141 Genome-wide analysis in E. coli unravels homoplasy associated with cefotaxime resistance Author contributions H. F. L. W., J. A. J. W. K. and M. A. H. conceived and supervised the study. J. P. M. C., E. P. M. D., E. K., J. A. S., J. J. V., W. J. G. M. and K. N. performed the data acquisition. J. P. M. C. and E. P. M. D. performed the data analysis. J. P. M. C. performed bioinformatic analysis. J. P. M. C., E. P. M. D. and M. A. H. performed the data interpretation and wrote the manuscript. All authors read and approved the final manuscript. Conflicts of interest The authors declare that there are no conflicts of interest. Footnotes Abbreviations: campC, chromosome-mediated ampC; CTX, cefotaxime; ESBL, extended-spectrum beta-lactamase; EUCAST, European Committee on Antimicrobial Susceptibility Testing; FDR, false discovery rate; FOX, cefoxitin; 3GC, third-generation cephalosporin; MIC, minimum inhibitory concentration; MLST, multilocus sequence typing; NCBI, National Center for Biotechnology Information; pampC, plasmidmediated ampC; qRT-PCR, quantitative reverse-transcriptase PCR; SMRT, singlemolecule real-time; ST, sequence type; VCF, variant calling file; WGS, whole-genome sequencing. All supporting data, code and protocols have been provided within the article or through supplementary data files. Four supplementary tables and three supplementary figures are available with the online version of this article. 7
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