Search

The study of common heritability, or co-heritability, among multiple traits has been widely established in quantitative and molecular genetics. However, in bacteria, genome-based estimation of heritability has only been considered very recently and no methods are currently available for considering co-heritability. Here we introduce such a method and demonstrate its usefulness by multi-trait analyses of the three major human pathogens \textit{Escherichia coli}, \textit{Neisseria gonorrhoeae} and \textit{Streprococcus pneumoniae}. We anticipate that the increased availability of high-throughput genomic and phenotypic screens of bacterial populations will spawn ample future opportunities to understand the common molecular basis of different traits in bacteria.

Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the “modern hospital” era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen., Enterococcus faecalis is a commensal microorganism of animals, insects and humans, but also a nosocomial pathogen. Here, the authors analyse genomic sequences from E. faecalis isolates from animals and humans, and find that the last common ancestors of multiple hospital-associated lineages date to the pre-antibiotic era.

Additional file 1: Figure 1. Venn diagrams showing the number of differentially expressedgenes in different treatment comparisons. Figure 2. Physiological measurements of the birds included in the study. Table 1. The number of up- and down-regulated genes when comparing expression between the groups. Table 2. Details on the 14 named genes showing a switching pattern. Table 3. Details on the six genes showing a switching pattern with chronically changed expression. Table 4. Details on the 45 named genes showing a chronically changed expression pattern.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic has placed enormous strain on intensive care units (ICUs) in Europe. Ensuring access to care, irrespective of COVID-19 status, in winter 2020-2021 is essential. METHODS: An integrated model of hospital capacity planning and epidemiological projections of COVID-19 patients is used to estimate the demand for and resultant spare capacity of ICU beds, staff and ventilators under different epidemic scenarios in France, Germany and Italy across the 2020-2021 winter period. The effect of implementing lockdowns triggered by different numbers of COVID-19 patients in ICUs under varying levels of effectiveness is examined, using a 'dual-demand' (COVID-19 and non-COVID-19) patient model. RESULTS: Without sufficient mitigation, we estimate that COVID-19 ICU patient numbers will exceed those seen in the first peak, resulting in substantial capacity deficits, with beds being consistently found to be the most constrained resource. Reactive lockdowns could lead to large improvements in ICU capacity during the winter season, with pressure being most effectively alleviated when lockdown is triggered early and sustained under a higher level of suppression. The success of such interventions also depends on baseline bed numbers and average non-COVID-19 patient occupancy. CONCLUSION: Reductions in capacity deficits under different scenarios must be weighed against the feasibility and drawbacks of further lockdowns. Careful, continuous decision-making by national policymakers will be required across the winter period 2020-2021.

Malaria burden is heavily concentrated in sub-Saharan Africa (SSA) where cases and deaths associated with COVID-19 are rising. In response, countries are implementing societal measures aimed at curtailing transmission. Despite this, the COVID-19 epidemic could still result in millions of deaths as local health facilities become overwhelmed. Advances in malaria control this century have been largely due to distribution of long-lasting insecticidal nets (LLINs), with many SSA countries planning campaigns for 2020. Here we use COVID-19 and malaria transmission models to estimate the impact of disruption of malaria prevention activities and other core health services under different COVID-19 epidemic scenarios. If activities are halted, the malaria burden in 2020 could be more than double that of 2019. Mitigating this negative impact is possible, and LLIN distributions in particular should be prioritised alongside access to antimalarial treatment to prevent substantial malaria epidemics.

Additional file 1 Additional file 1 includes all supplementary tables and figures.

Additional file 2 Review history.

