Publications

Page content

1. Journal articles

  1. Wan Y, Ganner M., Mumin Z., Ready D., Moore G., Potterill I., et al. Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom. Journal of Infection 2023; 87(3):210–219. DOI: 10.1016/j.jinf.2023.06.020.
  2. Wan Y, Sabnis A, Mumin Z, Potterill I, Jauneikaite E, Brown CS, et al. IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli. Microbial Genomics. 2023; 9(9):001102. DOI: 10.1099/mgen.0.001102.
  3. Wan Y, Myall A, Boonyasiri A, Bolt F, Ledda A, Mookerjee S, et al. Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. medRxiv; 2023. p. 2021.10.28.21265436. DOI: 10.1101/2021.10.28.21265436.
  4. Moore G, Barry A, Carter J, Ready J, Wan Y, et al. The detection, survival and persistence of Staphylococcus capitis NRCS-A in neonatal units in England. Journal of Hospital Infection. 2023; 140: 8e14. DOI: 10.1016/j.jhin.2023.06.030.
  5. Yuan JM, Nugent C, Wilson A, Verlander NQ, Alexander E, Fleming P, …, Wan Y, et al. Clinical outcomes of Staphylococcus capitis isolation from neonates, England, 2015–2021: a retrospective case–control study. Archives of Disease in Childhood - Fetal and Neonatal Edition. 2023; 9. DOI: 10.1136/archdischild-2023-325887.
  6. Jones NK, Coelho J, Logan JMJ, Broughton K, Hopkins KL, …, Wan Y, et al. Soft Tissue Infection of Immunocompetent Man with Cat-Derived Globicatella Species. Emerging Infectious Diseases. 2023; 29:1684–1687. DOI: 10.3201/eid2908.221770.
  7. Gregor R, Johnston J, Coe LSY, Evans N, Forsythe D, Jones R, …, Wan Y, et al. Building a queer- and trans-inclusive microbiology conference. mSystems. 2023 Oct 6; 0(0):e00433-23. DOI: 10.1128/msystems.00433-23.
  8. Paranthaman K, Wilson A, Verlander N, Rooney G, Macdonald N, Nsonwu O, …, Wan Y, et al. Trends in Coagulase negative Staphylococci (CoNS), England, 2010-2021. Access Microbiology. 2023; 5(6): 000491.v3. DOI: 10.1099/acmi.0.000491.v3.
  9. Myall A, Wiedermann M, Vasikasin P, Klamser P, Wan Y, et al. Reconstructing and predicting the spatial evolution of carbapenemase-producing Enterobacteriaceae outbreaks. International Journal of Infectious Diseases 2023; 130: S65. DOI: 10.1016/j.ijid.2023.04.163.
  10. Harvey EJ, Ashiru-Oredope D, Hill LF, Demirjian A, Jauneikaite E, Wan Y, et al. Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants. Clinical Microbiology and Infection, 2022; 29(1): 10–12. DOI: 10.1016/j.cmi.2022.09.016.
  11. Myall A, Peach R, Wan Y, Mookerjee S, Jauneikaite E, et al. Improved contact tracing using network analysis and spatial-temporal proximity. International Journal of Infectious Diseases 2022;116: S20. DOI: 10.1016/j.ijid.2021.12.047.
  12. Wan Y, Mills E, Leung RCY, Vieira A, Zhi X, Croucher NJ, et al. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microbial Genomics. 2021; 7(12):000702. DOI: 10.1099/mgen.0.000702.
  13. Wan Y, Wick R R, Zobel J, Ingle D J, Inouye M, & Holt K E. GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure. BMC Genomics, 2020; 21: 658. DOI: 10.1186/s12864-020-07019-6.
  14. Chen Q, Wan Y, Zhang X, Lei Y, Zobel J, & Verspoor K. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal of Data and Information Quality (JDIQ), 2018; 9(3): 17. DOI: 10.1145/3131611.
  15. Chen Q, Zhang X, Wan Y, Zobel J & Verspoor K. Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. Journal of Computational Biology, 2018. DOI:10.1089/cmb.2018.0198.
  16. Chen Q, Wan Y, Lei Y, Zobel J, & Verspoor K. Evaluation of CD-HIT for constructing non-redundant databases. 2016 IEEE International Conference on Bioinformatics and Biomedicine. 2016; 703-706. IEEE. DOI: 10.1109/BIBM.2016.7822604.
  17. Wan Y, Gorrie C L, Jenney A, Mirceta M, & Holt K E. Draft genome sequence of a clinical isolate of Serratia marcescens, strain AH0650_Sm1. Genome Announcements, 2015; 3(5): e01007-15. DOI: 10.1128/genomeA.01007-15.

