Effects of prior exposure to antibiotics on bacterial adaptation to phages

Understanding adaptation to complex environments requires information about how exposure to one selection pressure affects adaptation to others. For bacteria, antibiotics and viral parasites (phages) are two of the most common selection pressures and are both relevant for treatment of bacterial infections: increasing antibiotic resistance is generating significant interest in using phages in addition or as an alternative to antibiotics. However, we lack knowledge of how exposure to antibiotics affects bacterial responses to phages. Specifically, it is unclear how the negative effects of antibiotics on bacterial population growth combine with any possible mutagenic effects or physiological responses to influence adaptation to other stressors such as phages, and how this net effect varies with antibiotic concentration. Here, we experimentally addressed the effect of pre‐exposure to a wide range of antibiotic concentrations on bacterial responses to phages. Across 10 antibiotics, we found a strong association between their effects on bacterial population size and subsequent population growth in the presence of phages (which in these conditions indicates phage‐resistance evolution). We detected some evidence of mutagenesis among populations treated with fluoroquinolones and β‐lactams at sublethal doses, but these effects were small and not consistent across phage treatments. These results show that, although stressors such as antibiotics can boost adaptation to other stressors at low concentrations, these effects are weak compared to the effect of reduced population growth at inhibitory concentrations, which in our experiments strongly reduced the likelihood of subsequent phage‐resistance evolution.     

Ecology and evolution of antimicrobial resistance in bacterial communities

Accumulating evidence suggests that the response of bacteria to antibiotics is significantly affected by the presence of other interacting microbes. These interactions are not typically accounted for when determining pathogen sensitivity to antibiotics. In this perspective, we argue that resistance and evolutionary responses to antibiotic treatments should not be considered only a trait of an individual bacteria species but also an emergent property of the microbial community in which pathogens are embedded. We outline how interspecies interactions can affect the responses of individual species and communities to antibiotic treatment, and how these responses could affect the strength of selection, potentially changing the trajectory of resistance evolution. Finally, we identify key areas of future research which will allow for a more complete understanding of antibiotic resistance in bacterial communities. We emphasise that acknowledging the ecological context, i.e. the interactions that occur between pathogens and within communities, could help the development of more efficient and effective antibiotic treatments.Subject terms: Microbial ecology, Antibiotics, Bacterial evolution     

Geographical variation in cloacal microflora and bacterial antibiotic resistance in a threatened avian scavenger in relation to diet and livestock farming practices

The impact on wildlife health of the increase in the use of antimicrobial agents with the intensification of livestock production remains unknown. The composition, richness and prevalence of cloacal microflora as well as bacterial resistance to antibiotics in nestlings and full-grown Egyptian vultures Neophron percnopterus were assessed in four areas of Spain in which the degree of farming intensification differs. Differences in diet composition, especially the role of stabled livestock carrion, appear to govern the similarities of bacterial flora composition among continental populations, while the insular vulture population (Fuerteventura, Canary Islands) showed differences attributed to isolation. Evidence of a positive relationship between the consumption of stabled livestock carrion and bacterial resistance to multiple antibiotics was found. Bacterial resistance was high for semisynthetic penicillins and enrofloxacin, especially in the area with the most intensive stabled livestock production. The pattern of antibiotic resistance was similar for the different bacterial species within each area. Bacterial resistance to antibiotics may be determined by resistance of bacteria present in the livestock meat remains that constituted the food of this species, as indicated by the fact that resistance to each antibiotic was correlated in Escherichia coli isolated from swine carrion and Egyptian vulture nestlings. In addition, resistance in normal faecal bacteria (present in the microflora of both livestock and vultures) was higher than in Staphylococcus epidermidis, a species indicator of the transient flora acquired presumably through the consumption of wild rabbits. Potential negative effects of the use of antimicrobials in livestock farming included the direct ingestion of these drug residues and the effects of bacterial antibiotic resistance on the health of scavengers.     

Selection of resistant bacteria at very low antibiotic concentrations

The widespread use of antibiotics is selecting for a variety of resistance mechanisms that seriously challenge our ability to treat bacterial infections. Resistant bacteria can be selected at the high concentrations of antibiotics used therapeutically, but what role the much lower antibiotic concentrations present in many environments plays in selection remains largely unclear. Here we show using highly sensitive competition experiments that selection of resistant bacteria occurs at extremely low antibiotic concentrations. Thus, for three clinically important antibiotics, drug concentrations up to several hundred-fold below the minimal inhibitory concentration of susceptible bacteria could enrich for resistant bacteria, even when present at a very low initial fraction. We also show that de novo mutants can be selected at sub-MIC concentrations of antibiotics, and we provide a mathematical model predicting how rapidly such mutants would take over in a susceptible population. These results add another dimension to the evolution of resistance and suggest that the low antibiotic concentrations found in many natural environments are important for enrichment and maintenance of resistance in bacterial populations.     

