Investigation of potentially pathogenic Vibrionaceae in Saint-Louis city, Senegal.

Introduction: as cholera, due to toxigenic bacteria Vibrio cholera (serogroups O1 and O139), is a major public health threat in Africa, the aim of this work was to investigate potentially pathogenic Vibrionaceae bacteria firstly from human stool samples, and secondly from various environmental water points of Saint-Louis city in Senegal. Methods: a hospital-based study was conducted between 2013 and 2015. Stool samples were taken and cultured from daily incoming patients or hospitalized for acute diarrhea at Saint-Louis´ regional hospital. For environment, a monthly longitudinal sampling from January to October 2016 was carried out at 10 sites in the city. We used total DNA extracted from APW (alkaline peptone water) broth solutions and on suspect bacterial colonies to run PCR Multiplex targeting specific DNA fragments to detect Vibrio genus and specific species. In case of positivity, a simplex PCR was performed to test for cholera toxins Ctx, and V. parahaemolyticus TRH and TDH. Results: for 43 patients screened, bacterial culture was positive in 6% of cases but no strain of V. cholerae or other Vibrio sp. was isolated. PCR on 90 APW solutions were positive for Vibrio sp.(n = 43), V. cholera(n = 27), V. mimicus(n = 16), V. parahaemolyticus(8), V. alginolyticus(n = 4), and V. vulnificus(n = 2). Unlike for those on suspected colonies which were positive for a majority of V. parahaemolyticus (n = 40) and V. cholerae non-O1 / O139 (n = 35). Six strains of V. parahaemolyticus carried TRH gene, 3 of which expressed simultaneously virulence TRH and TDH genes. For physicochemical parameters, all temperatures varied similarly according to a unimodal seasonality, as well as salinity. Conclusion: despite the presence of natural populations of Vibrionaceae, even toxigenic ones, was noted in water environment, along with favorable habitat conditions that could play a role in transmission of Vibriosis in the Saint Louis population, we did not isolate any of them from patients screened at the hospital.

Complete genome sequences of two Klebsiella pneumoniae phages from Dakar, Senegal.

Two bacteriophages (phages) of Klebsiella pneumoniae were isolated from sewage water collected from Dakar, Senegal. Phage vKpIN17 belongs to the Przondovirus genus within the Autographiviridae family, with double-stranded DNA genomes, whereas vKpIN18 belongs to the Webervirus genus of the Drexlerviridae family.

Assessment of the global toxicity of marine sediments from the Dakar peninsula (Senegal, West Africa).

Marine pollution in West Africa is major threat particularly around coastal megacities. We assess the chemical and ecotoxicological quality of the marine sediments in various submerged sampling sites of Dakar. Analysis revealed that sediments were slightly basic in which fine and coarse sands predominated. High percentages of total organic carbon were found sometime above 6%. Higher levels of heavy metal were reported than in previous studies. Chromium and nickel were above the Probable Effect Concentration. Low trophic level appeared not affected by the overall toxicity, while medium trophic level was more affected. Indeed, the vast majority (91%) of sites studied revealed a net percentage of Magallana gigas embryolarval developmental abnormality over 20%. The assessment of the global toxicity of marine sediments from the Dakar sites Studied (n = 11) seemed, almost, as a whole, to be in a poor ecotoxicological state calling to take measures to improve the sanitary condition of this marine feature.

Influence of Community-Led Total Sanitation and Water Coverages in the Control of Cholera in Madarounfa, Niger (2018).

Every year, cholera affects 1.3-4.0 million people worldwide with a particularly high presence in Africa. Based on recent studies, effective targeting interventions in hotspots could eliminate up to 50% of cases in Sub-Saharan Africa. Those interventions include Water, Sanitation, and Hygiene (WASH) programs whose influence on cholera control, up to the present, has been poorly quantified. Among the few studies available, D'Mello-Guyett et al. underline how the distribution of hygiene kits is a promising form of intervention for cholera control and that the integration of a WASH intervention at the point of admission of suspected cases is new in cholera control efforts, particularly in outbreaks and complex emergencies. Considering the limited number of studies on Community-Led Total Sanitation (CLTS) and water coverages related to cholera control, the aim of our work is to determine whether these interventions in cholera hotspots (geographic areas vulnerable to disease transmission) have significant impact on cholera transmission. In this study, we consider data collected on 125 villages of the Madarounfa district (Niger) during the 2018 cholera outbreak. Using a hurdle model, our findings show that full access to improved sanitation significantly decreases the likelihood of cholera by 91% (P < 0.0001) compared to villages with no access to sanitation at all. Considering only the villages affected by cholera in the studied area, cholera cases decrease by a factor of 4.3 in those villages where there is partial access to at least quality water sources, while full access to improved water sources decreases the cholera cases by a factor of 6.3 when compared to villages without access to water (P < 0.001). In addition, villages without access to safe water and sanitation are 6.7 times (P < 0.0001) more likely to get cholera. Alternatively, villages with full sanitation and water coverage are 9.1 (P < 0.0001) less likely to get cholera. The findings of our study suggest that significant access to improved water and sanitation at the village level offer a strong barrier against cholera transmission. However, it requires full CLTS coverage of the village to observe a strong impact on cholera, as partial access only has a limited impact.

