QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments

Quantitative-genetic approaches have offered significant insights into phenotypic evolution. However, quantitative-genetic analyses fail to provide information about the evolutionary relevance of specific loci. One complex and ecologically relevant trait for plants is their resistance to herbivory because natural enemies can impose significant damage. To illustrate the insights of combined molecular and ecological research, we present the results of a field study mapping quantitative trait loci (QTL) for resistance and tolerance to natural rabbit herbivory in the genetic model, Arabidopsis thaliana. Replicates of the Ler x Col recombinant inbred lines were planted into field sites simulating natural autumn and spring seasonal germination cohorts. Shortly after flowering, herbivores removed the main flowering inflorescence (apical meristem). We found several main-effect QTL for resistance within each seasonal cohort and significant QTL-season interactions, demonstrating that the loci underlying resistance to a single herbivore differ across seasonal environments. The presence of QTL x environment also shows that variation at specific loci is only available to selection in some environments. Despite significant among-line variance components, no QTL for tolerance were detected. The combined results of the quantitative-genetic and QTL analyses demonstrate that many loci of small effect underlie tolerance to damage by rabbits, and counter the hypothesis of locus-specific tradeoffs between resistance and tolerance. The results also provide insights as to the locus-specific nature of evolutionary constraints, i.e. some loci influence flowering time and resistance in both seasonal cohorts. Our results show how linking molecular-genetic tools with field studies in ecologically relevant settings can clarify the role of specific loci in the evolution of quantitative traits.     

Functional role of bacterial multidrug efflux pumps in microbial natural ecosystems

Multidrug efflux pumps have emerged as relevant elements in the intrinsic and acquired antibiotic resistance of bacterial pathogens. In contrast with other antibiotic resistance genes that have been obtained by virulent bacteria through horizontal gene transfer, genes coding for multidrug efflux pumps are present in the chromosomes of all living organisms. In addition, these genes are highly conserved (all members of the same species contain the same efflux pumps) and their expression is tightly regulated. Together, these characteristics suggest that the main function of these systems is not resisting the antibiotics used in therapy and that they should have other roles relevant to the behavior of bacteria in their natural ecosystems. Among the potential roles, it has been demonstrated that efflux pumps are important for processes of detoxification of intracellular metabolites, bacterial virulence in both animal and plant hosts, cell homeostasis and intercellular signal trafficking.     

Antibiotic resistance of enterococci and related bacteria in an urban wastewater treatment plant

The main objective of this work was to study the ecology of enterococci and related bacteria in raw and treated wastewater from a treatment plant receiving domestic and pretreated industrial effluents in order to assess the influence of treatment on the prevalence of antibiotic resistance phenotypes among this group of bacteria. The predominant species found in the raw wastewater were Entercoccus hirae, Entercoccus faecium and Entercoccus faecalis. Wastewater treatment led to a reduction in E. hirae (alpha<0.1) and an increase in E. faecium (alpha<0.1); the relative proportions of E. faecalis remained the same in the raw and in the treated wastewater. Among the isolates tested, no vancomycin resistance was observed among the enterococci. Entercoccus faecium and E. faecalis showed resistance prevalence values reaching 33%, 40% and 57% for the antibiotics ciprofloxacin, erythromycin and tetracycline, respectively. Antibiotic-resistant strains of enterococci were not eliminated by wastewater treatment. A positive selection of ciprofloxacin-resistant enterococci was indicated by a significant increase in resistance prevalence (alpha<0.02) in treated wastewater compared with the raw wastewater.     