Meningitis is an infection of the meninges, a layer of tissue surrounding the brain. In cases of pneumococcal meningitis (where the bacterium Streptococcus pneumoniae is the causat- ive agent) this causes severe inflammation, requiring intensive care and rapid antibiotic treatment. The contribution of variation in host and pathogen genetics to pneumococcal meningitis is unknown. In this thesis I develop and apply statistical genetics techniques to identify genomic variation associated with the various stages of pneumococcal meningitis, including colonisation, invasion and severity. I start by describing the development of a method to perform genome-wide association studies (GWAS) in bacteria, which can find variation in bacterial genomes associated with bacterial traits such as antibiotic resistance and virulence. I then applied this method to longitudinal samples from asymptomatic carriage, and found lineages and specific variants associated with altered duration of carriage. To assess meningitis versus carriage samples I applied similar analysis techniques, and found that the bacterial genome is crucial in determining invasive potential. As well as bacterial serotype, which I found to be the main effect, I discovered many independent sequence variants associated with disease. Separately, I analysed within host-diversity during the invasive phase of disease and found it to be of less relevance to disease progression. Finally, I analysed host genotype data from four independent studies using GWAS and heritability estimates to determine the contribution of human sequence variation to pneumococcal meningitis. Host sequence accounted for some variation in susceptibility to and severity of meningitis. The work concludes with a combined analysis of pairs of bacterial and human sequences from meningitis cases, and finds variation correlated between the two., This work was funded by Wellcome and Medical Research Council studentship grant (1365620)

This is an edited version of the GWAS section of my thesis' introduction. I have also included some concluding thoughts.

One of the most striking things about many animals is that they can be defined by the ways in which they move. Moving costs metabolic energy and is a significant contributor to the daily energy balance of organisms and therefore fitness. Balancing energy needs is critically important to species inhabiting areas of limited resources. The metabolic cost of locomotion is influenced by physiological, morphological and behavioural factors that vary across species. The influence of these factors within species is less well understood. The objective of my PhD is to elucidate the potential for variation in locomotor performance, in particular the energy consumed and the biomechanics of locomotion within a species, in response to differences in season, sex, age and the nature of the terrain. The Svalbard ptarmigan (Lagopus muta hyperborea) is the only year-round avian resident of the Arctic archipelago of Svalbard. Svalbard is characterized by extreme photoperiodic and climatic conditions, with 24 hours of daylight in summer and continuous darkness in winter, when ice makes food unpredictable. As a result, ptarmigan annually gain significant fat stores, as much as doubling their body mass in winter. The consequences of such large gains in mass upon the metabolic cost and biomechanics of terrestrial locomotion are yet to be quantified. The Svalbard ptarmigan represents a unique opportunity to gain insight into avian adaptations.Using respirometry, I present evidence that winter birds are able to carry their fat stores at no metabolic cost. Using kinematic and force plate data, I show that acquiring fat results in reduced locomotor performance in terms of speed and take-off ability. As well as exhibiting phenotypic variation, male and female Svalbard ptarmigan are behaviourally very different. I present evidence that these behavioural differences are reflected in the metabolic cost of locomotion. In particular, males are both more efficient and faster than female birds during both summer and winter. I suggest that this results from sexual selection upon male locomotor performance. Furthermore, I present data demonstrating that sub-adult males experiencing their first winter possess the same metabolic and speed capabilities of adults. These data may indicate that selection for improved male locomotor performance may act upon sub-adult birds. Regardless of season, age or sex, Svalbard ptarmigan must locomote on a predominantly sloping terrain. The influence of inclines upon the metabolic cost of locomotion in birds is poorly understood. I provide evidence that at the same degree of incline, the cost of lifting 1 kg by 1 vertical metre is similar regardless of season and is therefore dictated by increased positive work. However, this cost varies according to the degree of incline and may be influenced by gait.The principal findings of the 5 first author papers presented are that behavioural, physiological and morphological variation within a species can have significant impacts upon the metabolic cost of locomotion and other aspects of locomotor performance. The potential for intraspecific differences should therefore be taken into account in future research regarding the patterns of energy expenditure in animals.

The illusion of distinct sound sources distributed throughout the three-dimensional space containing the listener is possible using only conventional stereo playback equipment by processing monaural sound signals prior to playback on two spaced-apart transducers. A plurality of such processed signals corresponding to different sound source positions may be mixed using conventional techniques without disturbing the positions of the individual images. Although two loudspeakers are required the sound produced is not conventional stereo, however, each channel of a left/right stereo signal can be separately processed according to the invention and then combined for playback. The sound processing involves dividing each monaural or single channel signal into two signals and then adjusting the differential phase and amplitude of the two channel signals on a frequency dependent basis in accordance with an empirically derived transfer function that has a specific phase and amplitude adjustment for each predetermined frequency interval over the audio spectrum. Each transfer function is empirically derived to relate to a different sound source location and by providing a number of different transfer functions and selecting them accordingly the sound source can be made to appear to move.

