Irenge et al 2020: Genome Sequence of a Pathogenic Vibrio cholerae 01 El Tor Strain Defective for the Entire Vibrio Pathogenicity Island 1

I have been reading the paper Irenge et al (2020): "Genome Sequence of a Pathogenetic Vibrio cholerae O1 El Tor Strain Defective for the Entire Vibrio Pathogenicity Island 1, Isolated in the Eastern Democratic Republic of the Congo". 

In this paper they describe a Vibrio cholerae isolate from a cholera patient from DRC, for which they have sequenced the genome. They found that the isolate belonged to the current pandemic lineage (7PET lineage). A previous paper from this team had reported a larger set of V. cholerae 7PET isolates from DRC, that mostly belonged to the T10 sublineage of 7PET. These previous isolates comprised two different clades of a phylogenetic tree, with ST515 and ST69 sequence types respectively. The isolate sequenced in this paper belonged to the ST515 clade, and was very unusual because it had a complete deletion (about 80 kb long) of the Vibrio pathogenicity island 1 (VPI-1). The island extended from gene VC_0774 to VC_0845. This was surprising as the VPI-1 includes the toxin coregulated pilus (TCP) cluster that plays a critical role in colonisation of the host gut.