The detection of diverse aminoglycoside phosphotransferases within natural populations of actinomycetes

The conserved nature of the genes that code for actinomycete secondary metabolite biosynthetic pathways suggests a common evolutionary ancestor and incidences of lateral gene transfer. Resistance genes associated with these biosynthetic pathways also display a high degree of similarity. Actinomycete aminoglycoside phosphotransferase antibiotic resistance enzymes (APH) are coded for by such genes and are therefore good targets for evaluating the bioactive potential of actinomycetes. A set of universal PCR primers for APH encoding genes was used to probe genomic DNA from three collections of actinomycetes to determine the utility of molecular screening. An additional monitoring of populations for the predominance of specific classes of enzymes to predict the potential of environmental sites for providing isolates with interesting metabolic profiles. Approximately one-fifth of all isolates screened gave a positive result by PCR. The PCR products obtained were sequenced and compared to existing APH family members. Sequence analysis resolved the family into nine groups of which six had recognizable phenotypes: 6′-phosphotransferase (APH(6)), 3′-phosphotransferase (APH(3)), hydroxyurea phosphotransferase (HUR), peptide phosphotransferase, hygromycin B phosphotransferase (APH(7″)) and oxidoreductase. The actinomycetes screened fell into seven groups, including three novel groups with unknown phenotypes. The strains clustered according to the environmental site from where they were obtained, providing evidence for the movement of these genes within populations. The value of this as a method for obtaining novel compounds and the significance to the ecology of antibiotic biosynthesis are discussed. Journal of Industrial Microbiology & Biotechnology (2002) 29, 60–69 doi:10.1038/sj.jim.7000260 Received 25 June 2001/ Accepted in revised form 26 March 2002     

Isolated cell behavior drives the evolution of antibiotic resistance

Bacterial antibiotic resistance is typically quantified by the minimum inhibitory concentration (MIC), which is defined as the minimal concentration of antibiotic that inhibits bacterial growth starting from a standard cell density. However, when antibiotic resistance is mediated by degradation, the collective inactivation of antibiotic by the bacterial population can cause the measured MIC to depend strongly on the initial cell density. In cases where this inoculum effect is strong, the relationship between MIC and bacterial fitness in the antibiotic is not well defined. Here, we demonstrate that the resistance of a single, isolated cell—which we call the single‐cell MIC (scMIC)—provides a superior metric for quantifying antibiotic resistance. Unlike the MIC, we find that the scMIC predicts the direction of selection and also specifies the antibiotic concentration at which selection begins to favor new mutants. Understanding the cooperative nature of bacterial growth in antibiotics is therefore essential in predicting the evolution of antibiotic resistance.     

Source-sink dynamics shape the evolution of antibiotic resistance and its pleiotropic fitness cost

Understanding the conditions that favour the evolution and maintenance of antibiotic resistance is the central goal of epidemiology. A crucial feature explaining the adaptation to harsh, or 'sink', environments is the supply of beneficial mutations via migration from a 'source' population. Given that antibiotic resistance is frequently associated with antagonistic pleiotropic fitness costs, increased migration rate is predicted not only to increase the rate of resistance evolution but also to increase the probability of fixation of resistance mutations with minimal fitness costs. Here we report in vitro experiments using the nosocomial pathogenic bacterium Pseudomonas aeruginosa that support these predictions: increasing rate of migration into environments containing antibiotics increased the rate of resistance evolution and decreased the associated costs of resistance. Consistent with previous theoretical work, we found that resistance evolution arose more rapidly in the presence of a single antibiotic than two. Evolution of resistance was also more rapid when bacteria were subjected to sequential exposure with two antibiotics (cycling therapy) compared with simultaneous exposure (bi-therapy). Furthermore, pleiotropic fitness costs of resistance to two antibiotics were higher than for one antibiotic, and were also higher under bi-therapy than cycling therapy, although the cost of resistance depended on the order of the antibiotics through time. These results may be relevant to the clinical setting where immigration is known to be important between chemotherapeutically treated patients, and demonstrate the importance of ecological and evolutionary dynamics in the control of antibiotic resistance.     

