Our data suggest that P. aeruginosa ST235 (a) has become prevalent across the globe potentially due to the selective pressure of fluoroquinolones and (b) readily became resistant to aminoglycosides, β-lactams and carbapenems through mutation and acquisition of resistance elements among local populations.

The treatment at the WWTP led to the relative enrichment of ESBLEC. We estimated that >600 billion of ESBLEC are released into the river Doubs daily and the sludge produced by the WWTP, used as fertilizer, contains 2.6 × 10(5) ESBLEC per gram.

Abstract-Traditionally, chaotic systems are built on the domain of infinite precision in mathematics. However, the quantization is inevitable for any digital devices, which causes dynamical degradation. To cope with this problem, many methods were proposed, such as perturbing chaotic states and cascading multiple chaotic systems. This paper aims at developing a novel methodology to design the higher-dimensional digital chaotic systems (HDDCS) in the domain of finite precision. The proposed system is based on the chaos generation strategy controlled by random sequences. It is proven to satisfy the Devaneys definition of chaos. Also, we calculate the Lyapunov exponents for HDDCS. The application of HDDCS in image encryption is demonstrated via FPGA platform. As each operation of HDDCS is executed in the same fixed precision, no quantization loss occurs. Therefore, it provides a perfect solution to the dynamical degradation of digital chaos.

Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.

BackgroundPseudomonas aeruginosa is a major human pathogen, which also affects animals. It is thought that P. aeruginosa has a non-clonal epidemic population structure, with distinct isolates found in humans, animals or the environment. However, very little is known about the structure of the P. aeruginosa population from diseased animals. Data on antimicrobial resistance are also scarce.ResultsThirty-four already registered and 19 new MLST profiles were identified. Interestingly, a few clones were more prevalent, and clones associated to human outbreaks were also detected. Multidrug resistance phenotypes were overall rare.ConclusionWe highlight the non clonal structure of the population and show a higher prevalence of specific clones, possibly correlating with higher pathogenicity. The low proportion of antimicrobial resistance contrasts with the high resistance rate of human isolates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12917-015-0324-x) contains supplementary material, which is available to authorized users.

In this paper, a novel formulation of discrete chaotic iterations in the field of dynamical systems is given. Their topological properties are studied: it is mathematically proved that, under some conditions, these iterations have a chaotic behavior in the meaning of Devaney. This chaotic behavior allows us to propose a way to generate new hash functions. An illustration example is detailed in order to show how to use our theoretical study in practice.

Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee ( Coffea arabica ) belongs to the Coffea genus, Robusta coffee ( Coffea canephora ) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species.

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