syndromes and multidrug resistance have increasingly been reported in the genus Shewanella. Some species are associated with various infections, such as skin and soft tissue infections, as well as bacteremia. Generally, these bacteria are opportunistic and mostly affect people with an impaired immune system. This genus is also a probable vehicle and progenitor of antibiotic resistance genes. In fact, several resistance genes and mobile genetic elements have been identified in some resistant species isolated from environmental or clinical settings. These genes confer resistance to different antibiotic classes, including those used in therapies such as β-lactams and quinolones, and are generally located on the chromosome. Recently, a multidrug-resistant (MDR) plasmid harboring several drug resistance genes associated with transposons and integrons has been identified in Shewanella xiamenensis. These antibiotic resistance genes can circulate in the environment and contribute to the emergence of antibiotic resistance. This review describes different aspects of Shewanella, focusing on the infections caused by this genus, as well as their role in the propagation of antibiotic resistance via mobile genetic elements.201728299457
3899180.9999Overview of Evidence of Antimicrobial Use and Antimicrobial Resistance in the Food Chain. Antimicrobial resistance (AMR) is a global health problem. Bacteria carrying resistance genes can be transmitted between humans, animals and the environment. There are concerns that the widespread use of antimicrobials in the food chain constitutes an important source of AMR in humans, but the extent of this transmission is not well understood. The aim of this review is to examine published evidence on the links between antimicrobial use (AMU) in the food chain and AMR in people and animals. The evidence showed a link between AMU in animals and the occurrence of resistance in these animals. However, evidence of the benefits of a reduction in AMU in animals on the prevalence of resistant bacteria in humans is scarce. The presence of resistant bacteria is documented in the human food supply chain, which presents a potential exposure route and risk to public health. Microbial genome sequencing has enabled the establishment of some links between the presence of resistant bacteria in humans and animals but, for some antimicrobials, no link could be established. Research and monitoring of AMU and AMR in an integrated manner is essential for a better understanding of the biology and the dynamics of antimicrobial resistance.202032013023
4297190.9999Predicting clinical resistance prevalence using sewage metagenomic data. Antibiotic resistance surveillance through regional and up-to-date testing of clinical isolates is a foundation for implementing effective empirical treatment. Surveillance data also provides an overview of geographical and temporal changes that are invaluable for guiding interventions. Still, due to limited infrastructure and resources, clinical surveillance data is lacking in many parts of the world. Given that sewage is largely made up of human fecal bacteria from many people, sewage epidemiology could provide a cost-efficient strategy to partly fill the current gap in clinical surveillance of antibiotic resistance. Here we explored the potential of sewage metagenomic data to assess clinical antibiotic resistance prevalence using environmental and clinical surveillance data from across the world. The sewage resistome correlated to clinical surveillance data of invasive Escherichia coli isolates, but none of several tested approaches provided a sufficient resolution for clear discrimination between resistance towards different classes of antibiotics. However, in combination with socioeconomic data, the overall clinical resistance situation could be predicted with good precision. We conclude that analyses of bacterial genes in sewage could contribute to informing management of antibiotic resistance.202033244050