Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)

Abstract

BackgroundOver the past recent years, Vibrio cholerae has been associated with outbreaks in sub-Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries. Conclusions/SignificanceCurrent data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years.

Vibrio cholerae multifaceted adaptive strategies in response to bacteriophage predation in an endemic region of the Democratic Republic of the Congo

“…We analyzed toxigenic V. cholerae O1 isolated from patients in the Great Lakes, a cholera endemic region of the Democratic Republic of the Congo (DRC), between 2013-2017. Bayesian phylogeography shows that all strains derived from the East Africa T10 introduction event 5 , consistent with establishment of a regional endemic focus, and identified two major lineages, with the most recent correlating to ST515, a cholera cluster previously found in the Lake Kivu and expanding northward 6 . We also identified a novel ICP1 bacteriophage, genetically distinct from previous ICP1 isolates detected in Asia 7,8 , from stool samples of cholera patients.…”

“…Twenty-one (87.5%) of 24 strains were V. cholerae O1 serotype Inaba, while 3 (12.5%) were serotype Ogawa, indicating that the two serotypes were co-circulating. All strains were ctxB genotype-I in wave 3 and were within the T10 introductory clade 5,6 .…”

Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa

“…During the workshop, we sequenced these isolates on the Oxford Nanopore MinION platform, producing 44 genomes covering at least 95% of the N16961 reference at >100x coverage ( Figure 2 , Figure 2—source data 1 ). We aligned these genomes to 1280 previously published V. cholerae O1 whole genome sequences ( Bwire et al, 2018 ; Irenge et al, 2020 ; Weill et al, 2019 ; Wick et al, 2017 ), which provide a broad overview of global seventh pandemic O1 cholera diversity. The majority of these sequences are from Africa and South Asia, and reported cases in West and Central Africa ( World Health Organization, 2019 ) are well represented by the sequence data ( Figure 2—source data 2 , Figure 2—figure supplement 1 , Figure 2—figure supplement 2 ).…”

“… Accession numbers, references, and basic metadata for sequences included in global phylogeny. The majority of these data were compiled by Weill et al, and the majority of background sequences were originally published in Weill et al, 2017 , Weill et al, 2017 , Irenge et al, 2020 , and Bwire et al, 2018 , among others. …”

“…As of this writing, there are no published V. cholerae O1 genomes from the nearby countries of Benin, Burkina Faso, or Mali, for example, from after 2010. Sequences from Central African Republic, South Sudan and Democratic Republic of the Congo from 2011 to 2018 suggest that the T10 lineage is predominant in Central Africa ( Irenge et al, 2020 ; Weill et al, 2019 ), but more recent data are needed to delineate the boundary between T10 and T12 circulation.…”