Evolution Of Antibiotic Resistance Genes Research Articles

Evolution of Antibiotic Resistance Genes and Bacterial Community During Erythromycin Fermentation Residue Composting Under High‐Salinity Stress

Evolution of Antibiotic Resistance Genes and Bacterial Community During Erythromycin Fermentation Residue Composting Under High‐Salinity Stress

Insight into the evolution of antibiotic resistance genes and microbial community during spiramycin fermentation residue composting process after thermally activated peroxydisulfate pretreatment

Previous research has been demonstrated that the residual unextracted antibiotics in spiramycin fermentation residue (SFR) could be efficiently removed by thermally activated peroxodisulfate (TAP) pretreatment, indicating the improvement of biodegradability. This study aimed to investigate the effect of TAP pretreatment on the succession of bacterial community and fate of antibiotic resistance genes (ARGs) during SFR composting. Results indicated that TAP pretreatment increased the composting temperature and promoted the decomposition of organic matters. Furthermore, TAP pretreatment could increase bacterial alpha diversity and significantly reduce the relative abundance of ARGs (1.13–1.75 times) and mobile genetic elements (MGEs) (1.13–1.32 times) after composting. The compost of pretreated SFR by TAP could reduce the enrichment of ARGs and MGEs in the bacterial community, especially the rRNA methylase genes of ermB (4–142-folds). Redundancy analysis showed that Actinobacteria, Bacteroidetes, Proteobacteria and horizontal gene transfer mediated by MGEs (intI1) was positively related to the changes in ARGs (accounted for 97.4%). Network analysis showed that Firmicutes was the main bacterial hosts of ARGs and MGEs. These findings demonstrated that TAP pretreatment combined composting was a promising strategy for SFR safe treatment and disposal that could reduce the proliferation and transfer of ARGs.

Diversity and Abundance of Antibiotic Resistance Genes in Tailings Ponds

Antibiotic resistance genes (ARGs) are considered emerging contaminants posing an increasing threat to the ecological environment and global human health. Profiling ARGs in tailings ponds is essential to better understand their spatial and temporal dynamics. In this study, high-throughput quantitative polymerase chain reaction (PCR) techniques were used to investigate the occurrence, diversity, abundance, and distribution of ARGs in a tailings pond. A total of 97, 52, 44, and 56 ARGs were detected in WK0, WK1, WK2, and HS, respectively, with 11, 6, 3, and 6 mobile genetic elements (MGEs) also being detected, respectively. The absolute abundance of ARGs in the pond water ranged from 6.39×107 to 1.75×108 copies·L-1. Additionally, the abundance of MGEs were higher than ARGs in WK1 and WK2, indicating the potential for horizontal gene transfer (HGT). Furthermore, Cu, TOC, and MGEs were significantly associated with ARGs. Indeed, redundancy analysis (RDA) revealed that Cu, TOC, and MGEs explained 61.64% of the alteration of the ARG profiles, implying their potential roles in the spread and evolution of ARGs in tailings ponds.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health.

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

Cyanobacterial blooms contribute to the diversity of antibiotic-resistance genes in aquatic ecosystems

Cyanobacterial blooms are a global ecological problem that directly threatens human health and crop safety. Cyanobacteria have toxic effects on aquatic microorganisms, which could drive the selection for resistance genes. The effect of cyanobacterial blooms on the dispersal and abundance of antibiotic-resistance genes (ARGs) of concern to human health remains poorly known. We herein investigated the effect of cyanobacterial blooms on ARG composition in Lake Taihu, China. The numbers and relative abundances of total ARGs increased obviously during a Planktothrix bloom. More pathogenic microorganisms were present during this bloom than during a Planktothrix bloom or during the non-bloom period. Microcosmic experiments using additional aquatic ecosystems (an urban river and Lake West) found that a coculture of Microcystis aeruginosa and Planktothrix agardhii increased the richness of the bacterial community, because its phycosphere provided a richer microniche for bacterial colonization and growth. Antibiotic-resistance bacteria were naturally in a rich position, successfully increasing the momentum for the emergence and spread of ARGs. These results demonstrate that cyanobacterial blooms are a crucial driver of ARG diffusion and enrichment in freshwater, thus providing a reference for the ecology and evolution of ARGs and ARBs and for better assessing and managing water quality.