Dynamics of cholera epidemics from Benin to Mauritania.

BACKGROUND: The countries of West Africa are largely portrayed as cholera endemic, although the dynamics of outbreaks in this region of Africa remain largely unclear. METHODOLOGY/PRINCIPAL FINDINGS: To understand the dynamics of cholera in a major portion of West Africa, we analyzed cholera epidemics from 2009 to 2015 from Benin to Mauritania. We conducted a series of field visits as well as multilocus variable tandem repeat analysis and whole-genome sequencing analysis of V. cholerae isolates throughout the study region. During this period, Ghana accounted for 52% of the reported cases in the entire study region (coastal countries from Benin to Mauritania). From 2009 to 2015, we found that one major wave of cholera outbreaks spread from Accra in 2011 northwestward to Sierra Leone and Guinea in 2012. Molecular epidemiology analysis confirmed that the 2011 Ghanaian isolates were related to those that seeded the 2012 epidemics in Guinea and Sierra Leone. Interestingly, we found that many countries deemed "cholera endemic" actually suffered very few outbreaks, with multi-year lulls. CONCLUSIONS/SIGNIFICANCE: This study provides the first cohesive vision of the dynamics of cholera epidemics in a major portion of West Africa. This epidemiological overview shows that from 2009 to 2015, at least 54% of reported cases concerned populations living in the three urban areas of Accra, Freetown, and Conakry. These findings may serve as a guide to better target cholera prevention and control efforts in the identified cholera hotspots in West Africa.

Identification of Atypical El TorV. cholerae O1 Ogawa Hosting SXT Element in Senegal, Africa.

Vibrio cholerae O1 is the causative agent of cholera with classical and El Tor, two well-established biotypes. In last 20 years, hybrid strains of classical and El Tor and variant El Tor which carry classical ctxB have emerged worldwide. In 2004-2005, Senegal experienced major cholera epidemic with a number of cases totalling more than 31719 with approximately 458 fatal outcomes (CFR, 1.44%). In this retrospective study, fifty isolates out of a total of 403 V. cholerae biotype El Tor serovar Ogawa isolates from all areas in Senegal during the 2004-2005 cholera outbreak were randomly selected. Isolates were characterized using phenotypic and genotypic methods. The analysis of antibiotic resistance patterns revealed the predominance of the S-Su-TCY-Tsu phenotype (90% of isolates). The molecular characterization of antibiotic resistance revealed the presence of the SXT element, a self-transmissible chromosomally integrating element in all isolates. Most of V. cholerae isolates had an intact virulence cassette (86%) (ctx, zot, ace genes). All isolates tested gave amplification with primers for classical CT, and 10/50 (20%) of isolates carried classical and El Tor ctxB. The study reveals the presence of atypical V. cholerae O1 El Tor during cholera outbreak in Senegal in 2004-2005.

Mobile phone data highlights the role of mass gatherings in the spreading of cholera outbreaks.

The spatiotemporal evolution of human mobility and the related fluctuations of population density are known to be key drivers of the dynamics of infectious disease outbreaks. These factors are particularly relevant in the case of mass gatherings, which may act as hotspots of disease transmission and spread. Understanding these dynamics, however, is usually limited by the lack of accurate data, especially in developing countries. Mobile phone call data provide a new, first-order source of information that allows the tracking of the evolution of mobility fluxes with high resolution in space and time. Here, we analyze a dataset of mobile phone records of ∼150,000 users in Senegal to extract human mobility fluxes and directly incorporate them into a spatially explicit, dynamic epidemiological framework. Our model, which also takes into account other drivers of disease transmission such as rainfall, is applied to the 2005 cholera outbreak in Senegal, which totaled more than 30,000 reported cases. Our findings highlight the major influence that a mass gathering, which took place during the initial phase of the outbreak, had on the course of the epidemic. Such an effect could not be explained by classic, static approaches describing human mobility. Model results also show how concentrated efforts toward disease control in a transmission hotspot could have an important effect on the large-scale progression of an outbreak.

