Vibrio cholerae O47 associated with a cholera-like diarrheal outbreak concurrent with seasonal cholera in Bangladesh

Abstract

The Ganges delta of the Bay of Bengal is a recognized hotspot for the emergence and spread of novel variants of Vibrio cholerae. Despite being a diverse species, very little information is available concerning environmental and human-associated aspects of V. cholerae serogroups, other than the two major epidemic-related serogroups O1 and O139. This represents a crucial gap in understanding the spectrum of diversity, ecology, and epidemiology of the species influencing the dynamics of global cholera. In this study, we describe an emerging variant of V. cholerae displaying the antigenic property of serogroup O47, associated with a cholera-like outbreak in coastal Bangladesh where cholera has been endemic for centuries. This outbreak coincides with a rise in cases of cholera caused by V. cholerae O1, as well as frequency of isolation of serogroups O47 and O1 from the environment. The V. cholerae O47 isolates proved clonal in nature, and their genome biology revealed distinct features, with respect to multidrug resistance (MDR), serogroup-specific genes, genomic island combinations, and overall phylogenetic properties. Genome comparison confirmed the absence of canonical virulence factors of V. cholerae O1 and O139, namely, cholera toxin (CTX) and toxin-co-regulated pili (TCP), and the presence of putative virulence factors including type 3 secretion system (T3SS) and an MDR pseudo-compound transposon, carrying genes for macrolide resistance and extended spectrum beta-lactamase. Results of the study suggest that V. cholerae O47 could represent an emerging Vibrio pathogen with the potential to spread virulence and antimicrobial resistance traits impacting the management of cholera-like diseases.IMPORTANCEDespite the global insurgence of human diseases caused by Vibrios in recent years, most research focuses only on the O1 serogroup of V. cholerae, leaving a significant gap concerning the environmental and human-associated aspects of other serogroups found in nature. Although other serogroups are often found associated with sporadic diarrhea cases, in 1992-1993, a massive cholera-like diarrhea epidemic was initiated by a "non-O1" serogroup, namely, O139 that temporally displaced O1 from endemic cholera in the Bay of Bengal villages of Bangladesh and India, highlighting the potential threat they might pose. This study describes yet another emerging variant of V. cholerae, displaying the antigenic property of serogroup O47, associated with a cholera-like outbreak in a coastal locality in Bangladesh. Findings of the study offer critical insights into the genome biology of V. cholerae O47 and its potential implications for understanding their ecology and epidemiology of cholera-like diseases.

Keywords: NOVC; Vibrio cholerae; antimicrobial resistance; cholera; genome analysis; genomic island; outbreak; serogroup.

Fig 1

Isolation history of V. cholerae O1 and NOVC by month from clinical (A) and environmental (B) samples collected in Mathbaria from December 2010 to December 2012. X-axis denotes. X-axis denotes the month, and Y-axis denotes the cumulative number of isolates from culture-based techniques in bi-weekly sampling scheme

Fig 2

Single nucleotide polymorphism (SNP)-based phylogeny of V. cholerae O47. Pandemic-generating (PG) and V. cholerae O47 clades are marked by colored bars. The tree was constructed from SNPs called against the V. cholerae El Tor reference genome N16961, and a V. paracholerae (EDC-792) was used as an outgroup to root the tree. The scale bar represents the number of substitutions per site per genome.

Fig 3

Comparison of gene content in (A) VPI-2 and (B) MDR pseudo-compound transposon found in V. cholerae O47 genome in respect to reference genomes. (A) VPI-2 region from reference V. cholerae El Tor strain N16961 and for panel B, MDR pseudo-compound transposon found in Yemen V. cholerae El Tor strain CNRVC19243 was used as reference.

Fig 4

Genome blast atlas comparison of V. cholerae O47, V. cholerae O1, V. cholerae O139, and other NOVC. Each ring in the atlas represents a genome with two chromosomes merged and colored by the chosen color representing a group of organisms. GCs are denoted by black bars, and predicted annotations are mentioned (described in Table 2) in the bottom right panel.

Fig 5

Comparison of the O-antigen-encoding region (wb*) of V. cholerae O47 MN06 isolated from Mathbaria outbreak and reference V. cholerae O47 RIMD2214285. The genetic orientation organization of the genes is denoted by arrows. Genes conserved across V. cholerae serogroups are marked by black arrows, genes that were only found in O47 serogroup are marked by pink arrows, and unique genes only found in Mathbaria outbreak isolates are marked as green arrows.