Biology subjects

Harris, S.

Publications and source records attributed to Harris, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Discovery of shared epigenetic pathways across human phenotypes

Omics-based association studies typically consider the marginal effects of a feature, such as CpG DNA methylation, on a trait (e.g, independent models for each feature). Although some methods can assess all features together in joint and conditional estimation, this is currently done on a trait-by-trait basis. Here, we introduce MAJA, a method to learn shared and outcome-specific effects for multiple traits in multi-omics data. MAJA determines the unique contribution of individual loci, genes, or molecular pathways, to variation in one or more traits, conditional on all other measured "omics" data genome-wide. Simulations show MAJA accurately finds shared and distinct associations between omics-data and multiple traits and estimates omics-specific (co)variances, allowing for sparsity and correlations within the data. Applying MAJA to 12 outcome traits in Generation Scotland methylation data (n=18,264), we find novel shared epigenetic pathways among cholesterol metabolism, osteoarthritis, blood pressure and asthma. In contrast to marginal testing, we find only 10 CpG probes with significant effects above the genome-wide background. This highlights the need for joint association testing in highly correlated methylation data from whole blood and for studies of increased sample size in order to refine epigenomic associations in observational data.

genetics↗

bioRxiv2024

Interferon Regulatory Factor 6 Determines Intestinal Epithelial Cell Development and Immunity

Intestinal epithelial cell (IEC) responses to interferon (IFN) favor antiviral defense with minimal cytotoxicity, but IEC-specific factors that regulate these responses remain poorly understood. Interferon regulatory factors (IRFs) are a family of nine related transcription factors, and IRF6 is preferentially expressed by epithelial cells, but its roles in IEC immunity are unknown. In this study, CRISPR screens found that Irf6 deficiency enhanced IFN-stimulated antiviral responses in transformed mouse IECs but not macrophages. Furthermore, KO of Irf6 in IEC organoids resulted in profound changes to homeostasis and immunity gene expression. Irf6 KO organoids grew more slowly, and single-cell RNA sequencing indicated reduced expression of genes in epithelial differentiation and immunity pathways. IFN-stimulated gene expression was also significantly different in Irf6 KO organoids, with increased expression of stress and apoptosis-associated genes. Functionally, the transcriptional changes in Irf6 KO organoids were associated with increased cytotoxicity upon IFN treatment or inflammasome activation. These data indicate a previously unappreciated role for IRF6 in IEC biology, including regulation of epithelial development and moderation of innate immune responses to minimize cytotoxicity and maintain barrier function.

immunology↗

bioRxiv2023

Efficient Multiplexing of Pollinator Metabarcodes Using Oxford Nanopore MinION Sequencing: Insights for Meadow Management from Floral Environmental DNA

Many pollinating species are experiencing declines globally, making effective, fast, and portable pollinator monitoring methods more important than ever before. Pollinators can leave DNA on the flowers they visit, and metabarcoding of these environmental DNA (eDNA) traces provides an opportunity to detect the presence of flower visitors. This study introduces an efficient, cost-effective workflow for utilizing DNA barcoding to monitor biodiversity through environmental DNA (eDNA) left on flowers from pollinators, employing the portable MinION and Nanopore sequencing. The developed method employs multiplexing with dual molecular tags on universal cytochrome oxidase 1 (COI) barcode primers. We used this approach to compare the arthropod diversity present in three meadows with different vegetation at three time points during the flowering season. The utility of eDNA metabarcoding in investigating pollinator biodiversity and interactions is highlighted through our results, revealing the presence and interactions of 65 species from 30 families. We multiplexed individual eDNA samples from hundreds of flowers and found plant-pollinator dynamics that showed differences in species richness between sampling times and meadow diversity. Comparative analyses with conventional methods showed eDNA metabarcodings ability to identify diverse species and ecological interactions compared to field sampling. While some DNA likely came from eggs or microscopic insects difficult to remove from flowers, traces of eDNA from various arthropods on multiple plant species confirmed the methods applicability, promising robust ecological monitoring and research potential in the wake of global pollinator declines. This is the first reported use of MinION based nanopore sequencing to detect arthropod species from eDNA samples collected from flowers using the described affordable multiplexing method.

