Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014

Abstract

Background: Cholera is endemic in Bangladesh, with outbreaks reported annually. Currently, the majority of epidemic cholera reported globally is El Tor biotype Vibrio cholerae isolates of the serogroup O1. However, in Bangladesh, outbreaks attributed to V. cholerae serogroup O139 isolates, which fall within the same phylogenetic lineage as the O1 serogroup isolates, were seen between 1992 and 1993 and in 2002 to 2005. Since then, V. cholerae serogroup O139 has only been sporadically isolated in Bangladesh and is now rarely isolated elsewhere.

Methods: Here, we present case histories of four cholera patients infected with V. cholerae serogroup O139 in 2013 and 2014 in Bangladesh. We comprehensively typed these isolates using conventional approaches, as well as by whole genome sequencing. Phenotypic typing and PCR confirmed all four isolates belonging to the O139 serogroup.

Findings: Whole genome sequencing revealed that three of the isolates were phylogenetically closely related to previously sequenced El Tor biotype, pandemic 7, toxigenic V. cholerae O139 isolates originating from Bangladesh and elsewhere. The fourth isolate was a non-toxigenic V. cholerae that, by conventional approaches, typed as O139 serogroup but was genetically divergent from previously sequenced pandemic 7 V. cholerae lineages belonging to the O139 or O1 serogroups.

Conclusion: These results suggest that previously observed lineages of V. cholerae O139 persist in Bangladesh and can cause clinical disease and that a novel disease-causing non-toxigenic O139 isolate also occurs.

Fig 1. Mid-point rooted maximum likelihood phylogeny of V. cholerae O139 isolates from this study, excluding the isolate from case 1 (strain 1) but including previously published V. cholerae isolates.

The scale bar represents the number of single nucleotide polymorphisms.

Fig 2. Multi-genome comparison using the Artemis Comparison Tool [29] showing the similarity and synteny of the O-antigen biosynthesis genes (coloured orange) of the O1 N16961 reference sequence (genes VC_0240 –VC_0264), and the draft de novo assemblies of the O139 MO10, the O139 from strain 3 in this study, the O-antigen biosynthesis genes from O139 MO45, and the O139 from strain 1 in this study.

Grey blocks indicate genetic similarity; vertical red lines indicate contig breaks in the draft assemblies. The PCR product of the primer sequences used in this study to identify O139 is shown in green in the genome sequence from strain 1.