Atypical El Tor Vibrio cholerae from the second major global seventh pandemic cholera wave is endemic in Sabah, Malaysia
Description
Cholera, caused by Vibrio cholerae, remains a significant diarrheal disease, especially in coastal regions of developing countries. In Malaysia, cholera is largely non-endemic except in Sabah, which has had recurrent outbreaks accounting for ∼75% of national cases between 2004 and 2014. To understand the origin and transmission of the disease, we sequenced the genomes of clinical isolates of V. cholerae O1 collected during an outbreak in 2019 and 2020. Genotypic analyses revealed that all Sabah isolates were atypical El Tor biotype harboring Classical CTX prophage elements. Notably, the strains carried two tandem CTX prophage copies and three tandem RS1 sequences, including a Classical type rstR, which is atypical for canonical El Tor. Genome comparisons revealed conserved seventh-pandemic genomic islands (VSP-1 and VSP-2) and variably arranged biotype-specific loci, suggesting pandemic-lineage markers and mobile elements linked to environmental adaptation. Phylogenetic reconstruction placed the Sabah strains within wave 2 of the seventh-pandemic clade, forming a distinct subclade with two genotypes, consistent with regional endemicity over the last few decades. Although Wave 3 strains have largely replaced Wave 2 globally, an established population of Wave 2 strains in Southeast Asia suggests that they are more resilient than previously thought.
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Institutions
- Universiti Malaysia Sabah