Origin Of Antibiotic Resistance Genes Research Articles

Metagenomic assemblies tend to break around antibiotic resistance genes

BackgroundAssembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.ResultsThe results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.ConclusionsOur study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.

High occurrence of antibiotic resistance genes in intensive aquaculture of hybrid snakehead fish

The increasing abundance of antibiotic resistance genes (ARGs), which are regarded as new pollutants, has raised public health concern. The use of antibiotics in aquaculture has promoted the evolution and spread of ARGs. The occurrence and abundance of ARGs in aquaculture has attracted extensive attention. However, the distribution and transmission of ARGs in aquaculture require further study. This study analyzed water and sediment from intensive culture of hybrid snakehead fish farm in Zhongshan, South China. Twenty-two types of ARGs were detected in all environmental samples. The relative abundance of sulfonamide resistance genes (sul1 and sul2) was the highest, ranging from 3.37×10-2 to 8.53×100 copies/16S rRNA gene. High occurrence of quinolones, phenicols, tetracycline resistance genes, and class 1 integrase gene (intI1) was also observed in pond water samples. This implies that pond water is one of the main reservoirs and origins of ARGs in the aquatic environment. Proteobacteria was the most abundant phylum in all the environmental samples, and its relative abundance ranged from 24.05% to 41.84%. Network and canonical correspondence analyses showed that a high abundance of ARGs (int1, sul1, sul2, qacEΔ1, aac6, and oqxA) was positively correlated with Proteobacteria, Cyanobacteria, and Bacteroidetes, and the abundance of Proteobacteria, Actinobacteria, and Patescibacteria was positively correlated with environmental factors (sulfide, nitrite nitrogen, pH, free chlorine, and ammonia nitrogen). These findings demonstrate the prevalence and persistence of ARGs in intensive fish farming in southern China. This suggests that ARG levels and microbiological community composition in aquaculture should be conventionally determined to assess potential risks to public health.

General principles of antibiotic resistance evolution in bacteria (review of literature).

Currently, the impact of antibiotic resistance on human health is a worldwide problem and its study is of great interest from a molecular genetic, environmental and clinical view-point. This review summarizes the latest data about antibiotic resistance, the classification of microorganisms as sensitive and resistant to the action of antibiotics, reveals the concept of minimum inhibitory concentration from modern positions. The resistance of microorganisms to antibacterial agents can be intrinsic and acquired, as well as being one of the examples of evolution that are currently available for study. Modern methods of whole-genome sequencing and complex databases of nucleotide-tagged libraries give an idea of the multifaceted nature of the mechanisms of intrinsic resistance to antibiotics and are able to provide information on genes encoding metabolic enzymes and proteins that regulate the basic processes of the physiology of bacteria. The article describes the main ways of spreading the resistance of microorganisms, reflects the concepts of "founder effect" and the fitness cost of bacteria, which underlie the emergence and evolution of antibiotic resistance. It is shown that the origin of antibiotic resistance genes that human pathogens currently possess can be traced by studying the surrounding not only clinical, but also non-clinical (ecological) habitats. As well as microorganisms of the surrounding ecosystems are the donors of resistance genes in horizontal gene transfer.

The mobile FOX AmpC beta-lactamases originated in Aeromonas allosaccharophila

ObjectiveIt is important to understand the origins of antibiotic resistance genes so that risks associated with the emergence of novel resistance genes can be assessed and managed. The chromosomal ampC gene (CAV-1) of Aeromonas caviae (A. caviae) has been reported as the origin of mobile FOX cephalosporinases. The recent identification of A. caviae as the origin of MOX-2 cephalosporinases and the comparably great sequence divergence between FOX and MOX genes makes it unlikely that both genes arose from the same species. Therefore, this study investigated the origin of FOX cephalosporinases using large-scale genomics. MethodsPublicly available genomes and plasmids were searched for FOX-like genes. Synteny and nucleotide identities of the identified FOX-like genes and their genetic environments were compared and a phylogenetic tree was generated. ResultsFOX-like genes were identified in > 230 Aeromonas genomes and in 46 Enterobacteriaceae isolates. Analysis of the genomic context of CAV-1 revealed a truncated insertion sequence directly upstream of the ampC gene. The chromosomal ampCs of A. caviae (n = 31) were 75–78% identical to CAV-1. In contrast, CAV-1, mobile FOX genes and their context were 95–98% similar to the chromosomal ampC-locus of Aeromonas allosaccharophila (A. allosaccharophila) (n = 6). The A. allosaccharophila ampCs formed a monophyletic branch with mobile FOX genes, whereas the A. caviae ampCs clustered with mobile MOX genes. ConclusionsThese findings show that FOX cephalosporinases originate not in A. caviae, as previously reported, but in A. allosaccharophila, which is a fish pathogen. This finding agrees with the hypothesis that antibiotic use in aquaculture could have contributed to the emergence of FOX genes in human pathogens.

