Seventh Pandemic Vibrio cholerae O1 Sublineages, Central African Republic

Cholera Outbreaks in Low- and Middle-Income Countries in the Last Decade: A Systematic Review and Meta-Analysis

Cholera is linked to penury, making low- and middle-income countries (LMICs) particularly vulnerable to outbreaks. In this systematic review, we analyzed the drivers contributing to these outbreaks, focusing on the epidemiology of cholera in LMICs. This review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and was registered in PROSPERO (ID: CRD42024591613). We searched PubMed, Scopus, Web of Science, and Google Scholar to include studies on cholera outbreaks that occurred in LMICs from 1 January 2014 to 21 September 2024. Studies on outbreaks outside LMICs and focusing on sporadic cases were excluded. The risk of bias among included studies was assessed using a modified Downes et al. appraisal tool. Thematic analysis was used to synthesize the qualitative data, and meta-analyses to estimate the pooled prevalence. From 1662 records, 95 studies met inclusion criteria, primarily documenting outbreaks in Africa (74%) and Asia (26%). Contaminated water was the main route of disease transmission. The pooled fatality prevalence was 1.3% (95% CI: 1.1-1.6), and the detection rate among suspected cases was 57.8% (95% CI: 49.2-66.4). Vibrio cholerae O1 was the dominant serogroup while Ogawa was the dominant serotype. All studies reporting biotypes indicated El Tor. Although the isolates were 100% susceptible to ofloxacin, levofloxacin, norfloxacin, cefuroxime, and doxycycline, they were also fully resistant to amikacin, sulfamethoxazole, trimethoprim, and furazolidone. The persistence of cholera outbreaks in destitute areas with limited access to clean water and sanitation emphasizes the need for socioeconomic improvements, infrastructure development, and ongoing surveillance to support timely responses and achieve long-term prevention.

Genomic insights into the 2022-2023Vibrio cholerae outbreak in Malawi

Malawi experienced its deadliest Vibrio cholerae (Vc) outbreak following devastating cyclones, with >58,000 cases and >1700 deaths reported between March 2022 and May 2023. Here, we use population genomics to investigate the attributes and origin of the Malawi 2022-2023 Vc outbreak isolates. Our results demonstrate the predominance of ST69 clone, also known as the seventh cholera pandemic El Tor (7PET) lineage, expressing O1 Ogawa (~ 80%) serotype followed by Inaba (~ 16%) and sporadic non-O1/non-7PET serogroups (~ 4%). Phylogenetic reconstruction revealed that the Malawi outbreak strains correspond to a recent importation from Asia into Africa (sublineage AFR15). These isolates harboured known antimicrobial resistance and virulence elements, notably the ICEGEN/ICEVchHai1/ICEVchind5 SXT/R391-like integrative conjugative elements and a CTXφ prophage with the ctxB7 genotype compared to historical Malawian Vc isolates. These data suggest that the devastating cyclones coupled with the recent importation of 7PET serogroup O1 strains, may explain the magnitude of the 2022-2023 cholera outbreak in Malawi.

Genetic approach toward linkage of Iran 2012-2016 cholera outbreaks with 7th pandemic Vibrio cholerae

