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>.

"further frequencies of resistant subpopulations from nitrofurantoin-heteroresistant isolates may challenge conventional nitrofurantoin susceptibility testing in clinical settings comparative genomics escherichia coli insertion sequences nitrofurantoin heteroresistance population analysis profiling whole-genome sequencing structural variation is1 elements resistance mechanism hybrid genome assembly openaccessembargo 0 whole-genome sequencing reads and genome assemblies generated in this study have been deposited under bioproject prjeb58678 in the european nucleotide archive (ena).; previously generated illumina whole-genome sequencing reads of progenitor isolates ec0026b and ec0880b are available under ena accessions err3142418 and err3142524 respectively.; illumina whole-genome sequencing (wgs) reads of ec0026b and ec0880b have been generated previously [ ] and are available under accessions err3142418 and err3142524 respectively in the ena."

"scripts used for aforementioned steps are available at github com/wanyuac/assembly_toolkit."

"Conflicts of interest The authors declare that there are no conflicts of interest."

"Funding information This study was funded by the UK Health Security Agency under United Kingdom National Action Plan on Antimicrobial Resistance (2019–2024)."