Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic

Daniel Rios Garza,Keley Nascimento Barbosa Nunes,Rodrigo Vellasco Duarte Silvestre,Edvaldo Carlos Brito Loureiro,Clayton Pereira Silva De Lima,Robert A Edwards,Jedson Ferreira Cardoso,Cristiane C Thompson,Bas E Dutilh,Lena Lillian Canto De Sá Morais,Davi Toshio Inada,Elisabeth C O Santos,Ana Carolina P Vicente,Márcio Roberto T Nunes,Edivaldo Costa Sousa Junior

doi:10.1371/journal.pone.0037283

Abstract

The 7th cholera pandemic reached Latin America in 1991, spreading from Peru to virtually all Latin American countries. During the late epidemic period, a strain that failed to ferment sucrose dominated cholera outbreaks in the Northern Brazilian Amazon region. In order to understand the genomic characteristics and the determinants of this altered sucrose fermenting phenotype, the genome of the strain IEC224 was sequenced. This paper reports a broad genomic study of this strain, showing its correlation with the major epidemic lineage. The potentially mobile genomic regions are shown to possess GC content deviation, and harbor the main V. cholera virulence genes. A novel bioinformatic approach was applied in order to identify the putative functions of hypothetical proteins, and was compared with the automatic annotation by RAST. The genome of a large bacteriophage was found to be integrated to the IEC224's alanine aminopeptidase gene. The presence of this phage is shown to be a common characteristic of the El Tor strains from the Latin American epidemic, as well as its putative ancestor from Angola. The defective sucrose fermenting phenotype is shown to be due to a single nucleotide insertion in the V. cholerae sucrose-specific transportation gene. This frame-shift mutation truncated a membrane protein, altering its structural pore-like conformation. Further, the identification of a common bacteriophage reinforces both the monophyletic and African-Origin hypotheses for the main causative agent of the 1991 Latin America cholera epidemics.

Highlights

Vibrio cholerae strains harboring the O1 or O139 surface antigen are the etiological agents of epidemic cholera
This study provides a broad comprehension of the Latin American seventh pandemic lineage
We show that out of the 332 genes that were located in low GC content/potentially mobile regions, only 55 have been directly implied in virulence, such as the A and B subunits of the cholera toxin (CTX) and the toxin co-regulated pilus cluster (TCP) (Supporting Table S2)

Summary

Introduction

Vibrio cholerae strains harboring the O1 or O139 surface antigen are the etiological agents of epidemic cholera. The choleragenic O1 lineages comprise the classical and El Tor biotypes, responsible for the sixth and seventh cholera pandemics, respectively [1]. They originated independently [2] and the estimated divergence date of their most recent common ancestor (MRCA) is the end of the nineteenth century [3]. The El Tor biotype became epidemic in Indonesia and spread to Asia, Africa, Europe and reached Latin America in 1991 [4]. Thirty years after its pandemic expansion in the 1960s, it reached Latin America at the harbor city of Chimbote/ Peru where it caused a major outbreak that quickly spread throughout the continent [6]. Latin America had not experienced a cholera epidemic since the fifth pandemic (1881–96) [7]

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