Using MALDI-ToF mass spectrometry to identify mushroom species: Proof of concept analysis of Amanita genus specimens.

Food poisoning caused by toxic mushrooms, such as species in the Amanita genus, occurs frequently around the world. To properly treat these patients, it is important to rapidly and accurately identify the causal species. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry is a rapid technique that has been used in medical laboratories for the past three decades to identify bacteria, yeasts, and filamentous fungi.Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-Tof MS) is a rapid method used for the past three decades to identify microorganisms. In this study, we created and internally validated a MALDI-Tof MS reference database comprising 15 Amanita species frequently encountered in France, and we challenged this database with 38 Amanita specimens from four French locations, using a free online application for MALDI-ToF spectra identifications.Assessment of the database showed that mass spectra can be obtained by analyzing any portion of a carpophore and that all portions enabled identification of the carpophore at the species level. Most carpophores were correctly identified using our database, with the exception of specimens from the Vaginatae section. Decay tests also demonstrated that decayed portions (like those found in the kitchen garbage can) of Amanita phalloides mushrooms could be properly identified using MALDI-ToF MS.Our findings provide important insight for toxicology laboratories that often rely on DNA sequencing to identify meal leftovers implicated in food poisoning. In future developments, this technique could also be used to detect counterfeit mushrooms by including other genera in the reference database. LAY SUMMARY: MALDI-ToF MS is a powerful identification tool for microorganisms. We demonstrate that the technique can be applied to Amanita specimens. This will prevent food intoxications as a rapid and definite identification can be obtained, and it can also be used for food remnants.

Delineating and Analyzing Locality-Level Determinants of Cholera, Haiti.

Centre Department, Haiti, was the origin of a major cholera epidemic during 2010-2019. Although no fine-scale spatial delineation is officially available, we aimed to analyze determinants of cholera at the local level and identify priority localities in need of interventions. After estimating the likely boundaries of 1,730 localities by using Voronoi polygons, we mapped 5,322 suspected cholera cases reported during January 2015-September 2016 by locality alongside environmental and socioeconomic variables. A hierarchical clustering on principal components highlighted 2 classes with high cholera risk: localities close to rivers and unimproved water sources (standardized incidence ratio 1.71, 95% CI 1.02-2.87; p = 0.04) and urban localities with markets (standardized incidence ratio 1.69, 95% CI 1.25-2.29; p = 0.0006). Our analyses helped identify and characterize areas where efforts should be focused to reduce vulnerability to cholera and other waterborne diseases; these methods could be used in other contexts.

Targeting Malaria Hotspots to Reduce Transmission Incidence in Senegal.

In central Senegal, malaria incidence declined in response to scaling-up of control measures from 2000 to 2010 and has since remained stable, making elimination unlikely in the short term. Additional control measures are needed to reduce transmission. We simulated chemoprophylaxis interventions targeting malaria hotspots using a metapopulation mathematical model, based on a differential-equation framework and incorporating human mobility. The model was fitted to weekly malaria incidence from 45 villages. Three approaches for selecting intervention targets were compared: (a) villages with malaria cases during the low transmission season of the previous year; (b) villages with highest incidence during the high transmission season of the previous year; (c) villages with highest connectivity with adjacent populations. Our results showed that intervention strategies targeting hotspots would be effective in reducing malaria incidence in both targeted and untargeted areas. Regardless of the intervention strategy used, pre-elimination (1-5 cases per 1000 per year) would not be reached without simultaneously increasing vector control by more than 10%. A cornerstone of malaria control and elimination is the effective targeting of strategic locations. Mathematical tools help to identify those locations and estimate the impact in silico.

Spatio-temporal variation of malaria hotspots in Central Senegal, 2008-2012.