Seasonal Patterns of Buruli Ulcer Incidence, Central Africa, 2002-2012.

To determine when risk for Buruli ulcer is highest, we examined seasonal patterns in a highly disease-endemic area of Cameroon during 2002-2012. Cases peaked in March, suggesting that risk is highest during the high rainy season. During and after this season, populations should increase protective behaviors, and case detection efforts should be intensified.

The niche reduction approach: an opportunity for optimal control of infectious diseases in low-income countries?

BACKGROUND: During the last century, WHO led public health interventions that resulted in spectacular achievements such as the worldwide eradication of smallpox and the elimination of malaria from the Western world. However, besides major successes achieved worldwide in infectious diseases control, most elimination/control programs remain frustrating in many tropical countries where specific biological and socio-economical features prevented implementation of disease control over broad spatial and temporal scales. Emblematic examples include malaria, yellow fever, measles and HIV. There is consequently an urgent need to develop affordable and sustainable disease control strategies that can target the core of infectious diseases transmission in highly endemic areas. DISCUSSION: Meanwhile, although most pathogens appear so difficult to eradicate, it is surprising to realize that human activities are major drivers of the current high rate of extinction among upper organisms through alteration of their ecology and evolution, i.e., their "niche". During the last decades, the accumulation of ecological and evolutionary studies focused on infectious diseases has shown that the niche of a pathogen holds more dimensions than just the immune system targeted by vaccination and treatment. Indeed, it is situated at various intra- and inter- host levels involved on very different spatial and temporal scales. After developing a precise definition of the niche of a pathogen, we detail how major advances in the field of ecology and evolutionary biology of infectious diseases can enlighten the planning and implementation of infectious diseases control in tropical countries with challenging economic constraints. SUMMARY: We develop how the approach could translate into applied cases, explore its expected benefits and constraints, and we conclude on the necessity of such approach for pathogen control in low-income countries.

How community ecology can improve our understanding of cholera dynamics.

Understanding the seasonal emergence and reemergence of cholera is challenging due to the complex dynamics of different protagonists. The abundance of Vibrio cholerae, the causative agent of cholera and a natural inhabitant of aquatic environments, fluctuates according to abiotic, and biotic factors. Among the biotic factors, the zooplankton community dynamics has been suggested to play a pivotal role in the survival, persistence, and natural competence of V. cholerae. However, factors regulating V. cholerae population structure and seasonal dynamics are still not fully understood. Investigation of the temporal shifts and variability in aquatic community composition in relation to the occurrence or abundance of V. cholerae appears very promising yet remained underexplored. Recent advances in metagenomics, facilitated by high-throughput ultra deep sequencing, have greatly improved our ability for a broader and deeper exploration of microbial communities including an understanding of community structure, function, as well as inter- and intra-specific competitions. Here, we discuss possible areas of research focusing how combination of community ecology and metagenomic approaches could be applied to study the cholera system.

Molecular diversity and predictability of Vibrio parahaemolyticus along the Georgian coastal zone of the Black Sea.

Vibrio parahaemolyticus is a leading cause of seafood-related gastroenteritis and is also an autochthonous member of marine and estuarine environments worldwide. One-hundred seventy strains of V. parahaemolyticus were isolated from water and plankton samples collected along the Georgian coast of the Black Sea during 28 months of sample collection. All isolated strains were tested for presence of tlh, trh, and tdh. A subset of strains were serotyped and tested for additional factors and markers of pandemicity. Twenty-six serotypes, five of which are clinically relevant, were identified. Although all 170 isolates were negative for tdh, trh, and the Kanagawa Phenomenon, 7 possessed the GS-PCR sequence and 27 the 850 bp sequence of V. parahaemolyticus pandemic strains. The V. parahaemolyticus population in the Black Sea was estimated to be genomically heterogeneous by rep-PCR and the serodiversity observed did not correlate with rep-PCR genomic diversity. Statistical modeling was used to predict presence of V. parahaemolyticus as a function of water temperature, with strongest concordance observed for Green Cape site samples (Percent of total variance = 70, P < 0.001). Results demonstrate a diverse population of V. parahaemolyticus in the Black Sea, some of which carry pandemic markers, with increased water temperature correlated to an increase in abundance of V. parahaemolyticus.

Cholera outbreak in Senegal in 2005: was climate a factor?

Cholera is an acute diarrheal illness caused by Vibrio cholerae and occurs as widespread epidemics in Africa. In 2005, there were 31,719 cholera cases, with 458 deaths in the Republic of Senegal. We retrospectively investigated the climate origin of the devastating floods in mid-August 2005, in the Dakar Region of Senegal and the subsequent outbreak of cholera along with the pattern of cholera outbreaks in three other regions of that country. We compared rainfall patterns between 2002 and 2005 and the relationship between the sea surface temperature (SST) gradient in the tropical Atlantic Ocean and precipitation over Senegal for 2005. Results showed a specific pattern of rainfall throughout the Dakar region during August, 2005, and the associated rainfall anomaly coincided with an exacerbation of the cholera epidemic. Comparison of rainfall and epidemiological patterns revealed that the temporal dynamics of precipitation, which was abrupt and heavy, was presumably the determining factor. Analysis of the SST gradient showed that the Atlantic Ocean SST variability in 2005 differed from that of 2002 to 2004, a result of a prominent Atlantic meridional mode. The influence of this intense precipitation on cholera transmission over a densely populated and crowded region was detectable for both Dakar and Thiès, Senegal. Thus, high resolution rainfall forecasts at subseasonal time scales should provide a way forward for an early warning system in Africa for cholera and, thereby, trigger epidemic preparedness. Clearly, attention must be paid to both natural and human induced environmental factors to devise appropriate action to prevent cholera and other waterborne disease epidemics in the region.

Role of zooplankton diversity in Vibrio cholerae population dynamics and in the incidence of cholera in the Bangladesh Sundarbans.

Vibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries. V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenic V. cholerae strains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenic V. cholerae and incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection of V. cholerae and/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions between V. cholerae, its plankton hosts, and the incidence of cholera.

Temporal and spatial variability in the distribution of Vibrio vulnificus in the Chesapeake Bay: a hindcast study.

Vibrio vulnificus, an estuarine bacterium, is the causative agent of seafood-related gastroenteritis, primary septicemia, and wound infections worldwide. It occurs as part of the normal microflora of coastal marine environments and can be isolated from water, sediment, and oysters. Hindcast prediction was undertaken to determine spatial and temporal variability in the likelihood of occurrence of V. vulnificus in surface waters of the Chesapeake Bay. Hindcast predictions were achieved by forcing a multivariate habitat suitability model with simulated sea surface temperature and salinity in the Bay for the period between 1991 and 2005 and the potential hotspots of occurrence of V. vulnificus in the Chesapeake Bay were identified. The likelihood of occurrence of V. vulnificus during high and low rainfall years was analyzed. From results of the study, it is concluded that hindcast prediction yields an improved understanding of environmental conditions associated with occurrence of V. vulnificus in the Chesapeake Bay.

A self-incompatibility system explains high male frequencies in an androdioecious plant.

Androdioecy is a sexual system in which males co-occur with hermaphrodites, which have both male and female function. Stable androdioecy is rare in nature, and theory suggests that it requires that males sire more than twice as many offspring as hermaphrodites. In several members of the olive family (Oleaceae), androdioecy occurs with higher frequencies of males than predicted by theory. In Phillyrea angustifolia L., we found that high male frequencies can be maintained in natural populations because hermaphrodites belong exclusively to one of two self-incompatibility groups, and thus, each can fertilize only half of all pollen recipients. In contrast, males can pollinate all hermaphrodites. Thus, in this species, the reproductive disadvantage that males face due to the loss of female function is offset by the fact that all males are fully compatible with all pollen recipients.

Cholera and climate: a demonstrated relationship.

Vibrio cholerae, the causative agent of cholera, is naturally present in the environment and autochthonous to coastal and estuarine ecosystems. V. cholerae is associated with copepods for its survival and multiplication in the natural environment. Changes in the density of its reservoir may result in modification of the bacterial population size in the environment. In this context, climate and/or environmental changes will influence the emergence of cholera in human populations. Several human pathogens are naturally occurring in the aquatic environment and can pose a threat to public health, including V. cholerae. We present results of a project, the goal of which was to improve the understanding of environmental factors associated with occurrence and distribution of the causative agent of cholera in time and space. The system that was developed provides real-time as well as short-term to seasonal forecasts of the likelihood of occurrence of V. cholerae in the Chesapeake Bay. The system, and potential future improved versions of it, may be useful to public health officials concerned with environmental factors influencing human health.

Meningococcal meningitis in Mali: a long-term study of persistence and spread.

