A Quinolinone Compound Inhibiting the Oligomerization of Nucleoprotein of Influenza A Virus Prevents the Selection of Escape Mutants

The emergence of resistance to currently available anti-influenza drugs has heightened the need for antivirals with novel mechanisms of action. The influenza A virus (IAV) nucleoprotein (NP) is highly conserved and essential for the formation of viral ribonucleoprotein (vRNP), which serves as the template for replication and transcription. Recently, using in silico screening, we identified an antiviral compound designated NUD-1 (a 4-hydroxyquinolinone derivative) as a potential inhibitor of NP. In this study, we further analyzed the interaction between NUD-1 and NP and found that the compound interferes with the oligomerization of NP, which is required for vRNP formation, leading to the suppression of viral transcription, protein synthesis, and nuclear export of NP. We further assessed the selection of resistant variants by serially passaging a clinical isolate of the 2009 H1N1 pandemic influenza virus in the presence of NUD-1 or oseltamivir. NUD-1 did not select for resistant variants after nine passages, whereas oseltamivir selected for resistant variants after five passages. Our data demonstrate that NUD-1 interferes with the oligomerization of NP and less likely induces drug-resistant variants than oseltamivir; hence, it is a potential lead compound for the development of novel anti-influenza drugs.

Glucocorticoids, male sexual signals, and mate choice by females: Implications for sexual selection

We review work relating glucocorticoids (GCs), male sexual signals, and mate choice by females to understand the potential for GCs to modulate the expression of sexually selected traits and how sexual selection potentially feeds back on GC regulation. Our review reveals that the relationship between GC concentrations and the quality of male sexual traits is mixed, regardless of whether studies focused on structural traits (e.g., coloration) or behavioral traits (e.g., vocalizations) or were examined in developmental or activational frameworks. In contrast, the few mate choice experiments that have been done consistently show that females prefer males with low GCs, suggesting that mate choice by females favors males that maintain low levels of GCs. We point out, however, that just as sexual selection can drive the evolution of diverse reproductive strategies, it may also promote diversity in GC regulation. We then shift the focus to females where we highlight evidence indicating that stressors or high GCs can dampen female sexual proceptivity and the strength of preferences for male courtship signals. Hence, even in cases where GCs are tightly coupled with male sexual signals, the strength of sexual selection on aspects of GC physiology can vary depending on the endocrine status of females. Studies examining how GCs relate to sexual selection may shed light on how variation in stress physiology, sexual signals, and mate choice are maintained in natural populations and may be important in understanding context-dependent relationships between GC regulation and fitness.

Heavy metal-induced co-selection of antibiotic resistance genes in the gut microbiota of collembolans

Heavy metal induced co-selection of antibiotic resistance genes (ARGs) has become an emerging environmental issue. The guts of soil fauna offer a unique habitat in the terrestrial ecosystem and harbor a variety of microorganisms. However, the effects of heavy metals on the gut-associated ARGs of soil fauna are poorly understood. In the present study, collembolans were cultivated with four types of heavy metals (Zn, Cu, Cd, and Cr) and one antibiotic (oxytetracycline), to investigate their impact on the gut-associated ARGs. High-throughput quantitative PCR and 16S rRNA gene amplicon sequencing were used to examine changes in the gut-associated ARGs and microbial composition caused by the metals and antibiotic. The results showed that heavy metals alone induced co-selection of ARGs in the collembolan gut, but the effects were weaker than selection by oxytetracycline. When Zn or Cu was present together with oxytetracycline, there was a strong synergistic effect between the compounds, which increased the selection of ARGs in the collembolan guts. Furthermore, redundancy analysis revealed that the gut microbiota and mobile genetic elements (MGEs) were significantly correlated with the ARG composition. These results extend our understanding on effects of heavy metals on the dispersal of ARGs in the soil food web.

Evidence of insecticide resistance selection in wild Anopheles coluzzii mosquitoes due to agricultural pesticide use

BACKGROUND

The wetlands used for some agricultural activities constitute productive breeding sites for many mosquito species. Thus, the agricultural use of insecticide targeting other pests may select for insecticide resistance in malaria mosquitoes. The purpose of this study is to clarify some knowledge gaps on the role of agrochemicals in the development of insecticide resistance in malaria vectors is of utmost importance for vector control.

METHODS

Using the CDC bottle test and the log-probit analysis, we investigated for the first time the resistance levels of Anopheles coluzzii mosquitoes to neonicotinoids, insecticides used exclusively for crop protection in Côte d'Ivoire. The study was conducted in two agricultural regions (Tiassale and Gagnoa) and one non-agricultural region (Vitre) between June and August 2017 using clothianidin, acetamiprid and imidacloprid.