Composting of oxytetracycline fermentation residue in combination with hydrothermal pretreatment for reducing antibiotic resistance genes enrichment

Hydrothermal pretreatment can efficiently remove the residual antibiotics in oxytetracycline fermentation residue (OFR), but its effect on antibiotic resistance genes (ARGs) during composting remains unclear. This study compared the shifts in bacterial community and evolutions in ARGs and integrons during different composting processes of OFRs with and without hydrothermal pretreatment. The results demonstrated that hydrothermal pretreatment increased the bacterial alpha diversity at the initial phase, and increased the relative abundances of Proteobacteria and Actinobacteria but decreased that of Bacteroidetes at the final phase by inactivating mycelia and removing residual oxytetracycline. Composting process inevitably elevated the abundance and relative abundance of ARGs. However, the increase in ARGs was significantly reduced by hydrothermal pretreatment, because the removal of oxytetracycline decreased their potential host bacteria and inhibited their horizontal gene transfer. The results demonstrated that hydrothermal pretreatment is an efficient strategy to reduce the enrichment of ARGs during the OFR composting.

Occurrence of antibiotics and antibiotic resistance genes in the Fuxian Lake and antibiotic source analysis based on principal component analysis-multiple linear regression model

In recent years, the dramatic increase in antibiotic use has led to the evolution of antibiotic resistant genes (ARGs), posing a potential risk to human and aquatic ecological safety. In this study, source contribution and correlations between twelve antibiotics and their corresponding ARGs were firstly investigated in surface water in the Fuxian Lake. The results showed that sulfamethoxazole (SMX) (0.98–14.32 ng L−1) and ofloxacin (OFL) (0.77–7.3 ng L−1) were the dominant antibiotics in surface water, whereas erythromycin-H2O (EM-H2O), SMX and OFL posed the medium risk to aquatic organisms. Meanwhile, the mean concentrations of MLs in inflowing rivers were 5.6 times more than those in the lake, which was related to dilution and degradation. Moreover, the facter1 (co-sources L (Living quarters), M (Mining area), A (Agricultural district) and T (tourist area)) contributed 78% of antibiotic concentrations, and the source L was predominant. The results also revealed the prevalence of intL1, sul1 and sul2 in all the sampling sites, and that the abundance of ARGs in the lake was significantly lower (P < 0.01) than that in inflowing rives. Additionally, significant correlations (p < 0.0001) between intL1 and sulfanilamide resistance genes (sul1, sul2) were detected, indicating that intL1 promoted the propagation and they originated from the same anthropogenic sources. Overall, our findings revealed the presence of antibiotics and ARGs and their inconsistent correlations in the Fuxian Lake, which provides a foundation to support further exploration of the occurrence and transmission mechanisms of antibiotics and ARGs.

Development, spread and persistence of antibiotic resistance genes (ARGs) in the soil microbiomes through co-selection.

