All Outputs (33)

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 need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance (2024)
Journal Article
Arnold, K. E., Laing, G., McMahon, B. J., Fanning, S., Stekel, D. J., Pahl, O., …McIntyre, K. M. (2024). The need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance. The Lancet Planetary Health, 8(2), E124-E133. https://doi.org/10.1016/S2542-5196%2823%2900278-4

Although the effects of antimicrobial resistance (AMR) are most obvious at clinical treatment failure, AMR evolution, transmission, and dispersal happen largely in environmental settings, for example within farms, waterways, livestock, and wildlife.... Read More about The need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance.

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.

Modeling of Space Crop-Based Dishes for Optimal Nutrient Delivery to Astronauts and Beyond on Earth (2023)
Journal Article
Liang, S., Rivera-Osorio, K., Burgess, A. J., Kumssa, D. B., Escribà-Gelonch, M., Fisk, I., …Hessel, V. (2024). Modeling of Space Crop-Based Dishes for Optimal Nutrient Delivery to Astronauts and Beyond on Earth. ACS Food Science & Technology, 4(1), 104–117. https://doi.org/10.1021/acsfoodscitech.3c00396

Future long-term human exploration of space will need a supply of resources for astronauts, including fresh food from space farms. This means it is necessary to identify combinations of crops that can be successfully grown together and which provide... Read More about Modeling of Space Crop-Based Dishes for Optimal Nutrient Delivery to Astronauts and Beyond on Earth.

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh (2023)
Journal Article
Williams, A. D., Rousham, E., Neal, A. L., Amin, M. B., Hobman, J. L., Stekel, D., & Islam, M. A. (2023). Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh. Microbiology Spectrum, 11(6), e0176323. https://doi.org/10.1128/spectrum.01763-23

Interactions between humans, animals, and the environment are considered critical foci for addressing antimicrobial resistance (AMR). However, One Health data on AMR in low- and middle-income countries are presently scarce. Using metagenomics, we inv... Read More about Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh.

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.

The role of multisystemic resilience in fostering critical agency: UK adolescents during the COVID-19 Pandemic (2023)
Journal Article
Weidman, S., Levine, D. T., Louwagie, F., Blackmore, K., Theron, L. C., & Stekel, D. J. (2024). The role of multisystemic resilience in fostering critical agency: UK adolescents during the COVID-19 Pandemic. Current Psychology, 43, 16833-16847. https://doi.org/10.1007/s12144-023-04578-1

Critical agency (CA) refers to an individual’s feeling of power in relation to social inequalities. Research has demonstrated that high CA is associated with positive adolescent outcomes, however, less is known about what supports are important for i... Read More about The role of multisystemic resilience in fostering critical agency: UK adolescents during the COVID-19 Pandemic.

Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK (2023)
Journal Article
Ibrahim, D. R., Dodd, C. E. R., Stekel, D. J., Meshioye, R. T., Diggle, M., Lister, M., & Hobman, J. L. (2023). Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK. Antibiotics, 12(1), Article 169. https://doi.org/10.3390/antibiotics12010169

Globally, cephalosporin therapy failure is a serious problem for infection control. One causative agent of cephalosporin-resistant infections is multidrug-resistant (MDR) E. coli producing extended-spectrum β-lactamases (ESBLs) and/or plasmid-encoded... Read More about Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK.

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., María Baena-Nogueras, R., Warry, A., Ortori, C. A., Todman, H., Gray-Hammerton, C. J., C. W. Pritchard, A., Iles, E., Cook, R., Emes, R. D., Jones, M. A., Kypraios, T., West, H., Barrett, D. A., Ramsden, S. J., …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.

A Model to Investigate the Impact of Farm Practice on Antimicrobial Resistance in UK Dairy Farms (2021)
Journal Article
Lanyon, C. W., King, J. R., Stekel, D. J., & Gomes, R. L. (2021). A Model to Investigate the Impact of Farm Practice on Antimicrobial Resistance in UK Dairy Farms. Bulletin of Mathematical Biology, 83(4), Article 36. https://doi.org/10.1007/s11538-021-00865-9

© 2021, The Author(s). The ecological and human health impact of antibiotic use and the related antimicrobial resistance (AMR) in animal husbandry is poorly understood. In many countries, there has been considerable pressure to reduce overall antibio... Read More about A Model to Investigate the Impact of Farm Practice on Antimicrobial Resistance in UK Dairy Farms.

Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids (2021)
Journal Article
Arya, S., Williams, A., Reina, S. V., Knapp, C. W., Kreft, J.-U., Hobman, J. L., & Stekel, D. J. (2021). Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids. Environmental Pollution, 275, Article 116602. https://doi.org/10.1016/j.envpol.2021.116602

© 2021 Elsevier Ltd Many antibiotic resistance genes co-occur with resistance genes for transition metals, such as copper, zinc, or mercury. In some environments, a positive correlation between high metal concentration and high abundance of antibioti... Read More about Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids.

A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer (2020)
Journal Article
Arya, S., Todman, H., Baker, M., Hooton, S., Millard, A., Kreft, J. U., …Stekel, D. J. (2020). A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiology Ecology, 96(7), https://doi.org/10.1093/femsec/fiaa100

© FEMS 2020. Antimicrobial resistance is a major global challenge. Of particular concern are mobilizable elements that can transfer resistance genes between bacteria, leading to pathogens with new combinations of resistance. To date, mathematical mod... Read More about A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer.

Roots or Flowers? Take a Guess (2020)
Book Chapter
Ajmera, I., Stekel, D., Band, L., & Hodgman, C. (2020). Roots or Flowers? Take a Guess. In F. Matthäus, S. Matthäus, S. Harris, & T. Hillen (Eds.), The Art of Theoretical Biology (66-67). Springer

Phosphorus is a growth-limiting nutrient for plants. The use of phosphate (Pi) fertiliser is unsustainable because its stocks are non-renew-able and the run-off of surplus fertiliser damages the environment.

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.

Removal of copper from cattle footbath wastewater with layered double hydroxide adsorbents as a route to antimicrobial resistance mitigation on dairy farms (2018)
Journal Article
Williams, O., Clark, I., Gomes, R. L., Perehinec, T., Hobman, J. L., Stekel, D. J., …Lester, E. (2019). Removal of copper from cattle footbath wastewater with layered double hydroxide adsorbents as a route to antimicrobial resistance mitigation on dairy farms. Science of the Total Environment, 655, 1139-1149. https://doi.org/10.1016/j.scitotenv.2018.11.330

Copper and zinc are routinely used in livestock antimicrobial footbaths in commercial farming. The footbath mix is a cost to farmers, and the disposal of spent footbath into slurry tanks leads to soil contamination, as well as the potential for antim... Read More about Removal of copper from cattle footbath wastewater with layered double hydroxide adsorbents as a route to antimicrobial resistance mitigation on dairy farms.

First report of antimicrobial resistance pre-dates penicillin (2018)
Journal Article
Stekel, D. (2018). First report of antimicrobial resistance pre-dates penicillin. Nature, 562(7726), 192. https://doi.org/10.1038/d41586-018-06983-0

Clinical antimicrobial resistance was first reported four years before Alexander Fleming’s discovery of penicillin in 1928 [...]

Investigating the association between the caecal microbiomes of broilers and Campylobacter burden (2018)
Journal Article
Sakaridis, I., Ellis, R. J., Cawthraw, S. A., van Vliet, A. H. M., Stekel, D. J., Penell, J., …Cook, A. J. (2018). Investigating the association between the caecal microbiomes of broilers and Campylobacter burden. Frontiers in Microbiology, 9, Article 927. https://doi.org/10.3389/fmicb.2018.00927

One of the major transmission routes for the foodborne bacterial pathogen Campylobacter is undercooked poultry meat, contaminated from intestinal contents during processing. In broilers, Campylobacter can grow to very high densities in the caeca, and... Read More about Investigating the association between the caecal microbiomes of broilers and Campylobacter burden.