RESULTS

Mosquito populations from Tiassale and Gagnoa (agricultural settings) were determined to be resistant to acetamiprid with mortality rates being < 85% at 24 h post-exposure. In Vitre (non-agricultural area) however, the mosquito population was susceptible to acetamiprid. In all three localities, mosquito populations were resistant to imidacloprid (mortality rates were 60% in Vitre, 37% in Tiassale, and 13% in Gagnoa) and completely susceptible to clothianidin (100% mortality). An. coluzzii represented 100% of mosquito collected in Gagnoa, 86% in Tiassale and 96% in Vitre.

CONCLUSIONS

This study provides strong evidence that agricultural use of insecticides can cause insecticide resistance in malaria vector populations. Insecticide resistance driven by agrochemical usage should be considered when vector control strategies are developed.

Mapping the drivers of within-host pathogen evolution using massive data sets

Differences among hosts, resulting from genetic variation in the immune system or heterogeneity in drug treatment, can impact within-host pathogen evolution. Genetic association studies can potentially identify such interactions. However, extensive and correlated genetic population structure in hosts and pathogens presents a substantial risk of confounding analyses. Moreover, the multiple testing burden of interaction scanning can potentially limit power. We present a Bayesian approach for detecting host influences on pathogen evolution that exploits vast existing data sets of pathogen diversity to improve power and control for stratification. The approach models key processes, including recombination and selection, and identifies regions of the pathogen genome affected by host factors. Our simulations and empirical analysis of drug-induced selection on the HIV-1 genome show that the method recovers known associations and has superior precision-recall characteristics compared to other approaches. We build a high-resolution map of HLA-induced selection in the HIV-1 genome, identifying novel epitope-allele combinations.

Does nano silver promote the selection of antibiotic resistance genes in soil and plant?

Growing evidences have demonstrated that heavy metal contamination can promote the proliferation of antibiotic resistance genes (ARGs) via co-selection. However, effects of nano-metal-materials on the occurrence and level of ARGs in the soil and plant, have not been fully explored. To gain insights into this impact, we conducted a pot experiment by adding nano‑silver particles (AgNPs) as a stimuli and Ag ion (AgNO₃) and tetracycline as a comparison. By using high throughput quantitative PCR, our results indicated that application of AgNPs (~20 nm and ~50 nm) at a concentration of 100 ppm resulted in no significant changes in the abundance of ARGs in either soil or phyllosphere (P > 0.05). Nevertheless, the overall pattern of resistome, especially in soil, was shifted following AgNPs application, with a significance increase in the relative abundance of efflux pumps genes, which is an important mechanism for co-selection of ARGs by heavy metals. By comparison, Ag ion at an equivalent Ag mass of AgNPs markedly increased ARGs abundance and shifted ARGs profile in soil, indicating that free Ag ion had a stronger impact on ARGs than AgNPs. These findings provide new insights in assessing the risks of manufactured nanomaterials accumulated in the environment.

Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae

Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.

Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer

Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism.

Evidence for rapid adaptive evolution of tolerance to chemical treatments in Phytophthora species and its practical implications

Chemical treatments are used widely in agricultural and natural settings to protect plants from diseases; however, they may exert an important selection pressure on plant pathogens, promoting the development of tolerant isolates through adaptive evolution. Phosphite is used to manage diseases caused by Phytophthora species which include a large number of the most economically damaging plant pathogens worldwide. Phosphite controls the growth of Phytophthora species in planta without killing it; as a result, isolates can develop tolerance to phosphite after prolonged exposure. We investigated the inter- and intra-specific variability in phosphite tolerance of eleven Phytophthora species, including P. ramorum, an internationally important, highly regulated pathogen. Phytophthora ramorum is a good model system because it is comprised of multiple genetically homogeneous lineages. Seven species were found to be consistently sensitive to phosphite based on the low Effective Concentration (EC) 50 values of all isolates tested (amount of phosphite required to inhibit mycelial growth by 50% relative to growth in the absence of phosphite). However, P. ramorum, P. lateralis, P. crassamura and P. cambivora showed intraspecific variability in sensitivity to phosphite, with at least one isolate showing significantly higher tolerance than the other isolates. Within the three P. ramorum evolutionarily divergent lineages tested, NA1 was the most susceptible to phosphite, the NA1 and EU1 lineages showed intralineage variability and the NA2 lineage showed a decreased sensitivity to phosphite overall as all isolates were relatively tolerant. This finding is relevant because NA1 is dominant in the wild and can be controlled using phosphite, while the EU1 lineage has recently been identified in the wild and is phosphite-tolerant, making the treatment approach potentially less effective. Phytophthora ramorum, P. lateralis and P. crassamura are either selfing, homothallic species, or are known to reproduce exclusively clonally, indicating tolerance to phosphite can emerge even in the absence of sexual recombination.

Evolution of high-level resistance during low-level antibiotic exposure

It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.