大熊猫源细菌耐药性研究进展

耐药菌和耐药基因已成为一种新型环境污染物,引发世界公共卫生问题。细菌耐药性尤其是多重耐药菌在人医临床、畜禽养殖以及环境传播等多个方面得到越来越多的关注,而关于大熊猫等野生动物的耐药性研究相对较少。大熊猫(Ailuropoda melanoleuca)是世界公认的珍稀野生动物,其种群数量易受到各种疾病的威胁,尤其是肠道细菌性疾病。随着抗菌药物在疾病预防和控制中的普遍使用,由此带来的耐药性危害日益明显。本文总结了关于大熊猫源细菌耐药的国内外研究报道,对其耐药表型、耐药基因型、耐药机制及水平传播机制等方面内容进行了综述,旨在为大熊猫源细菌耐药性的研究和防控提供依据,为临床科学用药提供理论参考,从而助力大熊猫迁地保护。     

培养法检测海滨浴场细菌多样性及耐药性研究

【目的】耐药基因细菌水平基因转移导致的耐药菌数量增加引发的公共安全问题日益引起人们关注,监测环境中耐药菌变得极为重要。【方法】采集湛江3处滨海浴场的水体、沙滩土样,通过平板稀释涂布和琼脂扩散法进行浴场微生物数量、多样性和抗生素耐药性分析。【结果】3处浴场水体无机氮含量偏高,浴场微生物数量随着客流量逐渐增加,沙滩中微生物数量显著高于水体。浴场细菌分布于3门12科18属,水体中变形菌门（Proteobacteria,49.64%）占优势,沙滩则是厚壁菌门（Firmicutes,54.74%）占优势。浴场细菌对β-内酰胺类耐药率较高,青霉素、万古霉素和头孢曲松耐药率分别达到23.25%、20.53%和17.42%,耐药菌株主要分布于芽孢杆菌属（Bacillus）、弧菌属（Vibrio）、假单胞菌属（Pseudomonas）、链霉菌属（Streptomyces）和肠杆菌属（Enterobacter）,水体中多重耐药细菌数量显著高于沙滩,集中于人流量多的浴场。【结论】滨海浴场环境中细菌耐药菌种类多,需持续监测以评估对当前地区公共卫生的潜在影响。     

Metabolic constraints on the evolution of antibiotic resistance

Despite our continuous improvement in understanding antibiotic resistance, the interplay between natural selection of resistance mutations and the environment remains unclear. To investigate the role of bacterial metabolism in constraining the evolution of antibiotic resistance, we evolved Escherichia coli growing on glycolytic or gluconeogenic carbon sources to the selective pressure of three different antibiotics. Profiling more than 500 intracellular and extracellular putative metabolites in 190 evolved populations revealed that carbon and energy metabolism strongly constrained the evolutionary trajectories, both in terms of speed and mode of resistance acquisition. To interpret and explore the space of metabolome changes, we developed a novel constraint‐based modeling approach using the concept of shadow prices. This analysis, together with genome resequencing of resistant populations, identified condition‐dependent compensatory mechanisms of antibiotic resistance, such as the shift from respiratory to fermentative metabolism of glucose upon overexpression of efflux pumps. Moreover, metabolome‐based predictions revealed emerging weaknesses in resistant strains, such as the hypersensitivity to fosfomycin of ampicillin‐resistant strains. Overall, resolving metabolic adaptation throughout antibiotic‐driven evolutionary trajectories opens new perspectives in the fight against emerging antibiotic resistance.     

Meta分析在细菌耐药性研究中的应用与展望

随着抗生素的大量不规范使用,细菌耐药性不断增强,导致耐药及多重耐药细菌的出现,严重威胁着人类健康。运用统计学方法对耐药性相关研究进行汇总与多元分析,有助于更好地了解全球细菌耐药性的流行与分布,明晰细菌耐药性形成规律与机制的共性问题。Meta分析是一种将多个同类型研究进行综合分析的统计学方法,已广泛应用于细菌耐药性的研究。本文简要描述了Meta分析的起源及基本流程,并采用文献计量的方法对2000-2020年关于Meta分析在细菌耐药性研究中的应用进行系统综述;进一步总结并阐述了Meta分析在细菌耐药性领域应用的成功案例和结论,而且对Meta分析方法在细菌耐药性领域中的进一步研究进行了展望,以期推动该方法在细菌耐药性研究中的应用,为耐药性问题的系统阐释和有效控制提供可靠的工具。     

Spatially resolved abundances of antibiotic resistance genes and intI1 in wastewater treatment biofilms