Inorganic and organic fertilizers application enhanced antibiotic resistome in greenhouse soils growing vegetables

Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in fertilizers pose risks to human health and their variation in soil after fertilization has been reported. However, some important questions, such as the origin of ARG and ARB observed in soil following fertilization, which are present in soil regardless of fertilizer type (i.e., core (shared) ARGs and ARB), and the contribution of various ARG subtypes to the soil antibiotic resistome, need to be addressed. In this study, the effects of a long-term (9-year) application of organic (manure) and inorganic (chemistry) fertilizers on ARGs in greenhouse soils growing vegetables were investigated using metagenomic sequencing. The results showed that both organic and inorganic fertilizers application increased the diversity and abundance of soil ARGs. The dominant ARG types in organic fertilizer (OF) were different from that in organic fertilizer treated soil (SO), inorganic fertilizer treated soil (SI) and no fertilizer control plots (SC). The difference of core ARGs abundance reflected the variation of ARG profiles among SC, SI and SO. The OF is likely a source of the elevated ARG subtypes in soil and almost all the soil core ARG subtypes can be detected in organic fertilizer. Fifteen ARG types were enriched in the soil with OF, and some ARG subtypes such as sul1, sul2, tetX and tetL might derived from OF while others including as vanR, tcmA, rosB, and mexF might be from indigenous microbes in soil. The nutrition factors were found to influence the ARG profiles in fertilized soil. In summary, this study revealed the possible reason for the soil total ARG numbers and their relative abundance increase after fertilization, which will facilitate the control of ARGs and ARB dissemination.

Permanent draft genome sequence of Bacillus flexus strain T6186-2, a multidrug-resistant bacterium isolated from a deep-subsurface oil reservoir

Previous studies suggest that antibiotic resistance genes have an ancient origin, which is not always linked to the use of antibiotics but can be enhanced by human activities. Bacillus flexus strain T6186-2 was isolated from the formation water sample of a deep-subsurface oil reservoir. Interestingly, antimicrobial susceptibility testing showed that this strain is susceptible to kanamycin, however, resistant to ampicillin, erythromycin, gentamicin, vancomycin, fosfomycin, fosmidomycin, tetracycline and teicoplanin. To explore our knowledge about the origins of antibiotic resistance genes (ARGs) in the relatively pristine environment, we sequenced the genome of B. flexus strain T6186-2 as a permanent draft. It represents the evidence for the existence of a reservoir of ARGs in nature among microbial populations from deep-subsurface oil reservoirs.

Antibiotic resistance: Origins, mechanisms, approaches to counter

Microbial resistance is emerging faster than we are replacing our armamentarium of antimicrobial agents. Resistance to penicillin developed soon after it was introduced into clinical practice in 1940s. Now resistance developed to every major class of antibiotics. In healthcare facilities around the world, bacterial pathogens that express multiple resistance mechanisms are becoming common. The origins of antibiotic resistance genes can be traced to the environmental microbiota. Mechanisms of antibiotic resistance include alterations in bacterial cell wall structure, growth in biofilms, efflux pump expression, modification of an antibiotic target or acquisition of a new target and enzymatic modification of the antibiotic itself. Specific examples of each mechanism are discussed in this review. Some approaches to counter resistance include antibiotic stewardship, co-administration with resistance inhibitors, exploiting genome data in search of new targets and use of non-antibiotic antimicrobials for topical indications. A coordinated effort from government, public and industry is needed to deal with antibiotic resistance health care crisis.

