Evolution of seventh cholera pandemic and origin of 1991 epidemic, Latin America.
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ABSTRACT:
SUBMITTER: Lam C
PROVIDER: S-EPMC3321917 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elements Vibrio seventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.
| S-EPMC5137724 | biostudies-literature
Project description:In 1970, the seventh pandemic of cholera (7 P) reached both Africa and Europe. Between 1970 and 2011, several European countries reported cholera outbreaks of a few to more than 2,000 cases. We report here a whole-genome analysis of 1,324 7 P V. cholerae El Tor (7 PET) isolates, including 172 from autochthonous sporadic or outbreak cholera cases occurring between 1970 and 2011 in Europe, providing insight into the spatial and temporal spread of this pathogen across Europe. In this work, we show that the 7 PET lineage was introduced at least eight times into two main regions: Eastern and Southern Europe. Greater recurrence of the disease was observed in Eastern Europe, where it persisted until 2011. It was introduced into this region from Southern Asia, often circulating regionally in the countries bordering the Black Sea, and in the Middle East before reaching Eastern Africa on several occasions. In Southern Europe, the disease was mostly seen in individual countries during the 1970s and was imported from North and West Africa, except in 1994, when cholera was imported into Albania and Italy from the Black Sea region. These results shed light on the geographic course of cholera during the seventh pandemic and highlight the role of humans in its global dissemination.
| S-EPMC7582136 | biostudies-literature
Project description:Vibrio cholerae is a globally important pathogen that is endemic in many areas of the world and causes 3-5 million reported cases of cholera every year. Historically, there have been seven acknowledged cholera pandemics; recent outbreaks in Zimbabwe and Haiti are included in the seventh and ongoing pandemic. Only isolates in serogroup O1 (consisting of two biotypes known as 'classical' and 'El Tor') and the derivative O139 can cause epidemic cholera. It is believed that the first six cholera pandemics were caused by the classical biotype, but El Tor has subsequently spread globally and replaced the classical biotype in the current pandemic. Detailed molecular epidemiological mapping of cholera has been compromised by a reliance on sub-genomic regions such as mobile elements to infer relationships, making El Tor isolates associated with the seventh pandemic seem superficially diverse. To understand the underlying phylogeny of the lineage responsible for the current pandemic, we identified high-resolution markers (single nucleotide polymorphisms; SNPs) in 154 whole-genome sequences of globally and temporally representative V. cholerae isolates. Using this phylogeny, we show here that the seventh pandemic has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s, and identify several transcontinental transmission events. Additionally, we show how the acquisition of the SXT family of antibiotic resistance elements has shaped pandemic spread, and show that this family was first acquired at least ten years before its discovery in V. cholerae.
| S-EPMC3736323 | biostudies-literature
Project description:After being cholera free for over 100 years, Peru experienced an unprecedented epidemic of Vibrio cholerae O1 that began in 1991 and generated multiple waves of disease over several years. We developed a mechanistic transmission model that accounts for seasonal variation in temperature to estimate spatial variability in the basic reproduction number ([Formula: see text]), the initial concentration of vibrios in the environment, and cholera reporting rates. From 1991-1997, cholera spread following a multi-wave pattern, with weekly incidence concentrated during warm seasons. The epidemic first hit the coastal departments of Peru and subsequently spread through the highlands and jungle regions. The correlation between model predictions and observations was high (range in R2: 58% to 97%). Department-level population size and elevation explained significant variation in spatial-temporal transmission patterns. The overall R0 across departments was estimated at 2.1 (95% CI: 0.8,7.3), high enough for sustained transmission. Geographic-region level [Formula: see text] varied substantially from 2.4 (95% CI: 1.1, 7.3) for the coastal region, 1.9 (0.7, 6.4) for the jungle region, and 1.5 (0.9, 2.2) for the highlands region. At the department level, mean [Formula: see text] ranged from 0.8 to 6.9. Department-level [Formula: see text] were correlated with overall observed attack rates (Spearman ρ = 0.59, P = 0.002), elevation (ρ = -0.4, P = 0.04), and longitude (ρ = -0.6, P = 0.004). We find that both [Formula: see text] and the initial concentration of vibrios were higher in coastal departments than other departments. Reporting rates were low, consistent with a substantial fraction of asymptomatic or mild cases associated with the El Tor cholera biotype. Our results suggest that cholera vibrios, autochthonous to plankton in the natural aquatic environment, may have triggered outbreaks in multiple coastal locations along the Pacific coast of Peru. Our methodology could be useful to investigate multi-wave epidemics of cholera and could be extended to conduct near real-time forecasts and investigate the impact of vaccination strategies.
| S-EPMC7360044 | biostudies-literature
Project description:BackgroundLatin America presently has the world's highest burden of Zika virus, but there are unexplained differences in national rates of congenital malformations collectively referred to as Congenital Zika Syndrome (CZS) in the region. While Zika virulence and case detection likely contribute to these differences, policy-related factors, including access to abortion, may play important roles. Our goal was to assess perspectives on, and access to, abortion in Latin America in the context of the Zika epidemic.MethodsWe conducted a scoping review of peer-reviewed and gray literature published between January 2015 and December 2016, written in English, Spanish, Portuguese, or French. We searched PubMed, Scielo, and Google Scholar for literature on Zika and/or CZS and abortion, and used automated and manual review methods to synthesize the existing information.Results36 publications met our inclusion criteria, the majority of which were qualitative. Publications were generally in favor of increased access to safe abortion as a policy-level response for mitigating the impact of CZS, but issues with implementation were cited as the main challenge. Aside from the reform of abortion regulation in Colombia, we did not find evidence that the Zika epidemic had triggered shifts in abortion policy in other countries.ConclusionAbortion policy in the region remained largely unchanged following the Zika epidemic. Further empirical research on abortion access and differential rates of CZS across Latin American countries is required.
