Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011

Farm animals are a potential reservoir for human Clostridium difficile infection (CDI), particularly PCR ribotype 078 which is frequently found in animals and humans. Here, whole genome single-nucleotide polymorphism (SNP) analysis was used to study the evolutionary relatedness of C. difficile 078 isolated from humans and animals on Dutch pig farms. All sequenced genomes were surveyed for potential antimicrobial resistance determinants and linked to an antimicrobial resistance phenotype. We sequenced the whole genome of 65 C. difficile 078 isolates collected between 2002 and 2011 from pigs (n = 19), asymptomatic farmers (n = 15) and hospitalised patients (n = 31) in the Netherlands. The collection included 12 pairs of human and pig isolates from 2011 collected at 12 different pig farms. A mutation rate of 1.1 SNPs per genome per year was determined for C. difficile 078. Importantly, we demonstrate that farmers and pigs were colonised with identical (no SNP differences) and nearly identical (less than two SNP differences) C. difficile clones. Identical tetracycline and streptomycin resistance determinants were present in human and animal C. difficile 078 isolates. Our observation that farmers and pigs share identical C. difficile strains suggests transmission between these populations, although we cannot exclude the possibility of transmission from a common environmental source

DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain

Eukaryotic replisomes are multiprotein complexes. Here the authors reveal two distinct stressed replisomes, associated with DONSON and FANCM, displaying a bias in replication timing and chromatin domain

Defining endemic cholera at three levels of spatiotemporal resolution within Bangladesh.

Although much focus is placed on cholera epidemics, the greatest burden occurs in settings in which cholera is endemic, including areas of South Asia, Africa and now Haiti1,2. Dhaka, Bangladesh is a megacity that is hyper-endemic for cholera, and experiences two regular seasonal outbreaks of cholera each year3. Despite this, a detailed understanding of the diversity of Vibrio cholerae strains circulating in this setting, and their relationships to annual outbreaks, has not yet been obtained. Here we performed whole-genome sequencing of V. cholerae across several levels of focus and scale, at the maximum possible resolution. We analyzed bacterial isolates to define cholera dynamics at multiple levels, ranging from infection within individuals, to disease dynamics at the household level, to regional and intercontinental cholera transmission. Our analyses provide a genomic framework for understanding cholera diversity and transmission in an endemic setting

Mapping of variations in child stunting, wasting and underweight within the states of India: the Global Burden of Disease Study 2000–2017

Background To inform actions at the district level under the National Nutrition Mission (NNM), we assessed the prevalence trends of child growth failure (CGF) indicators for all districts in India and inequality between districts within the states. Methods We assessed the trends of CGF indicators (stunting, wasting and underweight) from 2000 to 2017 across the districts of India, aggregated from 5 × 5 km grid estimates, using all accessible data from various surveys with subnational geographical information. The states were categorised into three groups using their Socio-demographic Index (SDI) levels calculated as part of the Global Burden of Disease Study based on per capita income, mean education and fertility rate in women younger than 25 years. Inequality between districts within the states was assessed using coefficient of variation (CV). We projected the prevalence of CGF indicators for the districts up to 2030 based on the trends from 2000 to 2017 to compare with the NNM 2022 targets for stunting and underweight, and the WHO/UNICEF 2030 targets for stunting and wasting. We assessed Pearson correlation coefficient between two major national surveys for district-level estimates of CGF indicators in the states. Findings The prevalence of stunting ranged 3.8-fold from 16.4% (95% UI 15.2–17.8) to 62.8% (95% UI 61.5–64.0) among the 723 districts of India in 2017, wasting ranged 5.4-fold from 5.5% (95% UI 5.1–6.1) to 30.0% (95% UI 28.2–31.8), and underweight ranged 4.6-fold from 11.0% (95% UI 10.5–11.9) to 51.0% (95% UI 49.9–52.1). 36.1% of the districts in India had stunting prevalence 40% or more, with 67.0% districts in the low SDI states group and only 1.1% districts in the high SDI states with this level of stunting. The prevalence of stunting declined significantly from 2010 to 2017 in 98.5% of the districts with a maximum decline of 41.2% (95% UI 40.3–42.5), wasting in 61.3% with a maximum decline of 44.0% (95% UI 42.3–46.7), and underweight in 95.0% with a maximum decline of 53.9% (95% UI 52.8–55.4). The CV varied 7.4-fold for stunting, 12.2-fold for wasting, and 8.6-fold for underweight between the states in 2017; the CV increased for stunting in 28 out of 31 states, for wasting in 16 states, and for underweight in 20 states from 2000 to 2017. In order to reach the NNM 2022 targets for stunting and underweight individually, 82.6% and 98.5% of the districts in India would need a rate of improvement higher than they had up to 2017, respectively. To achieve the WHO/UNICEF 2030 target for wasting, all districts in India would need a rate of improvement higher than they had up to 2017. The correlation between the two national surveys for district-level estimates was poor, with Pearson correlation coefficient of 0.7 only in Odisha and four small north-eastern states out of the 27 states covered by these surveys. Interpretation CGF indicators have improved in India, but there are substantial variations between the districts in their magnitude and rate of decline, and the inequality between districts has increased in a large proportion of the states. The poor correlation between the national surveys for CGF estimates highlights the need to standardise collection of anthropometric data in India. The district-level trends in this report provide a useful reference for targeting the efforts under NNM to reduce CGF across India and meet the Indian and global targets. Keywords Child growth failureDistrict-levelGeospatial mappingInequalityNational Nutrition MissionPrevalenceStuntingTime trendsUnder-fiveUndernutritionUnderweightWastingWHO/UNICEF target

