Defining shared/distinct genetic mechanisms for respiratory infections and subsequent respiratory disease

Respiratory infections refer to a range of respiratory diseases involving the respiratory tract which are characterised by generally short periods of infection and inflammation. While many individuals only experience benign, self-limiting infections, certain individuals are at risk of significant morbidity and mortality, with many lower respiratory infections, such as pneumonia, being some of the leading causes of death due to infectious disease worldwide. Environmental factors, such as smoking, have long been known to be risk factors for developing respiratory infections. Genetic factors may also play a role, however the biological mechanisms underlying existing statistical associations remain unclear. If respiratory infections had a degree of shared aetiology with related traits, then this may be informative for the development of novel therapeutics. In this thesis, genetic variants showing association with respiratory infection disease risk and/or frequency are investigated and the genome-wide genetic correlation between respiratory infections and other pulmonary traits is quantified.A genome-wide case-control analysis of respiratory infection disease risk revealed 56 putatively associated signals at a p-value The Extended Cohort for E-health, Environment and DNA (EXCEED) study of 10,000 individuals from Leicester, Leicestershire and Rutland was used to develop a primary care-based respiratory infection disease frequency phenotype, and was established as a resource for genetic studies.A further genome-wide analysis of respiratory infection disease frequency revealed 51 putatively associated signals using the same criteria as above. One signal achieved genome-wide significance after correction for genome-wide inflation. This signal was located in SEMA3F-AS1, an RNA gene. Despite this signal being located in SEMA3F-AS1, the sentinel variant was associated with increased expression of the proximal RBM6 gene across a very large number of tissues and cell types. Socioeconomic factors were highlighted as being significantly correlated with respiratory infection frequency, which warrants further study.Finally, there was significant, but not complete, genome-wide genetic correlation between the two respiratory infection analyses, suggesting a high degree of shared aetiology between risk and frequency, though there was little overlap in the top association signals from the two studies. With lung function, there was somewhat weak, yet highly significant, genome-wide genetic correlation with respiratory infection risk and frequency, highlighting shared aetiology between respiratory infections and measures of lung function.</div

Cardiac function during resuscitation from hemorrhagic shock with polymerized bovine hemoglobin-based oxygen therapeutic

<p>Hemorrhage impairs myocardial contractile function and decreases oxygen delivery. This study investigates how polymerized bovine hemoglobin (PolyHb) solutions affect cardiac function after resuscitation from hemorrhagic shock (HS). Hamsters were hemorrhaged and resuscitated with PolyHb at 8.5 g/dL and 11.5 g/dL. Left ventricle (LV) function was assessed during shock and resuscitation using a miniaturize conductance catheter. PolyHb resuscitation had no beneficial effects in cardiac function; it increased cardiac afterload and systemic vascular resistance (SVR) of 46 and 116% for 8.5 and 11.5 g/dL, respectively. Study findings indicate that preclinical evaluation of cardiac function is essential to develop safe and efficacious alternatives to blood transfusion.</p

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh

Interactions between humans, animals, and the environment are considered critical foci for addressing antimicrobial resistance (AMR). However, One Health data on AMR in low- and middle-income countries are presently scarce. Using metagenomics, we investigated whether and how the fecal antibiotic resistomes of humans are influenced by exposure to intensive and non-intensively reared poultry within contrasting settings of urban wet markets ( n = 13) and rural households ( n = 7) in Bangladesh. We also considered poultry ( n = 10) and wastewater ( n = 10) resistomes in these settings. We found that occupational poultry exposures did not significantly alter the human fecal resistome. In contrast, macrolide-lincosamide-streptogramin and streptothricin antibiotic resistance genes (ARGs) were enriched in poultry from urban wet markets relative to rural household chickens. Wastewater had the highest ARG richness, though this was only partially explained by poultry cecal and human fecal sources. Wastewater also contained clinically significant carbapenem ARGs. This study therefore provides critical insight into the distribution of ARGs in Bangladesh. IMPORTANCE Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.</p

The effect of sub-curative antibiotic doses on mice infected with <i>S. aureus</i> NewHG.

<p>Mice were infected intravenously with a 1∶1 mixture of NewHG EryR∶TetR bacteria and were treated by replacing their drinking water with the indicated concentrations of tetracycline prior to sacrifice two days later. (A) Total CFU per mouse at experimental endpoint. (B) Total EryR/TetR strain ratio per mouse at experimental endpoint. Solid lines indicate mean (A) and median (B) values.</p

The effect of sub-curative antibiotic doses on zebrafish embryos infected with a variety of pathogens.

<p>Embryos were infected with a 1∶1 mixture of (A) <i>S. aureus</i> NewHG EryR∶TetR bacteria (treated with 2.5 µg/ml tetracycline), (B) <i>P. aeruginosa</i> PAO1-L GmR∶TetR bacteria (treated with 50 µg/ml tetracycline), (C) <i>S. aureus</i> BH1CC OxS∶OxR bacteria (treated with 32 µg/ml oxacillin) or (D) <i>S. aureus</i> SH1000 EryR∶TetR bacteria (treated with 100 µg/ml erythromycin). Terminal sensitive/resistant strain ratio per embryo is shown in each case. Solid lines indicate median values.</p

The bacterial strain distribution in mouse organs at various time-points post infection.

<p>Mice were infected with a 1∶1∶1 mixture of three marked <i>S. aureus</i> NewHG strains (n = 8–10 mice per time-point). (A) The change in total CFU load over time in each organ (BD: below limit of detection). (B) The number of organs at each time-point that show either single-strain dominance (one strain ≥100× the other two), double-strain dominance (two strains ≥100× the third), spread dominance (highest and lowest strains differ by ≥100×, with the middle strain within 100× of both) or no dominance (all strains are within 100× of one another).</p

The stochastic distribution of bacterial strains <i>post mortem</i> in zebrafish embryos.

<p>Embryos were infected with a 1∶1∶1 mixture of three antibiotic resistance-marked, but otherwise isogenic, strains. Each pie chart represents a single embryo infected with <i>S. aureus</i> (A) SH1000 variants or (B) NewHG variants. Total bacterial load in each case was approximately 10⁶ CFU.</p

The effect of a sub-curative antibiotic dose on zebrafish embryos infected with <i>S. aureus</i> SH1000.

<p>Embryos were infected with a 1∶1 mixture of SH1000 EryR∶TetR bacteria and treated with 2.5 µg/ml or 10 µg/ml tetracycline as indicated. (A) Zebrafish mortality curve (n = 60–65 per group). (B) Total terminal bacterial load per embryo. (C) Terminal EryR/TetR strain ratio per embryo. (D) Terminal EryR/TetR strain ratio per <i>pu</i>.1 morphant (phagocyte-depleted embryo). Solid lines indicate mean (B) and median (C, D) values.</p

Multi-ancestry genome-wide association study improves resolution of genes, pathways and pleiotropy for lung function and chronic obstructive pulmonary disease

Lung function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry GWAS meta-analysis of lung function to date, comprising 580,869 participants, 1020 independent association signals identified 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score (GRS) showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies (PheWAS) for selected associated variants, and trait and pathway-specific GRS to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.</p