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Extended-spectrum beta-lactamases (ESBL) constitute a key antibiotic-resistance mechanism affecting Gram-negative bacteria, and also an excellent model for studying evolution in real time. A shift in the epidemiology of ESBLs is being observed, which is characterized by the explosive diversification and increase in frequency of the CTX-M-type β-lactamases in different settings. This provides a unique opportunity for studying a protein evolutionary radiation by the sequential acquisition of specific mutations enhancing protein efficiency and fitness concomitantly. The existence of driver antibiotic molecules favoring protein divergence has been investigated by combining evolutionary analyses and experimental site-specific mutagenesis. Phylogenetic reconstruction with all the CTX-M variants described so far provided a hypothetical evolutionary scenario showing at least three diversification events. CTX-M-3 was likely the enzyme at the origin of the diversification in the CTX-M-1 cluster, which was coincident with positive selection acting on several amino acid positions. Sixty-three CTX-M-3 derivatives containing all combinations of mutations under positively selected positions were constructed, and their phenotypic efficiency was evaluated. The CTX-M-3 diversification process can only be explained in a complex selective landscape with at least two antibiotics (cefotaxime and ceftazidime), indicating the need to invoke mixtures of selective drivers in order to understand the final evolutionary outcome. Under this hypothesis, we found congruent results between the in silico and in vitro analyses of evolutionary trajectories. Three pathways driving the diversification of CTX-M-3 towards the most complex and efficient variants were identified. Whereas the P167S pathway has limited possibilities of further diversification, the D240G route shows a robust diversification network. In the third route, drift may have played a role in the early stages of CTX-M-3 evolution. Antimicrobial agents should not be considered only as selectors for efficient mechanisms of resistance but also as diversifying agents of the evolutionary trajectories. Different trajectories were identified using a combination of phylogenetic reconstructions and directed mutagenesis analyses, indicating that such an approach might be useful to fulfill the desirable goal of predicting evolutionary trajectories in antimicrobial resistance., Author Summary Antimicrobial resistance in bacterial organisms is a worldwide problem widely discussed from clinical, economical and social points of view. The number of new resistance mechanisms and microorganisms resistant to new drugs is increasing all over the world. The development and spread of antibiotic resistance in bacterial communities represents an excellent model for testing the predictive potential of evolutionary principles at short time-scales. A number of studies have tried to predict the selection of resistant variants when a new drug is commercialized. However, in many cases there is no correlation between in vitro predictions and in-field observations. For this reason, it can be suspected that the ability to predict the emergence of new resistant variants might be incomplete unless we know the evolutionary forces acting on the genetic diversification processes. Using the CTX-M β-lactamases as a model, a combination of molecular phylogenetic approaches and experimental site-specific mutagenesis has allowed us to establish evolutionary trajectories. We have demonstrated that two synthetic antibiotics, cefotaxime and ceftazidime, were the selective forces driving the diversification of CTX-M enzymes, but only when both antibiotics were simultaneously present in the environment. We also predict that, if the current selective landscape is not modified, variants carrying the mutation D240G will be more prevalent and diverse in the future.

Introduction Human host immune response following infection with the new variant of A/H1N1 pandemic influenza virus (nvH1N1) is poorly understood. We utilize here systemic cytokine and antibody levels in evaluating differences in early immune response in both mild and severe patients infected with nvH1N1. Methods We profiled 29 cytokines and chemokines and evaluated the haemagglutination inhibition activity as quantitative and qualitative measurements of host immune responses in serum obtained during the first five days after symptoms onset, in two cohorts of nvH1N1 infected patients. Severe patients required hospitalization (n = 20), due to respiratory insufficiency (10 of them were admitted to the intensive care unit), while mild patients had exclusively flu-like symptoms (n = 15). A group of healthy donors was included as control (n = 15). Differences in levels of mediators between groups were assessed by using the non parametric U-Mann Whitney test. Association between variables was determined by calculating the Spearman correlation coefficient. Viral load was performed in serum by using real-time PCR targeting the neuraminidase gene. Results Increased levels of innate-immunity mediators (IP-10, MCP-1, MIP-1 beta), and the absence of anti-nvH1N1 antibodies, characterized the early response to nvH1N1 infection in both hospitalized and mild patients. High systemic levels of type-II interferon (IFN-gamma) and also of a group of mediators involved in the development of T-helper 17 (IL-8, IL-9, IL-17, IL-6) and T-helper 1 (TNF-alpha, IL-15, IL-12p70) responses were exclusively found in hospitalized patients. IL-15, IL-12p70, IL- 6 constituted a hallmark of critical illness in our study. A significant inverse association was found between IL- 6, IL- 8 and PaO2 in critical patients. Conclusions While infection with the nvH1N1 induces a typical innate response in both mild and severe patients, severe disease with respiratory involvement is characterized by early secretion of Th17 and Th1 cytokines usually associated with cell mediated immunity but also commonly linked to the pathogenesis of autoimmune/inflammatory diseases. The exact role of Th1 and Th17 mediators in the evolution of nvH1N1 mild and severe disease merits further investigation as to the detrimental or beneficial role these cytokines play in severe illness., This work has been made by an international team pertaining to the Spanish-Canadian Consortium for the Study of Influenza Immunopathogenesis. The authors would like to thank Lucia Rico and Veronica Iglesias for their assistance in the technical development of the multiplex cytokine assays, to Bego a Nogueira for her technical support, and to Nikki Kelvin for language revision of this article. This work was possible thanks to the financial support obtained from the Ministry of Science of Spain and Consejeria de Sanidad Junta de Castilla y Leon, Programa de investigacion comisionada en gripe, GR09/0021, Programa para favorecer la incorporacion de grupos de investigacion en las Instituciones del Sistema Nacional de Salud, EMER07/050, and Proyectos en Investigacion Sanitaria, PI081236. CIHR, NIH and LKSF-Canada support DJK. This sponsorship made possible reagent acquisition and sample transportation between participant groups.

