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Natural selection for grazer resistance to toxic cyanobacteria: evolution of phenotypic plasticity?

We studied the selection response of the freshwater grazing zooplankter, Daphnia galeata, to increased abundance of cyanobacteria in its environment. Cyanobacteria are a poor-quality and often toxic food. Distinct genotypes of D. galeata were hatched from diapausing eggs extracted from three time horizons in the sediments of Lake Constance, Europe, covering the period 1962 to 1997, a time of change in both the prevalence of planktonic cyanobacteria and levels of phosphorus pollution. We assessed whether the grazers evolved to become more resistant to dietary cyanobacteria by exposing genetically distinct clones to two diets, one composed only of the nutritious green alga, Scenedesmus obliquus (good food), and the other a mixture of S. obliquus and the toxic cyanobacterium Microcvstis aeruginosa (poor food). Genotype performance was measured as the specific rate of weight gain from neonate to maturity (gj). We evaluated evolutionary change in the Daphnia population using an analysis of reaction norms based on relative (log-transformed) changes in gj. Log(gj) is a measure of the proportional effect of dietary cyanobacteria on other fitness components of the Daphnia phenotype. For comparison, we also analyze absolute (i.e., nontransformed) changes in gj and discuss the interpretations of the two approaches. Statistical results using a general linear model demonstrate a significant effect of genotype (showing differences in gj among genotypes), a significant genotype x food-type interaction (showing differences in phenotypic plasticity among genotypes), and, in the case of log-transformed data, a significant sediment-genotype-age x food-type interaction. The latter shows that phenotypic plasticity evolved over the period studied. Two constraints act on response to selection in the D. galeata-Lake Constance system. First, gj on a diet containing poor food is highly correlated with gj on a diet of good food, thus evolving resistance also meant evolving an increase in gj on both diets. Second, because genotypes with a high gj also grow to a large adult body size, which in turn increases Daphnia vulnerability to fish predation, we suggest that selection only acted to favor genotypes possessing a high potential gj after cyanobacteria became prevalent. The presence of cyanobacteria depressed realized gj and led to animals of small adult body size even if their genotypes had the potential for high gj and large size. With realized gj reduced, genotypes with an inherently high value could be selected even in the presence of predatory fish. The joint action of selection by dietary cyanobacteria and vulnerability to fish predation provides an explanation for the observed evolution of resistance to poor food through reduced phenotypic plasticity.

Animals↗

Engineering aggregation-resistant proteins by directed evolution.

A method was recently described for selecting aggregation-resistant antibody domains. A repertoire of domains displayed on filamentous bacteriophage were heated/cooled and selected for binding to the affinity ligand protein A specific for the folded domains. Here we describe a generalization of the method based on the selection for retained phage infectivity and for the binding of an appended sequence tag, and applicable to any protein displayable in multivalent form on phage.

Evolution, Molecular↗

Evolution of drug-resistance genes in Plasmodium falciparum in an area of seasonal malaria transmission in Eastern Sudan.

We investigated the evolution of drug-resistant Plasmodium falciparum in a village in eastern Sudan. The frequencies of alleles of 4 genes thought to be determinants of drug resistance were monitored from 1990 through 2001. Changes in frequencies of drug-resistance genes between wet and dry seasons were monitored from 1998 through 2000. Parasites were also typed for 3 putatively neutral microsatellite loci. No significant variation in frequencies was observed for the microsatellite loci over the whole study period or between seasons. However, genes involved in resistance to chloroquine showed consistent, significant increases in frequencies over time (rate of annual increase, 0.027/year for pfcrt and 0.018/year for pfmdr1). Genes involved in resistance to the second-line drug used in the area (Fansidar) remained at low frequencies between 1990 and 1993 but increased dramatically between 1998 and 2000, which is consistent with the advent of Fansidar usage during this period. For mutant alleles of the primary drug-resistance targets for chloroquine and pyrimethamine, higher frequencies were seen during the dry season than during the wet season. This cyclical fluctuation in drug-resistance genes most likely reflects seasonal variation in drug pressure and differences in the fitness of resistant and sensitive parasites.

Alleles↗

Vaccines and their impact on the control of disease.