ecology↗

bioRxiv2021

Association between plasma phospho-tau181 and cognitive change from age 73 to 82: Lothian Birth Cohort 1936

INTRODUCTIONPlasma phospho-tau 181 (p-tau181) is a promising blood biomarker for Alzheimers disease. However, its predictive validity for age-related cognitive decline without dementia remains unclear. Several forms of p-tau have been shown to contribute to synapse degeneration, but it is unknown whether p-tau181 is present in synapses. Here, we tested whether plasma p-tau181predicts cognitive decline and whether it is present in synapses in human brain. METHODSGeneral cognitive ability and plasma p-tau181 concentration were measured in 195 participants at ages 72 and 82. Levels of p-tau181 in total homogenate and synaptic fractions were compared with western blot (n=10-12 per group), and synaptic localisation was examined using array tomography. RESULTSElevated baseline plasma p-tau181 and increasing p-tau181 over time predicted steeper general cognitive decline. We observe p-tau181 in neurites, presynapses, and post-synapses in the brain. DISCUSSIONBaseline and subsequent change in plasma p-tau181 may represent rare biomarkers of differences in cognitive ageing across the 8th decade of life and may play a role in synaptic function in the brain.

neuroscience↗

bioRxiv2021

Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference

AO_SCPLOWBSTRACTC_SCPLOWIn the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate {lambda} for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to [Formula] as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate (where < {lambda}), we also establish a similar result for birth-death trees, except that t/2 is replaced by t/2 {middle dot} (1 - /{lambda}). This complete tree may contain subtrees that have died out before time t; for the reduced tree that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.

evolutionary biology↗

bioRxiv2021

The relationship between mucosal microbiota, colitis and systemic inflammation in Chronic Granulomatous Disorder

BackgroundChronic granulomatous disorder (CGD) is a primary immunodeficiency which is frequently complicated by an inflammatory colitis and is associated with systemic inflammation. ObjectiveTo investigate the role of the microbiome in the pathogenesis of colitis and systemic inflammation. MethodsWe performed 16S rDNA sequencing on mucosal biopsy samples from each segment of 10 CGD patients colons, and conducted compositional and functional pathway prediction analyses. ResultsThe microbiota in samples from colitis patients demonstrated reduced taxonomic alpha diversity compared to unaffected patients, even in apparently normal bowel segments. Functional pathway richness was similar between the colitic and non-colitic mucosa, although metabolic pathways involved in butyrate biosynthesis or utilisation were enriched in patients with colitis and correlated positively with faecal calprotectin levels. One patient with very severe colitis was dominated by Enterococcus spp., while among other patients Bacteroides spp. abundance correlated with colitis severity measured by faecal calprotectin and an endoscopic severity score. In contrast, Blautia abundance associated with low severity scores and mucosal health. Several taxa and functional pathways correlated with concentrations of inflammatory cytokines in blood but not with colitis severity. Notably, dividing patients into High and Low systemic inflammation groups demonstrated clearer separation than on the basis of colitis status in beta diversity analyses. ConclusionThe microbiome is abnormal in CGD-associated colitis and altered functional characteristics probably contribute to pathogenesis. Furthermore, the relationship between the mucosal microbiome and systemic inflammation, independent of colitis status, implies that the microbiome in CGD can influence the inflammatory phenotype of the condition. Key MessagesThe colonic mucosal microbiome and bacterial metabolic pathways in patients with CGD colitis differ from patients without colitis, even in macroscopically normal bowel segments. The mucosal microbiome and bacterial metabolic pathways in patients with CGD also differ according to the extent of systemic inflammation, independently from the presence of colitis, suggesting a role for the gut microbiota in the inflammatory phenotype of this condition. Capsule summaryThe pathogenesis of chronic granulomatous disorder (CGD)-associated colitis and other inflammatory complications is unclear. We demonstrate potentially treatable alterations in the mucosa-associated microbiome in CGD colitis and microbial differences which associate with systemic inflammation independently of colitis status.

