Atypical El Tor Vibrio cholerae from the second major global seventh-pandemic cholera wave is endemic in Sabah, Malaysia

ABSTRACT 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. In particular, the strains carried two tandem CTX prophage copies in chromosome 2 and three tandem RS1 sequences on chromosome 1, including a Classical type rstR , which is atypical for canonical El Tor. Genome comparisons revealed conserved seventh-pandemic genomic islands (VSP1 and VSP2) 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. IMPORTANCE This study addresses a critical public health concern by investigating the genomic characteristics of Vibrio cholerae O1 strains responsible for recurrent cholera outbreaks in Sabah, Malaysia. Although cholera is largely non-endemic in most parts of Malaysia, Sabah remains an exception, contributing disproportionately to national case counts. By sequencing clinical isolations from the 2019 and 2020 outbreaks, this research provides essential insights into the origins, evolutionary dynamics, and transmission patterns of V. cholerae in a region with persistent endemicity. These findings underscore the importance of continuous genomic surveillance in geographically distinct settings and offer valuable data for informing public health strategies aimed at cholera control and prevention in Southeast Asia.