Insects Represent a Link between Food Animal Farms and the Urban Environment for Antibiotic Resistance Traits

Antibiotic-resistant bacterial infections result in higher patient mortality rates, prolonged hospitalizations, and increased health care costs. Extensive use of antibiotics as growth promoters in the animal industry represents great pressure for evolution and selection of antibiotic-resistant bacteria on farms. Despite growing evidence showing that antibiotic use and bacterial resistance in food animals correlate with resistance in human pathogens, the proof for direct transmission of antibiotic resistance is difficult to provide. In this review, we make a case that insects commonly associated with food animals likely represent a direct and important link between animal farms and urban communities for antibiotic resistance traits. Houseflies and cockroaches have been shown to carry multidrug-resistant clonal lineages of bacteria identical to those found in animal manure. Furthermore, several studies have demonstrated proliferation of bacteria and horizontal transfer of resistance genes in the insect digestive tract as well as transmission of resistant bacteria by insects to new substrates. We propose that insect management should be an integral part of pre- and postharvest food safety strategies to minimize spread of zoonotic pathogens and antibiotic resistance traits from animal farms. Furthermore, the insect link between the agricultural and urban environment presents an additional argument for adopting prudent use of antibiotics in the food animal industry.     

Bacterial tolerances to metals and antibiotics in metal-contaminated and reference streams

Anthropogenic-derived sources of selection are typically implicated as mechanisms for maintaining antibiotic resistance in the environment. Here we report an additional mechanism for maintaining antibiotic resistance in the environment through bacterial exposure to metals. Using a culture-independent approach, bacteria sampled along a gradient of metal contamination were more tolerant of antibiotics and metals compared to bacteria from a reference site. This evidence supports the hypothesis that metal contamination directly selects for metal tolerant bacteria while co-selecting for antibiotic tolerant bacteria. Additionally, to assess how antibiotic and metal tolerance may be transported through a stream network, we studied antibiotic and metal tolerance patterns over three months in bacteria collected from multiple stream microhabitats including the water column, biofilm, sediment and Corbicula fluminea (Asiatic clam) digestive tracts. Sediment bacteria were the most tolerant to antibiotics and metals, while bacteria from Corbicula were the least tolerant. Differences between microhabitats may be important for identifying reservoirs of resistance and for predicting how these genes are transferred and transported in metal-contaminated streams. Temporal dynamics were not directly correlated to a suite of physicochemical parameters, suggesting that tolerance patterns within microhabitats are linked to a complex interaction of the physicochemical characteristics of the stream.     

Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids

Inactivation of β ‐lactam antibiotics by resistant bacteria is a ‘cooperative’ behavior that may allow sensitive bacteria to survive antibiotic treatment. However, the factors that determine the fraction of resistant cells in the bacterial population remain unclear, indicating a fundamental gap in our understanding of how antibiotic resistance evolves. Here, we experimentally track the spread of a plasmid that encodes a β ‐lactamase enzyme through the bacterial population. We find that independent of the initial fraction of resistant cells, the population settles to an equilibrium fraction proportional to the antibiotic concentration divided by the cell density. A simple model explains this behavior, successfully predicting a data collapse over two orders of magnitude in antibiotic concentration. This model also successfully predicts that adding a commonly used β ‐lactamase inhibitor will lead to the spread of resistance, highlighting the need to incorporate social dynamics into the study of antibiotic resistance.     

The SOS response increases bacterial fitness,but not evolvability,under a sublethal dose of antibiotic

Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.     