immunology↗

bioRxiv2021

Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies

BackgroundComplex carbohydrates that escape digestion in the small intestine, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between particular microbes and the host, resulting in metabolic products that influence host gut health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes is not fully understood. Here we take the approach of combining data from long and short read sequencing allowing recovery of large numbers of high quality genomes, from which we can predict carbohydrate degrading functions, and impact of carbohydrate on microbial communities. ResultsIn this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. We found dynamic variations in the microbiome amongst carbohydrate treatments, and over time. Using these data, the MAGs were characterised as primary (0h to 6h) and secondary degraders (12h to 24h). Annotating the MAGs with the Carbohydrate Active Enzyme (CAZyme) database we are able to identify species which are enriched through time and have the potential to actively degrade carbohydrate substrates. ConclusionsRecent advances in sequencing technology allowed us to identify significant unexplored diversity amongst starch degrading species in the human gut microbiota including CAZyme profiles and complete MAGs. We have identified changes in microbial community composition in response to structurally distinct carbohydrate substrates, which can be directly related to the CAZyme complement of the enriched MAGs. Through this approach, we have identified a number of species which have not previously been implicated in starch degradation, but which have the potential to play an important role.

microbiology↗

bioRxiv2021

Novel insights in the pathophysiology of α-synuclein dysregulation on D2 receptor activity contributing to the vulnerability of dopamine neurons

Pathophysiological damages and loss of function of dopamine neurons precedes their demise and contributes to the early phases of Parkinsons disease. The presence of aberrant intercellular pathological inclusions of the protein -synuclein within ventral midbrain dopaminergic neurons is one of the cardinal features of Parkinsons disease. We employed multiple complementary approaches in molecular biology, electrophysiology, and live-cell imaging to investigate how excessive -synuclein levels alters multiple characteristics of dopaminergic neuronal dynamics and dopamine transmission prior to neuronal demise. These studies demonstrate that -synuclein dysregulation of D2 receptor autoinhibition contributes to the vulnerability of dopaminergic neurons, and that modulation thereof can ameliorate the resulting pathophysiology. These novel findings provide mechanistic insights in the insidious loss of dopaminergic function and neurons that characterize Parkinsons disease progression with significant therapeutic implications.

neuroscience↗

bioRxiv2020

Phage Commander, a software tool for rapid annotation of bacteriophage genomes using multiple programs

The number of sequenced phage genomes is growing at an exponential rate. The majority of newly sequenced phage genomes are annotated by one or more of several freely-available auto-annotation programs. No program has been shown to consistently outperform the others; thus the choice of which program to use is not obvious. We present the software Phage Commander for rapid annotation of phage genomes using multiple auto-annotation programs. Phage Commander runs a phage genome sequence through nine auto-annotation programs and integrates the results within a single output. Phage Commander generates properly formatted output files for direct export to NCBI GenBank. Users can select the threshold for determining which genes should be exported. Phage Commander was benchmarked using eight high-quality phage genomes whose genes have been identified through experiments. Results show that the best results are obtained by exporting genes identified by at least two or three of the nine auto-annotation programs.

bioinformatics↗

bioRxiv2020

Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity

Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered monomorphic, with little gene content variation between strains. Nevertheless, several genotypic and phenotypic factors separate the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum), from each other. However, genome variability and gene content especially of L5 and L6 strains have not been fully explored and may be potentially important for pathobiology and current approaches for genomic analysis of MTBC isolates, including transmission studies. We compared the genomes of 358 L5 clinical isolates (including 3 completed genomes and 355 Illumina WGS (whole genome sequenced) isolates) to the L5 complete genomes and H37Rv, and identified multiple genes differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found across L5 strains, including a split in the L5.3 sublineage into L5.3.1 and L5.3.2. These gene content differences had a small knock on effect on transmission cluster estimation, with clustering rates influenced by the selection of reference genome, and with potential over-estimation of recent transmission when using H37Rv as the reference genome. Our data show that the use of H37Rv as reference genome results in missing SNPs in genes unique for L5 strains. This potentially leads to an underestimation of the diversity present in the genome of L5 strains and in turn affects the transmission clustering rates. As such, a full capture of the gene diversity, especially for high resolution outbreak analysis, requires a variation of the single H37Rv-centric reference genome mapping approach currently used in most WGS data analysis pipelines. Moreover, the high within-lineage gene content variability suggests that the pan-genome of M. tuberculosis is at least several kilobases larger than previously thought, implying a concatenated or reference-free genome assembly (de novo) approach may be needed for particular questions. Data summarySequence data for the Illumina dataset are available at European Genome-phenome Archive (EGA; https://www.ebi.ac.uk/ega/) under the study accession numbers PRJEB38317 and PRJEB38656. Individual runs accession numbers are indicated in Table S8. PacBio raw reads for the L5 Benin genome are available on the ENA accession SAME3170744. The assembled L5 Benin genome is available on NCBI with accession PRJNA641267. To ensure naming conventions of the genes in the three L5 genomes can be followed, we have uploaded these annotated GFF files to figshare at https://doi.org/10.6084/m9.figshare.12911849.v1. Custom python scripts used in this analysis can be found at https://github.com/conmeehan/pathophy.