BACKGROUND: In malaria endemic areas, identifying spatio-temporal hotspots is becoming an important element of innovative control strategies targeting transmission bottlenecks. The aim of this work was to describe the spatio-temporal variation of malaria hotspots in central Senegal and to identify the meteorological, environmental, and preventive factors that influence this variation. METHODS: This study analysed the weekly incidence of malaria cases recorded from 2008 to 2012 in 575 villages of central Senegal (total population approximately 500,000) as part of a trial of seasonal malaria chemoprevention (SMC). Data on weekly rainfall and annual vegetation types were obtained for each village through remote sensing. The time series of weekly malaria incidence for the entire study area was divided into periods of high and low transmission using change-point analysis. Malaria hotspots were detected during each transmission period with the SaTScan method. The effects of rainfall, vegetation type, and SMC intervention on the spatio-temporal variation of malaria hotspots were assessed using a General Additive Mixed Model. RESULTS: The malaria incidence for the entire area varied between 0 and 115.34 cases/100,000 person weeks during the study period. During high transmission periods, the cumulative malaria incidence rate varied between 7.53 and 38.1 cases/100,000 person-weeks, and the number of hotspot villages varied between 62 and 147. During low transmission periods, the cumulative malaria incidence rate varied between 0.83 and 2.73 cases/100,000 person-weeks, and the number of hotspot villages varied between 10 and 43. Villages with SMC were less likely to be hotspots (OR = 0.48, IC95%: 0.33-0.68). The association between rainfall and hotspot status was non-linear and depended on both vegetation type and amount of rainfall. The association between village location in the study area and hotspot status was also shown. CONCLUSION: In our study, malaria hotspots varied over space and time according to a combination of meteorological, environmental, and preventive factors. By taking into consideration the environmental and meteorological characteristics common to all hotspots, monitoring of these factors could lead targeted public health interventions at the local level. Moreover, spatial hotspots and foci of malaria persisting during LTPs need to be further addressed. TRIAL REGISTRATION: The data used in this work were obtained from a clinical trial registered on July 10, 2008 at www.clinicaltrials.gov under NCT00712374.

Estimating effectiveness of case-area targeted response interventions against cholera in Haiti.

Case-area targeted interventions (CATIs) against cholera are conducted by rapid response teams, and may include various activities like water, sanitation, hygiene measures. However, their real-world effectiveness has never been established. We conducted a retrospective observational study in 2015-2017 in the Centre department of Haiti. Using cholera cases, stool cultures and CATI records, we identified 238 outbreaks that were responded to. After adjusting for potential confounders, we found that a prompt response could reduce the number of accumulated cases by 76% (95% confidence interval, 59 to 86) and the outbreak duration by 61% (41 to 75) when compared to a delayed response. An intense response could reduce the number of accumulated cases by 59% (11 to 81) and the outbreak duration by 73% (49 to 86) when compared to a weaker response. These results suggest that prompt and repeated CATIs were significantly effective at mitigating and shortening cholera outbreaks in Haiti.

Visceral Leishmaniasis in West Africa: Clinical Characteristics, Vectors, and Reservoirs.

Visceral leishmaniasis (VL) is the most serious form of human leishmaniasis. VL is understudied in West Africa. The increasing number of patients at-risk, including persons living with HIV and other chronic immunosuppressive diseases, and likely underreporting of VL related to diagnostic challenges advocate for review of existing data to understand VL regional epidemiology. Our review aims to describe the clinical characteristics and epidemiology of Human VL (HVL) in West Africa. We conducted a literature search to identify peer-reviewed articles and grey literature sources using the search terms "Visceral leishmaniasis West Africa", "Leishmania donovani West Africa"; and "Leishmania infantum West Africa". Thirty published articles report HVL from seven countries, including The Gambia, Niger, Nigeria, Ivory Coast, Togo, Burkina Faso, and Guinea Bissau. Three countries report cases of Canine Visceral Leishmaniasis (CVL), including The Gambia, Senegal, and Burkina Faso. Niger, Nigeria, and Ivory Coast report the greatest number of HVL cases. As VL is present in West Africa, active surveillance, increased diagnostic capacity, and studies of vectors and reservoirs are essential to better understand VL epidemiology in the region.

Epidemiologic Trends in Malaria Incidence Among Travelers Returning to Metropolitan France, 1996-2016.

Importance: Despite annually adapted recommendations to prevent malaria in travelers to endemic areas, France is still the industrialized country reporting the highest number of imported cases of malaria. Better understanding of the epidemiologic context and evolution during the past 2 decades may help to define a better preventive strategy. Objective: To study epidemiologic trends of imported cases of malaria in travelers in geographic territories of France on the European continent (metropolitan France) from 1996 through 2016 to potentially explain the persistence of high imported malaria incidence despite national preventive measures. Design, Setting, and Participants: In a cross-sectional study, between January 1 and May 31, 2018, data were extracted from the French National Reference Center of Malaria Surveillance. Trends in patients with imported malaria in association with age, sex, ethnicity, purpose of travel, malaria species, severity of illness, case mortality rate, and endemic countries visited were analyzed in 43 333 malaria cases among civilian travelers living in metropolitan France. Main Outcomes and Measures: Evolution of the main epidemiologic characteristics of patients with imported malaria. Results: Among the 43 333 patients with imported malaria in civilian travelers included in the study, 24 949 were male (62.4%), and 8549 were younger than 18 years (19.9%). A total of 28 658 malaria cases (71.5%) were among African individuals, and 10 618 cases (26.5%) among European individuals. From 1996 through 2016, the number of confirmed malaria cases peaked at 3400 cases in 2000, then declined to 1824 cases in 2005 and stabilized thereafter to approximately 1720 malaria cases per year. A total of 37 065 cases (85.5%) were due to Plasmodium falciparum. The proportion of malaria cases among African individuals rose from 53.5% in 1996 to 83.4% in 2016, and the most frequent motivation for traveling was visiting friends and relatives (25 329 [77.1%]; P < .001). Despite an increase in the proportion of severe cases, which rose from 131 cases (8.9%) in 1996 to 279 cases (16.7%) in 2016 (P < .001), mortality remained stable, being approximately 0.4% during the study period. Conclusions and Relevance: Beyond the apparent stability of the number of imported malaria cases in France, significant changes appear to have occurred among the population who developed malaria infection following travel in endemic areas. These changes may imply that adaptation of the preventive strategy is needed to reduce the burden of the disease among travelers.