Relating High Insecticide Residues in Larval Breeding Habitats in Urban Residential Areas to the Selection of Pyrethroid Resistance in Anopheles gambiae s.l. (Diptera: Culicidae) in Akim Oda, Ghana

The main objective of this study was to assess insecticide contamination in Anopheles breeding habitats in urban residential areas and pyrethroid susceptibility status of mosquitoes found in the habitats. A larval survey was conducted in Akim Oda between July and October 2016. The larvae that were reared to adult were used for susceptibility test against four different pyrethroid insecticides (deltamethrin 0.05%, permethrin 0.75%, cyfluthrin 0.15%, and etofenprox 0.5%). Gas chromatography was used to analyze pesticide residues in water collected from the breeding habitats. High levels of permethrin and deltamethrin plus traces of several organochlorine and organophosphate insecticides were detected in the larval-breeding habitats. None of the four pyrethroid insecticides caused more than 10% mortality. Anopheles coluzzii Coetzee & Wilkerson dominated in the study area with high frequency of kdr mutation (93.5%). We report for the first time in Ghana, high levels of pyrethroid insecticides contamination in Anopheles breeding habitats in urban residential areas where there are no major agricultural activities. The contamination is suspected to be the major cause of pyrethroid resistance in the Anopheles species. Improper disposal of old insecticide-treated net and other domestic insecticides and the use of herbicides are suspected to be the source of insecticide contamination.

The structure and diversity of human, animal and environmental resistomes

BACKGROUND

Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.

RESULTS

We provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n = 350), animals (n = 145) and external environments (n = 369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.

CONCLUSIONS

Our study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.

Environmental changes bridge evolutionary valleys

In the basic fitness landscape metaphor for molecular evolution, evolutionary pathways are presumed to follow uphill steps of increasing fitness. How evolution can cross fitness valleys is an open question. One possibility is that environmental changes alter the fitness landscape such that low-fitness sequences reside on a hill in alternate environments. We experimentally test this hypothesis on the antibiotic resistance gene TEM-15 β-lactamase by comparing four evolutionary strategies shaped by environmental changes. The strategy that included initial steps of selecting for low antibiotic resistance (negative selection) produced superior alleles compared with the other three strategies. We comprehensively examined possible evolutionary pathways leading to one such high-fitness allele and found that an initially deleterious mutation is key to the allele's evolutionary history. This mutation is an initial gateway to an otherwise relatively inaccessible area of sequence space and participates in higher-order, positive epistasis with a number of neutral to slightly beneficial mutations. The ability of negative selection and environmental changes to provide access to novel fitness peaks has important implications for natural evolutionary mechanisms and applied directed evolution.

Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance

The increasing rate of antibiotic resistance and slowing discovery of novel antibiotic treatments presents a growing threat to public health. Here, we consider a simple model of evolution in asexually reproducing populations which considers adaptation as a biased random walk on a fitness landscape. This model associates the global properties of the fitness landscape with the algebraic properties of a Markov chain transition matrix and allows us to derive general results on the non-commutativity and irreversibility of natural selection as well as antibiotic cycling strategies. Using this formalism, we analyze 15 empirical fitness landscapes of E. coli under selection by different β-lactam antibiotics and demonstrate that the emergence of resistance to a given antibiotic can be either hindered or promoted by different sequences of drug application. Specifically, we demonstrate that the majority, approximately 70%, of sequential drug treatments with 2-4 drugs promote resistance to the final antibiotic. Further, we derive optimal drug application sequences with which we can probabilistically 'steer' the population through genotype space to avoid the emergence of resistance. This suggests a new strategy in the war against antibiotic-resistant organisms: drug sequencing to shepherd evolution through genotype space to states from which resistance cannot emerge and by which to maximize the chance of successful therapy.

Does behaviour play a role in house fly resistance to imidacloprid-containing baits?

The objective of this research was to examine the role and type of behavioural mechanisms that function in house fly, Musca domestica L. (Diptera: Muscidae), resistance to an imidacloprid-containing commercial fly bait, QuickBayt(®) , using an insecticide-susceptible and an imidacloprid-resistant strain. Mortality and feeding behaviour were observed through choice bioassays of three post-imidacloprid selected house fly generations to determine whether flies would consume the bait in the presence of an alternative food source. Mortality rates in choice containers progressively decreased in post-selection flies as QuickBayt(®) no-choice selections proceeded. There were no differences between the proportions of flies observed contacting QuickBayt(®) and sugar, respectively, a finding that eliminates repellency as a mechanism of stimulus-dependent behavioural resistance. However, differences in QuickBayt(®) consumption and subsequent mortality between choice and no-choice containers provided strong support for the evolution of consumption irritancy- or taste aversion-related behavioural resistance. The results of this study support the responsible rotation of insecticide bait formulations for house fly control.