genetics↗

bioRxiv2020

Multi-proxy evidence for the impact of the Storegga Slide Tsunami on the early Holocene landscapes of the southern North Sea

Doggerland was a land mass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British land mass from the rest of Europe. The Storegga Slide, which triggered a tsunami reflected in sediment deposits in the Northern North Sea, North East coastlines of the British Isles and across the North Atlantic, was a major event during this transgressive phase. The spatial extent of the Storegga tsunami however remains unconfirmed because to date no direct evidence for the event has been recovered from the southern North Sea. We present evidence that Storegga associated deposits occur in the southern North Sea. Palaeo-river systems have been identified using seismic survey in the southwestern North Sea and sedimentary cores extracted to track the Mid Holocene inundation. At the head of one palaeo-river system near the Outer Dowsing Deep, the Southern River, we observed an abrupt and catastrophic inundation stratum. Based on lithostratigraphic, macro and microfossils and sedimentary ancient DNA (sedaDNA) evidence, supported by optical stimulation luminescence (OSL) and radiocarbon dating, we conclude these deposits were a result of the Storegga event. Seismic identification of this stratum to adjacent cores indicated diminished traces of the tsunami, largely removed by subsequent erosional processes. Our results demonstrate the catastrophic impact of Storegga within this area of the Southern North Sea, but indicate that these effects were temporary and likely localized and mitigated by the dense woodland and topography of the area. We conclude clear physical remnants of the wave are likely to be restricted to inland basins and incised river valley systems.

paleontology↗

bioRxiv2019

Genomes from Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy was revisited through a manual process using a combination of average nucleotide identity (ANI), concatenated marker gene phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then compared to the automated taxonomic assignment given by the recently proposed Genome Taxonomy Database (GTDB). We found the results of all three methods to be similar (25 out of the 33 had matching genera), but the GTDB approach was less subjective, and required far less labor. The primary differences in the remaining taxonomic assignments related to proposed taxonomy changes by the GTDB team.

bioinformatics↗

bioRxiv2018

The relative influence of niche versus neutral processes on Ediacaran communities

A fundamental question in community ecology is the relative influence of niche versus neutral processes in determining ecosystem dynamics. The extent to which these processes structured early animal communities is yet to be explored. Here we use spatial point process analyses (SPPA) to determine the influence of niche versus neutral processes on early total-group metazoan paleocommunities from the Ediacaran Period [~]565 million years in age. Preservation of these sessile organisms in large in-situ populations on exposed bedding planes enables inference of the most likely underlying processes governing their spatial distributions by SPPA. We conducted comprehensive spatial mapping of six of the largest Ediacaran paleocommunities in Newfoundland, Canada and Charnwood Forest, UK using LiDAR, photogrammetry and a laser-line probe. For each paleocommunity we determined the best-fit spatial model for each univariate and bivariate species distribution, comparing four sets of spatial models (complete spatial randomness, dispersal, habitat, and combined dispersal with habitat) using goodness-of-fit tests. Random and dispersal models are considered neutral processes while habitat and combined models are considered niche processes. We find the dynamics of these paleocommunities to be dominated by neutral processes, with limited influence from niche processes. Our findings are consistent with community model predictions of when neutral dynamics dominate, but are in stark contrast to the niche-dominated communities of the modern marine realm. Thus, while the underlying processes determining metazoan community assembly appear to have been in place since the appearance of the first macroscopic, complex animals, the dynamics of these early metazoan communities were fundamentally different to those of extant communities.\n\nSignificance statementThe extent to which habitat and dispersal processes structure the earliest animal communities found during the Ediacaran Period [~]565 million years ago, is unknown. In this study we analyse six of the largest and most diverse fossil assemblages from Newfoundland, Canada and Charnwood Forest, UK, using spatial point processes analyses to determine the relative influence of habitat processes (niche) and dispersal processes (neutral) on the spatial distribution of taxa. The vast majority of Ediacaran taxon distributions were controlled by neutral processes, in striking contrast to niche-dominated modern marine ecosystems, but consistent with model predictions of when neutral dynamics dominate communities. Thus the underlying processes determining metazoan community assembly have been in place since the appearance of the first macroscopic, complex animals.

