Publications
Selected publications
- Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes. (Journal article - 2024)
- Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom. (Journal article - 2023)
- IS<i>1</i>-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene <i>nfsB</i> causes nitrofurantoin heteroresistance in <i>Escherichia coli</i>. (Journal article - 2023)
- Alterations in chromosomal genes <i>nfsA</i>, <i>nfsB</i>, and <i>ribE</i> are associated with nitrofurantoin resistance in <i>Escherichia coli</i> from the United Kingdom. (Journal article - 2021)
- GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. (Journal article - 2020)
- Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates. (Journal article - 2025)
2025
Reviewer response for version 1
Wan, Y. (2025). Reviewer response for version 1. Microbiology Society. doi:10.1099/acmi.0.001025.v1.2
Evidence of a novel sublineage of<i>Streptococcus agalactiae</i>in elephants from zoo populations in Germany
67 Dynamic changes in throat swab positivity and Streptococcus pyogenes genotypes: Implications for outbreak prediction
Mills, E. A., Vieira, A., Zhu, N., Wan, Y., S’gro, V., Mok, K. Y., . . . Sriskandan, S. (2025). 67 Dynamic changes in throat swab positivity and Streptococcus pyogenes genotypes: Implications for outbreak prediction. Clinical Infection in Practice, 25, 100433. doi:10.1016/j.clinpr.2025.100433
Neonatal intensive care units as a driver and reservoir of invasive infections: an example of the emerging Staphylococcus capitis multidrug-resistant NRCS-A clone
Yu Wan, D., Jauneikaite, D. E., Gao, L., Pichon, D. B., Moore, D. G., Brown, D. C. S., . . . Ready, D. D. (2025). Neonatal intensive care units as a driver and reservoir of invasive infections: an example of the emerging Staphylococcus capitis multidrug-resistant NRCS-A clone. International Journal of Infectious Diseases, 152, 107674. doi:10.1016/j.ijid.2024.107674
Understanding the genomic landscape of Klebsiella pneumoniae: insights into bacteraemia across North-West London hospitals between April 2020-December 2021
Rodgus, M. J., Getino, D. M., Yu Wan, D., Davies, D. F., Holmes, P. A., & Jauneikaite, D. E. (2025). Understanding the genomic landscape of Klebsiella pneumoniae: insights into bacteraemia across North-West London hospitals between April 2020-December 2021. International Journal of Infectious Diseases, 152, 107754. doi:10.1016/j.ijid.2024.107754
Thinking outside the box: my reflections on ICID 2024 and CAMO-Net meeting in Cape Town
Wan, Y. (2025). Thinking outside the box: my reflections on ICID 2024 and CAMO-Net meeting in Cape Town. CAMO-Net. Retrieved from https://camonet.org/2025/02/20/dr-yu-wan-in-south-africa/
Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.
Wan, Y., Pike, R., Harley, A., Mumin, Z., Potterill, I., Meunier, D., . . . Pichon, B. (2025). Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.. BMC genomic data, 26(1), 12. doi:10.1186/s12863-025-01303-8
2024
Queer- and trans-inclusive faculty hiring-A call for change.
Weissman, J. L., Chappell, C. R., Francesco Rodrigues de Oliveira, B., Evans, N., Fagre, A. C., Forsythe, D., . . . Advancing Queer and Trans Equity in Science (AQTES) Consortium. (2024). Queer- and trans-inclusive faculty hiring-A call for change.. PLoS biology, 22(11), e3002919. doi:10.1371/journal.pbio.3002919
Exploring real-world vancomycin target attainment in neonatal intensive care in the context of Staphylococcal infections: a retrospective observational cohort study.
Blank, M., Wilson, R. C., Wan, Y., Peters, J., Davies, F., Tyszczuk, L., . . . Rawson, T. M. (2024). Exploring real-world vancomycin target attainment in neonatal intensive care in the context of Staphylococcal infections: a retrospective observational cohort study.. The Journal of infection, 89(2), 106191. doi:10.1016/j.jinf.2024.106191
Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.
Wan, Y., Myall, A. C., Boonyasiri, A., Bolt, F., Ledda, A., Mookerjee, S., . . . Davies, F. (2024). Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.. The Journal of infectious diseases, 230(1), e159-e170. doi:10.1093/infdis/jiae019
Rapid expansion and international spread of M1<sub>UK</sub> in the post-pandemic UK upsurge of Streptococcus pyogenes.
Vieira, A., Wan, Y., Ryan, Y., Li, H. K., Guy, R. L., Papangeli, M., . . . Sriskandan, S. (2024). Rapid expansion and international spread of M1<sub>UK</sub> in the post-pandemic UK upsurge of Streptococcus pyogenes.. Nature communications, 15(1), 3916. doi:10.1038/s41467-024-47929-7
Running a queer- and trans-inclusive microbiology faculty search
Clinical outcomes of <i>Staphylococcus capitis</i> isolation from neonates, England, 2015-2021: a retrospective case-control study.
Yuan, J. -M., Nugent, C., Wilson, A., Verlander, N. Q., Alexander, E., Fleming, P., . . . Demirjian, A. (2024). Clinical outcomes of <i>Staphylococcus capitis</i> isolation from neonates, England, 2015-2021: a retrospective case-control study.. Archives of disease in childhood. Fetal and neonatal edition, 109(2), 128-134. doi:10.1136/archdischild-2023-325887
2023
Building a queer- and trans-inclusive microbiology conference.
Gregor, R., Johnston, J., Coe, L. S. Y., Evans, N., Forsythe, D., Jones, R., . . . Weissman, J. L. (2023). Building a queer- and trans-inclusive microbiology conference.. mSystems, 8(5), e0043323. doi:10.1128/msystems.00433-23
Detection, survival, and persistence of Staphylococcus capitis NRCS-A in neonatal units in England.
