Genomic analysis of pathogenic isolates ofVibrio choleraefrom eastern Democratic Republic of the Congo (2014-2017)

Abstract

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Over the past recent years, <jats:italic>Vibrio cholerae</jats:italic> 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.</jats:p></jats:sec><jats:sec><jats:title>Methods/Principal findings</jats:title><jats:p>Phenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of <jats:italic>V. cholerae</jats:italic> associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were <jats:italic>V. cholerae</jats:italic> O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to <jats:italic>V. cholerae</jats:italic> isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other <jats:italic>V. cholerae</jats:italic> isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates.</jats:p></jats:sec><jats:sec><jats:title>Conclusions/Significance</jats:title><jats:p>Current 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. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.</jats:p></jats:sec><jats:sec><jats:title>Author’s summary</jats:title><jats:p>Cholera is a severe diarrheal disease caused by the Gram-negative bacterium <jats:italic>Vibrio cholerae.</jats:italic> After originating in Asia, the disease spread across sub-Saharan Africa, notably Democratic Republic of the Congo. The aim of our study was to assess the transmission pattern of <jats:italic>V. cholerae</jats:italic> strains prevailing in eastern DRC, and determine their genetic relatedness to strains from other African countries and other parts of the world. Between 2014 and 2017, we isolated <jats:italic>V. cholerae</jats:italic> from fecal samples of patients with acute diarrhea in eastern DRC, and subsequently examined the DNA of the bacteria. The results show that they all clustered in two genetic groups (ST69 and ST515) falling within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and T10 introduction event in East Africa. The genetic signature of ST515 may be involved in its adaptation to environmental conditions found in eastern DRC, and contribute to its extended geographic distribution. Indeed, unlike the locally endemic ST69, ST515 is spreading extensively through DRC cross-border countries such as South Sudan, Tanzania, Uganda and Zambia. This plainly justifies a regional strategy to strengthen the fight against cholera in eastern Africa.</jats:p></jats:sec>

Persistence of the T12 Vibrio cholerae O1 lineage in West Africa: Insights from a Regional Sequencing Workshop

“…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 2011–2018 suggest that the T10 lineage is predominant in Central Africa (2,12), but more recent data are needed to delineate the boundary between T10 and T12 circulation.…”

“…Forty-four genomes produced reference-based assemblies (covering at least 95% of the N16961 reference at >100x coverage, Appendix Table 2 ). We aligned these genomes to 1280 previously-published V. cholerae O1 whole genome sequences (1,2,11,12) and generated a maximum likelihood tree from these data, which showed that all 44 isolates belong to the T12 lineage. Two sequenced isolates did not align to the reference (NGA_148_2019, NGA_252_2019), and we found that the reads did not map to the wbe or wbf gene clusters associated with the O1 and O139 serogroups, respectively (or the ctxA cholera toxin) (13).…”

The Vibrio cholerae Seventh Pandemic islands act in tandem to defend against a circulating phage

“…However, so far, no V. cholerae phage has been reported to be sensitive to these two islands. Due to the prevalence of these two genomic islands in the circulating clinical isolates of V. cholerae [2,26,27], we hypothesize that novel phages that are sensitive to these islands exist and can be isolated. Therefore, we screened for novel phages from rice water stool (RWS) samples that had been collected from cholera patients in Bangladesh on permissive host, which is an O1 El Tor V. cholerae E7946 derivative lacking both VSP-I and VSP-II islands (ΔVSP) and deleted for prophages CTXΦ and K139 [28,29] .…”

Backward compatibility of whole genome sequencing data with MLVA typing using a newMLVAtypeshiny application: the example ofVibrio cholerae

“…Nine V. cholerae isolates were selected from a collection of isolates characterized in a recent study conducted between 2014 and 2017 in the DRC [7]. In addition, ten V. cholerae isolates collected between 2014 and 2016 in Uganda by G. Bwire and colleagues were selected based on their published data [8].…”