ecology↗

bioRxiv2018

Neurovascular coupling preserved in a chronic mouse model of Alzheimers disease: Methodology is critical.

Neurovascular coupling is the process by which neural activity causes localised changes in cerebral blood flow. Impaired neurovascular coupling has been suggested as an early pathogenic factor in Alzheimers disease (AD), and if so, could serve as an early biomarker of cerebral pathology. We have established an anaesthetic regime in which evoked hemodynamic responses are comparable to those in awake mice. This protocol was adapted to allow repeated measurements of neurovascular function over three months in the hAPP-J20 mouse model of AD (J20-AD) and wild-type (WT) controls. Animals were 9-12 months old at the start of the experiment, which is when deficits due to the disease condition would be expected. Mice were chronically prepared with a cranial window through which optical imaging spectroscopy (OIS) was used to generate functional maps of the cerebral blood volume and saturation changes evoked by whisker stimulation and vascular reactivity challenges. Unexpectedly, the hemodynamic responses were largely preserved in the J20-AD group. This result failed to confirm previous investigations using the J20-AD model. However, a final acute electrophysiology and OIS experiment was performed to measure both neural and hemodynamic responses concurrently. In this experiment, previously reported deficits in neurovascular coupling in the J20-AD model were observed. This suggests that J20-AD mice may be more susceptible to the physiologically stressing conditions of an acute experimental procedure compared to WT animals. These results therefore highlight the importance of experimental procedure when determining the characteristics of animal models of human disease.\n\nSignificance StatementUsing a chronic anaesthetised preparation, we measured hemodynamic responses evoked by sensory stimulation and respiratory gases in the J20-AD mouse model of Alzheimers Disease over a period of 3 months. We showed that neurovascular responses were preserved compared to age matched wildtype controls. These results failed to confirm previous investigations reporting a marked reduction of neurovascular coupling in the J20-AD mouse model. However, when our procedure involved acute surgical procedures, previously reported neurovascular deficits were observed. The effects of acute electrode implantation were caused by disturbances to baseline physiology rather than a consequence of the disease condition. These results highlight the importance of experimental procedure when determining the characteristics of animal models of human disease.

neuroscience↗

bioRxiv2018

Clinical data specification and coding for cross-analyses with omics data in autoimmune disease trials

ObjectivesAutoimmune and inflammatory diseases (AIDs) form a continuum of autoimmune and inflammatory diseases, yet AIDs nosology is based on syndromic classification. The TRANSIMMUNOM trial (NCT02466217) was designed to re-evaluate AIDs nosology through clinic-biological and multi-omics investigations of patients with one of 19 selected AIDs. To allow cross-analyses of clinic-biological data together with omics data, we needed to integrate clinical data in a harmonized database.\n\nMaterials and MethodsWe assembled a clinical expert consortium (CEC) to select relevant clinic-biological features to be collected for all patients and a cohort management team comprising biologists, clinicians and computer scientists to design an electronic case report form (eCRF). The eCRF design and implementation has been done on OpenClinica, an open-source CFR-part 11 compliant electronic data capture system.\n\nResultsThe CEC selected 865 clinical and biological parameters. The CMT selected coded the items using CDISC standards into 5835 coded values organized in 28 structured eCRFs. Examples of such coding are check boxes for clinical investigation, numerical values with units, disease scores as a result of an automated calculations, and coding of possible treatment formulas, doses and dosage regimens per disease.\n\nDiscussion21 CRFs were designed using OpenClinica v3.14 capturing the 5835 coded values per patients. Technical adjustment have been implemented to allow data entry and extraction of this amount of data, rarely achieved in classical eCRFs designs.\n\nConclusionsA multidisciplinary endeavour offers complete and harmonized CRFs for AID clinical investigations that are used in TRANSIMMUNOM and will benefit translational research team.

