Marie-Laure Quilici

While cholera imposes a substantial burden across the Democratic Republic of the Congo, its transmission dynamics vary by geography, socio-economic context or population habits. We investigated risk factors associated with laboratory-confirmed cholera among suspected cases in urban Goma and rural Bukama sites, across 2021-2022. Mixed-effects logistic regression models were fitted independently by site. Positivity rates were higher in Goma (70.2%, 1688/2405) than in Bukama (49.4%, 390/790). In both sites, rainy seasons increased odds of testing positive (OR=3.89, 95%CI [2.93-5.16] and 2.00 [1.39-2.86] for Goma and Bukama, respectively) while receiving ≥1 Oral Cholera Vaccine dose was protective (0.53 [0.37-0.74] and 0.58 [0.37-0.91]). Some risk factors were significant only in Goma, including displacement status (1.93 [1.11-3.35]), household cholera case exposure (1.79 [1.31-2.45]), consumption of surface water (2.11 (1.46-3.03]) or from water tankers (1.75 (1.24-2.47]). This study shows that cholera risk factors vary across endemic settings, giving insights for improved, locally-adapted control measures.

IncC plasmids played an important role in driving antimicrobial drug resistance development in the seventh pandemic Vibrio cholerae O1 El Tor (7PET) lineage during the 1970s and these have begun to re-emerge. In this study, we investigated a comprehensive dataset for 28 complete IncC plasmids - including 17 newly sequenced plasmid genomes - from 7PET isolates collected on various continents between 1979 and 2024 and distributed across the global phylogenetic tree for 7PET isolates. IncC type 2 predominated among the V. cholerae plasmids studied, and five new core genome sequence types (cgSTs) were identified. The antimicrobial resistance genes (ARGs) were arranged in islands inserted at specific hotspots within the common IncC backbone and were significantly associated with IncC types or islands. The IncC plasmid backbone has remained stable over the last 50 years, but the ARGs and their associated genomic islands displayed remarkable diversity, underscoring the complex evolution patterns of the 7PET lineage of V. cholerae and its considerable adaptability under selective pressure.

Since 1971, Cameroon has experienced several outbreaks of cholera due to strains of the seventh pandemic Vibrio cholerae O1 El Tor (7PET) lineage originating from South Asia. Over the last 6 years, more than 26,000 cholera cases have been reported. The aim of this study was to perform a genomic characterization of the V. cholerae O1 isolates collected during recent cholera outbreaks in Cameroon. We investigated the virulence, antimicrobial resistance (AMR) signatures and phylogenetic relationships of 164 clinical V. cholerae isolates representative of the successive outbreaks collected between 2018 and 2023. A phylogenomic analysis of more than 1,700 7PET genomes – including 45 from isolates collected in Cameroon between 1971 and 2011 – was performed to place the recent 7PET strains in a broader phylogenetic context. We found that all the recent Cameroonian isolates studied belonged to genomic wave 3 of the 7PET lineage. They clustered together within the AFR12 sublineage (which was identified for the first time in Cameroon in 2009) and with contemporary isolates from other countries in the same region. Serotyping and genome analysis revealed a reversion from serotype Inaba (all isolates between 2018 and 2019) to Ogawa (all isolates between 2021 and 2023) in two different strains originating from different regions of Cameroon. Finally, the AFR12 isolates studied here were less resistant to antimicrobial drugs than the AFR12 isolates identified in Cameroon between 2009 and 2011 due to a 10 kb deletion in the integrative conjugative element conferring multidrug resistance, ICEVchInd5, resulting in the loss of four AMR genes (strA, strB, floR and sul2). Our findings confirm the complementarity between traditional microbiological methods and microbial genomics for monitoring circulating 7PET strains and tracking their evolution and the development of AMR.

