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

Chaguza, Chrispin; Chibwe, Innocent; Chaima, David; Musicha, Patrick; Ndeketa, Latif; Kasambara, Watipaso; Mhango, Chimwemwe; Mseka, Upendo L.; Bitilinyu-Bangoh, Joseph; Mvula, Bernard; Kipandula, Wakisa; Bonongwe, Patrick; Munthali, Richard J.; Ngwira, Selemani; Mwendera, Chikondi A.; Kalizang’oma, Akuzike; Jambo, Kondwani C.; Kambalame, Dzinkambani; Kamng’ona, Arox W.; Steele, A. Duncan; Chauma-Mwale, Annie; Hungerford, Daniel; Kagoli, Matthew; Nyaga, Martin M.; Dube, Queen; French, Neil; Msefula, Chisomo L.; Cunliffe, Nigel A.; Jere, Khuzwayo C.

doi:10.1038/s41467-024-50484-w

Cited by 4 publications

(2 citation statements)

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“…Zambia and Malawi share many porous borders, and trade and intermarriage are common between the people. The Malawian study postulated that the strain of vibrio in their 2022/2023 outbreak, the worst in Malawian history, was a highly successful cone of pandemic potential worsened by humanitarian and climate crises and then propagated by suitable environmental factors [71]. This agrees with earlier findings suggesting that outbreaks in Kanyama and other hotspots like the fishing villages, were due to a combination of recent introduction of newer pathogenic strains, and favourable environmental factors like deplorable WASH status [29,30].…”

Section: Discussionsupporting

confidence: 81%

“…Isolates from the 2023/2024 outbreak in Zambia have yet to be fully analysed for host and pathogen genomics. However, recent sequencing results from Malawi give insight into a possible new transmission event into the subcontinent, that bears close resemblance to strains of Asian origin [71]. Zambia and Malawi share many porous borders, and trade and intermarriage are common between the people.…”

Section: Discussionmentioning

confidence: 99%

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Navigating the Cholera Elimination Roadmap in Zambia - a Scoping Review (2013-2023)

Mbewe,

Tembo,

Kasonde

et al. 2024

Preprint

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BackgroundCholera outbreaks are increasing in frequency and severity, particularly in Sub-Saharan Africa. Zambia, committed to ending cholera by 2025, is coming off its most significant outbreak in 2024. This review examines the perceived regression in elimination efforts by addressing two questions: (1) what is known about cholera in Zambia; and (2) what are the main suggested mechanisms and strategies to further elimination efforts in the region?Methodology/Principal FindingsA scoping literature search was conducted in PUBMED to identify relevant studies published between January 2013 and June 2024 using the search terms ‘cholera’ and ‘Zambia’. We identified 45 relevant publications. With the increasing influence of climate change, population growth, and rural-urban migration, further increases in outbreak frequency and magnitude are expected. Major risk factors for recurrent outbreaks include poor access to water, sanitation, and hygiene services in urban unplanned settlements and rural fishing villages. Interventions are best planned at a decentralized, community-centric approach to prevent elimination and reintroduction at the district level. Pre-emptive vaccination campaigns before the rainy season and climate-resilient WASH infrastructure are also recommended.Conclusions/SignificanceThe goal to eliminate cholera by 2025 was unrealistic as evidence points to the disease becoming endemic. Our findings confirm the need to align health and WASH investments with the Global Roadmap to Cholera Elimination by 2030 through a climate-focused lens. Recommendations for cholera elimination, including improved access to safe drinking water and sanitation, remain elusive in many low-income settings like Zambia. Patient-level information on survival and transmissibility is lacking. New research tailored to country-level solutions is urgently required. Insights from this review will be integrated into the next iteration of the National Cholera Control Plan and could be applicable to other countries with similar settings.Article SummaryDespite known evidence of the risks from insufficient safe water supplies, sanitation and hygiene (WASH), the protective effects of oral cholera vaccines, and a Roadmap from the Global Task Force on Cholera Control, there is a continuous increase in cholera outbreaks on the continent. Now endemic in many parts of Zambia, it is postulated that the true burden of cholera in the country is underreported due to inadequate completeness of data, particularly during outbreaks. With an increasing frequency related to climatic conditions and unplanned urbanization, it will be important to adopt a decentralised approach to cholera control in Zambia. There is a continued need to advocate strongly for multisectoral interventions aligning health and WASH investments. The findings expose gaps in the local literature, such as how to improve climate-resilient WASH infrastructure, strategies to boost vaccine availability, and also the host and environmental factors that may be protective at personal and household levels from being asymptomatic or dying of cholera. This work provides evidence-based recommendations for the next iteration of the National Cholera Control Plan for Zambia and for neighbouring countries that may be in the process of developing their own plans.