Attached growth bioprocesses that use biofilms to remove organic matter or nutrients from wastewater are known to harbor antibiotic resistance genes (ARGs). Biofilms in these processes are spatially heterogeneous, but little is known about depth stratification of ARGs in complex, mixed culture biofilms. To address this knowledge gap, we used an experimental approach combining cryosectioning and quantitative polymerase chain reaction to quantify the spatial distribution of three ARGs (sul1, ermB, and qnrS) and the class 1 integron-integrase gene intI1 in biofilms from a lab-scale rotating annular reactor fed with synthetic wastewater. We also used high throughput 16S ribosomal RNA (rRNA) gene sequencing to characterize community structure with depth in biofilms. The ARG sul1 and the integron-integrase gene intI1 were found in higher abundances in upper layers of biofilm near the fluid-biofilm interface than in lower layers and exhibited significant correlations between the distance from substratum and gene abundances. The genes ermB and qnrS were present in comparatively low relative abundances. Microbial community structure varied significantly by date of sampling and distance from the substratum. These findings highlight the genetic and taxonomic heterogeneity with distance from substratum in wastewater treatment biofilms and show that sul1 and intI1 are particularly abundant near fluid-biofilm interfaces where cells are most likely to detach and flow into downstream portions of treatment systems and can ultimately be released into the environment through effluent.     

基于代谢组学的抗生素与细菌间作用研究进展

抗生素杀菌是一个复杂的生理过程,杀菌抗生素与靶点作用后的下游代谢变化与抗生素作用效果紧密联系,其通过干扰细菌代谢状态加速死亡进程,而细菌改变代谢状态也能影响抗生素的有效性.代谢组学通过监测细菌在抗生素作用下的变化提供全面代谢信息,我们回顾近年来基于代谢组学对抗生素与细菌间作用的研究进展,以期为开发抗生素佐剂提高抗生素效...     

沈阳市某三甲医院呼吸重症监护室病原菌分布及其耐药性

分析沈阳市某三甲医院呼吸重症监护室（RICU）患者相关样本病原菌分布及其耐药性,为呼吸重症患者感染的治疗提供参考。

回顾性分析该院2021年6月至2022年6月收治的253例RICU患者的病例数据,通过API菌种鉴定系统及纸片扩散法药物敏感性试验检测送检的体液和组织标本中病原菌分布及其药敏情况。

RICU患者检出阳性标本共147例,阳性率58.10%;检出革兰阳性细菌39株（11.24%）、革兰阴性细菌206株（59.37%）、真菌102株（29.39%）。占比排名前5位的病原菌为鲍曼不动杆菌（21.90%）、白假丝酵母菌（12.10%）、肺炎克雷伯菌（10.37%）、热带假丝酵母菌（7.49%）、铜绿假单胞菌（5.19%）。病原菌耐药性分析显示,鲍曼不动杆菌对常见抗生素均耐药;白假丝酵母菌对常用的抗生素均表现为敏感,但热带假丝酵母菌对伏立康唑和氟康唑的耐药率超过50.00%;相比痰液,尿液中肺炎克雷伯菌的耐药率较高;铜绿假单胞菌对亚胺培南、替卡西林/克拉维酸的耐药率均超过50.00%。

该院RICU患者主要是以革兰阴性细菌和真菌感染为主,其中鲍曼不动杆菌和白假丝酵母菌所占比例较高,二者对常用的抗生素普遍耐药,临床可据此对病原菌耐药性的变化进行实时监测,为合理选用抗生素提供依据。

     

The cost of multiple drug resistance in Pseudomonas aeruginosa

The spread of bacterial antibiotic resistance mutations is thought to be constrained by their pleiotropic fitness costs. Here we investigate the fitness costs of resistance in the context of the evolution of multiple drug resistance (MDR), by measuring the cost of acquiring streptomycin resistance mutations (StrepR) in independent strains of the bacterium Pseudomonas aeruginosa carrying different rifampicin resistance (RifR) mutations. In the absence of antibiotics, StrepR mutations are associated with similar fitness costs in different RifR genetic backgrounds. The cost of StrepR mutations is greater in a rifampicin‐sensitive (RifS) background, directly demonstrating antagonistic epistasis between resistance mutations. In the presence of rifampicin, StrepR mutations have contrasting effects in different RifR backgrounds: StrepR mutations have no detectable costs in some RifR backgrounds and massive fitness costs in others. Our results clearly demonstrate the importance of epistasis and genotype‐by‐environment interactions for the evolution of MDR.     