The application of silvicultural systems in the B-19 Foothills, region of Alberta was examined in the light of current problems in management, silviculture, and utilisation. Following a regional description, in which a classification of site is developed, certain silvicultural systems were examined and recommended for the dominant stand types which occur on three major site groups, viz:- 1. Dry Upland 2. Moist Transition 3. Wet Consideration was given in each case to clearcutting, shelterwood and selection systems. Recommendations were based on the information presented in the preceding chapters and that available in those references cited in the bibliography. It has been pointed out in conclusion that there are three main phases in the development of control of the silviculture and management of the region. These are:- 1. The preparation of management plans for sustained yield. 2. The selection of silvicultural systems to, bring silvicultural control into the framework of sustained yield management. 3. The development and application of cultural treatments through research to improve local conditions and to help solve particular regeneration problems. The importance of the hypothesis presented in Chapter III is finally re-stressed with reference to the above mentioned development phases. That is - That there are already available to the practising forest management planner, silvicultural systems which are applicable, with or without further adaptation, to the forest stands of the region and to the sites described. Certain fields of research have been suggested throughout the text and these were summarised in a final recommendation.

Funder: the Joint Programming Initiative in Antimicrobial Resistance (JPIAMR2016-AC16/00039), Funder: FCT/MCTES Individual Call to Scientific Employment Stimulus (CEECIND/02268/2017), the Applied Molecular Biosciences Unit - UCIBIO which is financed by national funds from FCT (UIDP/04378/2020 e UIDB/04378/2020), Funder: Trond Mohn Foundation (Grant TMS2019TMT04), Funder: Trond Mohn Foundation (Grant TMS2019TMT04), ERC (Grant 742158), Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the “modern hospital” era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.

The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in Streptococcus pneumoniae. We analyze microbiological, genomic, and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is little evidence of HGT playing a major role in determining resistance frequencies. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages., Science Advances, 6 (21), ISSN:2375-2548

Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.

Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.

Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines.

n/a

Being able to identify the genetic variants responsible for specific bacterial phenotypes has been the goal of bacterial genetics since its inception and is fundamental to our current level of understanding of bacteria. This identification has been based primarily on painstaking experimentation, but the availability of large data sets of whole genomes with associated phenotype metadata promises to revolutionize this approach, not least for important clinical phenotypes that are not amenable to laboratory analysis. These models of phenotype-genotype association can in the future be used for rapid prediction of clinically important phenotypes such as antibiotic resistance and virulence by rapid-turnaround or point-of-care tests. However, despite much effort being put into adapting genome-wide association study (GWAS) approaches to cope with bacterium-specific problems, such as strong population structure and horizontal gene exchange, current approaches are not yet optimal. We describe a method that advances methodology for both association and generation of portable prediction models., Discovery of genetic variants underlying bacterial phenotypes and the prediction of phenotypes such as antibiotic resistance are fundamental tasks in bacterial genomics. Genome-wide association study (GWAS) methods have been applied to study these relations, but the plastic nature of bacterial genomes and the clonal structure of bacterial populations creates challenges. We introduce an alignment-free method which finds sets of loci associated with bacterial phenotypes, quantifies the total effect of genetics on the phenotype, and allows accurate phenotype prediction, all within a single computationally scalable joint modeling framework. Genetic variants covering the entire pangenome are compactly represented by extended DNA sequence words known as unitigs, and model fitting is achieved using elastic net penalization, an extension of standard multiple regression. Using an extensive set of state-of-the-art bacterial population genomic data sets, we demonstrate that our approach performs accurate phenotype prediction, comparable to popular machine learning methods, while retaining both interpretability and computational efficiency. Compared to those of previous approaches, which test each genotype-phenotype association separately for each variant and apply a significance threshold, the variants selected by our joint modeling approach overlap substantially.