Stress-induced selection of a single species from an entire meiobenthic nematode assemblage: is this possible using iron enrichment and does pre-exposure affect the ease of the process?

The present work proposes a new experimental design using iron enrichment to select a single species from an entire meiobenthic nematode community. The high diversity of nematodes makes it impossible to study their responses to stressors in terms of chemical biomarkers, as this kind of research demands a single species as a form of biological material. Two assemblages, one from a control site (Canal) and one from an iron-contaminated site (Fouledh) in Bizerte Lagoon (Tunisia), were used to validate the protocol and to study whether pre-exposure to iron could affect the ease of the selection process. Analyses of variance suggested that the abundance and species number of nematodes from the Canal and Fouledh sites decreased discernibly with exposure to iron. Multivariate analyses performed on nematode abundances revealed that Oncholaimus campylocercoides, Sabatieria granifer, Sabatieria punctata and Theristus flevensis were the most tolerant species, probably due to their deposit-feeding behaviour. Species with a restricted feeding spectrum showed a low tolerance potential. At the end of the experiment, O. campylocercoides became the unique component of the nematode community from both sites. The complete alteration of the community was achieved with more difficulty for nematodes from Fouledh than for those from Canal. The identity of the selected species was confirmed at both the morphological levels and by sequencing the nuclear small subunit ribosomal DNA (18S rDNA).

Environmental versus anthropogenic effects on population adaptive divergence in the freshwater snail Lymnaea stagnalis

Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using Q(ST)-F(ST) comparisons. Despite strong neutral differentiation (mean F(ST) = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment.

Mutans streptococci enumeration and genotype selection using different bacitracin-containing media

The primary etiological agents associated with dental caries include the mutans streptococci (MS) comprised of Streptococcus mutans and Streptococcus sobrinus. The effective cultivation and isolation of MS are necessary for the study of MS, including their proper clinical assessment in the epidemiological study of dental caries. Several selective media have been developed for the isolation, enumeration, and characterization of MS. However, inhibition of MS may occur, reducing counts and perhaps limiting selection of some strains. The purpose of this study was to compare five culture media containing bacitracin recommended for the isolation of MS. Five commonly used bacitracin-containing media (MSB, MSKB, GTSB, TYS20B, and TYCSB) used for MS isolation were quantitatively evaluated. Standard plate counts were performed in duplicate for 2 prototype MS strains (S. mutans UA159 and S. sobrinus 6715) and for MS isolates from clinical saliva samples obtained from 16 children (approximate age 5years) to determine total plate counts, and total S. mutans counts. Selected isolates (n=249) from all five media for 5 saliva samples were further confirmed as S. mutans with real-time PCR then subsequently evaluated qualitatively with rep-PCR for genotype determination. All media resulted in variable enumeration with no significant difference in MS counts. MS prototype strains grew well on all five media; clinical isolates demonstrated more variability in counts but no overall significant differences were found. MSB demonstrated comparable ability to grow S. mutans but allowed for more non-S. mutans growth. All 5 media identified a consistent predominant genotype by rep-PCR. Recovery of minor genotypes was not inhibited by media type.

Aggressive chemotherapy and the selection of drug resistant pathogens

Drug resistant pathogens are one of the key public health challenges of the 21^st century. There is a widespread belief that resistance is best managed by using drugs to rapidly eliminate target pathogens from patients so as to minimize the probability that pathogens acquire resistance de novo. Yet strong drug pressure imposes intense selection in favor of resistance through alleviation of competition with wild-type populations. Aggressive chemotherapy thus generates opposing evolutionary forces which together determine the rate of drug resistance emergence. Identifying treatment regimens which best retard resistance evolution while maximizing health gains and minimizing disease transmission requires empirical analysis of resistance evolution in vivo in conjunction with measures of clinical outcomes and infectiousness. Using rodent malaria in laboratory mice, we found that less aggressive chemotherapeutic regimens substantially reduced the probability of onward transmission of resistance (by >150-fold), without compromising health outcomes. Our experiments suggest that there may be cases where resistance evolution can be managed more effectively with treatment regimens other than those which reduce pathogen burdens as fast as possible.

Drug-resistance is a major public health problem. Conventional wisdom on resistance management is to use aggressive chemotherapy to kill pathogens as rapidly as possible so as to prevent them from acquiring resistance. This is the reason why physicians frequently exhort patients to finish drug courses even after they no longer feel sick. However, this approach is based on the notion that we need only prevent new resistant mutants from arising. We hypothesize that in the situation where such mutants are already present at the time of treatment, more aggressive chemotherapy will select for these the fastest by rapidly killing all sensitive competitors. Here we demonstrate in a rodent malaria model that such selection indeed occurs more intensely following aggressive treatment than following less aggressive treatment, without any benefit to host health or infectivity. This suggests that aggressive chemotherapy will not be the best way to retard resistance evolution in some - perhaps many - circumstances. We suggest that an evidence-based approach across a wide range of infectious diseases is needed to manage resistance evolution.

The rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs

The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments.

Assessing triclosan-induced ecological and trans-generational effects in natural phytoplankton communities: a trait-based field method

We exposed replicated phytoplankton communities confined in semi-permeable membrane-based mesocosms to 0, 0.1, 1 and 10 μg L(-1) triclosan (TCS) and placed them back in their original environment to investigate the occurrence of trans-generational responses at individual, population and community levels. TCS diffused out of mesocosms with a half-life of less than 8 h, so that only the parental generation was directly stressed. At the beginning of the experiment and after 7 days (approximately 2 generations) we analysed responses in the phytoplankton using scanning flow-cytometry. We acquired information on several individually expressed phenotypic traits, such as size, biovolume, pigment fluorescence and packaging, for thousands of individuals per replicated population and derived population and community aggregated traits. We found significant changes in community functioning (increased productivity in terms of biovolume and total fluorescence), with maximal effects at 1 μg L(-1) TCS. We detected significant and dose-dependent responses on population traits, such as changes in abundance for several populations, increased average size and fluorescence of cells, and strong changes in within-population trait mean and variance (suggesting micro-evolutionary effects). We applied the Price equation approach to partition community effects (changes in biovolume or fluorescence) in their physiological and ecological components, and quantified the residual component (including also evolutionary responses). Our results suggested that evolutionary or inheritable phenotypic plasticity responses may represent a significant component of the total observed change following exposure and over relatively small temporal scales.

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance

In principle, evolutionary outcomes could be largely predicted if all of the relevant physicochemical variants of a particular protein function under selection were known and integrated into an appropriate physiological model. We have tested this principle by generating a family of variants of the tetracycline resistance protein TetX2 and identified the physicochemical properties most correlated with organismal fitness. Surprisingly, small changes in the K(m(MCN)), less than twofold, were sufficient to produce highly successful adaptive mutants over clinically relevant drug concentrations. We then built a quantitative model directly relating the in vitro physicochemical properties of the mutant enzymes to the growth rates of bacteria carrying a single chromosomal copy of the tet(X2) variants over a wide range of minocycline (MCN) concentrations. Importantly, this model allows the prediction of enzymatic properties directly from cellular growth rates as well as the physicochemical-fitness landscape of TetX2. Using experimental evolution and deep sequencing to monitor the allelic frequencies of the seven most biochemically efficient TetX2 mutants in 10 independently evolving populations, we showed that the model correctly predicted the success of the two most beneficial variants tet(X2)(T280A) and tet(X2)(N371I). The structure of the most efficient variant, TetX2(T280A), in complex with MCN at 2.7 Å resolution suggests an indirect effect on enzyme kinetics. Taken together, these findings support an important role for readily accessible small steps in protein evolution that can, in turn, greatly increase the fitness of an organism during natural selection.

Decontamination treatments can increase the prevalence of resistance to antibiotics of Escherichia coli naturally present on poultry

The main objective of this study was to determine the ability of various decontaminants to increase the prevalence of resistance to antibiotics in Escherichia coli populations on poultry. Chicken legs were dipped for 15 min into aqueous solutions (wt/vol) of trisodium phosphate (TSP; 12%), acidified sodium chlorite (ASC; 1200 ppm), ascorbic acid (AA; 2%) or citric acid (CA; 2%), or tap water (control). Samples were analyzed immediately after treatment (day 0) and after five days of storage at 7 ± 1 °C. A total of 250 E. coli isolates (50 from each group of samples; 25 on day 0 and 25 on day 5) were tested against twelve antibiotics of clinical significance by means of a standard disc-diffusion technique. A high prevalence of resistance to antibiotics was observed for E. coli strains from control samples, with three (6.0%) isolates sensitive, three (6.0%) resistant to one antibiotic and 44 (88.0%) isolates resistant to two or more antibiotics. Isolates from control samples had a lower prevalence of resistance than those from treated samples to ampicillin-sulbactam (P < 0.01, samples treated with TSP), amoxicillin-clavulanic acid (P < 0.001, ASC, AA and CA), cephotaxime (P < 0.05, TSP), trimethoprim-sulphamethoxazole (P < 0.05, AA; P < 0.01, CA), tetracycline (P < 0.01, CA), ciprofloxacin (P < 0.001, ASC; P < 0.05, AA; P < 0.01, CA) and nitrofurantoin (P < 0.01, TSP). These results suggest that the chemical decontaminants tested could favor the emergence, selection and/or proliferation of antibiotic-resistant strains in microbial populations on poultry meat.

