Bacterial evolution: Resistance is a numbers game

Plasmids are well known for spreading antibiotic-resistance genes between bacterial strains. Recent experiments show that they can also act as catalysts for evolutionary innovation, promoting rapid evolution of novel antibiotic resistance

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

For a quantitative understanding of the process of adaptation, we need to understand its “raw material,” that is, the frequency and fitness effects of beneficial mutations. At present, most empirical evidence suggests an exponential distribution of fitness effects of beneficial mutations, as predicted for Gumbel-domain distributions by extreme value theory. Here, we study the distribution of mutation effects on cefotaxime (Ctx) resistance and fitness of 48 unique beneficial mutations in the bacterial enzyme TEM-1 β-lactamase, which were obtained by screening the products of random mutagenesis for increased Ctx resistance. Our contributions are threefold. First, based on the frequency of unique mutations among more than 300 sequenced isolates and correcting for mutation bias, we conservatively estimate that the total number of first-step mutations that increase Ctx resistance in this enzyme is 87 [95% CI 75–189], or 3.4% of all 2,583 possible base-pair substitutions. Of the 48 mutations, 10 are synonymous and the majority of the 38 non-synonymous mutations occur in the pocket surrounding the catalytic site. Second, we estimate the effects of the mutations on Ctx resistance by determining survival at various Ctx concentrations, and we derive their fitness effects by modeling reproduction and survival as a branching process. Third, we find that the distribution of both measures follows a Fréchet-type distribution characterized by a broad tail of a few exceptionally fit mutants. Such distributions have fundamental evolutionary implications, including an increased predictability of evolution, and may provide a partial explanation for recent observations of striking parallel evolution of antibiotic resistance

Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories

Understanding how novel functions evolve (genetic adaptation) is a critical goal of evolutionary biology. Among asexual organisms, genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion (epistasis). Non-linear interactions pose a formidable challenge for the computational prediction of mutation effects. Here we use the recent evolution of β-lactamase under antibiotic selection as a model for genetic adaptation. We build a network of coevolving residues (possible functional interactions), in which nodes are mutant residue positions and links represent two positions found mutated together in the same sequence. Most often these pairs occur in the setting of more complex mutants. Focusing on extended-spectrum resistant sequences, we use network-theoretical tools to identify triple mutant trajectories of likely special significance for adaptation. We extrapolate evolutionary paths (n = 3) that increase resistance and that are longer than the units used to build the network (n = 2). These paths consist of a limited number of residue positions and are enriched for known triple mutant combinations that increase cefotaxime resistance. We find that the pairs of residues used to build the network frequently decrease resistance compared to their corresponding singlets. This is a surprising result, given that their coevolution suggests a selective advantage. Thus, β-lactamase adaptation is highly epistatic. Our method can identify triplets that increase resistance despite the underlying rugged fitness landscape and has the unique ability to make predictions by placing each mutant residue position in its functional context. Our approach requires only sequence information, sufficient genetic diversity, and discrete selective pressures. Thus, it can be used to analyze recent evolutionary events, where coevolution analysis methods that use phylogeny or statistical coupling are not possible. Improving our ability to assess evolutionary trajectories will help predict the evolution of clinically relevant genes and aid in protein design

Initial Mutations Direct Alternative Pathways of Protein Evolution

Whether evolution is erratic due to random historical details, or is repeatedly directed along similar paths by certain constraints, remains unclear. Epistasis (i.e. non-additive interaction between mutations that affect fitness) is a mechanism that can contribute to both scenarios. Epistasis can constrain the type and order of selected mutations, but it can also make adaptive trajectories contingent upon the first random substitution. This effect is particularly strong under sign epistasis, when the sign of the fitness effects of a mutation depends on its genetic background. In the current study, we examine how epistatic interactions between mutations determine alternative evolutionary pathways, using in vitro evolution of the antibiotic resistance enzyme TEM-1 β-lactamase. First, we describe the diversity of adaptive pathways among replicate lines during evolution for resistance to a novel antibiotic (cefotaxime). Consistent with the prediction of epistatic constraints, most lines increased resistance by acquiring three mutations in a fixed order. However, a few lines deviated from this pattern. Next, to test whether negative interactions between alternative initial substitutions drive this divergence, alleles containing initial substitutions from the deviating lines were evolved under identical conditions. Indeed, these alternative initial substitutions consistently led to lower adaptive peaks, involving more and other substitutions than those observed in the common pathway. We found that a combination of decreased enzymatic activity and lower folding cooperativity underlies negative sign epistasis in the clash between key mutations in the common and deviating lines (Gly238Ser and Arg164Ser, respectively). Our results demonstrate that epistasis contributes to contingency in protein evolution by amplifying the selective consequences of random mutations

Significados e sentidos de saúde socializados por artefatos culturais: leituras das imagens de advertência nos maços de cigarro Senses and meanings of health socialized by cultural devices: readings of the warning images on cigarettes packs

Neste artigo, analisamos imagens veiculadas nas embalagens de cigarros, que fazem parte das estratégias do Ministério da Saúde no combate ao tabagismo e disponibilizadas pelo Instituto Nacional de Câncer. Tais imagens trazem o discurso oficial de especialistas e constroem narrativas, entendidas como verdades, alicerçadas no conhecimento científico. Apoiamo-nos no referencial teórico dos estudos culturais, pois suas reflexões ajudam a compreender que as subjetividades são social e culturalmente construídas por vários discursos e artefatos. Não negamos o que está representado, mas estabelecemos diálogos com outras possibilidades de leituras que podem estar presentes nestes artefatos. Entendemos essas imagens como pedagogias culturais - que se comportam como textos a serem lidos, construindo representações, as quais podem ser assumidas como efeitos de verdade - e que atribuem ao sujeito a necessidade de controlar constantemente suas ações. Ao reforçar a biomedicina, as instituições de saúde reproduzem uma visão unidimensional e desconsideram a complexidade desse problema. Entendemos que as pedagogias culturais fazem parte de um território de lutas, onde sentidos e significados podem ser reelaborados, produzindo identidades híbridas, que constroem suas matrizes identitárias nesse emaranhado de relações de poder.<br>This article analyzes the images publicized on cigarettes packs that are part of the strategies from the Ministry of Health to combat the tabagism and available from the Cancer National Institute. These images bring the official speech of specialists and build narratives, understood such as truths, based on scientific knowledge. We have supported our thesis on theoretical referential of Cultural Studies, since its reflections help to understand that the subjectiveness is social and culturally built by different speeches and devices. We do not deny what is represented, but we establish dialogues with other possibilities of readings that can be present at these devices.We understand the propagated images as cultural pedagogies that behave as texts to be read, building up representations that can be assumed as true effect, and attributes to the citizen the necessity of constant control of its action. Reassuring the biomedicine and the health institutions, an onedimensional vision is propagated disregarding the complexity of this problem. We understand that the cultural pedagogies are part of competition territories, where the directions and meanings can be re-prepared producing hybrid identities that build up its own identity origins over this tangle of power relations