Streptococcus pneumoniae is a common nasopharyngeal colonizer, but can also cause life-threatening invasive diseases such as empyema, bacteremia and meningitis. Genetic variation of host and pathogen is known to play a role in invasive pneumococcal disease, though to what extent is unknown. In a genome-wide association study of human and pathogen we show that human variation explains almost half of variation in susceptibility to pneumococcal meningitis and one-third of variation in severity, identifying variants in CCDC33 associated with susceptibility. Pneumococcal genetic variation explains a large amount of invasive potential (70%), but has no effect on severity. Serotype alone is insufficient to explain invasiveness, suggesting other pneumococcal factors are involved in progression to invasive disease. We identify pneumococcal genes involved in invasiveness including pspC and zmpD, and perform a human-bacteria interaction analysis. These genes are potential candidates for the development of more broadly-acting pneumococcal vaccines., Streptococcus pneumoniae is a causative agent of meningitis and bacteremia. In a combined pathogen and host GWAS, Lees et al. find that host genetic variation is associated with both susceptibility and severity of pneumococcal meningitis, and specific bacterial genetic variation associated with susceptibility.

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined 'true tree' using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

Streptococcus pneumoniaeis a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, and the duration of carriage is an important consideration in modelling transmission dynamics and vaccine response. Existing studies of carriage duration variability are based at the serotype level only, and do not probe variation within lineages or fully quantify interactions with other environmental factors.Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data. By combining these results with whole genome sequence data we estimate that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas host traits accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). For the locus effects, a genome-wide association study identified 16 loci which may have an effect on carriage duration independent of serotype. Hits at a genome-wide level of significance were to prophage sequences, suggesting infection by such viruses substantially affects carriage duration.These results show that both serotype and non-serotype specific effects alter carriage duration in infants and young children and are more important than other environmental factors such as host genetics. This has implications for models of pneumococcal competition and antibiotic resistance, and leads the way for the analysis of heritability of complex bacterial traits.Significance statementOther than serotype, the genetic determinants of pneumococcal carriage duration are unknown. In this study we used longitudinal sampling to measure the duration of carriage in infants, and searched for any associated variation in the pan-genome. While we found that the pathogen genome explains most of the variability in duration, serotype did not fully account for this. Recent theoretical work has proposed the existence of alleles which alter carriage duration to explain the puzzle of continued coexistence of antibiotic-resistant and sensitive strains. Here we have shown that these alleles do exist in a natural population, and also identified candidates for the loci which fulfil this role. Together these findings have implications for future modelling of pneumococcal epidemiology and resistance.

This thesis is about the White House staff. Primarily it covers the period from the 1930's to the 1970's: from being first established to being well embedded in the American political system. Although the main body of research and writing relates to the White House staff of six Presidents - Roosevelt, Truman, Eisenhower, Kennedy, Johnson and Nixon - additional reference where appropriate or where the opportunity arose is made to their successors: Ford, Carter and Reagan.\ud The argument of this thesis can be very simply stated. The White House staff are a very large and influential part of the modern Presidency. They now occupy a pre-eminent position in the presidential decision-making process. An understanding of the White House staff is now absolutely essential to an understanding of the framework of advice that culminates in any presidential decision. The prime characteristics of the staff are unique proximity to the President and virtually complete accountability to him alone. These contribute to a mutual confidence between President and staff that sustains the basis of staff influence. Over five decades they have far outgrown and transformed their original purposes both in size and power irrespective of the differences, and emerging similarities, in the ways Presidents have organized them. This progress was virtually uninterrupted and was not properly monitored. Experience has shown and evidence does confirm that the White House staff long inhabited a constitutional vacuum where the normal operation of the system of checks and balances effectively ceased to apply. Despite dramatic revelations of manifest abuses of power the position has been improved only partially. Although the permanent need for a staff has been recognised and they are now firmly entrenched in the structure of the Presidency of the United States the potential for abuse remains.

Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population structure in haploid genomes, has previously only been available as a MATLAB binary. We provide an R implementation which is both easier to install and use, automating the entire pipeline. Additionally, we allow for the use of multiple processors, improve on the default settings of the algorithm, and provide an interface with the ggtree library to enable informative illustration of the clustering results. Our aim is that this package aids in the understanding and dissemination of the method, as well as enhancing the reproducibility of population structure analyses.