Dr ADAM BLANCHARD's Outputs (31)

Euclid preparation: LV. Exploring the properties of proto-clusters in the Simulated Euclid Wide Survey (2025)
Journal Article
Euclid Collaboration, Böhringer, H., Chon, G., Cucciati, O., Dannerbauer, H., Bolzonella, M., De Lucia, G., Cappi, A., Moscardini, L., Giocoli, C., Castignani, G., Hatch, N. A., Andreon, S., Bañados, E., Ettori, S., Fontanot, F., Gully, H., Hirschmann, M., Maturi, M., Mei, S., …Verza, G. (2025). Euclid preparation: LV. Exploring the properties of proto-clusters in the Simulated Euclid Wide Survey. Astronomy and Astrophysics, 693, Article A59. https://doi.org/10.1051/0004-6361/202451683

Galaxy proto-clusters are receiving increased interest since most of the processes shaping the structure of clusters of galaxies and their galaxy population happen at the early stages of their formation. The Euclid Survey will provide a unique opport... Read More about Euclid preparation: LV. Exploring the properties of proto-clusters in the Simulated Euclid Wide Survey.

PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data (2024)
Journal Article
Blanchard, A. M., Taylor, A., Warry, A., Shephard, F., Curwen, A., Leigh, J. A., Emes, R. D., & Egan, S. A. (2024). PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data. Computational and Structural Biotechnology Journal, 23, 3780-3783. https://doi.org/10.1016/j.csbj.2024.10.025

Motivation: Current methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilit... Read More about PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data.

Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom (2024)
Journal Article
Hinds, J., Apaa, T., Parry, R. H., Withers, A. J., MacKenzie, L., Staley, C., Morrison, J., Bennett, M., Bremner-Harrison, S., Chadwick, E. A., Hailer, F., Harrison, S. W., Lambin, X., Loose, M., Mathews, F., Tarlinton, R., & Blanchard, A. (2024). Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom. Access Microbiology, 6(7), Article 000813.v4. https://doi.org/10.1099/acmi.0.000813.v4

The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, thoug... Read More about Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom.

Modelling the impact of wastewater flows and management practices on antimicrobial resistance in dairy farms (2024)
Journal Article
Todman, H., Helliwell, R., King, L., Blanchard, A., Gray-Hammerton, C. J., Hooton, S. P., Baker, M., Margerison, J., Wilson, P., Dodd, C. E. R., Morris, C., Raman, S., Hudson, C., Kreft, J.-U., Hobman, J. L., Kypraios, T., & Stekel, D. J. (2024). Modelling the impact of wastewater flows and management practices on antimicrobial resistance in dairy farms. npj Antimicrobials & Resistance, 2(1), Article 13. https://doi.org/10.1038/s44259-024-00029-4

Dairy slurry is a major source of environmental contamination with antimicrobial resistant genes and bacteria. We developed mathematical models and conducted on-farm research to explore the impact of wastewater flows and management practices on antim... Read More about Modelling the impact of wastewater flows and management practices on antimicrobial resistance in dairy farms.

PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data (2024)
Preprint / Working Paper
Blanchard, A. M., Taylor, A., Warry, A., Shephard, F., Curwen, A., Leigh, J. A., Emes, R. D., & Egan, S. A. (2024). PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data

Motivation Current methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilita... Read More about PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data.

A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen (2024)
Journal Article
Whiley, D., Jolley, K., Blanchard, A., Coffey, T., & Leigh, J. (2024). A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen. Microbial Genomics, 10(3), https://doi.org/10.1099/mgen.0.001225

Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly availa... Read More about A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen.

Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020–21 (2024)
Journal Article
Zachariah, A., Krishnankutty, S. P., Manazhi, J., Omanakuttan, V., Santosh, S., Blanchard, A., & Tarlinton, R. (2024). Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020–21. Access Microbiology, 6(1), Article 000686. https://doi.org/10.1099/acmi.0.000686.v3

Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in... Read More about Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020–21.

Advances in the understanding, detection and management of equine strangles (2023)
Journal Article
McLinden, L. A., Freeman, S. L., Daly, J., Blanchard, A., Kemp‐Symonds, J. G., & Waller, A. (2023). Advances in the understanding, detection and management of equine strangles. Equine Veterinary Education, 35(12), 662-672. https://doi.org/10.1111/eve.13845

Streptococcus equi subspecies equi (S. equi) is the causative organism of the upper respiratory disease of equids, strangles, characterised by pyrexia, lymphadenopathy and mucopurulent nasal discharge. Strangles was first reported over 750 years ago... Read More about Advances in the understanding, detection and management of equine strangles.