Bacterial pathogens resistant to multiple antibiotics are emergent threat to the public health which may evolve in the environment due to the co-selection of antibiotic resistance, driven by poly aromatic hydrocarbons (PAHs) and/or heavy metal contaminations. The co-selection of antibiotic resistance (AMR) evolves through the co-resistance or cross-resistance, or co-regulatory mechanisms, present in bacteria. The persistent toxic contaminants impose widespread pressure in both clinical and environmental setting, and may potentially cause the maintenance and spread of antibiotic resistance genes (ARGs). In the past few years, due to exponential increase of AMR, numerous drugs are now no longer effective to treat infectious diseases, especially in cases of bacterial infections. In this mini-review, we have described the role of co-resistance and cross-resistance as main sources for co-selection of ARGs; while other co-regulatory mechanisms are also involved with cross-resistance that regulates multiple ARGs. However, co-factors also support selections, which results in development and evolution of ARGs in absence of antibiotic pressure. Efflux pumps present on the same mobile genetic elements, possibly due to the function of Class 1 integrons (Int1), may increase the presence of ARGs into the environment, which further is promptly changed as per environmental conditions. This review also signifies that mutation plays important role in the expansion of ARGs due to presence of diverse types of anthropogenic pollutants, which results in overexpression of efflux pump with higher bacterial fitness cost; and these situations result in acquisition of resistant genes. The future aspects of co-selection with involvement of systems biology, synthetic biology and gene network approaches have also been discussed.

Simultaneous robust removal of tetracycline and tetracycline resistance genes by a novel UiO/TPU/PSF forward osmosis membrane

The accumulation of antibiotics in the environment fosters the evolution of antibiotic resistance genes (ARGs) that cause adverse an ecological impact. In this study, we fabricated a thermoplastic polyurethane/polysulfone (TPU/PSF) composite membrane with a low structural parameter and high mechanical strength using electrospinning. UiO-66-NH2 particles and particles interfacial polymerization thin-film nanocomposite forward osmosis (UTFN) membrane were then prepared and characterized with the best-performing substrate layer of the TPU/PSF (20/80) membrane. Furthermore, the co-rejection and mechanism of tetracycline (TC) and tetracycline resistance genes (TRGs) (commonly including tetA, tetC, tetM, tetO, and tetX, as well as int1 and 16S rRNA gene) were revealed. Results demonstrated that the as-prepared UTFN membrane with 0.075 wt% particle(UTFN-0.075) achieved the highest water flux (64 L m−2 h−1) and the rejection of TC was above 99.64% using 0.5 mol (NH4)2HPO4 as the draw solution. Meanwhile, the permeability of the TRGs was lower than 10% (particularly, less than 1.4% for tetC). The rejection of electrically neutral TC was likely affected by steric hindrance, whereas the TRGs rejection mechanism could be attributed to electrostatic repulsion and pore sieving effect. As for permeability, differences in various TRGs were mainly attributed to their distribution. Therefore, the simultaneous removal of TC and TRGs by the UTFN membrane has significant application prospects for wastewater treatment.

Temporal dynamics of antibiotic resistant genes and their association with the bacterial community in a water-sediment mesocosm under selection by 14 antibiotics

Antibiotics in aquatic environments at high concentrations and sub-inhibitory concentrations potentially select for the evolution of antibiotic resistant genes (ARGs), posing a potential risk to aquatic ecological safety. Our knowledge of the temporal and successive dynamics of ARGs and bacterial community under the selective pressure of antibiotics in natural water-sediment system was limited. This study used a 120-d operating hydrodynamic mesocosm to explore the temporal dynamics of ARGs in water-sediment systems, and the main selective mechanisms following the attenuation and transport of 14 commonly used antibiotics. Under the selective pressures by antibiotics, ARGs propagated transiently, and persisted after antibiotic removal; the bacterial community structures likewise changed. Mantel test and network analysis indicated that ARGs significantly correlated with the bacterial community in the water and surface sediments. Structural equation model (SEM) further revealed that the evolution of ARGs was mainly due to the direct effect of the change in bacterial community and horizontal gene transfer (HGT) via the class 1 integron-integrase gene (intI1), but antibiotics indirectly influenced ARG profiles. The migration of ARGs in deep layer sediments was not related to the bacterial community and intI1, but may be explained by antibiotic selective effects and ARG transformation.

