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

Abstract

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.

Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes

“…VSP-II constitutes a 26.9-kb genomic region composed of 24 open reading frames (ORFs) between VC0490 and VC0516 according to the annotation of V. cholerae N16961. Previous studies, including those by our laboratory, demonstrated diversity of VSP-II across the strains (18,23). In particular, we found that all strains partially lacked VSP-II and could be divided into five types: those with a deletion from VC0495 to VC0512 (type 1), those with a deletion from VC0495 to VC0498 (type 2), those with a deletion from VC0495 to VC0498 and a frameshift of VC0490 (type 3), those with a deletion from VC0492 to VC0498 and a frameshift of VC0490 (type 4), and those negative for VSP-II (type 5) ( 2009 contained strains carrying type 2 VSP-II and one VSP-II-negative strain (type 5).…”

“…The prototypical VSP-II was discovered in 2004 and encoded transcriptional regulators, methyl-accepting chemotaxis proteins, a putative RNase, a putative type IV pilin, a DNA repair protein, an integrase, and a number of hypothetical proteins. Although several variants have been identified from different continents, the role of VSP-II remains unclear (9,(13)(14)(15)(16)(17)23). ICEs constitute genetic elements transferable by conjugation and confer multiantimicrobial resistance.…”

Phenotypic and Genotypic Properties of Vibrio cholerae non-O1, non-O139 Isolates Recovered from Domestic Ducks in Germany

“…The role of VSP islands in infection is unclear. It is hypothesized that they increase the fitness advantage of the toxigenic strains [37,67]. In strain T58, a complete TTSS system was identified.…”

“…In toxigenic strains isolated since 1961 [37], two genomic islands are found that were designated Vibrio seventh pandemic islands 1 and 2 (VSP-1, VSP-2). Sequences related to these two islands were mostly absent in the four duck isolates.…”

“…A TTSS consisting of core genes and flanking 5 and 3 regions highly similar to the V. cholerae strain AM-19226 T3SS genomic island [33] is found in isolate T58. In toxigenic strains isolated since 1961 [37], two genomic islands are found that were designated Vibrio seventh pandemic islands 1 and 2 (VSP-1, VSP-2). Sequences related to these two islands were mostly absent in the four duck isolates.…”