Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants.

Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance to ensure early detection of novel resistance variants, but efficient strategies to do so remain undefined. We evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting antibiotic resistance and diagnostic escape variants in Neisseria gonorrhoeae, a pathogen associated with a high burden of disease and antibiotic resistance and the development of genotype-based diagnostics. We show that patient characteristic-informed sampling is not a reliable strategy for efficient variant detection. In contrast, sampling informed by pathogen characteristics, such as genomic diversity and genomic background, is significantly more efficient than random sampling in identifying genetic variants associated with resistance and diagnostic escape

Moss species on the move in East Antarctic terrestrial communities

Antarctica has experienced major changes in temperature, wind speed and stratospheric ozone levels over the last 50 years. Whilst West Antarctica and the peninsula showed rapid warming and associated ecosystem change, East Antarctica appeared to be little impacted by climate warming, thus biological changes were predicted to be relatively slow. Detecting the biological effects of Antarctic climate change has also been hindered by the paucity of long-term data sets, particularly for organisms that have been exposed to these changes throughout their lives. We monitored vegetation communities in the Windmill Islands, East Antarctica from 2000 to 2014 and found significant changes in moss species composition. In addition, we have shown that radiocarbon signals preserved along shoots of the dominant Antarctic moss flora can be used to determine accurate growth rates over a period of several decades, allowing us to explore the influence of environmental variables on growth. Carbon stable isotopic measurements suggest that the observed effects of climate variation on growth are mediated through changes in water availability and most likely linked to the more positive phase of the Southern Annular Mode and changing westerly wind patterns. For cold remote locations like Antarctica, where climate records are limited and of relatively short duration, this illustrates that mosses can act as microclimate proxies and have the potential to increase our knowledge of coastal Antarctic climate change

Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales

Antibiotic resistance is a significant global public health concern. Uropathogenic Escherichia coli sequence type (ST)131, a widely prevalent multidrug-resistant clone, is frequently associated with bacteraemia. This study investigates third-generation cephalosporin resistance in bloodstream infections caused by E. coli ST131. From 2013-2014 blood culture surveillance in Wales, 142 E. coli ST131 genomes were studied alongside global data. All three major ST131 clades were represented across Wales, with clade C/H30 predominant (n = 102/142, 71.8%). Consistent with global findings, Welsh strains of clade C/H30 contain β-lactamase genes from the blaCTX-M-1 group (n = 65/102, 63.7%), which confer resistance to third-generation cephalosporins. Most Welsh clade C/H30 genomes belonged to sub-clade C2/H30Rx (58.3%). A Wales-specific sub-lineage, named GB-WLS.C2, diverged around 1996-2000. An introduction to North Wales around 2002 led to a localised cluster by 2009, depicting limited genomic diversity within North Wales. This investigation emphasises the value of genomic epidemiology, allowing the detection of genetically similar strains in local areas, enabling targeted and timely public health interventions

It is hot in the sun: Antarctic mosses have high temperature optima for photosynthesis despite cold climate

The terrestrial flora of Antarctica’s frozen continent is restricted to sparse ice-free areas and dominated by lichens and bryophytes. These plants frequently battle sub-zero temperatures, extreme winds and reduced water availability; all influencing their ability to survive and grow. Antarctic mosses, however, can have canopy temperatures well above air temperature. At midday, canopy temperatures can exceed 15°C, depending on moss turf water content. In this study, the optimum temperature of photosynthesis was determined for six Antarctic moss species: Bryum pseudotriquetrum, Ceratodon purpureus, Chorisodontium aciphyllum, Polytrichastrum alpinum, Sanionia uncinata, and Schistidium antarctici collected from King George Island (maritime Antarctica) and/or the Windmill Islands, East Antarctica. Both chlorophyll fluorescence and gas exchange showed maximum values of electron transport rate occurred at canopy temperatures higher than 20°C. The optimum temperature for both net assimilation of CO2 and photoprotective heat dissipation of three East Antarctic species was 20–30°C and at temperatures below 10°C, mesophyll conductance did not significantly differ from 0. Maximum mitochondrial respiration rates occurred at temperatures higher than 35°C and were lower by around 80% at 5°C. Despite the extreme cold conditions that Antarctic mosses face over winter, the photosynthetic apparatus appears optimised to warm temperatures. Our estimation of the total carbon balance suggests that survival in this cold environment may rely on a capacity to maximize photosynthesis for brief periods during summer and minimize respiratory carbon losses in cold conditions

Bayesian methods for comparing species physiological and ecological response curves

Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species' responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. We developed a model that used Bayesian penalised splines to produce and compare response curves for any two given species. These splines allow the data to determine the shape of the response curves rather than making a priori assumptions. The models were implemented using the R2OpenBUGS package for R, which uses Markov Chain Monte Carlo simulation to repetitively fit alternative response curves to the data. As each iteration produces a different curve that varies in optima, niche breadth and limits, the model estimates the uncertainty in each of these attributes and the probability that the two curves are different. The models were tested using two datasets of mosses from Antarctica. Both datasets had a high degree of scatter, which is typical of ecological research. This noise resulted in considerable uncertainty in the optima and limits of species response curves, but substantive differences were found. Schistidium antarctici was found to inhabit wetter habitats than Ceratodon purpureus, and Polytrichastrum alpinum had a lower optimal temperature for photosynthesis than Chorisodontium aciphyllum under high light conditions. Our study highlights the importance of considering uncertainty in physiological optima and other attributes of species response curves. We found that apparent differences in optima of 7.5 degrees C were not necessarily substantive when dealing with noisy ecological data, and it is necessary to consider the uncertainty in attributes when comparing the curves for different species. The model introduced here could increase the robustness of research on niche partitioning, species coexistence and niche conservatism. (C) 2016 Elsevier B.V. All rights reserved

Acta technica napocensis / Series applied mathematics and mechanics

Many ecological questions require information on species\u27 optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species\u27 responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. We developed a model that used Bayesian penalised splines to produce and compare response curves for any two given species. These splines allow the data to determine the shape of the response curves rather than making a priori assumptions. The models were implemented using the R2OpenBUGS package for R, which uses Markov Chain Monte Carlo simulation to repetitively fit alternative response curves to the data. As each iteration produces a different curve that varies in optima, niche breadth and limits, the model estimates the uncertainty in each of these attributes and the probability that the two curves are different. The models were tested using two datasets of mosses from Antarctica. Both datasets had a high degree of scatter, which is typical of ecological research. This noise resulted in considerable uncertainty in the optima and limits of species response curves, but substantive differences were found. Schistidium antarcticiwas found to inhabit wetter habitats than Ceratodon purpureus, and Polytrichastrum alpinum had a lower optimal temperature for photosynthesis than Chorisodontium aciphyllum under high light conditions. Our study highlights the importance of considering uncertainty in physiological optima and other attributes of species response curves. We found that apparent differences in optima of 7.5 °C were not necessarily substantive when dealing with noisy ecological data, and it is necessary to consider the uncertainty in attributes when comparing the curves for different species. The model introduced here could increase the robustness of research on niche partitioning, species coexistence and niche conservatism

Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution of Escherichia coli ST131

A partir du XIe s. la simplification des décors et l’appauvrissement des formes, à côté d’une production de luxe imitant les modèles d’Iran et destinée à une petite élite, permettent de supposer que la « crise de l’argent » mise en évidence par les numismates a eu un impact significatif sur la masse des consommateurs

Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution of Escherichia coli ST131

Escherichia coli ST131 is the most frequently isolated fluoroquinolone-resistant (FQR) E. coli clone worldwide and a major cause of urinary tract and bloodstream infections. Although originally identified through its association with the CTXM- 15 extended-spectrum β-lactamase resistance gene, global genomic epidemiology studies have failed to resolve the geographical and temporal origin of the ST131 ancestor. Here, we developed a framework for the reanalysis of publically available genomes from different countries and used this data set to reconstruct the evolutionary steps that led to the emergence of FQR ST131. Using Bayesian estimation, we show that point mutations in chromosomal genes that confer FQR coincide with the first clinical use of fluoroquinolone in 1986 and illustrate the impact of this pivotal event on the rapid population expansion of ST131 worldwide from an apparent origin in North America. Furthermore, we identify virulence factor acquisition events that predate the development of FQR, suggesting that the gain of virulence-associated genes followed by the tandem development of antibiotic resistance primed the successful global dissemination of ST131. IMPORTANCE Escherichia coli sequence type 131 (ST131) is a recently emerged and globally disseminated multidrug-resistant clone frequently associated with human urinary tract and bloodstream infections. In this study, we have used two large publically available genomic data sets to define a number of critical steps in the evolution of this important pathogen. We show that resistance to fluoroquinolones, a class of broad-spectrum antibiotic used extensively in human medicine and veterinary practice, developed in ST131 soon after the introduction of these antibiotics in the United States, most likely in North America. We also mapped the acquisition of several fitness and virulence determinants by ST131 and demonstrate these events occurred prior to the development of fluoroquinolone resistance. Thus, ST131 has emerged by stealth, first acquiring genes associated with an increased capacity to cause human infection, and then gaining a resistance armory that has driven its massive population expansion across the globe