Rainfall and hydrological stability alter the impact of top predators on food web structure and function

Climate change will alter the distribution of rainfall, with potential consequences for the hydrological dynamics of aquatic habitats. Hydrological stability can be an important determinant of diversity in temporary aquatic habitats, affecting species persistence and the importance of predation on community dynamics. As such, prey are not only affected by drought‐induced mortality but also the risk of predation [a non‐consumptive effect (NCE)] and actual consumption by predators [a consumptive effect (CE)]. Climate‐induced changes in rainfall may directly, or via altered hydrological stability, affect predator–prey interactions and their cascading effects on the food web, but this has rarely been explored, especially in natural food webs. To address this question, we performed a field experiment using tank bromeliads and their aquatic food web, composed of predatory damselfly larvae, macroinvertebrate prey and bacteria. We manipulated the presence and consumption ability of damselfly larvae under three rainfall scenarios (ambient, few large rainfall events and several small rainfall events), recorded the hydrological dynamics within bromeliads and examined the effects on macroinvertebrate colonization, nutrient cycling and bacterial biomass and turnover. Despite our large perturbations of rainfall, rainfall scenario had no effect on the hydrological dynamics of bromeliads. As a result, macroinvertebrate colonization and nutrient cycling depended on the hydrological stability of bromeliads, with no direct effect of rainfall or predation. In contrast, rainfall scenario determined the direction of the indirect effects of predators on bacteria, driven by both predator CEs and NCEs. These results suggest that rainfall and the hydrological stability of bromeliads had indirect effects on the food web through changes in the CEs and NCEs of predators. We suggest that future studies should consider the importance of the variability in hydrological dynamics among habitats as well as the biological mechanisms underlying the ecological responses to climate change.     

Antibiotics affect the growth responses of <Emphasis Type="Italic">Daphnia magna</Emphasis> to poor food quality

We tested the hypothesis that exposure to antibiotics alters the growth and reproductive responses of Daphnia magna to changing stoichiometric food quality. To do so, we measured growth and reproduction of differentially P-nourished Daphnia in the presence and absence of sublethal concentrations of antibiotics. We found that exposure to an antibiotic cocktail significantly reduced an index of the microbial load of Daphnia and altered its growth responses to changing dietary P-content. Growth rates of Daphnia consuming the most P-rich and P-poor food increased with antibiotic exposure but were negatively or not affected in animals eating mildly to moderately P-limiting food. Similar effects were found in a subsequent experiment where daphnid neonates were exposed to natural bacterial communities prior to receiving antibiotics and being fed different food C:P ratios. In contrast, antibiotic effects on Daphnia reproduction were either not detected (number and size of broods) or were relatively minor (day of first reproduction). We also found no evidence that gut flora provides defense against pathogenic bacterial infection; instead, infection rates in Daphnia by a bacterial microparasite, Pasteuria ramosa, decreased in animals that had experienced prior antibiotic exposure. Our results demonstrate that antibiotic exposure reduced the microbial load and altered growth rates of an important zooplankton herbivore. Given the mediating role of animal’s food C:P ratio, our results show that interactions between Daphnia and its microbial symbionts vary in strength and nature partly with the host’s nutritional state.     

The effects of salicylate on bacteria

Salicylate and related compounds, such as aspirin, have a variety of effects in eucaryotic systems and are well known for their medicinal properties. Salicylate also has numerous effects on bacteria, yet only a handful of individuals within the scientific community appreciate these findings. From a bacterial viewpoint, growth in the presence of salicylate can be both beneficial and detrimental. On one hand, growth of certain bacteria in the presence of salicylate can induce an intrinsic multiple antibiotic resistance phenotype. On the other hand, growth in the presence of salicylate can reduce the resistance to some antibiotics and affect virulence factor production in some bacteria. This review provides an overview of the effects salicylate has on various bacterial species.     

Genomic Analysis Reveals Distinct Concentration-Dependent Evolutionary Trajectories for Antibiotic Resistance in Escherichia coli

Evolution of bacteria under sublethal concentrations of antibiotics represents a trade-off between growth and resistance to the antibiotic. To understand this trade-off, we performed in vitro evolution of laboratory Escherichia coli under sublethal concentrations of the aminoglycoside kanamycin over short time durations. We report that fixation of less costly kanamycin-resistant mutants occurred earlier in populations growing at lower sublethal concentration of the antibiotic, compared with those growing at higher sublethal concentrations; in the latter, resistant mutants with a significant growth defect persisted longer. Using deep sequencing, we identified kanamycin resistance-conferring mutations, which were costly or not in terms of growth in the absence of the antibiotic. Multiple mutations in the C-terminal end of domain IV of the translation elongation factor EF-G provided low-cost resistance to kanamycin. Despite targeting the same or adjacent residues of the protein, these mutants differed from each other in the levels of resistance they provided. Analysis of one of these mutations showed that it has little defect in growth or in synthesis of green fluorescent protein (GFP) from an inducible plasmid in the absence of the antibiotic. A second class of mutations, recovered only during evolution in higher sublethal concentrations of the antibiotic, deleted the C-terminal end of the ATP synthase shaft. This mutation confers basal-level resistance to kanamycin while showing a strong growth defect in the absence of the antibiotic. In conclusion, the early dynamics of the development of resistance to an aminoglycoside antibiotic is dependent on the levels of stress (concentration) imposed by the antibiotic, with the evolution of less costly variants only a matter of time.     

