SPODT: An R Package to Perform Spatial Partitioning

International audienceSpatial cluster detection is a classical question in epidemiology: Are cases located near other cases? In order to classify a study area into zones of different risks and determine their boundaries, we have developed a spatial partitioning method based on oblique decision trees, which is called spatial oblique decision tree (SpODT). This non-parametric method is based on the classification and regression tree (CART) approach introduced by Leo Breiman. Applied to epidemiological spatial data, the algorithm recursively searches among the coordinates for a threshold or a boundary between zones, so that the risks estimated in these zones are as different as possible. While the CART algorithm leads to rectangular zones, providing perpendicular splits of longitudes and latitudes, the SpODT algorithm provides oblique splitting of the study area, which is more appropriate and accurate for spatial epidemiology. Oblique decision trees can be considered as non-parametric regression models. Beyond the basic function, we have developed a set of functions that enable extended analyses of spatial data, providing: inference, graphical representations, spatio-temporal analysis, adjustments on covariates, spatial weighted partition, and the gathering of similar adjacent final classes. In this paper, we propose a new R package, SPODT, which provides an extensible set of functions for partitioning spatial and spatio-temporal data. The implementation and extensions of the algorithm are described. Function usage examples are proposed, looking for clustering malaria episodes in Bandiagara, Mali, and samples showing three different cluster shapes

Letter to the Editor Questioning the Effectiveness of Oral Cholera Vaccine in Port-au-Prince Slums

International audienceOral cholera vaccination (OCV) has been validated by the World Health Organization (WHO) as a valuable tool to complement water, sanitation, and hygiene (WASH) activities in cholera prevention for high-risk areas and populations. We read with great interest the recent study published by Sévère and others, which evaluated the effectiveness of a mass OCV campaign targeting approximately 70,000 inhabitants in several slums of Port-au-Prince, Haiti, between April and June 2012. The authors reported a 75% vaccine coverage and, using a cohort design, a striking 97.5% vaccine effectiveness in the 37 months postvaccination, whereas controlled clinical trials have measured OCV vaccine efficacy around 57% [95% confidence interval, 44–67%] during the first 2 years. Although it was expected that 56% of cholera cases would occur among vaccinated individuals according to the WHO screening method, the same proportion was 5% in the Sévère and others cohort. A thorough analysis of this study shows that the authors did not evaluate the isolated effectiveness of OCV. They rather estimated its combined effectiveness together with WASH-associated measures. To assess the importance of such methodological bias, we computed provided data using a bias-indicator cohort analysis, as previously described in another OCV campaign, and found that their strategy exhibited a 95% effectiveness [93–97%] against noncholeric diarrheas as well. Pondering such bias would require adjusting the results on the observance of WASH prevention methods, which may have differed between nonvaccinated and vaccinated groups

Antimicrobial susceptibility of autochthonous aquatic Vibrio cholerae in Haiti

We investigated the antimicrobial susceptibility of 50 environmental isolates of Vibrio cholerae non-O1/non-O139 collected in surface waters in Haiti in July 2012, during an active cholera outbreak. A panel of 16 antibiotics was tested on the isolates using the disk diffusion method and PCR detection of seven resistance-associated genes (strA/B, sul1/2, ermA/B and mefA). All isolates were susceptible to amoxicillin-clavulanic acid, cefotaxime, imipenem, ciprofloxacin, norfloxacin, amikacin and gentamicin. Nearly a quarter (22.0%) of the isolates were susceptible to all 16 antimicrobials tested and only 8.0% of the isolates (n=4) were multidrug-resistant. The highest proportions of resistant isolates were observed for sulfonamide (70.0%), amoxicillin (12.0%) and trimethoprim-sulfamethoxazole (10.0%). One strain was resistant to erythromycin and one to doxycycline, two antibiotics used to treat cholera in Haiti. Among the 50 isolates, 78% possessed at least two resistance-associated genes, and the genes sul1, ermA and strB were detected in all four multidrug-resistant isolates. Our results clearly indicate that the autochthonous population of V. cholerae non-O1/non-O139 found in surface waters in Haiti shows antimicrobial patterns different from that of the outbreak strain. The presence in the Haitian aquatic environment of V. cholerae non-O1/non-O139 with reduced susceptibility or resistance to antibiotics used in human medicine may constitute a mild public health threat