Antibiotic resistance in bacteria associated with coarse atmospheric particulate matter in an urban area

To assess antibiotic resistance in airborne bacteria associated with coarse particulate matter (PM10) in an urban area, with specific considerations about the Staphylococcus genus. Disc diffusion test was performed on 243 microbial strains, isolated from PM10 in winter and summer and belonging to families Pseudomonadaceae and Enterobacteriaceae and genera Acinetobacter, Enterococcus and Staphylococcus. Staphylococci resistances were the most heterogeneous, being distributed among almost all tested antibiotics. Staphylococcus isolates resistant to some selected antibiotics were further investigated for the presence of the corresponding genetic determinants. Only tetK, which mediates the tetracycline resistance through the action of an efflux protein, was found in almost all resistant isolates. The lack of specific genetic determinants makes their transmission among staphylococci less likely. This may reduce the theoretical risk associated with the inhalation of airborne micro-organisms. Although the spreading of antibiotic resistant micro-organisms is of particular concern in clinical settings, the origin of antibiotic resistance genes can be traced in natural environments. As behaviour, viability and transport of bacteria in the atmospheric compartment suffer from a lack of information, the evaluation of the actual risk posed by airborne micro-organisms to human health is still challenging.

Metagenomic Analysis of Apple Orchard Soil Reveals Antibiotic Resistance Genes Encoding Predicted Bifunctional Proteins

To gain insight into the diversity and origins of antibiotic resistance genes, we identified resistance genes in the soil in an apple orchard using functional metagenomics, which involves inserting large fragments of foreign DNA into Escherichia coli and assaying the resulting clones for expressed functions. Among 13 antibiotic-resistant clones, we found two genes that encode bifunctional proteins. One predicted bifunctional protein confers resistance to ceftazidime and contains a natural fusion between a predicted transcriptional regulator and a beta-lactamase. Sequence analysis of the entire metagenomic clone encoding the predicted bifunctional beta-lactamase revealed a gene potentially involved in chloramphenicol resistance as well as a predicted transposase. A second clone that encodes a predicted bifunctional protein confers resistance to kanamycin and contains an aminoglycoside acetyltransferase domain fused to a second acetyltransferase domain that, based on nucleotide sequence, was predicted not to be involved in antibiotic resistance. This is the first report of a transcriptional regulator fused to a beta-lactamase and of an aminoglycoside acetyltransferase fused to an acetyltransferase not involved in antibiotic resistance.

Genomic evidence for antibiotic resistance genes of actinomycetes as origins of antibiotic resistance genes in pathogenic bacteria simply because actinomycetes are more ancestral than pathogenic bacteria

Although in silico analysis have suggested that the antibiotic resistance genes in actinomycetes appear to be the origins of some antibiotic resistance genes, we have shown that recent horizontal transfer of antibiotic resistance genes from actinomycetes to other medically important bacteria have not taken place. Although it has been speculated in Benveniste and Davies' attractive hypothesis that antibiotic resistance genes of actinomycetes are origins of antibiotic resistance genes in pathogenic bacteria because the actinomycetes require mechanisms such as metabolic enzymes (encoded by the antibiotic resistance genes) to degrade the antibiotics they produce or to transport the antibiotics outside the bacterial cells, this hypothesis has never been proven. Both the phylogenetic tree constructed using 16S rRNA gene sequences and that constructed using concatenated amino acid sequences of 15 housekeeping genes extracted from 90 bacterial genomes showed that the actinomycetes is more ancestral to most other bacteria, including the pathogenic Gram-negative bacteria, Gram-positive bacteria, and Chlamydia species. Furthermore, the tetracycline resistance gene of Bifidobacterium longum is more ancestral to those of other pathogenic bacteria and the actinomycetes, which is in line with the ancestral position of B. longum. These suggest that the evolution of antibiotic resistance genes of antibiotic-producing bacteria in general parallels the evolution of the corresponding bacteria. The ancestral position of the antibiotic resistance genes in actinomycetes is probably unrelated to the fact that they produce antibiotics, but simply because actinomycetes are more ancestral than pathogenic bacteria.