Molecular epidemiology of geographically dispersed Vibrio cholerae, Kenya, January 2009-May 2010

Abstract

Numerous outbreaks of cholera have occurred in Kenya since 1971. To more fully understand the epidemiology of cholera in Kenya, we analyzed the genetic relationships among 170 Vibrio cholerae O1 isolates at 5 loci containing variable tandem repeats. The isolates were collected during January 2009-May 2010 from various geographic areas throughout the country. The isolates grouped genetically into 5 clonal complexes, each comprising a series of genotypes that differed by an allelic change at a single locus. No obvious correlation between the geographic locations of the isolates and their genotypes was observed. Nevertheless, geographic differentiation of the clonal complexes occurred. Our analyses showed that multiple genetic lineages of V. cholerae were simultaneously infecting persons in Kenya. This finding is consistent with the simultaneous emergence of multiple distinct genetic lineages of V. cholerae from endemic environmental reservoirs rather than recent introduction and spread by travelers.

Figure 1

Geographic/climatic regions as defined in a study of the genetic relatedness of O1 Vibrio cholerae isolates, Kenya, January 2009–May 2010.

Figure 2

Genetic relatedness of O1 Vibrio cholerae isolates from an outbreak of cholera, Kenya, January 2009–May 2010. The 3 largest clonal complexes are shown; smaller clonal complexes consisted of 2 or 3 genotypes. A) Clonal complex 1 was observed in each geographic/climatic region. B) Clonal complex 2 was detected in the Rift Valley (western part of the arid and semi-arid region) and in the coastal, lower eastern, and highland (primarily in informal settlements around Nairobi, represented by asterisks) regions. C) Clonal complex 3 was detected in the coastal, lake, and highland regions and in the Rift Valley (arid and semi-arid region).Genetic relatedness was determined by using eBURSTv3 (http://eburst.mlst.net/). Each genotype is represented by a node in the diagram; each connecting line represents an allelic change at a single locus.

Figure 3

Distribution of Vibrio cholerae isolates, by clonal complex and month of isolation, Kenya, January 2009–May 2010. A) Highland region, including informal settlements around Nairobi. B) Coastal region. C) Arid and semi-arid region. D) Lower eastern region.