Since 1971, Cameroon has experienced several outbreaks of cholera due to strains of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage originating from South Asia. Over the last six years, more than 26,000 cholera cases have been reported. The aim of this study was to perform a genomic characterisation of the V. cholerae O1 isolates collected during recent cholera outbreaks in Cameroon. We investigated the virulence, antimicrobial resistance (AMR) signatures and phylogenetic relationships between 164 clinical V. cholerae isolates representative of the successive outbreaks that were collected between 2018 and 2023. A phylogenomic analysis of more than 1,700 7PET genomes —including 45 from isolates collected in Cameroon between 1971 and 2011 — was performed to place the recent 7PET strains in a broader phylogenetic context. We found that all the recent Cameroonian isolates studied belonged to genomic wave 3 of the 7PET lineage. They clustered together within the AFR12 sublineage (which was identified for the first time in Cameroon in 2009 and with contemporary isolates from other countries in the same region). Serotyping and genome analysis revealed a reversion from serotype Inaba (all isolates between 2018 and 2019) to Ogawa (all isolates between 2021 and 2023) in two different strains originating from different regions of Cameroon. Finally, the AFR12 isolates studied here were less resistant to antimicrobial drugs than the AFR12 isolates identified in Cameroon between 2009 and 2011 due to a 10-kb deletion in the integrative conjugative element conferring multidrug resistance, ICE Vch Ind5, resulting in the loss of four antimicrobial resistance (AMR) genes ( strA , strB , floR and sul2 ). Our findings confirm the complementarity between traditional microbiological methods and microbial genomics for monitoring circulating 7PET strains and tracking their evolution development and that of AMR in particular. IMPACT STATEMENT: The number of cholera cases has fallen since the beginning of 2024 (only 49 cases reported up to July 28), but Cameroon, in Central Africa, experienced a number of cholera epidemics between 2018 and 2023, with 26,411 cholera cases in total and 735 deaths (case fatality rate: 2.8%). We performed a phenotypic and genomic analysis of 164 V. cholerae O1 isolates representative of the successive outbreaks that were collected from 2018 to 2023 from seven of the 10 regions of Cameroon, which revealed that these isolates were very similar and closely related to other West African isolates. All belonged to the same pandemic lineage thought to have been introduced into West Africa from South Asia in 2007. The strains of this lineage have become less resistant to antimicrobial drugs over time, due to a single genetic event (i.e., deletion of a region of the bacterial chromosome containing several antimicrobial resistance genes) and have reverted to the Ogawa serotype (the original serotype of wild-type strains). Neither of these changes were anticipated. Furthermore, our findings support the hypothesis that the causal agent of cholera is permanently circulating in the countries around the Lake Chad basin and those of West Africa. They stress the importance of combining a genomic approach with traditional microbiology for the epidemiological surveillance of cholera. Furthermore, transborder collaborative efforts are strongly advised to ensure effective cholera control in this region.

Background: The number of cholera cases reported to the World Health Organization (WHO) in 2022 was more than double that of 2021. Nine countries of the WHO European Region reported 51 cases of cholera in 2022 vs five reported cases in 2021. Aim: We aimed to confirm that the Vibrio cholerae O1 isolates reported by WHO European Region countries in 2022 belonged to the seventh pandemic El Tor lineage (7PET). We also studied their virulence, antimicrobial resistance (AMR) determinants and phylogenetic relationships. Methods: We used microbial genomics to study the 49 V. cholerae O1 isolates recovered from the 51 European cases. We also used > 1,450 publicly available 7PET genomes to provide a global phylogenetic context for these 49 isolates. Results: All 46 good-quality genomes obtained belonged to the 7PET lineage. All but two isolates belonged to genomic Wave 3 and were grouped within three sub-lineages, one of which, Pre-AFR15, predominated (34/44). This sub-lineage, corresponding to isolates from several countries in Southern Asia, the Middle East and Eastern or Southern Africa, was probably a major contributor to the global upsurge of cholera cases in 2022. No unusual AMR profiles were inferred from analysis of the AMR gene content of the 46 genomes. Conclusion: Reference laboratories in high-income countries should use whole genome sequencing to assign V. cholerae O1 isolates formally to the 7PET or non-epidemic lineages. Periodic collaborative genomic studies based on isolates from travellers can provide useful information on the circulating strains and their evolution, particularly as concerns AMR.