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.

Ecologic Features of Plague Outbreak Areas, Democratic Republic of the Congo, 2004-2014.

During 2004-2014, the Democratic Republic of the Congo (DRC) declared 54% of plague cases worldwide. Using national data, we characterized the epidemiology of human plague in DRC for this period. All 4,630 suspected human plague cases and 349 deaths recorded in DRC came from Orientale Province. Pneumonic plague cases (8.8% of total) occurred during 2 major outbreaks in mining camps in the equatorial forest, and some limited outbreaks occurred in the Ituri highlands. Epidemics originated in 5 health zones clustered in Ituri, where sporadic bubonic cases were recorded throughout every year. Classification and regression tree characterized this cluster by the dominance of ecosystem 40 (mountain tropical climate). In conclusion, a small, stable, endemic focus of plague in the highlands of the Ituri tropical region persisted, acting as a source of outbreaks in DRC.

Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library.

Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani, L. guyanensis, and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers.

Populations at risk for alveolar echinococcosis, France.

During 1982-2007, alveolar echinococcosis (AE) was diagnosed in 407 patients in France, a country previously known to register half of all European patients. To better define high-risk groups in France, we conducted a national registry-based study to identify areas where persons were at risk and spatial clusters of cases. We interviewed 180 AE patients about their way of life and compared responses to those of 517 controls. We found that almost all AE patients lived in 22 départements in eastern and central France (relative risk 78.63, 95% CI 52.84-117.02). Classification and regression tree analysis showed that the main risk factor was living in AE-endemic areas. There, most at-risk populations lived in rural settings (odds ratio [OR] 66.67, 95% CI 6.21-464.51 for farmers and OR 6.98, 95% CI 2.88-18.25 for other persons) or gardened in nonrural settings (OR 4.30, 95% CI 1.82-10.91). These findings can help sensitization campaigns focus on specific groups.

Spatio-temporal dynamics of cholera during the first year of the epidemic in Haiti.

BACKGROUND: In October 2010, cholera importation in Haiti triggered an epidemic that rapidly proved to be the world's largest epidemic of the seventh cholera pandemic. To establish effective control and elimination policies, strategies rely on the analysis of cholera dynamics. In this report, we describe the spatio-temporal dynamics of cholera and the associated environmental factors. METHODOLOGY/PRINCIPAL FINDINGS: Cholera-associated morbidity and mortality data were prospectively collected at the commune level according to the World Health Organization standard definition. Attack and mortality rates were estimated and mapped to assess epidemic clusters and trends. The relationships between environmental factors were assessed at the commune level using multivariate analysis. The global attack and mortality rates were 488.9 cases/10,000 inhabitants and 6.24 deaths/10,000 inhabitants, respectively. Attack rates displayed a significantly high level of spatial heterogeneity (varying from 64.7 to 3070.9 per 10,000 inhabitants), thereby suggesting disparate outbreak processes. The epidemic course exhibited two principal outbreaks. The first outbreak (October 16, 2010-January 30, 2011) displayed a centrifugal spread of a damping wave that suddenly emerged from Mirebalais. The second outbreak began at the end of May 2011, concomitant with the onset of the rainy season, and displayed a highly fragmented epidemic pattern. Environmental factors (river and rice fields: p<0.003) played a role in disease dynamics exclusively during the early phases of the epidemic. CONCLUSION: Our findings demonstrate that the epidemic is still evolving, with a changing transmission pattern as time passes. Such an evolution could have hardly been anticipated, especially in a country struck by cholera for the first time. These results argue for the need for control measures involving intense efforts in rapid and exhaustive case tracking.

The 2009 A(H1N1) influenza pandemic in the French Armed Forces: evaluation of three surveillance systems.

