140 Chapter 7 Conclusions To conclude, our method demonstrates extreme levels of homoplasy in E. coli that are significantly associated with CTX resistance. Greater access to WGS data provides new opportunities to perform large-scale genome-wide analysis. Homoplasy-based methods can have a potential role in future studies as they constitute an effective strategy to relate phenotypic traits to variable genomic positions. Funding information The authors received no specific grant from any funding agency. Acknowledgements Special thanks to A. C. J. Soer (Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands), B. A. Lamberts (Department of Medical Microbiology and Immunology, Rijnstate, Arnhem, The Netherlands) and C. Verhulst (Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands and Laboratory for Microbiology, Microvida, Breda, The Netherlands) for handling the samples in the laboratory and creating the Illumina sequence libraries. Many thanks to M. P. Kwint and R. Derks (Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands) for helping with SMRT sequencing on the PacBio Sequel I. Many thanks also to M. Janssens (Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands), S. Van Leest (Laboratory for Microbiology, Microvida, Bravis Hospital, The Netherlands), K. T. Veldman and D. J. Mevius (Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands), E.A. Reuland (Medical Microbiology and Infection Control, Amsterdam UMC VUmc, Amsterdam, The Netherlands), W. H. F. Goessens (Erasmus University Medical Center, Rotterdam, The Netherlands), R. W. Bosboom (Department of Medical Microbiology and Immunology, Rijnstate, Arnhem, The Netherlands) and P. Vos (Check-Points, Wageningen, The Netherlands) for providing samples of which some are included in this study.
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