Several authors have attributed the explosive outbreak of gastroenteritis that occurred in Czechoslovakia in 1965 to a toxigenic strain of Vibrio cholerae serogroup O37 based on unverified metadata associated with three particular strains from the American Type Culture Collection. Here, by sequencing the original strain preserved at the Czech National Collection of Type Cultures since 1966, we show that the strain responsible for this outbreak was actually a V. cholerae O5 that lacks the genes encoding the cholera toxin, the toxin-coregulated pilus protein and Vibrio pathogenicity islands present in V. cholerae O37 strains.

Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods and microbial genomics to study 34 clinical and environmental Vibrio cholerae isolates collected throughout this outbreak. All isolates are identified as V. cholerae O1, serotype Ogawa strains from wave 3 of the seventh pandemic El Tor (7PET) lineage. Phylogenomic analysis unexpectedly reveals the presence of two different strains of the seventh pandemic El Tor (7PET) lineage. The dominant strain has a narrow antibiotic resistance profile and is phylogenetically related to South Asian V. cholerae isolates and derived African isolates from the AFR15 sublineage. The second strain is geographically restricted and extensively drug-resistant. It belongs to the AFR13 sublineage and clusters with V. cholerae isolates collected in Yemen. In conclusion, the 2022-2023 Lebanese cholera outbreak is caused by the simultaneous introduction of two different 7PET strains. Genomic surveillance with cross-border collaboration is therefore crucial for the identification of new introductions and routes of circulation of cholera, improving our understanding of cholera epidemiology.

Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.

The humanitarian crisis in Yemen led in 2016 to the biggest cholera outbreak documented in modern history, with more than 2.5 million suspected cases to date. In late 2018, epidemiological surveillance showed that V. cholerae isolated from cholera patients had turned multi-drug resistant (MDR). We generated genomes from 260 isolates sampled in Yemen between 2018 and 2019 to identify a possible shift in circulating genotypes. 84% of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sublineage T13 – same as in 2016 and 2017 – while the remaining 16% of strains were non-toxigenic and belonged to divergent V. cholerae lineages, likely reflecting sporadic gut colonisation by endemic strains. Phylogenomic analysis reveals a succession of T13 clones, with 2019 dominated by a clone that carried an IncC-type plasmid harbouring an MDR pseudo-compound transposon (PCT). Identical copies of these mobile elements were found independently in several unrelated lineages, suggesting exchange and recombination between endemic and epidemic strains. Treatment of severe cholera patients with macrolides in Yemen from 2016 to early 2019 coincides with the emergence of the plasmid-carrying T13 clone. The unprecedented success of this genotype where an SXT-family integrative and conjugative element (SXT/ICE) and an IncC plasmid coinhabit show the stability of this MDR plasmid in the 7PET background, which may durably reduce options for epidemic cholera case management. We advocate a heightened genomic epidemiology surveillance of cholera to help control the spread of this highly-transmissible, MDR clone.

In 2022, the burden of cholera—an acute watery diarrheal disease caused by Vibrio cholerae serogroup O1 (or more rarely O139) bacteria, which produce cholera toxin—remains high in many African and Asian countries. In the last few years, microbial genomics has made it possible to define the bacterial populations responsible for cholera more precisely. It has been shown that the current, seventh pandemic is due to a single lineage with a reservoir in the countries of the Bay of Bengal (India and Bangladesh). There have been several transmissions of the causal agent of cholera from this region to Africa, Asia and Latin America, suggesting a human-to-human transmission of the disease. Microbial genetics can help to fight this scourge by providing insight into cholera epidemiology and through its use in disease monitoring, thereby contributing to the achievement of the World Health Organization’s goal of reducing cholera deaths by 90% by 2030.