The MinION nanopore sequencer, a device the size of a large USB memory stick, has been successfully used with Illumina HiSeq data to identify a previously uncharacterized insertion site of a chromosomal antibiotic resistance island (which is flanked by repetitive sequence and likely to have been horizontally transferred) in a strain of Salmonella enterica subsp. enterica serovar Typhi. Nanopore technology can produce long sequence reads that are necessary for characterizing such complex repetitive sequence regions, and this proof-of-principle study demonstrates the potential of this technology for tracking the spread of bacterial pathogens and, ultimately, its future applicability in the clinic.