Disease control exerts evolutionary pressures that can lead to the evolution of resistance. This has been seen in a spectacular fashion in the evolution of resistance to antibiotics, anti-virals and anti-parasitics. Despite intense (and often successful) attempts to control infectious diseases through vaccination, there is still rather little evidence of the emergence of strains of pathogen resistant to vaccines. This chapter asks why this should be so and what are the exceptions indicating that the evolution of vaccine resistance, though currently rare, is a possibility that should be planned for.

Communicable Disease Control↗

Evolution of drug-resistant tuberculosis: a tale of two species.

The history of the disease tuberculosis is briefly discussed. Now human societal failures have potentiated the evolution of drug-resistant strains of the tubercle bacillus in the United States and around the world. Until recently, this evolutionary change largely posed a threat to the health and survival of the individual in whom inadequate therapy promoted the drug resistance. However, the human immunodeficiency virus epidemic threatens to promote wholesale transmission of multidrug-resistant tuberculosis with the potential for immense morbidity and mortality. Reinforced treatment and control programs for tuberculosis are vital.

Biological Evolution↗

Effect of inhaled interferon-β1a on SARS-CoV-2 diversity and evolution.

Interferon resistance has been implicated in SARS-CoV-2 escape from innate immunity, but exogenous interferon's impact on viral evolution and diversity is unknown. SNG001, an inhaled interferon-β1a treatment, was evaluated in the ACTIV-2/A5401 randomized controlled trial of therapeutics for COVID-19. We measured viral kinetics and performed whole-genome sequencing on longitudinal nasal swabs collected from ACTIV-2 participants who received either SNG001 or placebo to assess viral sequence diversity. No difference in nasal viral load decay was detected between study arms when stratifying by SARS-CoV-2 variant or by viral culture conversion. Compared to placebo participants, the SNG001-treated participants displayed significantly lower nonsynonymous amino acid average pairwise distance, indicating lower sequence diversity. Similarly, SNG001-treated individuals also developed numerically fewer nonsynonymous mutations during their infection in ORF1a, ORF1b, Spike, and Nucleocapsid. No specific emerging SARS-CoV-2 nonsynonymous amino acid changes indicating signatures of viral escape were enriched in those receiving SNG001. These in vivo data provide an intriguing signal that exogenous interferon-β1a may restrict SARS-CoV-2 viral diversity and add to growing evidence that interferon levels play a critical role in antiviral responses during COVID-19.IMPORTANCESARS-CoV-2 encodes several genes which can antagonize the interferon signaling cascade, preventing it from activating antiviral responses and thereby facilitating viral establishment and dissemination. It is unknown how the administration of exogenous interferon might affect viral evolution and immune escape. ACTIV-2/A5401 represents a unique opportunity to study the virologic effects of interferon treatment in a rigorous randomized, placebo-controlled clinical trial setting. Our characterization of longitudinal nasal samples shows that interferon-treated individuals had lower viral diversity and no evidence of viral escape mutations.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT04518410.

Humans↗

Induction and inhibition of ciprofloxacin resistance-conferring mutations in hypermutator bacteria.

The emergence of drug-resistant bacteria poses a serious threat to human health. Bacteria often acquire resistance from a mutation of chromosomal genes during therapy. We have recently shown that the evolution of resistance to ciprofloxacin in vivo and in vitro requires the induction of a mutation that is mediated by the cleavage of the SOS repressor LexA and the associated derepression of three specialized DNA polymerases (polymerase II [Pol II], Pol IV, and Pol V). These results led us to suggest that it may be possible to design drugs to inhibit these proteins and that such drugs might be coadministered with antibiotics to prevent mutation and the evolution of resistance. For the approach to be feasible, there must not be any mechanisms through which bacteria can induce mutations and acquire antibiotic resistance that are independent of LexA and its repressed polymerases. Perhaps the most commonly cited mechanism to elevate bacterial mutation rates is the inactivation of methyl-directed mismatch repair (MMR). However, it is unclear whether this represents a LexA-independent mechanism or if the mutations that arise in MMR-deficient hypermutator strains are also dependent on LexA cleavage and polymerase derepression. In this work, we show that LexA cleavage and polymerase derepression are required for the evolution of clinically significant resistance in MMR-defective Escherichia coli. Thus, drugs that inhibit the proteins responsible for induced mutations are expected to efficiently prevent the evolution of resistance, even in MMR-deficient hypermutator strains.