| S-EPMC5932843 | biostudies-literature
Project description:Zika is one of the most challenging emergent vector-borne diseases, yet its future public health impact remains unclear. Zika was of little public health concern until recent reports of its association with congenital syndromes. By 3 August 2017 ?217,000 Zika cases and ?3,400 cases of associated congenital syndrome were reported in Latin America and the Caribbean. Some modelling exercises suggest that Zika virus infection could become endemic in agreement with recent declarations from the The World Health Organisation.We produced high-resolution spatially-explicit projections of Zika cases, associated congenital syndromes and monetary costs for Latin America and the Caribbean now that the epidemic phase of the disease appears to be over. In contrast to previous studies which have adopted a modelling approach to map Zika potential, we project case numbers using a statistical approach based upon reported dengue case data as a Zika surrogate. Our results indicate that ?12.3 (0.7-162.3) million Zika cases could be expected across Latin America and the Caribbean every year, leading to ?64.4 (0.2-5159.3) thousand cases of Guillain-Barré syndrome and ?4.7 (0.0-116.3) thousand cases of microcephaly. The economic burden of these neurological sequelae are estimated to be USD ?2.3 (USD 0-159.3) billion per annum.Zika is likely to have significant public health consequences across Latin America and the Caribbean in years to come. Our projections inform regional and federal health authorities, offering an opportunity to adapt to this public health challenge.
| S-EPMC5683651 | biostudies-literature
Project description:The seventh pandemic of cholera in Europe revisited by microbial genomics
| PRJEB38484 | ENA
Project description:BackgroundZika virus (ZIKV) emerged in Latin America and the Caribbean (LAC) region in 2013, with serious implications for population health in the region. In 2016, the World Health Organization declared the ZIKV outbreak a Public Health Emergency of International Concern following a cluster of associated neurological disorders and neonatal malformations. In 2017, Zika cases declined, but future incidence in LAC remains uncertain due to gaps in our understanding, considerable variation in surveillance and the lack of a comprehensive collation of data from affected countries.MethodsOur analysis combines information on confirmed and suspected Zika cases across LAC countries and a spatio-temporal dynamic transmission model for ZIKV infection to determine key transmission parameters and projected incidence in 90 major cities within 35 countries. Seasonality was determined by spatio-temporal estimates of Aedes aegypti vectorial capacity. We used country and state-level data from 2015 to mid-2017 to infer key model parameters, country-specific disease reporting rates, and the 2018 projected incidence. A 10-fold cross-validation approach was used to validate parameter estimates to out-of-sample epidemic trajectories.ResultsThere was limited transmission in 2015, but in 2016 and 2017 there was sufficient opportunity for wide-spread ZIKV transmission in most cities, resulting in the depletion of susceptible individuals. We predict that the highest number of cases in 2018 would present within some Brazilian States (Sao Paulo and Rio de Janeiro), Colombia and French Guiana, but the estimated number of cases were no more than a few hundred. Model estimates of the timing of the peak in incidence were correlated (p?<?0.05) with the reported peak in incidence. The reporting rate varied across countries, with lower reporting rates for those with only confirmed cases compared to those who reported both confirmed and suspected cases.ConclusionsThe findings suggest that the ZIKV epidemic is by and large over within LAC, with incidence projected to be low in most cities in 2018. Local low levels of transmission are probable, but the estimated rate of infection suggests that most cities have a population with high levels of herd immunity.
| S-EPMC6169075 | biostudies-literature
Project description:Latin American governments swiftly implemented income assistance programs to sustain families' livelihoods during COVID-19 stay-at-home orders. This paper analyzes the potential coverage and generosity of these measures and assesses the suitability of current safety nets to deal with unexpected negative income shocks in 10 Latin American countries. The expansion of pre-existing programs (most notably conditional cash transfers and non-contributory pensions) during the COVID-19 crisis was generally insufficient to compensate for the inability to work among the poorest segments of the population. When COVID-19 ad hoc programs are analyzed, the coverage and replacement rates of regular labor income among households in the first quintile of the country's labor income distribution increase substantially. Yet, these programs present substantial coverage challenges among families composed of fundamentally informal workers who are non-poor, but are at a high risk of poverty. These results highlight the limitations of the fragmented nature of social protection systems in the region.
| S-EPMC8568185 | biostudies-literature
Project description:This article examines how Argentina, Brazil, Chile, Colombia, Mexico, and Peru addressed the COVID-19 pandemic and the effectiveness of these policy responses from the date each country declared a sanitary emergency, between middle and late March 2020 to the most recent available measurement on 23 September 2020. To analyze how governments responded to the COVID-19 pandemic in these six Latin American countries, we use an index of government response, created by the University of Oxford. To explore the effects of these governmental mitigation policies on reducing social mobility, we use Google mobility reports. We also analyze how these policies may have influenced COVID-19 mortality rates. Overall, the results showed that both timelier and more stringent implementation of the public policies analyzed to address the COVID-19 pandemic seem to be associated with higher mobility reductions and lower mortality rates. We draw five policy lessons from the way each country implemented these mitigation policies. KEY MESSAGE: Timelier and more stringent implementation of these public policies may contribute to a higher mobility reduction in several public spaces and to lower mortality rates. The effectiveness of the closure and containment policies in each Latin American country seem to depend on the degree of compliance of their respective populations and to their socioeconomic living conditions. Economic and social policies of income support and debt relief provided by governments allowed people to comply with closure and containment policies. Health systems should maintain high levels of policy stringency together with effective surveillance through testing policy and contact tracing.
| S-EPMC7841039 | biostudies-literature