BACKGROUND: The French military forces had to modify their epidemiological surveillance systems at the time of the 2009 A(H1N1) influenza pandemic. The aim of this article was to present an evaluation of the different systems used. METHODS: Two influenza surveillance systems are usually used in the French forces: one permanent (Surveillance épidémiologique des armées or SEA) and one seasonal (Système militaire d'observation de la grippe or SMOG). The pandemic required the implementation of a daily surveillance system (Surveillance quotidienne--SQ), which aimed to monitor disrupted activity owing to 2009 A(H1N1) influenza. The qualitative evaluation of these three systems during the period from September 2009 to February 2010 was performed using 11 criteria based on the list defined by Centers for Disease Control and Prevention of Atlanta. RESULTS: Although it included only 30 sentinel units vs. 320 for the other systems, the SMOG system was the best-performing system in terms of relevance, feasibility, efficacy, quality of data, usefulness, acceptability, efficiency and cost/benefits/costs ratio. The SQ proved very expensive in terms of logistics. CONCLUSION: The SQ did not bring any significant advantage compared with the weekly surveillance schemes. In the eventuality of another similar episode, influenza surveillance could be significantly improved by using the SMOG system extended to more units for better geographical coverage.

Dynamics of cholera outbreaks in Great Lakes region of Africa, 1978-2008.

Cholera outbreaks have occurred in Burundi, Rwanda, Democratic Republic of Congo, Tanzania, Uganda, and Kenya almost every year since 1977-1978, when the disease emerged in these countries. We used a multiscale, geographic information system-based approach to assess the link between cholera outbreaks, climate, and environmental variables. We performed time-series analyses and field investigations in the main affected areas. Results showed that cholera greatly increased during El Nino warm events (abnormally warm El Ninos) but decreased or remained stable between these events. Most epidemics occurred in a few hotspots in lakeside areas, where the weekly incidence of cholera varied by season, rainfall, fluctuations of plankton, and fishing activities. During lull periods, persistence of cholera was explained by outbreak dynamics, which suggested a metapopulation pattern, and by endemic foci around the lakes. These links between cholera outbreaks, climate, and lake environments need additional, multidisciplinary study.

Understanding the cholera epidemic, Haiti.

After onset of a cholera epidemic in Haiti in mid-October 2010, a team of researchers from France and Haiti implemented field investigations and built a database of daily cases to facilitate identification of communes most affected. Several models were used to identify spatiotemporal clusters, assess relative risk associated with the epidemic's spread, and investigate causes of its rapid expansion in Artibonite Department. Spatiotemporal analyses highlighted 5 significant clusters (p<0.001): 1 near Mirebalais (October 16-19) next to a United Nations camp with deficient sanitation, 1 along the Artibonite River (October 20-28), and 3 caused by the centrifugal epidemic spread during November. The regression model indicated that cholera more severely affected communes in the coastal plain (risk ratio 4.91) along the Artibonite River downstream of Mirebalais (risk ratio 4.60). Our findings strongly suggest that contamination of the Artibonite and 1 of its tributaries downstream from a military camp triggered the epidemic.

Understanding the cholera epidemic, Haiti

This article Understanding the Cholera Epidemic, Haiti, of the journal Emerging Infectious Diaseases give information how, morbidity and mortality survey, statistics, discussion and others topics with relationship at the epidemic cholera.

Clinical features and evolution of alveolar echinococcosis in France from 1982 to 2007: results of a survey in 387 patients.

BACKGROUND & AIMS: Alveolar echinococcosis (AE) is a rare disease in humans, caused by the larval stage of the fox tapeworm Echinococcus multilocularis. METHODS: We present here 387 detailed AE cases diagnosed in France from 1982 to 2007 actively identified by a retrospective survey performed in 1997-1998 and prospectively thereafter. RESULTS: Male:female ratio was 1.03 and mean age 57.8 years at time of diagnosis. Among the 362 complete files (including 347 non dead-out and 15 dead-out lesions), 73% of the patients were symptomatic at first admittance. Among them, 83% presented with clinical patterns evocative either of a digestive or a hepatic disorder. Other symptomatic patients presented with erratic clinical pictures, generally due to metastasis or extra-hepatic location of the parasite. Except for a few patients with particularly severe AE who died shortly after the diagnosis, most patients were treated using benzimidazoles. Their mortality tends to merge with that of the general French population, matched by sex, age, and calendar year. This study also highlights an unexpectedly high frequency of blood-tied family cases (13% of patients submitted to a specific questionnaire). CONCLUSIONS: Even though the broad set of clinical features provoked by E. multilocularis makes AE a potential diagnostic trap for many physicians, our study revealed an improvement of its prognosis. However, as shown by our findings about the frequency of family cases, there is still a need for studies aimed at better describing this uncommon parasitic disease.