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology (2023)
Journal Article
Apaa, T., Withers, A. J., Staley, C. E., Blanchard, A. M., Bennett, M., Bremner-Harrison, S., Chadwick, E. A., Hailer, F., Harrison, S. W. R., Loose, M., Mathews, F., & Tarlinton, R. E. (2023). Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology. Journal of General Virology, 104(6), Article 001859. https://doi.org/10.1101/2023.02.14.528476

Horseshoe bats are the natural hosts of the Sarbecovirus subgenus that includes SARS-CoV and SARS-CoV- 2. Despite the devastating impact of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecovi... Read More about Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology.

RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance (2023)
Journal Article
Stockdale, S. R., Blanchard, A. M., Nayak, A., Husain, A., Nashine, R., Dudani, H., McClure, C. P., Tarr, A. W., Nag, A., Meena, E., Sinha, V., Shrivastava, S. K., Hill, C., Singer, A. C., Gomes, R. L., Acheampong, E., Chidambaram, S. B., Bhatnagar, T., Vetrivel, U., Arora, S., …Monaghan, T. M. (2023). RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. The Lancet Regional Health – Southeast Asia, 14, Article 100205. https://doi.org/10.1016/j.lansea.2023.100205

Background: The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectio... Read More about RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance.

High genetic diversity and zoonotic potential of Staphylococcus aureus strains recovered from bovine intramammary infections in Colombians dairy herds (2022)
Journal Article
Torres, G., Vargas, K., Reyes-Vélez, J., Jiménez, N., Blanchard, A., & Olivera-Angel, M. (2023). High genetic diversity and zoonotic potential of Staphylococcus aureus strains recovered from bovine intramammary infections in Colombians dairy herds. Comparative Immunology, Microbiology and Infectious Diseases, 93, Article 101940. https://doi.org/10.1016/j.cimid.2022.101940

Genotyping of Staphylococcus aureus isolated from mastitis has become a fundamental tool to understand its complex epidemiology and to evaluate spillover events. The aim of this study was to describe the frequency of genotypes of the S. aureus strain... Read More about High genetic diversity and zoonotic potential of Staphylococcus aureus strains recovered from bovine intramammary infections in Colombians dairy herds.

Genome Reference Assembly for Bottlenecked Southern Australian Koalas (2022)
Journal Article
Blanchard, A. M., Emes, R. D., Greenwood, A. D., Holmes, N., Loose, M. W., McEwen, G. K., Meers, J., Speight, N., & Tarlinton, R. E. (2023). Genome Reference Assembly for Bottlenecked Southern Australian Koalas. Genome Biology and Evolution, 15(1), Article evac176. https://doi.org/10.1093/gbe/evac176

Koala populations show marked differences in inbreeding levels and in the presence or absence of the endogenous Koala retrovirus (KoRV). These genetic differences among populations may lead to severe disease impacts threatening koala population viabi... Read More about Genome Reference Assembly for Bottlenecked Southern Australian Koalas.

The persistence of equine strangles (2022)
Preprint / Working Paper
Mclinden, L., Freeman, S., Daly, J., Blanchard, A., Kemp-Symonds, J., & Waller, A. The persistence of equine strangles

Streptococcus equi subspecies equi (S. equi) is the causative organism of the upper respiratory disease of equids, strangles, characterised by pyrexia, lymphadenopathy, and mucopurulent nasal discharge. Strangles was first reported over 750 years ago... Read More about The persistence of equine strangles.

Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens (2022)
Journal Article
Blanchard, A. M., Baumbach, C. M., Michler, J. K., Pickwell, N. D., Staley, C. E., Franklin, J. M., Wattegedera, S. R., Entrican, G., & Tötemeyer, S. (2022). Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens. Animals, 12(23), Article 3235. https://doi.org/10.3390/ani12233235

Ovine footrot is a complex multifactorial infectious disease, causing lameness in sheep with major welfare and economic consequences. Dichelobacter nodosus is the main causative bacterium; however, footrot is a polymicrobial disease with Fusobacteriu... Read More about Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens.