clinical trials↗

bioRxiv2018

Genomics of Cryptococcus neoformans

C. neoformans var. grubii (C. neoformans) is an environmentally acquired pathogen causing 181 000 HIV-associated deaths each year. We used whole genome sequencing (WGS) to characterise 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. We found that 91% of our clinical isolates belonged to one of three highly clonal sub-clades of VNIa, which we have termed VNIa-4, VNIa-5 and VNIa-93. Parsimony analysis revealed frequent, long distance transmissions of C. neoformans; international transmissions took place on 13% of VNIa-4 branches, and intercontinental transmissions on 7% of VNIa-93 branches. The median length of within sub-clade internal branches was 3-6 SNPs, while terminal branches were 44.5-77.5 SNPs. The short median internal branches were partly driven by the large number (12-15% of internal branches) of polytomies in the within-sub-clade trees. To simultaneously explain our observation of no apparent molecular clock, short internal branches and frequent polytomies we hypothesise that C. neoformans VNIa spends much of its time in the environment in a quiescent state, while, when it is sampled, it has almost always undergone an extended period of growth. Infections with VNIa-93 were associated with a significantly reduced risk of death by 10 weeks compared with infections with VNIa-4 (Hazard Ratio = 0.45, p = 0.003). We detected a recombination in the mitochondrial sequence of VNIa-5, suggesting that mitochondria could be involved in the propensity of this sub-clade to infect HIV-uninfected patients. These data highlight the insight into the biology and epidemiology of pathogenic fungi which can be gained from WGS data.

microbiology↗

bioRxiv2018

Oxford Nanopore MinION genome sequencer: performance characteristics, optimised analysis workflow, phylogenetic analysis and prediction of antimicrobial resistance in Neisseria gonorrhoeae

Antimicrobial resistant (AMR) Neisseria gonorrhoeae strains are common and compromise gonorrhoea treatment internationally. Rapid identification and characterisation of AMR gonococcal strains could ensure appropriate and even personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of the emergence and dissemination of AMR determinants that predict AMR in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that can generate bacterial genomes within one day. However, the accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench, we show that ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended therapeutic antimicrobials. We also show that the ONT-derived sequences can be useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.

genomics↗

bioRxiv2018

Linked mutations at adjacent nucleotides have shaped human population differentiation and protein evolution

Despite the fundamental importance of single nucleotide polymorphisms (SNPs) to human evolution there are still large gaps in our understanding of the forces that shape their distribution across the genome. SNPs have been shown to not be distributed evenly, with directly adjacent SNPs found unusually frequently. Why this is the case is unclear. We illustrate how neighbouring SNPs that cant be explained by a single mutation event (that we term here sequential dinucleotide mutations, SDMs) are driven by distinct mutational processes and selective pressures to SNPs and multinucleotide polymorphisms (MNPs). By studying variation across multiple populations, including a novel cohort of 1,358 Scottish genomes, we show that, SDMs are over twice as common as MNPs and like SNPs, display distinct mutational spectra across populations. These biases are though not only different to those observed among SNPs and MNPs, but also more divergent between human population groups. We show that the changes that make up SDMs are not independent, and identify a distinct mutational profile, CA [->] CG [->] TG, that is observed an order of magnitude more often than other SDMs, including others that involve the gain and subsequent deamination of CpG sites. This suggests these specific changes are driven by a distinct process. In coding regions particular SDMs are favoured, and especially those that lead to the creation of single codon amino acids. Intriguingly selection has favoured particular pathways through the amino acid code, with epistatic selection appearing to have disfavoured sequential non-synonymous changes.

genomics↗