Moore, G., Barry, A., Carter, J., Ready, J., Wan, Y., Elsayed, M., . . . UK Health Security Agency Staphylococcus capitis Environment Task and Finish Group. (2023). Detection, survival, and persistence of Staphylococcus capitis NRCS-A in neonatal units in England.. The Journal of hospital infection, 140, 8-14. doi:10.1016/j.jhin.2023.06.030
IS<i>1</i>-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene <i>nfsB</i> causes nitrofurantoin heteroresistance in <i>Escherichia coli</i>.
Wan, Y., Sabnis, A., Mumin, Z., Potterill, I., Jauneikaite, E., Brown, C. S., . . . Sriskandan, S. (2023). IS<i>1</i>-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene <i>nfsB</i> causes nitrofurantoin heteroresistance in <i>Escherichia coli</i>.. Microbial genomics, 9(9). doi:10.1099/mgen.0.001102
Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom.
Wan, Y., Ganner, M., Mumin, Z., Ready, D., Moore, G., Potterill, I., . . . Pichon, B. (2023). Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom.. The Journal of infection, 87(3), 210-219. doi:10.1016/j.jinf.2023.06.020
Soft Tissue Infection of Immunocompetent Man with Cat-Derived Globicatella Species.
Jones, N. K., Coelho, J., Logan, J. M. J., Broughton, K., Hopkins, K. L., Pichon, B., . . . Gouliouris, T. (2023). Soft Tissue Infection of Immunocompetent Man with Cat-Derived Globicatella Species.. Emerging infectious diseases, 29(8), 1684-1687. doi:10.3201/eid2908.221770
Trends in coagulase-negative staphylococci (CoNS), England, 2010-2021.
Paranthaman, K., Wilson, A., Verlander, N., Rooney, G., Macdonald, N., Nsonwu, O., . . . Demirjian, A. (2023). Trends in coagulase-negative staphylococci (CoNS), England, 2010-2021.. Access microbiology, 5(6), acmi000491.v3. doi:10.1099/acmi.0.000491.v3
RECONSTRUCTING AND PREDICTING THE SPATIAL EVOLUTION OF CARBAPENEMASE-PRODUCING ENTEROBACTERIACEAE OUTBREAKS
Myall, A., Wiedermann, M., Vasikasin, P., Klamser, P., Wan, Y., Zachariae, A., . . . Brockmann, D. (2023). RECONSTRUCTING AND PREDICTING THE SPATIAL EVOLUTION OF CARBAPENEMASE-PRODUCING ENTEROBACTERIACEAE OUTBREAKS. International Journal of Infectious Diseases, 130, S65. doi:10.1016/j.ijid.2023.04.163
Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants.
Harvey, E. J., Ashiru-Oredope, D., Hill, L. F., Demirjian, A., & United Kingdom Health Security Agency Staphylococcus capitis Incident Management Team. (2023). Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants.. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 29(1), 10-12. doi:10.1016/j.cmi.2022.09.016
2022
Good IPC practice for the cleaning and handling of incubators and other equipment in neonatal units
Wan, Y. (2022). Good IPC practice for the cleaning and handling of incubators and other equipment in neonatal units. UK Health Security Agency. Retrieved from https://www.gov.uk/
Improved contact tracing using network analysis and spatial-temporal proximity
Myall, A., Peach, R., Wan, Y., Mookerjee, S., Jauneikaite, E., Bolt, F., . . . Barahona, M. (2022). Improved contact tracing using network analysis and spatial-temporal proximity. International Journal of Infectious Diseases, 116, S20. doi:10.1016/j.ijid.2021.12.047
2021
Alterations in chromosomal genes <i>nfsA</i>, <i>nfsB</i>, and <i>ribE</i> are associated with nitrofurantoin resistance in <i>Escherichia coli</i> from the United Kingdom.
Wan, Y., Mills, E., Leung, R. C. Y., Vieira, A., Zhi, X., Croucher, N. J., . . . Sriskandan, S. (2021). Alterations in chromosomal genes <i>nfsA</i>, <i>nfsB</i>, and <i>ribE</i> are associated with nitrofurantoin resistance in <i>Escherichia coli</i> from the United Kingdom.. Microbial genomics, 7(12). doi:10.1099/mgen.0.000702
Characterising contact in disease outbreaks via a network model of spatial-temporal proximity
2020
GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.
Wan, Y., Wick, R. R., Zobel, J., Ingle, D. J., Inouye, M., & Holt, K. E. (2020). GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.. BMC genomics, 21(1), 658. doi:10.1186/s12864-020-07019-6
GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure
2019
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.
Chen, Q., Zhang, X., Wan, Y., Zobel, J., & Verspoor, K. (2019). Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.. Journal of computational biology : a journal of computational molecular cell biology, 26(6), 605-617. doi:10.1089/cmb.2018.0198
2017
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases
Chen, Q., Wan, Y., Zhang, X., Lei, Y., Zobel, J., & Verspoor, K. (2017). Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal of Data and Information Quality, 9(3), 1-27. doi:10.1145/3131611
2016
Evaluation of CD-HIT for constructing non-redundant databases
Qingyu Chen., Yu Wan., Yang Lei., Zobel, J., & Verspoor, K. (2016). Evaluation of CD-HIT for constructing non-redundant databases. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). doi:10.1109/bibm.2016.7822604
2015
Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.
Wan, Y., Gorrie, C. L., Jenney, A., Mirceta, M., & Holt, K. E. (2015). Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.. Genome announcements, 3(5), e01007-e01015. doi:10.1128/genomea.01007-15