Bacterial Proteins↗

Multigenerational versus single generation studies to estimate herbicide resistance fitness cost in Arabidopsis thaliana.

The evolution of resistance in response to pesticide selection is expected to be delayed if fitness costs are associated with resistance genes. The estimate of fitness costs usually involves comparing major growth traits of resistant versus susceptible individuals in the absence of pesticide. Ideally, a measure of changes in resistance allele frequency over several generations would allow the best estimate of the overall fitness cost of a resistance gene. In greenhouse conditions, we monitored the dynamics of the evolution of the frequencies of six herbicide-resistant mutations (acetolactate synthase, cellulose synthase, and auxin-induced target genes) in the model species Arabidopsis thaliana in a multigenerational study covering five to seven nonoverlapping generations. The microevolutionary dynamics in experimental populations indicated a mean fitness cost of 38%, 73%, and 94% for the ixr1-2, axr1-3, and axr2-1 resistances, respectively; no fitness cost for the csr1-1, and ixr2-1 resistances; and a transient advantage for the aux1-7 resistance. The result for the csr1-1 resistance contrasts with a cost of 37% based on total seed number in a previous study, demonstrating that single generation studies could have limitation for detecting cost. A positive frequency dependence for the fitness cost was also detected for the ixr1-2 resistance. The results are discussed in relation to the maintenance of polymorphism at resistance loci.

2,4-Dichlorophenoxyacetic Acid↗

Evolution of multidrug-resistant Acinetobacter baumannii isolates obtained from elderly patients with respiratory tract infections.

OBJECTIVES: To study the evolution between 1999 and 2002 and mechanisms of antibiotic resistance in a multidrug-resistant Acinetobacter baumannii clone predominant in isolates from elderly patients with respiratory tract infections. METHODS: Susceptibility to antimicrobials was determined using an agar dilution method. Bacterial clones were identified by PCR-fingerprinting and PFGE with ApaI. Carbapenemases were detected by phenotypic tests; by PCR with primers specific for bla (OXA-40), bla(IMP), bla(VIM-1) and bla(VIM-2); and by hybridization with DNA probes. Class 1 integrons were detected using PCR. RESULTS: In 1999 isolates were grouped into two main genotypes: clone I (33%) and clone II (55%). These were also detected in 2002 with a different distribution: clone I (69%), clone II (22%). Resistance to amikacin, meropenem and imipenem increased significantly in clone I over this time, whereas clone II was not affected. In 2002, the incidence of bla(OXA-40) rose to 91% in clone I isolates with some also harbouring bla(VIM-2) and bla(IMP) genes. Different class 1 integrons were detected ranging in size from 550 to 1200 bp. No relationship was found between carbapenemases and class 1 integrons. CONCLUSIONS: In elderly patients, a single clone became predominant among A. baumannii isolates, coinciding with an increase in antibiotic resistance rates. The majority of isolates harboured the bla(OXA-40) carbapenemase gene and some of them also harboured bla(VIM-2) and bla(IMP) genes. The presence of class 1 integrons also increased over time.

Acinetobacter Infections↗

Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.

Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.

Biofilms↗

Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution.

Antibiotic resistant bacteria are a constant threat in the battle against infectious diseases. One strategy for reducing their effect is to temporarily discontinue the use of certain antibiotics in the hope that in the absence of the antibiotic the resistant strains will be replaced by the sensitive strains. An experiment where this strategy is employed in vitro produces data which showed a slow accumulation of sensitive mutants. Here we propose a mathematical model and statistical analysis to explain this data. The stochastic model elucidates the trend and error structure of the data. It provides a guide for developing future sampling strategies, and provides a framework for long term predictions of the effects of discontinuing specific antibiotics on the dynamics of resistant bacterial populations.

Bacteria↗

[The chloroquine resistance of Plasmodium falciparum in Vanuatu (1980-1984): appearance, evolution, distribution].

