Prevalent chromosome fusion in Vibrio cholerae O1

Abstract

Two circular chromosomes are a defining feature of the bacterial family Vibrionaceae, including the pathogen Vibrio cholerae, with rare reports of isolates with a single, fused chromosome. Here, we use long-read sequencing to analyse 467 V. cholerae O1 isolates from 47 cholera patients and household contacts in Bangladesh. We identify several independent chromosome fusion events that are likely transmissible within a household. Fusions occur in a 12 kilobase-pair homologous sequence shared between the two chromosomes and are stable for at least 200 generations under laboratory conditions. We find no detectable effect of fusion on V. cholerae growth, virulence factor expression, or biofilm formation. The factors promoting fusion, affecting chromosome stability, and subtle phenotypic or clinical consequences merit further investigation.

Fig. 1. V. cholerae with a fused chromosome identified in multiple patients and households.

A Schematic representation of the study design; B PFGE results for the putatively fused (light blue) and non-fused (dark blue) chromosomes identified by sequencing. Schizosaccharomyces pombe was used as a DNA size marker and V. cholerae strain N16961 as a well-characterized isolate with two chromosomes. PFGE was conducted twice. PFGE: Pulsed-Field Gel Electrophoresis; Mbp: Mega base pair; Vc: Vibrio cholerae; S. pombe: Schizosaccharomyces pombe. Source data is provided as a Source Data file.

Fig. 2. Chromosome fusion events occur in V. cholerae sublineages with a shared homologous sequence on each chromosome.

A Schematic representation of the chromosome fusion with the location of HS1, crtS, the origins of replications and pathogenicity islands indicated. Chr. 2 does in rare cases carry an additional copy of VSP-I; (B) Annotation of genes within the homologous sequence (HS1) at the fusion site; (C) Phylogenetic tree based on 281 high-quality SNVs, along with household membership, the 7PET sublineage designation, the number of chromosomes identified by sequencing, and the number of times HS1 was detected in the genome. Highlighted in light blue are five branches or clades (numbered in red) that include genomes with a fused chromosome. The red diamonds in the tree depict their parent nodes. Branches are color-coded according to ultrafast bootstrap (UF) approximation support; (D) Distribution of fused and non-fused chromosome genomes amongst index cases and household contacts for all five households in which at least one fusion was detected. Mbp: Mega base pair; Kbp: Kilo base pair; Chr: Chromosome; HS1: Homologous Sequence 1; Vc: Vibrio cholerae; UF: UltraFast bootstrap approximation. Source data are provided as a Source Data file.