The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin (2022)
Journal Article
Marshall, H. J., Blanchard, A. M., Kelly, K. R., Goh, J. N., Williams, A. D., King, L., Lovatt, F., Davies, P. L., & Tötemeyer, S. (2022). The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin. Veterinary Microbiology, 272, Article 109459. https://doi.org/10.1016/j.vetmic.2022.109459

Ovine footrot, is a highly contagious polymicrobial bacterial infection, primarily caused by Dichelobacter nodosus. Preventative bactericidal footbaths are commonly used in the sheep industry to reduce the spread of bacteria. However, their effect on... Read More about The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin.

A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions (2021)
Journal Article
Blanchard, A. M., Staley, C. E., Shaw, L., Wattegedera, S. R., Baumbach, C.-M., Michler, J. K., Rutland, C., Back, C., Newbold, N., Entrican, G., & Tötemeyer, S. (2021). A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions. Infection and Immunity, 89(10), Article e00270-21. https://doi.org/10.1128/iai.00270-21

Footrot is a polymicrobial infectious disease in sheep causing severe lameness, leading to one of the industry’s largest welfare problems. The complex etiology of footrot makes in situ or in vitro investigations difficult. Computational methods offer... Read More about A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions.

A paradox in bacterial pathogenesis: Activation of the local macrophage inflammasome is required for virulence of streptococcus uberis (2020)
Journal Article
Archer, N., Egan, S. A., Coffey, T. J., Emes, R. D., Addis, M. F., Ward, P. N., Blanchard, A. M., & Leigh, J. A. (2020). A paradox in bacterial pathogenesis: Activation of the local macrophage inflammasome is required for virulence of streptococcus uberis. Pathogens, 9(12), 1-23. https://doi.org/10.3390/pathogens9120997

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the h... Read More about A paradox in bacterial pathogenesis: Activation of the local macrophage inflammasome is required for virulence of streptococcus uberis.

Complete genome sequence of Streptococcus agalactiae strain 01173, isolated from Kuwaiti wild fish (2020)
Journal Article
Santi, M., Egan, S. A., Leigh, J. A., Verner-Jeffreys, D. W., & Blanchard, A. M. (2020). Complete genome sequence of Streptococcus agalactiae strain 01173, isolated from Kuwaiti wild fish. Microbiology Resource Announcements, 9(36), Article e00674-20. https://doi.org/10.1128/MRA.00674-20

© 2020 Santi et al. Here, we report the complete genome of piscine Streptococcus agalactiae 01173 serotype Ia, which was generated using long-read sequencing technology. The bacteria were isolated from wild fish displaying signs of streptococcosis, f... Read More about Complete genome sequence of Streptococcus agalactiae strain 01173, isolated from Kuwaiti wild fish.

Characterisation of Listeria monocytogenes isolates from cattle using a bovine caruncular epithelial cell model (2020)
Journal Article
Blanchard, A. M., Billenness, R., Warren, J., Glanvill, A., Roden, W., Drinkall, E., Maboni, G., Robinson, R. S., Rees, C. E., Pfarrer, C., & Tötemeyer, S. (2020). Characterisation of Listeria monocytogenes isolates from cattle using a bovine caruncular epithelial cell model. Heliyon, 6(7), Article e04476. https://doi.org/10.1016/j.heliyon.2020.e04476

© 2020 Listeria monocytogenes is an important foodborne pathogen in human and veterinary health, causing significant morbidity and mortality including abortion. It has a particular tropism for the gravid uterus, however, the route of infection in rep... Read More about Characterisation of Listeria monocytogenes isolates from cattle using a bovine caruncular epithelial cell model.

Metagenomics Reveals Impact of Geography and Acute Diarrhoeal Disease on the Central Indian Human Gut Microbiome (2020)
Journal Article
Monaghan, T. M., Sloan, T. J., Stockdale, S. R., Blanchard, A. M., Emes, R. D., Wilcox, M., Biswas, R., Nashine, R., Manke, S., Gandhi, J., Jain, P., Bhotmange, S., Ambalkar, S., Satav, A., Draper, L. A., Hill, C., & Singh Kashyap, R. (2020). Metagenomics Reveals Impact of Geography and Acute Diarrhoeal Disease on the Central Indian Human Gut Microbiome. Gut Microbes, 12(1), Article 1752605

Background: The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrhoeal diseases, particularly Clostridioides difficile, in rural-agricultural and urban popula... Read More about Metagenomics Reveals Impact of Geography and Acute Diarrhoeal Disease on the Central Indian Human Gut Microbiome.