The Transmission and Antibiotic Resistance Variation in a Multiple Drug Resistance Clade of Vibrio cholerae Circulating in Multiple Countries in Asia

Abstract

Vibrio cholerae has caused massive outbreaks and even trans-continental epidemics. In 2008 and 2010, at least 3 remarkable cholera outbreaks occurred in Hainan, Anhui and Jiangsu provinces of China. To address the possible transmissions and the relationships to the 7th pandemic strains of those 3 outbreaks, we sequenced the whole genomes of the outbreak isolates and compared with the global isolates from the 7th pandemic. The three outbreaks in this study were caused by a cluster of V. cholerae in clade 3.B which is parallel to the clade 3.C that was transmitted from Nepal to Haiti and caused an outbreak in 2010. Pan-genome analysis provided additional evolution information on the mobile element and acquired multiple antibiotic resistance genes. We suggested that clade 3.B should be monitored because the multiple antibiotic resistant characteristics of this clade and the 'amplifier' function of China in the global transmission of current Cholera pandemic. We also show that dedicated whole genome sequencing analysis provided more information than the previous techniques and should be applied in the disease surveillance networks.

Fig 1. Maximum-likelihood phylogenetic tree of V. cholerae in wave 3 based on SNPs across the whole core genome, excluding possible recombination regions.

The wave and clade designation is same to Mutreja et al. paper[3] and our previous study[6]. The labels of the strains (SNXXX) in wave 3 were same to our previous study[6] except for the 5 strains isolated in 2008 and 2010 China cholera outbreaks. The pre-seventh pandemic isolate M66 was used as an outgroup to root the tree. The terminal branches are colored according to the areas where the strains were isolated.

Fig 2. Sequence comparisons of SXT elements in O139 strain MO10, the 5 Chinese outbreak strains and Alteromonas macleodii Aegaean Sea MED64.

Arrows with a black line represent the SXTs and CDSs, and the gray blocks represent the alignments. The colored arrows represent different types of genes (black: int, light blue: tnp, brown: tra, purple: ssb, dark blue: set, and others for resistance genes). The attL and attR sequences located on both ends of each SXT are displayed with red triangles. The read coverages in SXTs from the Chinese strains are displayed using green curves. Five hotspots are represented by gray triangles linked by gray dashed lines. The highly recombined region between tnp genes carrying resistance genes is marked using red triangles linked by red dashed lines. Three pairs of direct repeat sequences are represented by red, dark blue and purple lines. The scale at the bottom indicates the locations of the sequences.

Fig 3. Transmission routes of the 3 V. cholerae clades in Wave 3.

V. cholerae Clade 3.B and Clade 3.C circulated in South Asia. Clade 3.B reached China, (a) Hainan; (b) Anhui; (c) Jiangsu. Clade 3.C and Clade 3.A reached Haiti and Africa, respectively. The blue and red circles indicate the circulation of Clade 3.B and Clade 3.C. The map was generated with ArcGIS.