Objectives To determine the effect of food on the antiviral activity of enteric-coated (EC) capsules of didanosine (ddI). Methods We conducted a pilot, randomized, open-label study of 28-day ddI-EC capsules monotherapy-administered in a fasted state (group 1, n=11) or with food (group 2, n=10) to treatment-naive chronically HIV-1-infected individuals. To assess the antiviral efficacy, HIV-1 RNA was determined at baseline, day 3, day 7 and weekly thereafter. The area under the HIV-1 RNA curve minus baseline weighted by time (AUCMB/day) was calculated. Results Mean baseline HIV-1 RNA was 4.2 log10 copies/mL in group 1 and 3.8 log10 copies/mL in group 2. After 28 days, the mean HIV-1 RNA reduction was 0.99 log10 copies/mL [95% confidence interval (CI) 0.45–1.53] for group 1 and 0.89 log10 copies/mL (95% CI 0.38–1.40) for group 2. AUCMB/day values were 0.775 log10 copies/mL (95% CI 0.33–1.22) and 0.774 log10 copies/mL (95% CI 0.48–1.07), respectively, showing no difference in the rate of decrease of HIV-1 RNA (P=0.995). Mean ddI plasma levels at day 28 were 0.0234 mg/L for group 1 and 0.0227 mg/L for group 2 (P=0.96). Conclusions In this pilot study, the administration of food did not have any significant effect on the antiviral activity of ddI-EC capsules.

This work was supported by the grants BIO2005-04278, LSHM-CT-2005-018705 and LSHM-CT-2005-518152.

The evolution of Chlamydia trachomatis is mainly driven by recombination events. This fact can be fuelled by the coincidence in several European regions of the high prevalence of non-invasive urogenital genotypes and lymphogranuloma venereum (LGV) outbreaks. This scenario could modify the local epidemiology and favor the selection of new C. trachomatis variants. Quantifying the prevalence of co-infection could help to predict the potential risk in the selection of new variants with unpredictable results in pathogenesis or transmissibility. In the 2009-2013 period, 287 clinical samples with demonstrated presence of C. trachomatis were selected. They were divided in two groups. The first group was constituted by 137 samples with C. trachomatis of the LGV genotypes, and the second by the remaining 150 samples in which the presence of LGV genotypes was previously excluded. They were analyzed to detect the simultaneous presence of non-LGV genotypes based on pmpH and ompA genes. In the first group, co-infections were detected in 10.9% of the cases whereas in the second group the prevalence was 14.6%, which is the highest percentage ever described among European countries. Moreover, bioinformatic analyses suggested the presence among men who have sex with men of a pmpH-recombinant variant, similar to strains described in Seattle in 2002. This variant was the result of genetic exchange between genotypes belonging to LGV and members of G-genotype. Sequencing of other genes, phylogenetically related to pathotype, confirmed that the putative recombinant found in Madrid could have a common origin with the strains described in Seattle. Countries with a high prevalence of co-infections and high migration flows should enhance surveillance programs in at least their vulnerable population.