Chloroquine resistance of P. falciparum was studied in Vanuatu from March 1981 to July 1984, with limited means, and a non-systematic procedure; it was first evidenced in 1980. In vivo chloroquine resistance criteria were those established by W. H. O. In vitro testing methods were the standard W. H. O. macro-test and micro-test. 124 in vivo chloroquine resistant cases were seen: 111 cases in hospital (63 R III, 28 R II and 20 R I) and 13 cases in field studies (1 R III, 4 R II and 8 R I). 87 in vitro chloroquine sensitivity tests were carried out. A high failure rate was apparently due to a defective batch of lyophilised culture medium. Out of the 25 isolates successfully tested, 22 showed in vitro chloroquine resistance (88%). Correlation between in vivo and in vitro resistance was good in 13 cases studied by both methods. Moreover, 13 in vitro mefloquine sensitivity tests evidenced a high sensitivity to this drug. Chloroquine resistant malaria thus appears to be extended to the whole country. Its prevalence remains unknown but was estimated at 60% at least in 1984. Moreover, a geographical spread of chloroquine resistance from north to south of the group was evidenced between 1980 and 1984, identical to that of the dramatic increase of P. falciparum incidence at the same period of time. Possible mechanisms of the advent of chloroquine resistance in Vanuatu are discussed.

Adolescent↗

Molecular evolution of multiply-antibiotic-resistant staphylococci.

Methicillin-resistant Staphylococcus aureus (MRSA) is an intractable nosocomial pathogen. The chemotherapeutic intransigence of this organism stems from its predilection to antimicrobial resistance as a consequential response to selective pressures prevailing in the clinical environment. MRSA isolates are frequently resistant to all practicable antimicrobials except the glycopeptide, vancomycin. Although antimicrobial resistance sometimes arises via chromosomal mutation, the emergence of multiply-antibiotic-resistant staphylococci is primarily due to the acquisition of pre-existent resistance genes; such determinants can be encoded chromosomally or by plasmids and are often associated with transposons or insertion sequences. Clinical staphylococci commonly carry one or more plasmids, ranging from small replicons that are phenotypically cryptic or contain only a single resistance gene, to larger episomes that possess several such determinants and sometimes additionally encode systems that mediate their own conjugative transmission and the mobilization of other plasmids. The detection of closely related plasmids, elements and/or genes in other hosts, including coagulase-negative staphylococci and enterococci, attests to interspecific and intergeneric genetic exchange facilitated by mobile genetic elements and DNA transfer mechanisms. The extended genetic reservoir accessible to staphylococci afforded by such horizontal gene flux is fundamental to the acquisition, maintenance and dissemination of staphylococcal antimicrobial resistance in general, and multiresistance in particular.

Drug Resistance, Microbial↗

Taking stock of herbicide-resistant crops ten years after introduction.

Since transgenic, bromoxynil-resistant cotton and glufosinate-resistant canola were introduced in 1995, planting of transgenic herbicide-resistant crops has grown substantially, revolutionizing weed management where they have been available. Before 1995, several commercial herbicide-resistant crops were produced by biotechnology through selection for resistance in tissue culture. However, non-transgenic herbicide-resistant crops have had less commercial impact. Since the introduction of glyphosate-resistant soybean in 1996, and the subsequent introduction of other glyphosate-resistant crops, where available, they have taken a commanding share of the herbicide-resistant crop market, especially in soybean, cotton and canola. The high level of adoption of glyphosate-resistant crops by North American farmers has helped to significantly reduce the value of the remaining herbicide market. This has resulted in reduced investment in herbicide discovery, which may be problematic for addressing future weed-management problems. Introduction of herbicide-resistant crops that can be used with selective herbicides has apparently been hindered by the great success of glyphosate-resistant crops. Evolution of glyphosate-resistant weeds and movement of naturally resistant weed species into glyphosate-resistant crop fields will require increases in the use of other herbicides, but the speed with which these processes compromise the use of glyphosate alone is uncertain. The future of herbicide-resistant crops will be influenced by many factors, including alternative technologies, public opinion and weed resistance. Considering the relatively few recent approvals for field testing new herbicide-resistant crops and recent decisions not to grow glyphosate-resistant sugarbeet and wheat, the introduction and adoption of herbicide-resistant crops during the next 10 years is not likely to be as dramatic as in the past 10 years.

Agriculture↗

Horizontal genetic exchange, evolution, and spread of antibiotic resistance in bacteria.