Spectinomycin resistance mutations in the rrn16 gene are new plastid markers in Medicago sativa

We report here the isolation of spectinomycin-resistant mutants in cultured cells of Medicago sativa line RegenSY-T2. Spectinomycin induces bleaching of cultured alfalfa cells due to inhibition of protein synthesis on the prokaryotic type 70S plastid ribosomes. Spontaneous mutants resistant to spectinomycin bleaching were identified by their ability to form green shoots on plant regeneration medium containing selective spectinomycin concentrations in the range of 25-50 mg/l. Sequencing of the plastid rrn16 gene revealed that spectinomycin resistance is due to mutations in a conserved stem structure of the 16S rRNA. Resistant plants transferred to the greenhouse developed normally and produced spectinomycin-resistant seed progeny. In light of their absence in soybean, a related leguminous plant, the isolation of spectinomycin-resistant mutants in M. sativa was unexpected. The new mutations are useful for the study of plastid inheritance, as demonstrated by detection of predominantly paternal plastid inheritance in the RegenSY-T2 × Szapko57 cross, and can be used as selective markers in plastid transformation vectors to obtain cisgenic plants.

Do pollutants affect insecticide-driven gene selection in mosquitoes? Experimental evidence from transcriptomics

The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, the emergence of insecticide resistance threatens mosquito control programs. Until now, most research efforts have been focused on elucidating resistance mechanisms caused by insecticide treatments. Less attention has been paid to the impact of the mosquito chemical environment on insecticide-driven selection mechanisms. Here the mosquito Aedes aegypti was used as a model species to conduct laboratory experiments combining the exposure of mosquito larvae to a sub-lethal concentration of xenobiotics and their selection with the insecticide permethrin. After 10 generations, bioassays and a transcriptome profiling with a 15 k microarray were performed comparatively on all strains. The three selected strains showed a small but significant increase of permethrin resistance compared to the susceptible parental strain. Microarray analysis revealed that the transcription of many genes was altered by insecticide selection. Exposing larvae to sub-lethal concentrations of the pollutant fluoranthene or the insecticide permethrin prior to selection at each generation affected the selection of several genes, including those involved in detoxification, transport and cell metabolism. Genes potentially involved in permethrin resistance and cross-responses between xenobiotics and insecticide were identified. The present study investigated for the first time the impact of the presence of pollutants in mosquito environment on insecticide-driven selection mechanisms. Our results revealed that mosquitoes exposed to xenobiotics show a different adaptive response to insecticide selection pressure. This suggests that insect chemical environment can shape the long-term selection of metabolic mechanisms leading to insecticide resistance.

Modeling HIV-1 drug resistance as episodic directional selection

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance.

When exposed to treatment, HIV-1 and other rapidly evolving viruses have the capacity to acquire drug resistance mutations (DRAMs), which limit the efficacy of antivirals. There are a number of experimentally well characterized HIV-1 DRAMs, but many mutations whose roles are not fully understood have also been reported. In this manuscript we construct evolutionary models that identify the locations and targets of mutations conferring resistance to antiretrovirals from viral sequences sampled from treated and untreated individuals. While the evolution of drug resistance is a classic example of natural selection, existing analyses fail to detect the majority of DRAMs. We show that, in order to identify resistance mutations from sequence data, it is necessary to recognize that in this case natural selection is both episodic (it only operates when the virus is exposed to the drugs) and directional (only mutations to a particular amino-acid confer resistance while allowing the virus to continue replicating). The new class of models that allow for the episodic and directional nature of adaptive evolution performs very well at recovering known DRAMs, can be useful at identifying unknown resistance-associated mutations, and is generally applicable to a variety of biological scenarios where similar selective forces are at play.

Identification of innate immunity elicitors using molecular signatures of natural selection

The innate immune system is an ancient and broad-spectrum defense system found in all eukaryotes. The detection of microbial elicitors results in the up-regulation of defense-related genes and the elicitation of inflammatory and apoptotic responses. These innate immune responses are the front-line barrier against disease because they collectively suppress the growth of the vast majority of invading microbes. Despite their critical role, we know remarkably little about the diversity of immune elicitors. To address this paucity, we reasoned that hosts are more likely to evolve recognition to "core" pathogen proteins under strong negative selection for the maintenance of essential cellular functions, whereas repeated exposure to host-defense responses will impose strong positive selective pressure for elicitor diversification to avoid host recognition. Therefore, we hypothesized that novel bacterial elicitors can be identified through these opposing forces of natural selection. We tested this hypothesis by examining the genomes of six bacterial phytopathogens and identifying 56 candidate elicitors that have an excess of positively selected residues in a background of strong negative selection. We show that these positively selected residues are atypically clustered, similar to patterns seen in the few well-characterized elicitors. We then validated selected candidate elicitors by showing that they induce Arabidopsis thaliana innate immunity in functional (virulence suppression) and cellular (callose deposition) assays. These finding provide targets for the study of host-pathogen interactions and applied research into alternative antimicrobial treatments.