Enhancement of methane production and antibiotic resistance genes reduction by ferrous chloride during anaerobic digestion of swine manure

In this study, effects of ferrous chloride (FeCl2) addition on methane production and antibiotic resistance genes (ARGs) reduction were investigated during anaerobic digestion (AD) of swine manure. FeCl2 could both improve the accumulative methane production and reduce the abundance of total ARGs, i.e., the maximum increase of CH4 production of 21.5% at FC5, and the maximum ARGs reduction of 33.3% at FC25. The reduction of pathogenic bacteria and metal resistance genes (MRGs) was enhanced. Acetate and propionate utilization were intensified by enhancing H2 utilization and direct interspecies electron transfer (DIET), where DIET was further enhanced by the reaction of the FeCl2 and acetic acid. The bacterial community played important role in the evolution of ARGs (68.26%), which were also affected by MRGs, mobile genetic elements (MGEs), and environmental factors. Therefore, FeCl2-based AD is a feasible and attractive way to improve methane production and ARG reduction.

Effects of endogenous inhibitors on the evolution of antibiotic resistance genes during high solid anaerobic digestion of swine manure

Livestock manure is a reservoir of antibiotic resistance genes (ARGs). The endogenous inhibitors that emerge during high solid anaerobic digestion (HSAD) greatly influence the bioprocess performance and the ARGs. The effect of endogenous inhibitors including volatile fatty acids (VFAs) and free ammonia (FA) on the ARG occurrences during HSAD of swine manure was investigated in this study. The ARG properties during HSAD (8%–14% total solids (TS)) largely differed from the low TS control (4%). The endogenous inhibitors and microbial communities greatly contributed to the three-phase changes in ARGs. The concentrations of VFAs and abundances of Proteobacteria and intI1 were correlated with the changes in ARGs. FA inhibition and VFA accumulation (especially propionate) delayed and restricted the decline of ARGs. The relatively slow rate of changes in ARGs and high ARGs in the end product suggested the high risk of the HSAD digestate for land application.

Антибиотикорезистентность: эволюционные предпосылки, механизмы, последствия

The article focuses on the problem of studying the antibiotic resistance of microorganisms inhabiting the natural environments of the human and animal organism. It analyzes some data published in Russian and world literature on the importance of this problem in the field of public health, veterinary medicine, the existing mechanisms of the emergence of antibiotic resistance in pathogens and forms of acquired resistance. Widespread use of antibiotics in medicine and veterinary led to the emergence of highly resistant pathogens thus creating both an epizootic and epidemiological problem (A.N. Panin et al., 2017). Extensive use of antimicrobials resulted in the selection of resistant strains among the species of commensal, saprophytic and opportunistic microflora. While resisting the effects of antimicrobial agents, bacteria use different sets of defense mechanisms simultaneously and create new counteraction strategies during the evolution (M.A. Shkurat, I.O. Pokudina, D.V. Battalov, 2014). On the one hand, this is due to the evolution of antibiotic resistance genes determining the formation of new molecular mechanisms of resistance, and, on the other hand, to the formation of new mechanisms of adaptation and maintenance in microecosystems. The latter led to the evolution of microbial communities and the emergence of new nosological units. Microbial communities, interacting with each other, create a barrier (biofilm) as a protective factor against antibacterial agents (D. Hughes, D.I. Andersson, 2017). Currently, the microbial communities of the potentially pathogenic microflora, which are stable by species composition, are widely spread, which is manifested by the occurrence of mixed infections. That raises new problems of ensuring the health of animals and humans.

The mobile dso-gene-sso element in rolling-circle plasmids of staphylococci reflects the evolutionary history of its resistance gene.

We have analysed five resistance genes in Staphylococcus aureus that are positioned between the replication elements of rolling-circle plasmids. For three of these genes, evidence was obtained indicative of recent mobilization. The historical use of the antibiotics to which the genes produce resistance could be related to the number of mutations collected in these genes. However, two other resistance genes have not collected any mutations over time, and the reasons for this are discussed. The analyses presented provide insights into the spread and evolution of antibiotic resistance genes.

Ancient Resistome.

Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides. The investigation of the resistome of ancient bacteria is a recent and emerging field of research, and technological advancements such as next-generation sequencing will further contribute to its growth. It is hoped that the knowledge gained from this research will help us to better understand the evolution of antibiotic resistance genes and will also be used in drug design as a proactive measure against antibiotic resistance.

CfxA expression in oral clinical Capnocytophaga isolates

Capnocytophaga spp. are commensal bacteria involved in oral and systemic diseases, with a variable susceptibility to beta-lactams. The cfxA gene expression level was assessed using quantitative RT-PCR, and reasons of the observed misexpression were discussed, as insertion of foreign genetic material, contributing to dissemination and evolution of antibiotic resistance genes.

Genome sequence of type strain of Staphylococcus aureus subsp. aureus

BackgroundStaphylococcus aureus is a pathogen that causes food poisoning and community-associated infection with antibiotic resistance. This species is an indigenous intestinal microbe found in infants and not found in adult intestine. The relatively small genome size and rapid evolution of antibiotic resistance genes in the species have been drawing an increasing attention in public health. To extend our understanding of the species and use the genome data for comparative genomic studies, we sequenced the type strain of S. aureus subsp. aureus DSM 20231T.ResultsSeventeen contigs were generated using hybrid assembly of sequences derived from the Roche 454 and Illumina systems. The length of the genome sequence was 2,902,619 bases with a G + C content of 32.8%. Among the 2,550 annotated CDSs, 44 CDSs were annotated to antibiotic resistance genes and 13 CDSs were related to methicillin resistance. It is interesting to note that this strain was first isolated in 1884 before methicillin was generally used on patients.ConclusionsThe present study analyzed the genome sequence of S. aureus subsp. aureus type strain as the reference sequence for comparative genomic analyses of clinical isolates. Methicillin resistance genes found in the genome indicate the presence of antibiotic resistance mechanism prior to the usage of antibiotics. Further comparative genomic studies of methicillin-resistant strains based on this reference genome would help to understand the evolution of resistance mechanism and dissemination of resistance genes.

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.

Multiple resistance in Gram-negative bacteria

When extended spectrum cephalosporins were introduced into clinical practice some 20 years ago it was widely predicted that these agents would effectively remove the problem of infections caused by resistant Enterobacteriaceae. It very rapidly became clear that the rapid evolution of antibiotic resistance genes in Gram-negative bacteria, particularly with their fluid gene pool, could circumvent the pharmaceutical industry's efforts. In the last 10 years, extended-spectrum beta-lactamases have become the major mechanism of resistance in Enterobacteriaceae to these valuable antimicrobials. In many parts of the world resistance levels have reached the point where these agents can no longer be used, this has resulted in greatly increased usage of fluoroquinolones and carbepenem antibiotics and, once again, a variety of mechanisms of resistance have been recognized which are becoming increasingly common. The review discusses various aspects of the molecular evolution of resistance to these three major groups of antibiotics and reviews the role of mobile elements in Gram-negative bacteria in the dissemination of genes encoding resistance to these classes of antimicrobial. It is concluded that there is already a growing problem of potentially untreatable infections caused by Enterobacteriaceae and Pseudomonas aeruginosa which, unless novel agents are introduced, could pose a major threat to the health of both hospitalized patients and, with the movement of these genes into faecally carried community Gram-negative bacteria, patients with infections in the community.

Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus.

The kanamycin resistance gene from Staphylococcus aureus has been sequenced and its structure compared with similar genes isolated from Streptomyces fradiae and from two transposons, Tn5 and Tn903, originally isolated from Klebsiella pneumoniae and Salmonella typhimurium, respectively. The genes are all homologous but, since their common ancestor, have undergone extensive divergence, with more than 43% divergence between the closest pair. The phylogeny of the genes cannot be made congruent to the phylogeny of the taxa from which they were isolated without requiring rather improbable differences in rates. One is therefore led to conclude that there have been multiple occurrences of gene transfer between these species. Thus, although they are homologous, they are neither orthologous nor paralogous. It is suggested that homologous genes of this type be called xenologous.