Some transformable bacteria have acquired target-mediated antibiotic resistance by horizontal genetic exchange of fragments of chromosomal genes. The resistant strains express variants of the antibiotic target that are metabolically active but exhibit a lowered affinity for the antibiotic. The alleles encoding these resistant proteins are mosaics comprising DNA derived from the host and other bacteria, often members of a different species. Examples include penicillin-resistant penicillin-binding proteins (PBPs) in Streptococcus pneumoniae and the pathogenic Neisseria species and sulfonamide-resistant dihydropterate synthase in Neisseria meningitidis. Distinct mosaic alleles encoding antibiotic resistance have arisen on multiple occasions, indicating the mobility of chromosomal genes in these species. Mosaic genes can arise at any chromosomal locus, and S. pneumoniae organisms with high-level penicillin resistance have acquired mosaic PBP genes at three bacterial bpb loci. Furthermore, horizontal genetic exchange permits movement of alleles among bacterial lineages, increasing the opportunities for the spread of antibiotic resistance.

Animals↗

How evolution of mutations conferring drug resistance affects viral dynamics and clinical outcomes of cytomegalovirus-infected hematopoietic cell transplant recipients.

Infection with cytomegalovirus (CMV) remains a significant cause of morbidity and mortality among hematopoietic cell transplant (HCT) recipients. We describe two pediatric HCT recipients who developed persistent and severe drug-resistant CMV infections. CMV resistance to foscarnet and ganciclovir was detected after only 6 and 11 weeks of therapy, respectively. Viral pol mutations associated with drug resistance in these patients included T838A (a novel mutation) and D588N, which were shown by marker transfer to confer foscarnet and multidrug resistance, respectively. Each of these mutations significantly reduced in vitro replication of CMV, suggesting that they may decrease viral fitness. This finding was further supported by the disappearance of mutations upon withdrawal of antiviral pressure in one patient. Novel antivirals or combination therapy may be required for the treatment of drug-resistant CMV in HCT recipients and perhaps in other severely immunocompromised patients.

Adolescent↗

Modeling the dynamics of adaptation to transgenic corn by western corn rootworm (Coleoptera: Chrysomelidae).

A simulation model of the population dynamics and genetics of the western corn rootworm, Diabrotica virgifera virgifera LeConte, was created for a landscape of corn, soybean, and other crops. Although the model was created to study a 2-locus problem for beetles having genes for resistance to both crop rotation and transgenic corn, during this first phase of the project, the model was simulated to evaluate only resistance management plans for transgenic corn. Allele expression in the rootworm and toxin dose in the corn plant were the two most important factors affecting resistance development. A dominant resistance allele allowed quick evolution of resistance to transgenic corn, whereas a recessive allele delayed resistance >99 yr. With high dosages of toxin and additive expression, the time required to reach 3% resistance allele frequency ranged from 13 to >99 yr. With additive expression, lower dosages permitted the resistant allele frequency to reach 3% in 2-9 yr with refuges occupying 5-30% of the land. The results were sensitive to delays in emergence by susceptible adults and configuration of the refuge (row strips versus blocks).

Adaptation, Physiological↗

Effects of Bt cotton and crylac toxin on survival and development of pink bollworm (Lepidoptera: Gelechiidae).

We evaluated the effects of Bacillus thuringiensis (Bt) toxin CrylAc on survival and development of a susceptible strain and laboratory-selected resistant strains of pink bollworm, Pectinophora gossypiella (Saunders). For susceptible and resistant strains tested on artificial diet, increases in CrylAc concentration reduced developmental rate and pupal weight. In greenhouse tests, survival of resistant larvae on transgenic cotton that produces CrylAc (Bt cotton) was 46% relative to their survival on non-Bt cotton. In contrast, Bt cotton killed all susceptible larvae tested. F1 hybrid progeny of resistant and susceptible adults did not survive on Bt cotton, which indicates recessive inheritance of resistance. Compared with resistant or susceptible larvae reared on non-Bt cotton, resistant larvae reared on Bt cotton had lower survival and slower development, and achieved lower pupal weight and fecundity. Recessive resistance to Bt cotton is consistent with one of the basic assumptions of the refuge strategy for delaying resistance to Bt cotton. Whereas slower development of resistant insects on Bt cotton could increase the probability of mating between resistant adults and accelerate resistance, negative effects of Bt cotton on the survival and development of resistant larvae could delay evolution of resistance.

Animals↗