Delaying selection for fungicide insensitivity by mixing fungicides at a low and high risk of resistance development: a modeling analysis

This study used mathematical modeling to predict whether mixtures of a high-resistance-risk and a low-risk fungicide delay selection for resistance against the high-risk fungicide. We used the winter wheat and Mycosphaerella graminicola host-pathogen system as an example, with a quinone outside inhibitor fungicide as the high-risk and chlorothalonil as the low-risk fungicide. The usefulness of the mixing strategy was measured as the "effective life": the number of seasons that the disease-induced reduction of the integral of canopy green area index during the yield forming period could be kept <5%. We determined effective lives for strategies in which the dose rate (i) was constant for both the low-risk and high-risk fungicides, (ii) was constant for the low-risk fungicide but could increase for the high-risk fungicide, and (iii) was adjusted for both fungicides but their ratio in the mixture was fixed. The effective life was highest when applying the full label-recommended dose of the low-risk fungicide and adjusting the dose of the high-risk fungicide each season to the level required to maintain effective control. This strategy resulted in a predicted effective life of ≤ 12 years compared with 3 to 4 years when using the high risk fungicide alone.

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.

Antibiotic resistance has emerged as a very significant health care problem due to the extensive use and misuse of antibiotics in human and veterinary medicine and in agriculture. It remains unclear where most of the resistant bacteria have been selected, and in particular if the low antibiotic concentrations that are present in natural environments or in human/animal body compartments during therapeutic or growth promotion use, are important for the selection and enrichment of resistant mutants. The presented data shows that for several clinically used antibiotics extremely low concentrations, similar to the concentrations found in natural environments, can select for resistant bacteria. These results suggest that antibiotic release into the environment might be a significant contributor to the emergence and maintenance of resistance and emphasize the importance of introducing measures to reduce antibiotic pollution.

Within-host dynamics of the hepatitis C virus quasispecies population in HIV-1/HCV coinfected patients

HIV/HCV coinfected individuals under highly active antiretroviral therapy (HAART) represent an interesting model for the investigation of the role played by the immune system in driving the evolution of the HCV quasispecies. We prospectively studied the intra-host evolution of the HCV heterogeneity in 8 coinfected subjects, selected from a cohort of 32 patients initiating HAART: 5 immunological responders (group A) and 3 immunological non-responders (group B), and in two HCV singly infected controls not assuming drugs (group C). For all these subjects at least two serial samples obtained at the first observation (before HAART) and more than 1 year later, underwent clonal sequence analysis of partial E1/E2 sequences, encompassing the whole HVR1. Evolutionary rates, dated phylogenies and population dynamics were co-estimated by using a Bayesian Markov Chain Monte Carlo approach, and site specific selection pressures were estimated by maximum likelihood-based methods. The intra-host evolutionary rates of HCV quasispecies was 10 times higher in subjects treated with HAART than in controls without immunodeficiency (1.9 and 2.3×10⁻³ sub/site/month in group A and B and 0.29×10⁻³ sub/site/month in group C individuals). The within-host Bayesian Skyline plot analysis showed an exponential growth of the quasispecies populations in immunological responders, coinciding with a peak in CD4 cell counts. On the contrary, quasispecies population remained constant in group B and in group C controls. A significant positive selection pressure was detected in a half of the patients under HAART and in none of the group C controls. Several sites under significant positive selection were described, mainly included in the HVR1. Our data indicate that different forces, in addition to the selection pressure, drive an exceptionally fast evolution of HCV during HAART immune restoration. We hypothesize that an important role is played by the enlargement of the viral replicative space.

Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure

Using quantitative deep HIV-1 sequencing in a subject who developed virological failure to deep salvage therapy with raltegravir, we found that most Q148R and N155H mutants detected at the time of virological failure originated from pre-existing minority Q148R and N155H variants through independent evolutionary clusters. Double 148R+N155H mutants were also detected in 1.7% of viruses at virological failure in association with E138K and/or G163R. Our findings illustrate the ability of HIV-1 to escape from suboptimal antiretroviral drug pressure through selection of pre-existing drug-resistant mutants, underscoring the importance of using fully active antiretroviral regimens to treat all HIV-1-infected subjects.

New capabilities for Mycosphaerella graminicola research

Mycosphaerella graminicola is a major pathogen of wheat worldwide, causing Septoria leaf blotch disease. Targeted gene disruption in M. graminicola, by Agrobacterium tumefaciens-mediated transformation, has become an established functional genomics tool for M. graminicola research in recent years. However, in order to advance research into this economically important pathogen, further functional genomics tools need to be developed. Here, we report three new capabilities for M. graminicola research: (i) two selectable markers have been shown to work robustly in M. graminicola, namely G418 and the fungicide carboxin; (ii) the generation of a strain of M. graminicola in which the KU70 (MUS-51) homologue has been disrupted; in this strain, homologous recombination efficiencies increased to more than 95%, whilst maintaining wild-type growth in vitro and full pathogenicity on wheat leaves; (iii) the ability to efficiently target and generate precise mutations of specific genes in the genomic context in M. graminicola. In addition, the insertion of the E198A mutation into the beta-tubulin gene (MgTUB1), conferring resistance to the fungicide benomyl, suggests that this mutant allele may provide an additional selectable marker. The collective use of these tools will permit further advancements in our knowledge of the biology and pathogenicity of this important plant pathogen.