A global view of antibiotic resistance

Antibiotic resistance is one of the few examples of evolution that can be addressed experimentally. The present review analyses this resistance, focusing on the networks that regulate its acquisition and its effect on bacterial physiology. It is widely accepted that antibiotics and antibiotic resistance genes play fundamental ecological roles – as weapons and shields, respectively – in shaping the structures of microbial communities. Although this Darwinian view of the role of antibiotics is still valid, recent work indicates that antibiotics and resistance mechanisms may play other ecological roles and strongly influence bacterial physiology. The expression of antibiotic resistance determinants must therefore be tightly regulated and their activity forms part of global metabolic networks. In addition, certain bacterial modes of life can trigger transient phenotypic antibiotic resistance under some circumstances. Understanding resistance thus requires the analysis of the regulatory networks controlling bacterial evolvability, the physiological webs affected and the metabolic rewiring it incurs.     

Contribution of ethylamine degrading bacteria to atrazine degradation in soils

Bacterial communities that cooperatively degrade atrazine commonly consist of diverse species in which the genes for atrazine dechlorination and dealkylation are variously distributed among different species. Normally, the first step in degradation of atrazine involves dechlorination mediated by atzA, followed by stepwise dealkylation to yield either N-ethylammelide or N-isopropylammelide. As the liberated alkylamine moieties are constituents of many organic molecules other than atrazine, it is possible that a large number of alkylamine-degrading bacteria other than those previously described might contribute to this key step in atrazine degradation. To examine this hypothesis, we isolated 82 bacterial strains from soil by plating soil water extracts on agar media with ethylamine as a sole carbon source. Among the relatively large number of isolates, only 3 were able to degrade N-ethylammelide, and in each case were shown to carry the atzB gene and atzC genes. The isolates, identified as Rhizobium leguminosarum, Flavobacterium sp., and Arthrobacter sp., were all readily substituted into an atrazine-degrading consortium to carry out N-ethylammelide degradation. The distribution of these genes among many different species in the soil microbial population suggests that these genes are highly mobile and over time may lead to generation of various atrazine-degrading consortia.     

The evolution of alternative mating strategies in variable environments

Summary We assessed the influence of phenotypic plasticity in age at maturity on the maintenance of alternative mating strategies in male Atlantic salmon,Salmo salar. We calculated the fitness,r, associated with the parr and the anadromous strategies, using age-specific survival data from the field and strategy-specific fertilization data from the laboratory. The fitness of each strategy depended largely on mate competition (numbers of parr per female, i.e. parr frequency) and on age at maturity. Fitness declined with increasing numbers of parr per female with equilibrium frequencies (at which the fitnesses of each strategy are equal) being within the range observed in the wild. Equilibrium parr frequencies declined with decreasing growth rate and increasing age at maturity. Within populations, the existence of multiple age-specific sets of fitness functions suggests that the fitnesses of alternative strategies are best represented as multidimensional surfaces. The points of intersection of these surfaces, whose boundaries encompass natural variation in age at maturity and mate competition, define an evolutionarily stable continuum (ESC) of strategy frequencies along which the fitnesses associated with each strategy are equal. We propose a simple model that incorporates polygenic thresholds of a largely environmentally-controlled trait (age at maturity) to provide a mechanism by which an ESC can be maintained within a population. An indirect test provides support for the prediction that growth-rate thresholds for parr maturation exist and are maintained by stabilizing selection. Evolutionarily stable continua, maintained by negative frequency-dependent selection on threshold traits, provide a theoretical basis for understanding how alternative life histories can evolve in variable environments.