Analysis of Vibrio seventh pandemic island II and novel genomic islands in relation to attachment sequences among a wide variety of Vibrio cholerae strains

Vibrio cholerae O1 El Tor, the pathogen responsible for the current cholera pandemic, became pathogenic by acquiring virulent factors including Vibrio seventh pandemic islands (VSP)‐I and −II. Diversity of VSP‐II is well recognized; however, studies addressing attachment sequence left (attL) sequences of VSP‐II are few. In this report, a wide variety of V. cholerae strains were analyzed for the structure and distribution of VSP‐II in relation to their attachment sequences. Of 188 V. cholerae strains analyzed, 81% (153/188) strains carried VSP‐II; of these, typical VSP‐II, and a short variant was found in 36% (55/153), and 63% (96/153), respectively. A novel VSP‐II was found in two V. cholerae non‐O1/non‐O139 strains. In addition to the typical 14‐bp attL, six new attL‐like sequences were identified. The 14‐bp attL was associated with VSP‐II in 91% (139/153), whereas the remaining six types were found in 9.2% (14/153) of V. cholerae strains. Of note, six distinct types of the attL‐like sequence were found in the seventh pandemic wave 1 strains; however, only one or two types were found in the wave 2 or 3 strains. Interestingly, 86% (24/28) of V. cholerae seventh pandemic strains harboring a 13‐bp attL‐like sequence were devoid of VSP‐II. Six novel genomic islands using two unique insertion sites to those of VSP‐II were identified in 11 V. cholerae strains in this study. Four of those shared similar gene clusters with VSP‐II, except integrase gene.