Chasing the Genetics of Ascites in Broilers using Whole Genome Resequencing

We are using whole genome resequencing to identify chromosomal regions associated with resistance or susceptibility to ascites, a form of pulmonary hypertension syndrome, meat-type chickens. Previous Genome Wide Association Studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs) have identified regions on chromosomes 2, 9 and Z. Despite several GWAS and further genotyping, there are no reliable or potential markers for ascites phenotype. We have completed screening of Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms in ascites resistant and susceptible birds from the relaxed, REL, line derived from a commercial elite broiler line. DNA samples from resistant and susceptible birds were purified, quantified and pooled in two pools of 10 DNAs from each phenotype for both genders. Eight pools (2 pools x 2 phenotypes x 2 genders) were generated. Each pool was submitted for bar-coded library generation, and 2x125 paired end reads on Illumina HiSeq 2500 and with 66X genome coverage. The sequence reads were mapped onto Galgal5 using Bowtie for initial CNV mapping cn.mops (R package). Further mapping to chromosomes were done using NGen and ArrayStar (DNAStar ver 13). So far, we have identified two potential regions for CNVs and 31 regions for SNPs with potential association with ascites phenotype. CPQ gene on chromosome 2 and LRRTM4 gene on chromosome 22 have been validated for containing ascites QTLs. However, their exact role in ascites is yet to be discovered. Further, we screened the regions from REL line in DNAs from an unrelated commercial broiler line using WGR

Insights into the functional role of tea microbes on tea growth, quality and resistance against pests and diseases

Tea is an economical and most widely used beverage across the globe owing to its unique fragrance and flavor. Plant microbe interaction has emerged as an important topic which got the attention of scientists to improve plant performance. Tea microbes remained a prominent research topic for scientists over the years as tea microbes helps in nutrient cycling and stress management which in turn improve the tea growth, yield and quality. The roots of tea plants are colonized by various microbes including arbuscular mycorrhizal fungi (AMF), bacterial communities, and endophytes increase root growth, development and nutrient uptake which in turn improve tea growth, yield and quality. These microbes also increase the concentration of nutrients, amino acids, soluble proteins, flavonoids, catechuic acid, glucose, fructose, sucrose contents caffeine, and polyphenols concentration in tea plants. Besides this, these microbes also protect the tea plants from harmful pest and diseases which in turn leads to an appreciable improvement in plant growth and development. The most important goal of any farming system is to establish a system with production of maximum food while minimizing impacts on the environment. The present review article highlights the role of various microbes in improving the growth, yield and quality of tea plants. In addition, we also discussed the research gaps to improve our understanding about the role of tea microbes in improving tea growth, yield, pest and diseases resistance. We believe that this review will provide a better insight into the existing knowledge of tea microbes in improving tea growth and yield

Substantial and sustained reduction in under-5 mortality, diarrhea, and pneumonia in Oshikhandass, Pakistan : Evidence from two longitudinal cohort studies 15 years apart

Funding Information: Study 1 was funded through the Applied Diarrheal Disease Research Program at Harvard Institute for International Development with a grant from USAID (Project 936–5952, Cooperative Agreement # DPE-5952-A-00-5073-00), and the Aga Khan Health Service, Northern Areas and Chitral, Pakistan. Study 2 was funded by the Pakistan US S&T Cooperative Agreement between the Pakistan Higher Education Commission (HEC) (No.4–421/PAK-US/HEC/2010/955, grant to the Karakoram International University) and US National Academies of Science (Grant Number PGA-P211012 from NAS to the Fogarty International Center). The funding bodies had no role in the design of the study, data collection, analysis, interpretation, or writing of the manuscript. Publisher Copyright: © 2020 The Author(s).Peer reviewedPublisher PD

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

<i>CPQ</i> coding and 3’-UTR SNPs.

<p><i>CPQ</i> coding and 3’-UTR SNPs.</p

Scatterplot representing GBS data on chromosome 2.

<p>Difference in SNP frequencies (Y-axis) is plotted between the average non-reference SNP frequencies of the two replicate pools (resistant less susceptible) relative to chromosome 2 position (X-axis) in Mbp. Positive values indicate that non-reference SNP favors resistance, whereas negative values indicate the SNP favors susceptibility for ascites. <b>(Panel 1A):</b> Entire chromosome 2 for males. The black arrow indicates the peak associated with the <i>CPQ</i> gene locus. <b>(Panel 1B):</b> An expanded view of the peak region ((black arrow) from Panel 1A. <b>(Panel 1C):</b> The same region as Panel 1B only for females.</p

Primers, probes, and conditions for RT-qPCR.

<p>For each <i>CPQ</i> locus: position is the [chromosome]:[chromosomal position] of the 5’ base according to the <i>Gallus_gallus-5</i> assembly; Primers are 5’-3’ for forward (F) and reverse (R); Probes are 5’-3’ with allele 1 (P1) labeled with FAM and allele 2 (P2) labeled with HEX. Annealing temperatures for qPCR are indicated in °C.</p