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Section: Discussionsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 99%

Navigating the Cholera Elimination Roadmap in Zambia - a Scoping Review (2013-2023)

Mbewe,

Tembo,

Kasonde

et al. 2024

Preprint

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Effectiveness of a single dose of oral cholera vaccine: findings from epidemiological and genomic surveillance ofVibrio Choleraein the Democratic Republic of the Congo (PICHA7 Program)

George,

Namunesha,

Endres

et al. 2024

Preprint

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This study investigated whole-cell oral cholera vaccine (kOCV) single-dose effectiveness and transmission dynamics ofVibrio choleraethrough 4 years of epidemiological and genomic surveillance in Democratic Republic of the Congo (DRC). Whole genome sequencing was performed on clinical and waterV. choleraestrains from 200 patient households and found annual bimodal peaks ofV. choleraeclade AFR10e. 1154 diarrhea patients were enrolled with 342 culture confirmed cholera patients. A large clonal cholera outbreak occurred 18 months after a kOCV campaign of >1 million doses of Euvichol-Plus, likely because of low vaccine coverage in informal settlements (9%). Clinical and waterV. choleraestrains in the same household were more closely related than different households suggesting both person-to-person and water-to-person transmission. Single-dose kOCV vaccine effectiveness in the first 24 month after vaccination was 56.9% (95% CI: 18.6%-77.2%), suggesting a single-dose provided modest protection against medically attended cholera during the 24 months post-vaccination.

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Genomic Diversity and Antimicrobial Resistance ofVibrio choleraeIsolates from Africa: A PulseNet Africa Initiative Using Nanopore Sequencing to Enhance Genomic Surveillance

Foster-Nyarko,

Able-Thomas,

Adade

et al. 2024

Preprint

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Objectives: Vibrio cholerae remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of V. cholerae isolates from Cote d'Ivoire, Ghana, Zambia and South Africa to assess genomic diversity, AMR profiles, and virulence, demonstrating the utility of WGS for enhanced surveillance within the PulseNet Africa network. Methods: We analysed Vibrio isolates from clinical and environmental sources (2010-2024) using Oxford Nanopore sequencing and hybracter assembly. Phylogenetic analysis, multilocus sequence typing (MLST), virulence and AMR gene detection were performed using Terra, Pathogenwatch, and Cloud Infrastructure for Microbial Bioinformatics (CLMB) platforms, with comparisons against 88 global reference genomes for broader genomic context. Results: Of 79 high-quality assemblies, 67 were confirmed as V. cholerae, with serogroup O1 accounting for the majority (43/67, 67%). ST69 accounted for 60% (40/67) of isolates, with eight sequence types identified overall. Thirty-seven isolates formed novel sub-clades within AFR12 and AFR15 O1 lineages, suggesting local clonal expansions. AMR gene analysis revealed high resistance to trimethoprim (96%) and quinolones (83%), while resistance to azithromycin, rifampicin, and tetracycline remained low (less than or equal to 7%). A significant proportion of the serogroup O1 isolates (41/43, 95%) harboured resistance genes in at least three antibiotic classes. Conclusions: This study highlights significant genetic diversity and AMR prevalence in African V. cholerae isolates, with expanding AFR12 and AFR15 clades in the region. The widespread resistance to trimethoprim and quinolones raises concerns for treatment efficacy, although azithromycin and tetracycline remain viable options. WGS enables precise identification of species and genotyping, reinforcing PulseNet Africa's pivotal role in advancing genomic surveillance and enabling timely public health responses to cholera outbreaks.

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

Cited by 4 publications

References 100 publications

Navigating the Cholera Elimination Roadmap in Zambia - a Scoping Review (2013-2023)

Navigating the Cholera Elimination Roadmap in Zambia - a Scoping Review (2013-2023)

Effectiveness of a single dose of oral cholera vaccine: findings from epidemiological and genomic surveillance ofVibrio Choleraein the Democratic Republic of the Congo (PICHA7 Program)

Genomic Diversity and Antimicrobial Resistance ofVibrio choleraeIsolates from Africa: A PulseNet Africa Initiative Using Nanopore Sequencing to Enhance Genomic Surveillance

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