Biology subjects

White, R. T.

Publications and source records attributed to White, R. T..

6 recordsLinked to original sources

bioRxiv2026

NEXCISION: exact, validated, and scalable excision of genomic regions from phylogenomic NEXUS matrices

Coordinate-based exclusion of genomic regions is routine in microbial phylogenomics, yet the editing step often relies on ad hoc scripts or manual alignment manipulation. This simple but high-consequence task can alter the character matrix, retain unwanted signal, or leave invalid NEXUS dimensions. This study presents NEXCISION, a dependency-free Python command-line tool for exact removal of coordinate-labelled rows from transposed NEXUS matrices. NEXCISION uses 1-based inclusive intervals, preserves retained rows and surrounding NEXUS content, updates matrix dimensions, reports interval-specific removal counts, and can generate deterministic provenance reports with SHA-256 checksums. Correctness was evaluated using three genuine SPANDx-derived matrices, an independent oracle, 17 correctness and preservation cases, 26 malformed-input challenges, 1,000 synthetic matrices containing 304,000 site rows, nine property-based invariants across 1,800 examples, and 12 deliberately faulted implementations. All expected rows were removed, retained rows and state strings were preserved, malformed inputs failed safely, and all deliberate faults were detected. In 105 measured scalability runs, NEXCISION remained correct and deterministic across 21 configurations. Runtime scaled near-linearly from [~]100 MB to 5 GB, processing a 4.83 GiB matrix in [~]24.2 seconds on one pinned logical central processing unit. Up to 100,000 intervals added modest runtime, while peak memory increased by [~]4.85 GiB per GiB of input. NEXCISION makes a fragile bespoke editing step exact, testable, and provenance-rich for microbial phylogenomics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/740842v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1035228org.highwire.dtl.DTLVardef@106c1a3org.highwire.dtl.DTLVardef@92dcddorg.highwire.dtl.DTLVardef@1e25457_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementRemoving defined genomic regions from a phylogenomic matrix seems simple, but errors can alter alignments, retain unwanted signal, or leave invalid NEXUS dimensions. NEXCISION replaces manual or bespoke editing with a focused command-line tool that removes only intended coordinate-labelled rows, preserves all other content, and records the operation. It is a trustworthy bridge between region detection and downstream phylogenetic inference for microbial genomic epidemiology, outbreak analysis, recombination masking, mobile-element studies, and workflows that excise reference-defined sites from transposed NEXUS matrices. NEXCISION was tested against genuine files, an independent oracle, 1,000 synthetic matrices, generated edge cases, and deliberately faulted implementations. It runs locally as a dependency-free, single-process Python utility. On a computer with 16 GB random-access memory (RAM), [~]2 GB matrices are practical; the largest tested matrix was 5.2 GB and required [~]25 GB RAM. NEXCISION is compact, transparent, and supported by evidence for correctness, failure safety, and scalability. Data summaryNo new biological sequence data were generated. Supporting software, validation assets, benchmarks, analysis code, figure sources, and reproducibility instructions are available from: NEXCISION software repository: https://github.com/RhysWhite/nexcision NEXCISION benchmarking repository: https://github.com/RhysWhite/nexcision-benchmarking The evaluated software was NEXCISION v0.1.0 (MIT licence; Python >=3.10). The benchmarking repository includes the wheel checksum, deterministic data generator, manifests, independent oracle, compact results, summaries, and analysis scripts. The 1,000 synthetic matrices are reproducible from the version-controlled generator and manifest; the regenerated corpus has deterministic tree digest 9ed25d7e2dd4fee380f2f0f32ddcf653694715926905bd54179e7003e64f1c28. Three SPANDx-derived matrices were used only to confirm compatibility with real matrix syntax; no biological inference was made. Their metadata and checksums are recorded in the benchmarking repository. All data, code, and protocols needed to reproduce the deterministic and performance results are provided in the article, supplementary material, or linked repositories. Software versions, computational environments, deterministic controls, and immutable provenance identifiers are summarized in Table S6.

bioinformatics↗

bioRxiv2025

Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing

The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem resistance. We here evaluate the use of long-read nanopore sequencing to investigate carbapenem resistance dynamics and the role of plasmid transfers and environmental reservoirs in the hospital setting. Over 13 months, routine clinical diagnostics identified recurring isolates of carbapenem-resistant Citrobacter species carrying Klebsiella pneumoniae carbapenemases (KPC) and/or OXA-48-like carbapenemases from patient screening and hospital drain samples. While routine diagnostic approaches provided limited insights into the carbapenem resistance dynamics, we show that near-complete de novo assembly of chromosomes and plasmids by long-read nanopore sequencing allowed for high-resolution strain identification, plasmid profiling, and antibiotic resistance gene detection. Notably, genomically nearly indistinguishable Citrobacter freundii of the high-risk sequence type ST91 genomes were recovered from screening samples collected in the same hospital room one year apart. We further provide evidence of a KPC-2 encoding IncN plasmid that is likely to have spread across bacterial species and between patient and drain isolates, which emphasizes the role of contaminated drains in the persistence and dissemination of resistances within the hospital environment. Overall, this study demonstrates the value of long-read nanopore sequencing for uncovering the complex dynamics of carbapenem resistance spread and persistence in the hospital setting, and its potential implications for Infection Prevention and Control. Impact statementThis study demonstrates how long-read nanopore sequencing can resolve the complex dynamics of plasmid-mediated antimicrobial resistance in clinical and environmental samples within the hospital setting. By linking patient- and drain-derived isolates through near-complete de novo assemblies, we reveal hidden reservoirs and dynamics behind the persistence of cabapenem resistance over extended time periods. This work shows how long-read sequencing approaches can uncover resistance dynamics that are missed using standard diagnostic methods, with implications for infection control and surveillance. Data SummaryThe study sequences are available at the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA1297122. The raw sequence read data is available at NCBI sequence read archive (SRA (https://www.ncbi.nlm.nih.gov/sra)) under accession numbers SRR34727947-59. The chromosomal assemblies of all ST91 strains are available at NCBI GenBank under the Biosample accession numbers SAMN50449475-80. All other supporting data are provided in the article and supplementary data files.

