Outputs (8)

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., …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.

The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies (2024)
Journal Article
Cook, R., Brown, N., Rihtman, B., Michniewski, S., Redgwell, T., Clokie, M., …Millard, A. (2024). The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies. Microbial Genomics, 10(2), Article 0.001198. https://doi.org/10.1099/mgen.0.001198

Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial... Read More about The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.

A model of antibiotic resistance genes accumulation through lifetime exposure from food intake and antibiotic treatment (2023)
Journal Article
Todman, H., Arya, S., Baker, M., & Stekel, D. J. (2023). A model of antibiotic resistance genes accumulation through lifetime exposure from food intake and antibiotic treatment. PLoS ONE, 18(8), Article e0289941. https://doi.org/10.1371/journal.pone.0289941

Antimicrobial resistant bacterial infections represent one of the most serious contemporary global healthcare crises. Acquisition and spread of resistant infections can occur through community, hospitals, food, water or endogenous bacteria. Global ef... Read More about A model of antibiotic resistance genes accumulation through lifetime exposure from food intake and antibiotic treatment.

Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics (2023)
Journal Article
Chio, H., Guest, E. E., Hobman, J. L., Dottorini, T., Hirst, J. D., & Stekel, D. J. (2023). Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics. Journal of Molecular Graphics and Modelling, 123, Article 108508. https://doi.org/10.1016/j.jmgm.2023.108508

Antibiotics enter the environment through waste streams, where they can exert selective pressure for antimicrobial resistance in bacteria. However, many antibiotics are excreted as partly metabolized forms, or can be subject to partial breakdown in w... Read More about Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics.

Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control (2022)
Journal Article
Baker, M., Williams, A. D., Hooton, S. P., Helliwell, R., King, E., Dodsworth, T., …Stekel, D. J. (2022). Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control. Environment International, 169, Article 107516. https://doi.org/10.1016/j.envint.2022.107516

Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial res... Read More about Antimicrobial resistance in dairy slurry tanks: a critical point for measurement and control.

Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming (2022)
Journal Article
Peng, Z., Maciel-Guerra, A., Baker, M., Zhang, X., Hu, Y., Wang, W., …Dottorini, T. (2022). Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PLoS Computational Biology, 18(3), Article e1010018. https://doi.org/10.1371/journal.pcbi.1010018

Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs... Read More about Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens (2021)
Journal Article
Cook, R., Hooton, S., Trivedi, U., King, L., Dodd, C. E., Hobman, J. L., …Millard, A. D. (2021). Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. Microbiome, 9, Article 65. https://doi.org/10.1186/s40168-021-01010-3

Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle... Read More about Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens.

DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples (2019)
Journal Article
Shaw, L. M., Blanchard, A., Chen, Q., An, X., Davies, P., Totemeyer, S., …Stekel, D. J. (2019). DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples. Scientific Reports, 9, Article 2373. https://doi.org/10.1038/s41598-019-38873-4

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test... Read More about DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples.