Publications
Selected publications
- Enhancing Infectious Intestinal Disease diagnosis through metagenomic and metatranscriptomic sequencing of over 1000 human diarrhoeal samples (Preprint - 2023)
- Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship (Preprint - 2024)
- Innovations in genomic antimicrobial resistance surveillance. (Journal article - 2023)
- Emerging Variants of Canine Enteric Coronavirus Associated with Outbreaks of Gastroenteric Disease. (Journal article - 2024)
- Quantifying the bystander effect of antimicrobial use on the diversity and resistome of the gut microbiome in Malawian adults (Preprint - 2025)
2025
Complete genome sequence of <i>Pseudomonas</i> sp. PP3, a dehalogenase-producing bacterium, confirms the unusual mobile genetic element <i>DEH</i>.
Webster, G., Baldwin, A. J., Cunningham-Oakes, E., Mullins, A. J., Dodds, R., Hill, K. E., . . . Weightman, A. J. (2025). Complete genome sequence of <i>Pseudomonas</i> sp. PP3, a dehalogenase-producing bacterium, confirms the unusual mobile genetic element <i>DEH</i>.. Microbiology resource announcements, 14(5), e0008925. doi:10.1128/mra.00089-25
Emergence Risks from Within? Metagenomic Analysis of Mosquito Viromes from Two Zoos Reveals Mosquito-associated Orthobunyaviruses in the UK
Importance of diversity and representation in science: benefits towards strengthening our response to global challenges.
Perez-Sepulveda, B. M., Cunningham-Oakes, E., & Waters, E. V. (2025). Importance of diversity and representation in science: benefits towards strengthening our response to global challenges.. npj antimicrobials and resistance, 3(1), 26. doi:10.1038/s44259-025-00101-7
Quantifying the bystander effect of antimicrobial use on the diversity and resistome of the gut microbiome in Malawian adults
Building an inclusive culture at scientific meetings: foundations for future progress.
Maringer, K., Cunningham-Oakes, E., Lane, F., Jones, K. L., Rodrigues de Oliveira, B. F., Baba-Dikwa, A., . . . Khan, C. M. A. (2025). Building an inclusive culture at scientific meetings: foundations for future progress.. Microbiology (Reading, England), 171(2). doi:10.1099/mic.0.001527
2024
Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship
Emerging Variants of Canine Enteric Coronavirus Associated with Outbreaks of Gastroenteric Disease.
Cunningham-Oakes, E., Pilgrim, J., Darby, A. C., Appleton, C., Jewell, C., Rowlingson, B., . . . Radford, A. D. (2024). Emerging Variants of Canine Enteric Coronavirus Associated with Outbreaks of Gastroenteric Disease.. Emerging infectious diseases, 30(6), 1240-1244. doi:10.3201/eid3006.231184
2023
Innovations in genomic antimicrobial resistance surveillance.
Wheeler, N. E., Price, V., Cunningham-Oakes, E., Tsang, K. K., Nunn, J. G., Midega, J. T., . . . SEDRIC Genomics Surveillance Working Group. (2023). Innovations in genomic antimicrobial resistance surveillance.. The Lancet. Microbe, 4(12), e1063-e1070. doi:10.1016/s2666-5247(23)00285-9
Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.
Cunningham-Oakes, E., Bronowski, C., Chinyama, E., Jere, K. C., Sindhu, K. N. C., Kang, G., . . . Parker, E. P. K. (2023). Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.. BMC microbiology, 23(1), 354. doi:10.1186/s12866-023-03098-z
Yeast lacking the sterol C-5 desaturase Erg3 are tolerant to the anti-inflammatory triterpenoid saponin escin.
Johnston, E. J., Tallis, J., Cunningham-Oakes, E., Moses, T., Moore, S. J., Hosking, S., & Rosser, S. J. (2023). Yeast lacking the sterol C-5 desaturase Erg3 are tolerant to the anti-inflammatory triterpenoid saponin escin.. Scientific reports, 13(1), 13617. doi:10.1038/s41598-023-40308-0
Enhancing Infectious Intestinal Disease diagnosis through metagenomic and metatranscriptomic sequencing of over 1000 human diarrhoeal samples
2022
Tracking outbreak dynamics using within-host variation
Donovan-Banfield, I., & Cunningham-Oakes, E. (2022). Tracking outbreak dynamics using within-host variation. NATURE MICROBIOLOGY, 7(12), 1947-1948. doi:10.1038/s41564-022-01274-x
Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis
Cunningham-Oakes, E., Pointon, T., Murphy, B., Campbell-Lee, S., Connor, T. R., & Mahenthiralingam, E. (2022). Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis. MICROBIAL GENOMICS, 8(11). doi:10.1099/mgen.0.000884
Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic
Cunningham-Oakes, E., & Trivett, H. (2022). Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic. MICROBIAL GENOMICS, 8(1). doi:10.1099/mgen.0.000757
2021
Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as <i>Burkholderia lata</i>.
Cunningham-Oakes, E., Pointon, T., Murphy, B., Campbell-Lee, S., Webster, G., Connor, T. R., & Mahenthiralingam, E. (2021). Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as <i>Burkholderia lata</i>.. Microbial genomics, 7(4). doi:10.1099/mgen.0.000564
2020
Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India
Webster, G., Mullins, A. J., Cunningham-Oakes, E., Renganathan, A., Aswathanarayan, J. B., Mahenthiralingam, E., & Vittal, R. R. (2020). Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India. FEMS MICROBIOLOGY ECOLOGY, 96(9). doi:10.1093/femsec/fiaa147
Genome Sequence of <i>Pluralibacter gergoviae</i> ECO77, Multireplicon Isolate of Industrial Origin
Cunningham-Oakes, E., Pointon, T., Murphy, B., Connor, T. R., & Mahenthiralingam, E. (2020). Genome Sequence of <i>Pluralibacter gergoviae</i> ECO77, Multireplicon Isolate of Industrial Origin. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 9(9). doi:10.1128/MRA.01561-19
2019
Understanding the challenges of non-food industrial product contamination
Cunningham-Oakes, E., Weiser, R., Pointon, T., & Mahenthiralingam, E. (2019). Understanding the challenges of non-food industrial product contamination. FEMS MICROBIOLOGY LETTERS, 366(23). doi:10.1093/femsle/fnaa010
The Genome Sequences of Three <i>Paraburkholderia</i> sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential
Webster, G., Mullins, A. J., Bettridge, A. S., Jones, C., Cunningham-Oakes, E., Connor, T. R., . . . Mahenthiralingam, E. (2019). The Genome Sequences of Three <i>Paraburkholderia</i> sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 8(34). doi:10.1128/MRA.00778-19
Not all <i>Pseudomonas aeruginosa</i> are equal: strains from industrial sources possess uniquely large multireplicon genomes
Weiser, R., Green, A. E., Bull, M. J., Cunningham-Oakes, E., Jolley, K. A., Maiden, M. C. J., . . . Mahenthiralingam, E. (2019). Not all <i>Pseudomonas aeruginosa</i> are equal: strains from industrial sources possess uniquely large multireplicon genomes. MICROBIAL GENOMICS, 5(7). doi:10.1099/mgen.0.000276
Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, <i>Methanococcoides</i> spp., Isolated from Marine Sediments
Webster, G., Mullins, A. J., Watkins, A. J., Cunningham-Oakes, E., Weightman, A. J., Mahenthiralingam, E., & Sass, H. (2019). Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, <i>Methanococcoides</i> spp., Isolated from Marine Sediments. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 8(18). doi:10.1128/MRA.00342-19
2018
Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen <i>Pseudomonas baetica </i>a390T sequenced by Ion semiconductor and Nanopore technologies
Beaton, A., Lood, C., Cunningham-Oakes, E., MacFadyen, A., Mullins, A. J., El Bestawy, W., . . . Tucker, N. P. (2018). Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen <i>Pseudomonas baetica </i>a390T sequenced by Ion semiconductor and Nanopore technologies. FEMS MICROBIOLOGY LETTERS, 365(9). doi:10.1093/femsle/fny069
2015
Nordihydroguaiaretic acid enhances the activities of aminoglycosides against methicillin- sensitive and resistant <i>Staphylococcus aureus in vitro</i> and <i>in vivo</i>
Cunningham-Oakes, E., Soren, O., Moussa, C., Rathor, G., Liu, Y., Coates, A., & Hu, Y. (2015). Nordihydroguaiaretic acid enhances the activities of aminoglycosides against methicillin- sensitive and resistant <i>Staphylococcus aureus in vitro</i> and <i>in vivo</i>. FRONTIERS IN MICROBIOLOGY, 6. doi:10.3389/fmicb.2015.01195