microbiology↗

bioRxiv2025

Convergent evolution of distinct D-ribulose utilisation pathways in attaching and effacing pathogens

Attaching and effacing pathogens overcome colonisation resistance by competing with metabolically similar organisms for limited resources. Enterohaemorrhagic E. coli (EHEC) utilises the pathogenicity island-encoded Accessory -arabinose Uptake (Aau) transporter to effectively colonise the mouse gut, hypothesised to be achieved via an enhanced capacity to scavenge -arabinose. Aau is regulated exclusively in response to -arabinose, but it is unclear how this system specifically benefits EHEC in vivo. Here, we show that Aau displays a >200-fold higher affinity for the monosaccharide D-ribulose, over -arabinose. EHEC cannot grow on D-ribulose as a sole carbon source and this sugar does not trigger aau transcription. However, Aau effectively transports D-ribulose into the cell only in the presence of -arabinose, where it feeds into the pentose phosphate pathway, after phosphorylation by the -ribulokinase AraB, thus providing EHEC a significant fitness advantage. EHEC has therefore evolved a mechanism of hijacking the canonical -arabinose utilisation machinery to promote D-ribulose utilisation in vivo. Furthermore, Citrobacter rodentium encodes an analogous system that exclusively transports D-ribulose and metabolises it via a dedicated D-ribulokinase. These unique mechanisms of D-ribulose utilisation suggest that convergent evolution has driven the ability of distinct pathogenic species to exploit this nutrient during invasion of the gut niche.

microbiology↗

bioRxiv2024

Resolving a neonatal intensive care unit outbreak of methicillin-resistant Staphylococcus aureus to the SNV level using Oxford Nanopore simplex reads and HERRO error correction

ObjectivesOur laboratory began prospective genomic surveillance for healthcare-associated organisms in 2022 using Oxford Nanopore Technologies (ONT) sequencing as a standalone platform. This has permitted the early detection of outbreaks but has been insufficient for single-nucleotide variant (SNV)-level analysis due to lower read accuracy than Illumina sequencing. This study aimed to determine whether Haplotype-aware ERRor cOrrection (HERRO) of ONT data could permit high-resolution comparison of outbreak isolates. MethodsWe used ONT simplex reads from isolates involved in a recent outbreak of methicillin-resistant Staphylococcus aureus (MRSA) in our neonatal unit. The raw sequence data were re-basecalled and adapter-trimmed using Dorado v0.7.0. The simplex reads then underwent HERRO correction. The resulting genome assemblies and phylogenies were compared with previous analyses (using Dorado v0.3.4, no HERRO correction and data generated by Illumina sequencing). ResultsFive of nine outbreak isolates were included in the analysis. The remaining four isolates had insufficient read lengths (N50 values <10,000 bp) and did not provide complete chromosome coverage after HERRO correction. The average chromosome sequencing depth for nanopore data was 147x (range: 44-220x) with an average read N50 of 12,215 bp (interquartile range (IQR): 11,439-12,711 bp). The median pairwise SNV distance between outbreak isolates from the original investigation was 51 SNVs (range: 40-68), which decreased to 3 SNVs (range: 1-15) with HERRO correction. Illumina sequencing generated a median SNV distance of 2 (range: 0-13). The resulting standalone ONT HERRO-corrected phylogeny was almost indistinguishable from the standalone Illumina-generated phylogeny. ConclusionsThe addition of HERRO correction meant isolates from this MRSA outbreak could be resolved to a level on par with Illumina sequencing. ONT data following HERRO correction represents a viable standalone option for high-resolution genomic analysis of hospital outbreaks, provided sufficient read lengths can be generated.

genomics↗

bioRxiv2023

Metabolism of ʟ -arabinose converges with virulence regulation to promote enteric pathogen fitness

Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified a novel transporter of the dietary monosaccharide -arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive fitness in the mouse gut and highly expressed during human infection. Accordingly, we discovered that -arabinose induces expression of the EHEC type 3 secretion system, enhancing its ability to attach to host cells, and that the underlying mechanism is dependent on products of its catabolism rather than the sensing of -arabinose as a signal. Finally, using the murine pathogen Citrobacter rodentium, we show that -arabinose metabolism provides a fitness benefit during enteric infection via virulence factor regulation, as opposed to supporting pathogen growth. This study describes an intrinsic mechanism of integrating central sugar metabolism with virulence regulation and highlights the unexpected impact that nutrient utilisation can have in enteric pathogens.

microbiology↗

bioRxiv2020

Extreme suction attachment performance from specialised insects living in mountain streams (Diptera: Blephariceridae)

Suction is widely used by animals for strong controllable underwater adhesion but is less well understood than adhesion of terrestrial climbing animals. Here we investigate the attachment of an aquatic insect larva (Blephariceridae), which clings to rocks in torrential streams using the only known muscle-actuated suction organs in insects. We measured their attachment forces on well-defined rough substrates and found their adhesion was much less reduced by micro-roughness than terrestrial climbing insects. In vivo visualisation of the suction organs in contact with microstructured substrates revealed that they can mould around large asperities to form a seal. Moreover, we showed that spine-like microtrichia on the organ are stiff cuticular structures that only make tip contact on smooth and microstructured substrates. Our results highlight the performance and versatility of blepharicerid suction organs and introduce a new study system to explore biological suction.

ecology↗