Static recipient cells as reservoirs of antibiotic resistance during antibiotic therapy

How does taking the full course of antibiotics prevent antibiotic resistant bacteria establishing in patients? We address this question by testing the possibility that horizontal/lateral gene transfer (HGT) is critical for the accumulation of the antibiotic-resistance phenotype while bacteria are under antibiotic stress. Most antibiotics prevent bacterial reproduction, some by preventing de novo gene expression. Nevertheless, in some cases and at some concentrations, the effects of most antibiotics on gene expression may not be irreversible. If the stress is removed before the bacteria are cleared from the patients by normal turnover, gene expression restarts, converting the residual population to phenotypic resistance. Using mathematical models we investigate how static recipients of resistance genes carried by plasmids accumulate resistance genes, and how specifically an environment cycling between presence and absence of the antibiotic uniquely favors the evolution of horizontally mobile resistance genes. We found that the presence of static recipients can substantially increase the persistence of the plasmid and that this effect is most pronounced when the cost of carriage of the plasmid decreases the cell's growth rate by as much as a half or more. In addition, plasmid persistence can be enhanced even when conjugation rates are as low as half the rate required for the plasmid to persist as a parasite on its own.     

Biological filtering of correlated environments: towards a generalised Moran theorem

Many species from diverse taxa are known to display synchronous fluctuations across vast geographical ranges. It is often thought that climate factors influencing the growth of conspecific populations are correlated over large distances and hence produce the synchronous population dynamics – an effect known as the Moran effect. However, for species embedded in a food web the Moran effect needs not necessarily influence the focal species directly, but can act indirectly through other species. Such an indirect synchronization can also occur in an age-structured population, where the correlated environment of one age-class causes synchronous fluctuations of another. Here, we investigate this indirect Moran effect. We find first of all that synchrony is readily transferred through food webs or between age classes, which complicates the identification of the underlying synchronizing factor. Secondly, we find puzzling cases, where synchrony is enhanced as it is filtered through a food web or between age-classes. Our results also apply to systems of different species, but with closely matching dynamics.     

Two ways to skin a cat: acyldepsipeptides antibiotics can kill bacteria through activation or inhibition of ClpP activity

Infection by Mycobacterium tuberculosis (Mtb) has had a devastating effect on the world population. Acyldepsipeptide antibiotics (ADEPs) are known to kill some bacteria by over activating the bacterial ClpP peptidase. ADEP antibiotics also target Mtb, with the assumption that uncontrolled ADEP‐activated proteolysis by ClpP is the common mode of killing. In this issue of Molecular Microbiology, Famulla, et al. now show that ADEP's effectiveness in mycobacteria is likely due to inhibition of ClpP‐dependent protease activity rather than activation. This finding of how the same antibiotic can kill bacteria by either inhibiting or activating proteases illustrates the utility of targeting these enzymes for sorely needed new antibiotics.     

植物干旱胁迫对植食性昆虫及其天敌的影响

全球正经历以变暖为主要特征的气候变化,由此带来的干旱将对农业生态系统造成重要影响。本文综述了干旱胁迫下寄主植物对植食性昆虫及其天敌影响的国内外最新研究进展。在干旱胁迫下,寄主植物物理性状、营养状况和次生代谢物质等均发生变化,这些变化导致植食性昆虫的生存环境和营养物质的获取等方面发生改变,从而影响了害虫生长发育和种群动态。干旱胁迫还导致寄主物候变化与昆虫发生不同步,使害虫缺乏食物。另外干旱也会引起植食性害虫天敌的种群发生变化,从而对植食性昆虫种群数量产生间接的影响。     

Assessing the potential for indirect interactions between tropical tree species via shared insect seed predators

Natural enemies of plants have the potential to influence the dynamics of plant populations and the structure of plant communities. In diverse tropical forests, research on the effects of plant enemies has largely focused on the diversity-enhancing effects of highly specialized enemies, while the community-level effects of enemies with broader diets have rarely been considered. We investigated the community of insect seed predators interacting with seven tree species in the family Lauraceae on Barro Colorado Island (Panama). We present one of the first quantitative food webs for pre-dispersal insect seed predators and their host plants, and use the information in the web to assess the potential for indirect interactions between the tree species. Our data suggest that there is high potential for indirect interactions between Lauraceae species via their shared seed predators. The strength and direction of these interactions are largely unrelated to the phylogenetic distance and trait similarity between species but are likely governed by the volume of fruit produced by each tree species.     