2. Conference or workshop presentations

  1. Oral presentation (online): Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes. 20 Sep 2023. EMBO Workshop: Plasmids as vehicles of AMR spread.
  2. Poster [04]: Staphylococcus capitis NRCS-A clone is widespread in neonatal units across the United Kingdom. Staph GBI Conference. 22–23 Jun 2023. Galway, Ireland.
  3. Poster [P684]: IS1-related large-scale deletion of chromosomal nfsB regions causes nitrofurantoin heteroresistance in Escherichia coli. Microbiology Society Annual Conference. 17–20 Apr 2023. Birmingham, UK.
  4. Poster and five-min oral presentation: Staphylococcus capitis NRCS-A clone is widespread among neonatal units across the United Kingdom. 1st UKHSA Conference. 18–19 Oct. Leeds, UK.
  5. Poster [04672]: Genomic investigation of increased Staphylococcus capitis infections in neonatal intensive care units across England. 23–26 Apr 2022. 32nd European Congress of Clinical Microbiology & Infectious Diseases (online).
  6. Poster [03080]: Genomic and phylogenetic analyses of multidrug-resistant Pseudomonas aeruginosa isolates from a persistent nosocomial outbreak. 23–26 Apr 2022. 32nd European Congress of Clinical Microbiology & Infectious Diseases (online).
  7. Poster [07422] (co-author): Persistence, susceptibility and environmental reservoirs of NRCS-A Staphylococcus capitis in English neonatal intensive care units. 23–26 Apr 2022. 32nd European Congress of Clinical Microbiology & Infectious Diseases (online).
  8. Poster [P002]: Nitrofurantoin-resistant Escherichia coli in the UK: genetic basis, diversity, and undetected occurrences. Annual Conference Online 2021. 26 Apr 2021. London, UK. Microbial Society. Abstract: doi.org/10.1099/acmi.ac2021.po0086.
  9. Oral presentation: A network approach for detecting horizontal co-transfer of antimicrobial resistance genes in bacteria. 27–28 Nov 2018. ABACBS-2018, Parkville, VIC, Australia. Australian Bioinformatics and Computational Biology Society.
  10. Poster [POA-341]: Network analysis of bacterial genes to predict horizontal co-transfer and mobile genetic elements. Registration Award based on research summary. 8–12 Jul 2018. SMBE2018, Yokohama, Japan. Society of Molecular Biology and Evolution.
  11. Poster: Integrative analysis of DNA methylation and gene expression in breast cancer. 11–12 Oct 2014. ABiC 2014, Parkville, VIC, Australia. Australian Bioinformatics and Computational Biology Society.
  12. Poster: Integrative analysis of DNA methylation and gene expression in breast cancer. ABiC 2014 Conference, Parkville, VIC, Australia. 11–12 Oct 2014.
  13. A comparison of three approaches to prokaryotic genome annotation. MESB19 course, Gothenburg, Sweden, 25–29 Aug 2019. DOI: 10.13140/RG.2.2.21120.79365.

3. Doctor of Philosophy

Thesis

Wan, Y. Detecting horizontal co-transfer of antimicrobial resistance genes in bacteria: a network approach. (The University of Melbourne, 2019).

This is the final version of my PhD thesis, which was submitted to the University of Melbourne on 9 August 2019.

Oration

I presented the work for my thesis on Friday 17 August 2018 in Bio21 Institute to the Department of Biochemistry and Molecular Biology in which I enrolled. A poster of the oration can be accessed via this link.