Heterozygous effects on fitness of EMS-treated chromosomes in Drosophila melanogaster

The heterozygous effects on fitness of second chromosomes carrying mutants induced with different doses of EMS were ascertained by monitoring changes in chromosome frequencies over time. These changes were observed in populations in which the treated chromosomes, as well as untreated competitors, remained heterozygous in males generation after generation. This situation was achieved by using a translocation which links the second chromosome to the X chromosome; however, only untranslocated second chromosomes were mutagenized. Chromosomes were classified according to their effects on viability in homozygous condition. A preliminary homozygosis identified completely lethal chromosomes; secondary tests distinguished between drastic (viability index < 0.1) and nondrastic chromosomes. Chromosomes that were nondrastic after treatment were found to reduce the fitness of their heterozygous carriers by 3-5%. The data show that flies homozygous for these chromosomes were about 2.7% less viable per treatment with 1 mm EMS than flies homozygous for untreated chromosomes. By comparing the fitness-depressing effects of nondrastic EMS-induced mutants in heterozygous condition with the corresponding viability-depressing effects measured by Temin, it is apparent that the total fitness effects are several times larger than the viability effects alone. Completely lethal chromosomes derived from the most heavily treated material reduced fitness by 11% in heterozygous condition; approximately half of this reduction was due to the lethal mutations themselves.

[Selection of active strains of Actinomadura carminata, the producer of carminomycin]

The method of selecting active strains among a definite group of analogue-resistant mutants was used on the basis of studying the dependence of the carminomycin-producing organism growth and the antibiotic synthesis level on some metabolites. As a result, gamma-ray induced mutants 4 times more active than the parent strains were obtained.

Variation in the direction of selection applied by pentenol to the alcohol dehydrogenase locus in Drosophila melanogaster

This paper describes selective effects of pentenol-impregnated media on six genotypes at the alcohol dehydrogenase (Adh) locus in D. melanogaster. In the laboratory population studied, developmental times of pre-adults homozygous for an alcohol dehydrogenase "null" allele increased with increasing pentenol concentrations. The developmental times of the other five genotypes, which produced active alcohol dehydrogenases, increased slightly at pentenol concentrations up to 0-0033%, but above this concentration they decreased markedly. In fact on 0-067% pentenol, the highest concentration tested, developmental times of these five genotypes were between 9 and 24 h less than their developmental times on media lacking pentenol. The magnitude of the reduction in developmental time differed significantly between genotypes and was positively correlated with alcohol dehydrogenase activity. Pentenol had toxic effects on adults and significant differences were found between survival percentages of adults of different genotypes on pentenol-impregnated media. These survival percentages were negatively correlated with alcohol dehydrogenase activities. Therefore selective differences between genotypes in adult survival were negatively correlated with those in developmental times. The variations in the direction of selection are discussed in terms of their possible biochemical basis and their effects on the maintenance of Adh polymorphisms.

[Genetic bases for the selection of microorganisms using analogs]

The main mechanisms are considered for biosynthesis processes regulation by means of repression and inhibition with final products. On the basis of these mechanisms the state and prospects of the directed alteration of various stages in regulating the synthesis of primary and secondary metabolites, using breeding selection of mutants resistant to analogues are discussed. The main regularities are presented for using analogues of primary metabolites in the breeding strains with overproduction of various biologically active compounds.

[Production of active mutants of a new species of rifamycin producer resistant to specific actinophage]

Selection of a phage-stable strain of a new species of the rifamycin-producing organism was carried out. The phage-stable mutants were selected with respect to the virulent phage 2739 isolated from a lysogenic culture of the rifamycin-producing organism. Spontaneous phage-stable mutants formed at a rate of 0.8 per cent. Most of them belonged to the morphological colony type with a decreased activity level. No shifts in variation with respect to the property of the antibiotic production were noted under the action of phage 2739. 62 per cent of the phage-stable variants isolated from the secondary growth colonies after infection with the phage were lysogenic and liberated phage 2739 to the culture fluid. Induction of mutations with MNNG, UV and gamma(Co30) rays increased the frequency of the phage-stable mutanta by 1.5 times. Active phage-resistant mutants stable to the phage because of its adsorption and liberating no phage 2739 into liquid media during its cultivation were selected.