Genome Dynamics of Vibrio cholerae Isolates Linked to Seasonal Outbreaks of Cholera in Dhaka, Bangladesh

Abstract

The temporal switching of serotypes from serotype Ogawa to Inaba and back to Ogawa was identified in Vibrio cholerae O1, which was responsible for seasonal outbreaks of cholera in Dhaka during the period 2015 to 2018. In order to delineate the factors responsible for this serotype transition, we performed whole-genome sequencing (WGS) of V. cholerae O1 multidrug-resistant strains belonging to both the serotypes that were isolated during this interval where the emergence and subsequent reduction of the Inaba serotype occurred. The whole-genome-based phylogenetic analysis revealed clonal expansion of the Inaba isolates mainly responsible for the peaks of infection during 2016 to 2017 and that they might have evolved from the prevailing Ogawa strains in 2015 which coclustered with them. Furthermore, the wbeT gene in these Inaba serotype isolates was inactivated due to insertion of a transposable element at the same position signifying the clonal expansion. Also, V. cholerae isolates in the Inaba serotype dominant clade mainly contained classical ctxB allele and revealed differences in the genetic composition of Vibrioseventh pandemic island II (VSP-II) and the SXT integrative and conjugative element (SXT-ICE) compared to those of Ogawa serotype strains which remerged in 2018. The variable presence of phage-inducible chromosomal island-like element 1 (PLE1) was also noted in the isolates of the Inaba serotype dominant clade. The detailed genomic characterization of the sequenced isolates has shed light on the forces which could be responsible for the periodic changes in serotypes of V. cholerae and has also highlighted the need to analyze the mobilome in greater detail to obtain insights into the mechanisms behind serotype switching.IMPORTANCE The switching of serotype from Ogawa to Inaba and back to Ogawa has been observed temporally in Vibrio cholerae O1, which is responsible for endemic cholera in Bangladesh. The serospecificity is key for effective intervention and for preventing cholera, a deadly disease that continues to cause significant morbidity and mortality worldwide. In the present study, WGS of V. cholerae allowed us to better understand the factors associated with the serotype switching events observed during 2015 to 2018. Genomic data analysis of strains isolated during this interval highlighted variations in the genes ctxB, tcpA, and rtxA and also identified significant differences in the genetic content of the mobilome, which included key elements such as SXT ICE, VSP-II, and PLE. Our results indicate that selective forces such as antibiotic resistance and phage resistance might contribute to the clonal expansion and predominance of a particular V. cholerae serotype responsible for an outbreak.

Keywords: Vibrio cholerae; genomics; seasonality; serogroups.

FIG 1

Temporal distribution of Vibrio cholerae serotypes from 2005 to 2018. The graph shows the serotype distribution of V. cholerae isolates identified at icddr,b, Dhaka, Bangladesh, for a 14-year period (2005 to 2018). The Ogawa and Inaba serotypes of V. cholerae are indicated in blue and red, respectively. The non-O1/O139 serotypes are represented in green.

FIG 2

Whole-genome-based phylogeny. The whole-genome-based phylogenetic tree of 34 in-house-sequenced V. cholerae isolates along with genomes of reference strain N16961 and outgroup strain M66 revealed broad correlation between the year of isolation and serotype. The colors of the node labels indicate the serotypes as follows: blue, Ogawa; red, Inaba. Clades A and B are marked in orange and green, respectively. The adjacent colored bars indicate the year of isolation, ctxB allele, SXT ICE (integrative conjugative element), and PLE1 (phage-inducible chromosomal island-like element 1), respectively.

FIG 3

Genetic organization of VSP-II. The open reading frames (ORFs) of the VSP-II island (VC_490 to VC_516) in the genome of V. cholerae strain N16961 are represented in black at the bottom of the figure. The ORFs in each line in the top panel indicate their status in 34 in-house-sequenced V. cholerae isolates, and blue and red data indicate serotypes Ogawa and Inaba, respectively. The comparison was generated using BLAST Atlas.

FIG 4

Variations in SXT ICE. The SXT pangenome was constructed iteratively by appending unique regions of SXT elements of 34 in-house-sequenced isolates and the Ogawa RND6878 strain onto that of the IDH_1986 strain which served as the initial seed. The SXT pangenome is represented in the outer circle (black), and the pink and yellow innermost circles represent individual SXT ICE elements of strains Ogawa RND6878 and IDH_1986, respectively. The red and green color coding of the rest of the inner circles indicates in-house-sequenced isolates belonging to clade A and clade B, respectively, as shown in Fig. 2.