Genomic Microevolution of Vibrio cholerae O1, Lake Tanganyika Basin, Africa

Abstract

C holera is an acute life-threatening diarrheal disease responsible for ≈4.3 million cases and 142,000 deaths annually worldwide (1). Excluding epidemic peaks in Haiti and Yemen (2,3), most cases of cholera originate from sub-Saharan Africa, predominantly the African Great Lakes Region (AGLR); specifically, the countries of the Lake Tanganyika basin (4). Many recurrent cholera outbreaks in the Democratic Republic of the Congo (DRC), Tanzania, Burundi, and Zambia have been linked to a common hotspot area around the Lake Tanganyika basin (5-8).By the end of 2018, the World Health Organization had noted a steady decline in cholera cases throughout the world, including the AGLR (9). Continuous genomic surveillance of circulating Vibrio cholerae bacteria strains is required to understand the transmission dynamics and genetic evolution of V. cholerae and potentially to guide prevention and response interventions to continue the trend toward decreasing case numbers, in line with the global cholera roadmap to 2030 (10). One lineage, seventh pandemic V. cholerae O1 El Tor (7PET), is responsible for the current pandemic, which began in 1961 (11); Africa was hit by 7PET in 1970 (11). During 1970-2014, >11 different 7PET sublineages were introduced from South Asia into Africa, and sublineage AFR10 (previously T10) replaced AFR5 (previously T5) in the AGLR in the late 1990s (11). Sublineage AFR13 (previously T13) was identified in East Africa (Tanzania, Uganda, Kenya) and Zimbabwe (12). We tracked the 7PET populations circulating in the Lake Tanganyika basin by studying recent V. cholerae O1 isolates collected in the region by conventional bacteriology and genomics and placing these genomes in a broader phylogenetic context to elucidate their evolutionary history. The StudyWe analyzed 96 V. cholerae O1 isolates collected during 2015-2020 in DRC (86 clinical isolates, including 39 collected in 2018-2020) and Tanzania (10 environmental isolates from fish and lake water) (Appendix 1, https://wwwnc.cdc.gov/EID/article/29/1/22-0641-App1.pdf; Appendix 2 Table 1, https://wwwnc. cdc.gov/EID/article/29/1/22-0641-App2.xlsx). We subjected the isolates to antimicrobial susceptibility testing, whole-genome sequencing, genomic characterization, and phylogenetic analyses, as previously Genomic Microevolution ofVibrio cholerae O1,

Genomic evolution and rearrangement of CTX-Φ prophage elements in Vibrio cholerae during the 2018-2022 cholera outbreaks in The Democratic Republic of Congo

“…Furthermore, our findings are in line with recent studies that show an AFR10d decline and the dominance of the AFR10e sublineage (23). In particular, we demonstrate that V.…”

“…Furthermore, our findings are in line with recent studies that show an AFR10d decline and the dominance of the AFR10e sublineage (23). In particular, we demonstrate that V. cholerae O1 isolates from Kasaï Oriental province, the first from central DRC to be molecularly characterised, belong to the AFR10e sublineage.…”

“…The objective of this study was to phylogenetically characterise V. cholerae isolates associated with cholera outbreaks in DRC from 2018 to 2022, building upon a previous study that analysed isolates from the eastern DRC between 2014 and 2017 (22). Our results are consistent with previous reports that V. cholerae O1 isolates from the third wave and T10 transmission (AFR10) remain the major clade responsible for cholera outbreaks in the eastern part of the country (13, 22, 23). This evidence marks the sustained prevalence of a single clade as unprecedented when compared to the establishment of other V .…”

“…Additionally, all AFR10e isolates presented the S85L substitution in the parC protein, a combination associated with reduced susceptibility to quinolones in V. cholerae (23). Notably, no AFR10d isolate in this study was found to carry both the S83I substitution in gyrA and the S85L substitution in parC.…”

Impact of a multi-pronged cholera intervention in an endemic setting

“…Confirming our estimates of population immunity and the source of bacterial infection would require serological data and substantial microbiological monitoring of the lake water in the area. Evidence of environmental presence of toxigenic V. cholerae is scarce but it has been found in Lake Tanganyika on the Tanzanian shore in fish and water samples with some evidence of increased positive samples during rainy seasons (40–42). Evidence of fecal contamination in coastal water would support the importance of the strong amplification of environmental presence through environmental contamination during outbreaks (43).…”