The clinical use of cefaclor has been shown to enrich Haemophilus influenzae populations harboring cefaclor-hydrolyzing ROB-1 β-lactamase. Such a selective process may lead to the increased use of extended-spectrum cephalosporins or β-lactams plus β-lactamase inhibitors and, eventually, resistance to these agents, which has not previously been observed in H. influenzae . In order to establish which bla ROB-1 mutations, if any, could confer resistance to extended-spectrum cephalosporins and/or to β-lactamase inhibitors, a plasmid harboring bla ROB-1 was transformed into hypermutagenic strain Escherichia coli GB20 (Δ ampC mutS ::Tn 10 ), and this construct was used in place of H. influenzae bla ROB-1 . Strain GB20 with the cloned gene was submitted to serial passages in tubes containing broth with increasing concentrations of selected β-lactams (cefotaxime or amoxicillin-clavulanate). Different mutations in the bla ROB-1 gene were obtained during the passages in the presence of the different concentrations of the selective agents. Mutants resistant to extended-spectrum cephalosporins harbored either the Leu169→Ser169 or the Arg164→Trp164 substitution or the double amino acid change Arg164→Trp164 and Ala237→Thr237. ROB-1 mutants that were resistant to β-lactams plus β-lactamase inhibitors and that harbored the Arg244→Cys244 or the Ser130→Gly130 replacement were also obtained. The cefaclor-hydrolyzing efficiencies of the ROB-1 variants were strongly decreased in all mutants, suggesting that if bla ROB-1 mutants were selected by cefaclor, this drug would prevent the further evolution of this β-lactamase toward molecular forms able to resist extended-spectrum cephalosporins or β-lactamase inhibitors.

Acidaminococcus intestini belongs to the family Acidaminococcaceae , order Selenomonadales , class Negativicutes , phylum Firmicutes . Negativicutes show the double-membrane system of Gram-negative bacteria, although their chromosomal backbone is closely related to that of Gram-positive bacteria of the phylum Firmicutes . The complete genome of a clinical A. intestini strain is here presented.

Eighty percent (21 of 26) of macrolide-resistant Peptostreptococcus strains studied harbored the ermTR gene. This methyltransferase gene is also the most frequently found gene among macrolide-lincosamide-streptogramin B-resistant Streptococcus pyogenes strains. Transfer of the ermTR gene from Peptostreptococcus magnus to macrolide-susceptible S. pyogenes strains indicates that this resistance determinant may circulate among gram-positive aerobic and anaerobic species of the oropharyngeal bacterial flora.

The rate at which mutations are generated is central to the pace of evolution. Although this rate is remarkably similar amongst all cellular organisms, bacterial strains with mutation rates 100 fold greater than the modal rates of their species are commonly isolated from natural sources and emerge in experimental populations. Theoretical studies postulate and empirical studies teort the hypotheses that these "mutator" strains evolved in response to selection for elevated rates of generation of inherited variation that enable bacteria to adapt to novel and/or rapidly changing environments. Less clear are the conditions under which selection will favor reductions in mutation rates. Declines in rates of mutation for established populations of mutator bacteria are not anticipated if such changes are attributed to the costs of augmented rates of generation of deleterious mutations. Here we report experimental evidence of evolution towards reduced mutation rates in a clinical isolate of Escherichia coli with an hyper-mutable phenotype due a deletion in a mismatch repair gene, (ΔmutS). The emergence in a ΔmutS background of variants with mutation rates approaching those of the normal rates of strains carrying wild-type MutS was associated with increase in fitness with respect to ancestral strain. We postulate that such an increase in fitness could be attributed to the emergence of mechanisms driving a permanent "aerobic style of life", the negative consequence of this behavior being regulated by the evolution of mechanisms protecting the cell against increased endogenous oxidative radicals involved in DNA damage, and thus reducing mutation rate. Gene expression assays and full sequencing of evolved mutator and normo-mutable variants supports the hypothesis. In conclusion, we postulate that the observed reductions in mutation rate are coincidental to, rather than, the selective force responsible for this evolution.

The frequency of mutation to rifampin resistance of 200 clinical Streptococcus pneumoniae isolates was examined. Two peaks were observed in the distribution, with mode frequencies of 2.5 × 10 −7 (20% of isolates) and 2.5 × 10 −8 . The hexA and hexB gene entire sequences were analyzed in 13 isolates. Sequences from both hypermutable and “normomutable” strains were conserved relative to that of the R6 S. pneumoniae control strain. The phenotypic Hex system proficiency, in terms of transforming efficiency, was also maintained irrespective of the variations in mutation frequency values.

The modification of the anti-epileptic activity of clonazepam by other anticonvulsivants is studied. The results vary according to the drug and technique used. The usefulness of the 2 techniques employed is discussed.