Vibrio cholerae, as a natural inhabitant of the marine environment is among the world-leading causes of diarrheal diseases. The present study aimed to investigate the genetic relatedness of Iran 2012-2016 V. cholerae outbreaks with 7th pandemic cholera and to further characterize the non-ST69/non-ST75 sequence types strains by whole-genome sequencing (WGS).Twenty V. cholerae isolates related to 2012, 2013, 2015 and 2016 cholera outbreaks were studied by two genotyping methods - Pulsed-field Gel Electrophoresis (PFGE) and Multi-locus Sequence Typing (MLST)-and by antimicrobial susceptibility testing. Seven sequence types (STs) and sixteen pulsotypes were detected. Sequence type 69 was the most abundant ST confirming that most (65%, 13/20) of the studied isolates collected in Iran between 2012 and 2016 belonged to the 7th pandemic clone. All these ST69 isolates (except two) exhibited similar pulsotypes. ST75 was the second most abundant ST. It was identified in 2015 and 2016. ST438, ST178, ST579 and STs of 983 and 984 (as newfound STs) each were only detected in one isolate. All strains collected in 2016 appeared as distinct STs and pulsotypes indicative of probable different originations. All ST69 strains were resistant to nalidixic acid. Moreover, resistance to nalidixic acid, trimethoprim-sulfamethoxazole and tetracycline was only observed in strains of ST69. These properties propose the ST69 as a unique genotype derived from a separate lineage with distinct resistance properties. The circulation of V. cholerae ST69 and its traits in recent years in Iran proposes the 7th pandemic strains as the ongoing causes of cholera outbreaks in this country, although the role of ST75 as the probable upcoming dominant ST should not be ignored.Genomic analysis of non-ST69/non-ST75 strains in this study showed ST579 is the most similar ST type to 7th pandemic sequence types, due to the presence of wild type-El Tor sequences of tcpA and VC-1319, VC-1320, VC-1577, VC-1578 genes (responsible for polymyxin resistance in El Tor biotype), the traits of rstC of RS1 phage in one strain of this ST type and the presence of VPI-1 and VSP-I islands in ST579 and ST178 strains. In silico analysis showed no significant presence of resistance genes/cassettes/plasmids within non-ST69/non-ST75 strains genomes. Overall, these data indicate the higher susceptibility of V. cholerae non-ST69/non-ST75 strains in comparison with more ubiquitous and more circulating ST69 and ST75 strains.In conclusion, the occurrence of small outbreaks and sporadic cholera cases due to V. cholerae ST69 in recent years in Iran shows the 7th pandemic strains as the persistent causes of cholera outbreaks in this country, although the role of ST75 as the second most contributed ST should not be ignored. The occurrence of non-ST69/non-ST75 sequence types with some virulence factors characteristics in border provinces in recent years is noteworthy, and further studies together with surveillance efforts are expected to determine their likely route of transport.

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

Africa's Lake Tanganyika basin is a cholera hotspot. During 2001-2020, Vibrio cholerae O1 isolates obtained from the Democratic Republic of the Congo side of the lake belonged to 2 of the 5 clades of the AFR10 sublineage. One clade became predominant after acquiring a parC mutation that decreased susceptibility to ciprofloxacin.

Modalities and preferred routes of geographic spread of cholera from endemic areas in eastern Democratic Republic of the Congo

Cholera is endemic along the Great Lakes Region, in eastern Democratic Republic of the Congo (DRC). From these endemic areas, also under perpetual conflicts, outbreaks spread to other areas. However, the main routes of propagation remain unclear. This research aimed to explore the modalities and likely main routes of geographic spread of cholera from endemic areas in eastern DRC. We used historical reconstruction of major outbreak expansions of cholera since its introduction in eastern DRC, maps of distribution and spatiotemporal cluster detection analyses of cholera data from passive surveillance (2000–2017) to describe the spread dynamics of cholera from eastern DRC. Four modalities of geographic spread and their likely main routes from the source areas of epidemics to other areas were identified: in endemic eastern provinces, and in non-endemic provinces of eastern, central and western DRC. Using non-parametric statistics, we found that the higher the number of conflict events reported in eastern DRC, the greater the geographic spread of cholera across the country. The present study revealed that the dynamics of the spread of cholera follow a fairly well-defined spatial logic and can therefore be predicted.

The spread of cholera in western Democratic Republic of the Congo is not unidirectional from East-West: a spatiotemporal analysis, 1973-2018

BACKGROUND

Cholera outbreaks in western Democratic Republic of the Congo (DRC) are thought to be primarily the result of westward spread of cases from the Great Lakes Region. However, other patterns of spatial spread in this part of the country should not be excluded. The aim of this study was to explore alternative routes of spatial spread in western DRC.

METHODS

A literature review was conducted to reconstruct major outbreak expansions of cholera in western DRC since its introduction in 1973. We also collected data on cholera cases reported at the health zone (HZ) scale by the national surveillance system during 2000-2018. Based on data from routine disease surveillance, we identified two subperiods (week 45, 2012-week 42, 2013 and week 40, 2017-week 52, 2018) for which the retrospective space-time permutation scan statistic was implemented to detect spatiotemporal clusters of cholera cases and then to infer the spread patterns in western DRC other than that described in the literature.

RESULTS

Beyond westward and cross-border spread in the West Congo Basin from the Great Lakes Region, other dynamics of cholera epidemic propagation were observed from neighboring countries, such as Angola, to non-endemic provinces of southwestern DRC. Space-time clustering analyses sequentially detected clusters of cholera cases from southwestern DRC to the northern provinces, demonstrating a downstream-to-upstream spread along the Congo River.

CONCLUSIONS

The spread of cholera in western DRC is not one-sided. There are other patterns of spatial spread, including a propagation from downstream to upstream areas along the Congo River, to be considered as preferential trajectories of cholera in western DRC.