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Kirk, T.

Publications and source records attributed to Kirk, T..

3 recordsLinked to original sources
bioRxiv2024

BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis

Bacterial single-cell RNA sequencing has the potential to elucidate within-population heterogeneity of prokaryotes, as well as their interaction with host systems. Despite conceptual similarities, the statistical properties of bacterial single-cell datasets are highly dependent on the protocol, making proper processing essential to tap their full potential. We present BacSC, a fully data-driven computational pipeline that processes bacterial single-cell data without requiring manual intervention. BacSC performs data-adaptive quality control and variance stabilization, selects suitable parameters for dimension reduction, neighborhood embedding, and clustering, and provides false discovery rate control in differential gene expression testing. We validated BacSC on a broad selection of bacterial single-cell datasets spanning multiple protocols and species. Here, BacSC detected subpopulations in Klebsiella pneumoniae, found matching structures of Pseudomonas aeruginosa under regular and low-iron conditions, and better represented subpopulation dynamics of Bacillus subtilis. BacSC thus simplifies statistical processing of bacterial single-cell data and reduces the danger of incorrect processing.

bioinformatics↗
bioRxiv2024

Molecular characterisation of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022-23 UK upsurge

At the end of 2022 into early 2023 the UK Health Security Agency reported unusually high levels of scarlet fever and invasive disease caused by Streptococcus pyogenes (StrepA or group A Streptococcus). During this time, we collected and genome sequenced 341 non-invasive throat and skin S. pyogenes isolates identified during routine clinical diagnostic testing in Sheffield, a large UK city. We compared the data with that obtained from a similar collection of 165 isolates from 2016-17. Numbers of throat-associated isolates collected peaked in early December 2022, reflecting the national scarlet fever upsurge, while skin infections peaked later in December. The most common emm-types in 2022-23 were emm1 (28.7%), emm12 (24.9%), and emm22 (7.7%) in throat; and emm1 (22%), emm12 (10%), emm76 (18%), and emm49 (7%) in skin. Whilst all emm1 isolates were the M1UK lineage, comparison with 2016-17 revealed diverse lineages in other emm-types, including emm12, and emergent lineages within other types including a new acapsular emm75 lineage, demonstrating that the upsurge was not completely driven by a single genotype. Analysis of the capsule locus predicted only 51% of throat isolates would produce capsule compared to 78% of skin isolates. 90% of throat isolates were also predicted to have high NADase and Streptolysin O (SLO) expression, based on the promoter sequence, compared to only 56% of skin isolates. Our study has highlighted the value in analysis of non-invasive isolates to characterise tissue tropisms, as well as changing strain diversity and emerging genomic features which may have implications for spillover into invasive disease and future S. pyogenes upsurges. Data summaryAll new genome sequence data is available on the NCBI short read archive under the bioproject PRJNA1062601 and individual accession numbers are listed in Supplementary Table 1 and Table 2. Impact statementThe human bacterial pathogen Streptococcus pyogenes, also known as group A Streptococcus or StrepA, caused a dramatic and sudden upsurge in scarlet fever in the UK at the end of 2022 into early 2023. We present molecular characterisation of this upsurge, through genome sequence analysis of throat, skin and other types of non-severe infection isolates collected by the microbiology diagnostic lab at the Northern General Hospital in Sheffield, England. We found that, whilst two strain types were the predominant cause of infections during the upsurge, other types had emerged or changed when compared to a similar collection from 2016-17. We also identified differences between throat-associated isolates and skin-associated isolates and highlighted important bacterial factors that might influence infection types. Isolates from non-severe throat/skin types of infections are rarely saved and therefore our knowledge of them is limited. However, here we demonstrate that study of such isolates may be key to understanding upsurges of more severe infections.

microbiology↗
bioRxiv2022

Unified surface and volumetric projection of physiological imaging data

Projection of volumetric data onto the cortical surface is an important precursor to performing surface-based analysis. Numerous projection methods have been reported in the literature, many of which make assumptions which tie them to use with specific modalities, notably blood oxygenation level dependent (BOLD) imaging. This means that they may not be appropriate for use with modalities where subcortical tissue contributes a signal of interest. This work details a new projection that provides a number of generalisations and extensions to existing methods. Namely, it may be used to project arbitrary data without making modality-specific assumptions and can produce unified surface and volumetric representations of data (a concept also known as grayordinates space). When constrained to the same assumptions as existing methods, a comparison using simulation data shows that it produces similar outputs. When these assumptions are relaxed to project simulation data containing both cortical and subcortical signals to and from a unified surface and volume space, substantial and statistically significant differences in recovery of ground truth are observed compared to existing methods.

neuroscience↗