OBJECTIVES: Meningococcal meningitis (MM) is still a huge threat in the African meningitis belt. To fight against epidemics, a strengthened health information system, based upon weekly collected data, was set up in Mali. We aimed to study the spatio-temporal dynamics of MM in this country between 1992 and 2003. METHODS: We were first interested in the impact of population size on the disease persistence. We then used cross-correlation analysis to study the spread of the disease on three different spatial scales, i.e., inter-region (global) and inter-district and intra-district (local) levels. RESULTS: We found no persistence of MM at district level in Mali during the whole of the study period. However, we found persistence on a nationwide scale after the 1997 big epidemics, as opposed to the 1992-1996 time periods. In terms of spread, two main regions seem to lead MM dynamics in Mali, even if on a local scale the 'cities-villages' diffusion pattern was not systematically observed. CONCLUSIONS: This study improves knowledge on the spread and persistence of MM in Mali in recent years. It constitutes a first spatial study describing persistence and spread of MM in an African meningitis belt country. The next step should be the integration of vaccination and genetic variability data to clarify the route of spread of the disease in the human population.

Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study.

Vibrio cholerae, the causative agent of cholera, is a naturally occurring inhabitant of the Chesapeake Bay and serves as a predictor for other clinically important vibrios, including Vibrio parahaemolyticus and Vibrio vulnificus. A system was constructed to predict the likelihood of the presence of V. cholerae in surface waters of the Chesapeake Bay, with the goal to provide forecasts of the occurrence of this and related pathogenic Vibrio spp. Prediction was achieved by driving an available multivariate empirical habitat model estimating the probability of V. cholerae within a range of temperatures and salinities in the Bay, with hydrodynamically generated predictions of ambient temperature and salinity. The experimental predictions provided both an improved understanding of the in situ variability of V. cholerae, including identification of potential hotspots of occurrence, and usefulness as an early warning system. With further development of the system, prediction of the probability of the occurrence of related pathogenic vibrios in the Chesapeake Bay, notably V. parahaemolyticus and V. vulnificus, will be possible, as well as its transport to any geographical location where sufficient relevant data are available.

Environmental signatures associated with cholera epidemics.

The causative agent of cholera, Vibrio cholerae, has been shown to be autochthonous to riverine, estuarine, and coastal waters along with its host, the copepod, a significant member of the zooplankton community. Temperature, salinity, rainfall and plankton have proven to be important factors in the ecology of V. cholerae, influencing the transmission of the disease in those regions of the world where the human population relies on untreated water as a source of drinking water. In this study, the pattern of cholera outbreaks during 1998-2006 in Kolkata, India, and Matlab, Bangladesh, and the earth observation data were analyzed with the objective of developing a prediction model for cholera. Satellite sensors were used to measure chlorophyll a concentration (CHL) and sea surface temperature (SST). In addition, rainfall data were obtained from both satellite and in situ gauge measurements. From the analyses, a statistically significant relationship between the time series for cholera in Kolkata, India, and CHL and rainfall anomalies was determined. A statistically significant one month lag was observed between CHL anomaly and number of cholera cases in Matlab, Bangladesh. From the results of the study, it is concluded that ocean and climate patterns are useful predictors of cholera epidemics, with the dynamics of endemic cholera being related to climate and/or changes in the aquatic ecosystem. When the ecology of V. cholerae is considered in predictive models, a robust early warning system for cholera in endemic regions of the world can be developed for public health planning and decision making.

Comparative study of meningitis dynamics across nine African countries: a global perspective.

BACKGROUND: Meningococcal meningitis (MM) represents an important public health problem especially in the "meningitis belt" in Africa. Although seasonality of epidemics is well known with outbreaks usually starting in the dry season, pluri-annual cycles are still less understood and even studied. In this context, we aimed at study MM cases time series across 9 sahelo-sudanian countries to detect pluri-annual periodicity and determine or not synchrony between dynamics. This global and comparative approach allows a better understanding of MM evolution in time and space in the long-term. RESULTS: We used the most adapted mathematical tool to time series analyses, the wavelet method. We showed that, despite a strong consensus on the existence of a global pluri-annual cycle of MM epidemics, it is not the case. Indeed, even if a clear cycle is detected in all countries, these cycles are not as permanent and regular as generally admitted since many years. Moreover, no global synchrony was detected although many countries seemed correlated. CONCLUSION: These results of the first large-scale study of MM dynamics highlight the strong interest and the necessity of a global survey of MM in order to be able to predict and prevent large epidemics by adapted vaccination strategy. International cooperation in Public Health and cross-disciplines studies are highly recommended to hope controlling this infectious disease.