Biology subjects

Coyle, N. M.

Publications and source records attributed to Coyle, N. M..

4 recordsLinked to original sources

bioRxiv2026

Environmental Drivers and Distribution of Pathogenic Vibrio Species in the Teign Estuary, UK

Climate-driven increases in sea surface temperature have been associated with the expansion of Vibrio species and a corresponding rise in vibriosis cases in both human populations and aquaculture systems. Coastal waters across the south of England are increasingly becoming suitable for the growth and establishment of both human- and aquaculture-associated Vibrio species, potentially increasing vulnerability to the types of infections and disease outbreaks already reported elsewhere in the world. In this study, we report the presence of a diverse and well-established Vibrio community within the Teign Estuary, (Southwest, UK), including the human-pathogenic species V. parahaemolyticus, V. cholerae (non-O1/non-O139), V. alginolyticus, and V. diabolicus, as well as the important aquaculture pathogens V. jasicida, V. aestuarianus, and V. anguillarum. We identified V. diabolicus, a species that was indistinguishable from V. alginolyticus using conventional biochemical identification methods and could only be accurately resolved by whole-genome sequencing and developed novel PCR targets to differentiate these species in the lab. Using the insect infection model Galleria mellonella, we demonstrate that environmental isolates of V. cholerae (non-O1/non-O139), V. parahaemolyticus, and V. alginolyticus possess virulence potential. We also investigated the effects of sewage effluent on the growth of Vibrio isolates from the Teign Estuary and found that sewage can preferentially promote the growth of Vibrio species. Furthermore, several Vibrio isolates were multidrug resistant and carried antimicrobial resistance genes, highlighting the potential role of environmental Vibrio populations in the Teign Estuary as reservoirs of antimicrobial resistance. Together, these findings demonstrate how rising sea surface temperatures and sewage pollution may influence the emergence, persistence, and public health and aquaculture significance of Vibrio species in UK coastal waters.

microbiology↗

bioRxiv2025

Detection of Macrobrachium rosenbergii golda virus (MrGV) in giant river prawn larvae across Asia through NCBI sequence read archive (SRA) data mining

1Macrobrachium rosenbergii golda virus (MrGV) was first characterised in Macrobrachium rosenbergii larvae in 2020, associated with mass mortalities in multiple Southern Bangladesh prawn hatcheries. MrGV has since been detected in two metatranscriptomic datasets from M. rosenbergii in China and in relation to a larval mortality event in India. The major objective of this study was to further characterise the geographical spread of the virus by mining the NCBI Sequence Read Archive (SRA) database. Utilising a new database, Logan, generated from assembling each SRA dataset, and a custom Snakemake pipeline, we discovered MrGV sequence data in M. rosenbergii SRA datasets from China, Thailand, and India, and determined that presence and relative abundance of MrGV is mostly associated with the larval life stage of M. rosenbergii. These results provide insights into the current prevalence of MrGV globally, suggest the life stages of prawn that should be screened to prevent spread of the virus, and demonstrate how the Logan database can be used to inform epidemiological studies.

bioinformatics↗

bioRxiv2023

Vibrio aestuarianus Clade A and Clade B isolates are associated with Pacific oyster (Crassostrea gigas) disease outbreaks across Ireland

2.Bacteria from the Vibrionaceae family have been implicated in mass mortalities of farmed Pacific oysters (Crassostrea gigas) in multiple countries, leading to substantial impairment for growth in the sector. In Ireland there has been concern that Vibrio have been involved in serious summer outbreaks. There is evidence that Vibrio aestuarianus is increasingly becoming the main pathogen of concern for the Pacific Oyster industry in Ireland. While bacteria belonging to the Vibrio splendidus clade are also detected frequently in mortality episodes, their role in the outbreaks of summer mortality are not well understood. To identify and characterise strains involved in these outbreaks, 43 Vibrio isolates were recovered from Pacific oyster summer mass mortality episodes in Ireland from 2008-2015 and these were whole genome sequenced. Among these, 25 were found to be V. aestuarianus (implicated in disease) and 18 V. splendidus sensu lato (role in disease undetermined). Two distinct clades of V. aestuarianus - Clade A and Clade B - were found that had previously been described as circulating within French oyster culture. The high degree of similarity between the Irish and French V. aestuarianus isolates points to translocation of the pathogen between Europes two major oyster producing countries, probably via trade in spat and other age classes. V. splendidus isolates were more diverse, but the data reveal a single clone of this species that has spread across oyster farms in Ireland. This underscores that Vibrio could be transmitted readily across oyster farms. The presence of V. aestuarianus Clades A and B in not only France but also Ireland adds weight to growing concern that this pathogen is spreading and impacting Pacific oyster production within Europe. 3. OutcomePacific oyster culture in Ireland has increasingly suffered from summer mass mortality events. Many of these mortalities in recent years have been associated with Vibrio aestuarianus; the role of another pathogen, Vibrio splendidus has, so far, remained inconclusive. Here we show that two clades of V. aestuarianus are circulating in Ireland, and that these are members of two clades that have previously caused extensive oyster die offs in France. Their discovery in Ireland is consistent with transport of infected oyster stock between the two countries. Although V. splendidus-like strains in Ireland were highly diverse, a small clonal group was detected that appears to have spread rapidly from a single source to disparate locations in Ireland. Combined, these findings highlight the appearance of a highly pathogenic Vibrio in Ireland, and the risk of transmission between interconnected oyster production industries in Europe. 4. Data summarySequences generated in this study were deposited on the NCBI. Accession number: PRJNA797364. Publicly accessed genomes are listed in Table S2. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2019

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly classify paralogous gene families into either putative fission/fusion events or gene duplications. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.\n\nAvailabilityPIRATE is implemented in Perl and is freely available under an GNU GPL 3 open source license from https://github.com/SionBayliss/PIRATE.\n\nSupplementary InformationSupplementary data is available online.

bioinformatics↗