Nations within a nation: variations in epidemiological transition across the states of India, 1990–2016 in the Global Burden of Disease Study

18% of the world's population lives in India, and many states of India have populations similar to those of large countries. Action to effectively improve population health in India requires availability of reliable and comprehensive state-level estimates of disease burden and risk factors over time. Such comprehensive estimates have not been available so far for all major diseases and risk factors. Thus, we aimed to estimate the disease burden and risk factors in every state of India as part of the Global Burden of Disease (GBD) Study 2016

Fabrication of free-standing casein Devices with micro- and nanostructured regular and bioimprinted surface features

This work introduces a novel process for the fabrication of free-standing biodegradable casein devices with micro- and nanoscale regular and biomimetic surface features. Fabrication of intermediate polydimethylsiloxane (PDMS) moulds from photoresist masters and liquid-casting of casein is used to transfer arbitrary geometrical shapes onto the surface of casein devices. Casein film composition was optimized for mechanical stability and pattern resolution. It was found that 15% casein in 0.2% NaOH solution, mixed with 10% glycerol, and cross-linked by addition of 2% glutaraldehyde produced the best pattern transfer results. Biomimetic cell-like shapes were transferred onto casein by use of bioimprinting of two-dimensional cell-cultures into PDMS. To demonstrate this process, C2C12 mouse myoblasts were cultured on microscope slides, replicated into PDMS and casein using liquid casting and drying. Recessed alignment grids were integrated into the microscope glass slides to facilitate direct comparison of original cells and their bioimprints on PDMS and casein. Optical microscopy and atomic force microscopy confirmed the transfer of micron-scale morphological features, such as cell outlines, nuclei and larger lamellipodia, into the casein surface. Nanoscale feature resolution in casein was found to be limited compared to the PDMS intermediate moulds, which was attributed to limited wetting of the aqueous casein solution. Strategies to increase resolution of the casein transfer step, as well as degradation behavior of the fabricated devices in cell culture media are currently underway. Substrates fabricated with this process have applications in stem cell engineering, regenerative medicine, and implantable device

Micro- and Nanopatterning of Freestanding Protein Films

Biodegradable casein films have significant potential for use as non-supported stand-alone sheeting in orthopaedic implants and tissue engineering substrates. Multi-scale surface patterns can be used to modulate and guide cell interaction by means of an engineered construct. The majority of work on cell-pattern interaction has so far focused on non-degradable materials. In this paper we demonstrate for the first time the fabrication of micro- and nano-scale geometric patterns on the surface of a crosslinked biodegradable casein film. To achieve this we introduce a two-step fabrication procedure based on polydimethylsiloxane (PDMS) soft-lithography. We will show the reproduction of micro- and nano-scale patterns in liquid-cast casein films. We also demonstrate film formation and cross-linking using glutaraldehyde and discuss the use of these films as cell-culture substrates

Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011

Farm animals are a potential reservoir for human Clostridium difficile infection (CDI), particularly PCR ribotype 078 which is frequently found in animals and humans. Here, whole genome single-nucleotide polymorphism (SNP) analysis was used to study the evolutionary relatedness of C. difficile 078 isolated from humans and animals on Dutch pig farms. All sequenced genomes were surveyed for potential antimicrobial resistance determinants and linked to an antimicrobial resistance phenotype. We sequenced the whole genome of 65 C. difficile 078 isolates collected between 2002 and 2011 from pigs (n = 19), asymptomatic farmers (n = 15) and hospitalised patients (n = 31) in the Netherlands. The collection included 12 pairs of human and pig isolates from 2011 collected at 12 different pig farms. A mutation rate of 1.1 SNPs per genome per year was determined for C. difficile 078. Importantly, we demonstrate that farmers and pigs were colonised with identical (no SNP differences) and nearly identical (less than two SNP differences) C. difficile clones. Identical tetracycline and streptomycin resistance determinants were present in human and animal C. difficile 078 isolates. Our observation that farmers and pigs share identical C. difficile strains suggests transmission between these populations, although we cannot exclude the possibility of transmission from a common environmental source

Characterizations and analysis of the antioxidant, antimicrobial, and dye reduction ability of green synthesized silver nanoparticles

The current study was conducted to assess the potential of ginger rhizome extract (Zingiber officinale) for the synthesis of silver nanoparticles (AgNPs) through the green method and its mitigating activity against pathogenic bacterial strains. AgNPs were synthesized through a simple one-step approach and characterized by UV-Visible (UV-Vis) spectroscopy, powder X-ray diffraction (PXRD), transmission electronic microscopy (TEM), and energy dispersive X-rays spectroscopy (EDS). PXRD and TEM results of AgNPs showed the face central cubic structures and predominantly spherical structures with a size of 6.5 nm. EDS analysis confirms the elemental silver in nanoparticles. Moreover, the impact of the pH, as well as temperature, during the synthesis of AgNPs has also been investigated. At 25°C and pH 5, there was no significant peak for AgNPs in the absorption spectra. However, with an increase in temperature from 25°C to 85°C and pH 5 to pH 11, particles started attaining the spherical shape of different sizes due to an increase in the reduction rate. The AgNPs displayed effective results against selected pathogenic strains, Pseudomonas aeruginosa (MTCC 424), Methicillin-resistant Staphylococcus aureus (ATCC 43300), and fungus Candida albicans (KACC 30003). The prepared AgNPs exhibited excellent antioxidant activity and catalytic reduction of methyl orange with the pseudo-first-order rate constant of 3.9 × 10−3