Failure of antibiotic treatment in microbial populations

The tolerance of bacterial populations to biocidal or antibiotic treatment has been well documented in both biofilm and planktonic settings. However, there is still very little known about the mechanisms that produce this tolerance. Evidence that small, non-mutant subpopulations of bacteria are not affected by an antibiotic challenge has been accumulating and provides an attractive explanation for the failure of typical dosing protocols. Although a dosing challenge can kill the susceptible bacteria, the remaining persister cells can serve as a source of population regrowth. We give a condition for the failure of a periodic dosing protocol for a general chemostat model, which supports the simulations of an earlier, more specialized batch model. Our condition implies that the treatment protocol fails globally, in the sense that a mixed bacterial population will ultimately persist above a level that is independent of the initial composition of the population. We also give a sufficient condition for treatment success, at least for initial population compositions near the steady state of interest, corresponding to bacterial washout. Finally, we investigate how the speed at which the bacteria are wiped out depends on the duration of administration of the antibiotic. We find that this dependence is not necessarily monotone, implying that optimal dosing does not necessarily correspond to continuous administration of the antibiotic. Thus, genuine periodic protocols can be more advantageous in treating a wide variety of bacterial infections.      

基于幼虫粪便的小菜蛾肠道细菌分离鉴定及其抗生素敏感性分析

【目的】昆虫肠道微生物对于其食物消化、生长发育以及环境适应性等方面都具有重要作用,本研究旨在探究小菜蛾 Plutella xylostella (L.)幼虫肠道可培养细菌的菌群结构及抗生素敏感性。【方法】对小菜蛾3龄幼虫粪便进行了细菌分离培养和16S rDNA分子鉴定,并采用纸片扩散法对之进行了药敏试验。【结果】小菜蛾3龄幼虫肠道有5属6种细菌,即蒙氏肠球菌 Enterococcus mundtii、欧文氏菌属 Erwinia 2种、成团泛菌 Pantoea agglomerans 、类芽孢杆菌Paenibacillus sp.和栖稻假单胞菌 Pseudomonas oryzihabitans,均与小菜蛾中肠细菌已知种不同,其中蒙氏肠球菌数量最多;蒙氏肠球菌、桃色欧文氏菌和成团泛菌对青霉素、氨苄青霉素、麦迪霉素、克拉霉素和洁霉素均不敏感,而对磷霉素、万古霉素和强力霉素等表现出相似的敏感性。【结论】小菜蛾幼虫肠道细菌菌群组成具有多样性,且存在天然耐药性现象。本研究为进一步开展小菜蛾幼虫肠道细菌微生物区系及功能细菌的研究提供了菌株材料和研究基础。     

Evolution of dispersal in a multi‐trophic community context

Much is known about the evolution of dispersal when species interact with their resources or natural enemies, but very little is known about dispersal evolution when species interact with both resources and natural enemies. Here I investigate how the dispersal of an intermediate consumer evolves in response to its interactions with a basal resource and top predator. I find that dispersal evolution is possible even when the consumer species is not directly affected by environmental variability, but rather experiences the consequences that such variability has on its resource and predator. Spatial variation in the consumer's fitness is driven by spatial heterogeneity in resource productivity, which determines whether a predator can colonize a resource‐consumer community. Temporal variation in the consumer's fitness is driven by random disturbances that cause periodic local extinctions of the predator, followed by recolonizations that lead to transient fluctuations in consumer abundance. When spatial variation in resource productivity is low and the predator can colonize all patches in the landscape, there is no spatial variation in consumer fitness but temporal variation in fitness favors the evolution of a dispersal monomorphism. When spatial variation in resource productivity is high and the predator cannot colonize many patches in the landscape, spatial variation in fitness selects against dispersal. In this case, temporal variation can promote the evolution of a dispersal polymorphism with sedentary and mobile phenotypes, but only for certain types of tri‐trophic interactions. This finding underscores the importance of indirect interactions in shaping the evolution of dispersal. While the ecological community can provide a strong selective environment for the evolution of dispersal, the nature of interactions between trophic levels can also impose constraints on evolution.