Illumina sequencing was performed at UKHSA and followed the same protocol as described by Chattaway et al. (2017) (link). The QIAsymphony system (Qiagen) was used to extract genomic DNA from selected DEC samples. The Nextera XP kit (Illumina) was used to prepare the sequence library for sequencing on the HiSeq 2,500 instrument (Illumina), run with the fast protocol. Trimmomatic v0.27 was utilised to remove bases with a PHRED score of <30 from the leading and trailing ends on the FASTQ reads, with reads <50 bp after quality trimming discarded (Bolger et al., 2014 (link)).
Sequence type (ST) was determined from reads using MOST (v1.0) as previously described by Tewolde et al. (2016) (link) and eBurst Group (eBG) as described in Achtman et al. (2012 (link);Figure 1 ).
Sequence type (ST) was determined from reads using MOST (v1.0) as previously described by Tewolde et al. (2016) (link) and eBurst Group (eBG) as described in Achtman et al. (2012 (link);
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