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Point pattern simulation modelling of extensive and intensive chicken farming in Thailand: Accounting for clustering and landscape characteristics

Ag Systems mar19Celia Chaiban, Christophe Biscio, Weerapong Thanapongtharm, Michael Tildesley, Xiangming Xiao, Timothy P Robinson, Sophie O Vanwambeke, Marius Gilbert

The recent intensification of animal production economies to meet the growing demands of increasingly urban populations comes with significant environmental, health and social impacts. To assess these impacts, detailed maps of livestock distributions have been developed, providing estimates of the density of animals However, many epidemiological or environmental science applications would make better use of data where the distribution and size of farms are predicted rather than the number of animals per pixel. We investigated the spatial point pattern distribution of extensive and intensive chicken farms in Thailand. Our point-pattern simulation models could be particularly valuable in countries where farm location data are unavailable.

Agricultural Systems, march 2019

Fri 26 Apr 2019, 08:01

Assessing evolutionary risks of resistance for new antimicrobial therapies

Nature, Ecol & Evol mar19Brockhurst MA, Harrison F, Veening J-W, Harrison E, Blackwell G, Iqbal Zamin and Maclean C

New antibiotics are urgently needed to combat rising rates of resistance against all existing classes of antimicrobials. We highlight key issues that complicate the prediction of resistance evolution in the real world and outline the ways in which these can be overcome.

Nature, Ecology & Evolution. March 2019

Tue 23 Apr 2019, 08:26

Xavier Didelot publications

mBioA Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078

Kate E Dingle, Xavier Didelot, T Phuong Quan, David W Eyre, Nicole Stoesser, Charis A Marwick, John Coia, Derek Brown, Sarah Buchanan, Umer Z Ijaz, Cosmika Goswami, Gill Douce, Warren N Fawley, Mark H Wilcox, Timothy EA Peto, A Sarah Walker, Derrick W Crook

The increasing clinical importance of human infections caused by Clostridium difficile PCR ribotype 078 (RT078) was first reported in 2008. The severity of symptoms (mortality of ≤30%) and the higher proportion of infections among community and younger patients raised concerns. Farm animals, especially pigs, have been identified as RT078 reservoirs. We aimed to understand the recent changes in RT078 epidemiology by investigating a possible role for antimicrobial selection in its recent evolutionary history. Our work indicates that the use of antimicrobials outside the health care environment has selected for resistant organisms, and in the case of RT078, has contributed to the emergence of a human pathogen. mBio. March 2019


Microbial Genomics mar19Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains

Lucy van Dorp, Qi Wang, Liam P. Shaw, Mislav Acman, Ola B. Brynildsrud, Vegard Eldholm, Ruobing Wang, Hua Gao, Yuyao Yin, Hongbin Chen, Chuling Ding, Rhys A. Farrer, Xavier Didelot, Francois Balloux, Hui Wang

Carbapenem-resistant Klebsiella pneumoniae (CRKP) increasingly cause high-mortality outbreaks in hospital settings globally. Following a patient fatality at a hospital in Beijing due to a bla KPC-2-positive CRKP infection, close monitoring was put in place over the course of 14 months to characterize all bla KPC-2-positive CRKP in circulation in the hospital. Our findings highlight the epidemiological value of whole genome sequencing for investigating multi-drug-resistant hospital infections and illustrate that standard typing schemes cannot capture the extraordinarily fast genome evolution of CRKP isolates. Microbial Genomics. March 2019

Mon 15 Apr 2019, 08:22

A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria

Env International mar19Dae-Wi Kim, Cung Nawl Thawng, Kihyun Lee, Elizabeth M.H.Wellington, Chang-Jun Cha

Sulfonamide-degrading bacteria have been discovered in various environments, suggesting the presence of novel resistance mechanisms via drug inactivation. In this study, Microbacterium sp. CJ77 capable of utilizing various sulfonamides as a sole carbon source was isolated from a composting facility. Our results suggest that the sulfonamide metabolism may have evolved in sulfonamide-resistant bacteria which had already acquired the class 1 integron under sulfonamide selection pressures. This is the first study to report that sulX responsible for both sulfonamide degradation and resistance is prevalent in sulfonamide-degrading acti-nobacteria and its genetic signatures indicate horizontal gene transfer of the novel resistance gene.

Environment International. March 2019

Fri 12 Apr 2019, 08:25 | Tags: Environmental Bioscience

The RNA helicase 1 UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci

eLife logoAnand K. Singh, Subhendu Roy Choudhury, Sandip De, Jie Zhang, Stephen Kissane, Vibha Dwivedi, Preethi Ramanathan, Marija Petric, Luisa Orsini , Daniel Hebenstreit  and Saverio Brogna

UPF1 is an RNA helicase that is required for efficient nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3'UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm by a mechanism that requires its RNA helicase activity. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNAs, and cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and mRNA export from the nucleus.

eLife. March 2019

Wed 10 Apr 2019, 08:01

Kevin Purdy publications

Water Research mar19COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters

Zeynep Cetecioglu, Jan Dolfing, JessicaTaylor, Kevin J Purdy, Özge Eyice

Anaerobic digestion of organic matter is the major route of biomethane production. However, in the presence of sulfate, sulfate-reducing bacteria (SRB) typically outcompete methanogens, which may reduce or even preclude methane production from sulfate-containing wastewaters. Our data showed that sulfate removal and methane generation occurred in varying efficiencies and the carbon source had limited effect on the methane yield. Importantly, the results demonstrated that methanogenic and SRB diversities were only affected by the carbon source and not by the COD/SO42− ratio. Water Research. March 2019


 AJUR mar19Sex Bias in Tuberculosis in the Developing World

Sophie Shaw & Kevin J Purdy

Tuberculosis (TB) kills nearly twice as many men as women. One third of the world’s population is estimated to be infected TB, with Low and Middle Income Countries (LMIC) bearing the greatest disease burden. In LMIC sex bias in TB is influenced by sociocultural, behavioural as well as biological factors, with dynamic interactions between reporting variables, other confounding variables and physiological mechanisms, which each influence one another to produce the male-biased sex ratio observed in TB transmission, prevalence and mortality. It is the biological aspects of sex bias in TB that present specific challenges for diagnosis and treatment in men and women as they potentially influence future immunological-based interventions to treat TB.

American Journal of Undergraduate Research. March 2019

Mon 08 Apr 2019, 08:38

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