Exploring the presence of the T6SS

The 18 components of the full T6SS were extracted from the annotated Nanopore sequence of S. sonnei CIP 106347 and compiled into a singular multi-FASTA file. SRST2 v0.2.0⁵⁴ was then utilised for the purpose of T6SS component gene detection as a custom database. The T6SS components within the multi-FASTA were not pre-clustered and therefore were assigned to gene clusters based on 90% nucleotide similarity via CD-HIT v4.8.1.⁵⁵ Python scripts provided as part of the SRST2 package were utilised to parse the clusters and generate a SRST2 compatible database. SRST2 gene detection was then run utilising the custom T6SS database.