Proof of concept study on early forecasting of antimicrobial resistance in hospitalized patients using machine learning and simple bacterial ecology data.

Antibiotic resistance in bacterial pathogens is a major threat to global health, exacerbated by the misuse of antibiotics. In hospital practice, results of bacterial cultures and antibiograms can take several days. Meanwhile, prescribing an empirical antimicrobial treatment is challenging, as clinicians must balance the antibiotic spectrum against the expected probability of susceptibility. We present here a proof of concept study of a machine learning-based system that predicts the probability of antimicrobial susceptibility and explains the contribution of the different cofactors in hospitalized patients, at four different stages prior to the antibiogram (sampling, direct examination, positive culture, and species identification), using only historical bacterial ecology data that can be easily collected from any laboratory information system (LIS) without GDPR restrictions once the data have been anonymised. A comparative analysis of different state-of-the-art machine learning and probabilistic methods was performed using 44,026 instances over 7 years from the Hôpital Européen Marseille, France. Our results show that multilayer dense neural networks and Bayesian models are suitable for early prediction of antibiotic susceptibility, with AUROCs reaching 0.88 at the positive culture stage and 0.92 at the species identification stage, and even 0.82 and 0.92, respectively, for the least frequent situations. Perspectives and potential clinical applications of the system are discussed.

Reviving health mediation during the COVID-19 crisis and beyond: an implementation study in deprived neighbourhoods of Marseille, France.

Introduction: In 2020, during France's COVID-19 response, healthcare professionals from a hospital and an association initiated health mediation interventions in Marseille's vulnerable neighbourhoods, funded by the regional health authorities. This mixed method research evaluates the CORHESAN program that lasted until June 2022. Methods: We examined CORHESAN documents and reports, conducted interviews, and analysed activity data, comparing it to the COVID-19 hotspots identified on a weekly basis at the neighbourhood level, using generalised linear mixed models (GLMMs). Results: CORHESAN was implemented by a team of up to nine health mediators, six private nurses hired on an ad hoc basis, supervised by a general coordinator and two part-time medical and nursing coordinators. Multiple partnerships were established with shelters, associations, social-housing landlords and local institutions. The team accompanied 6,253 people affected by COVID-19 or contact in the practical implementation of their isolation and contact tracing. Of the 5,180 nasopharyngeal samples for RT-PCR and 1,875 for antigenic testing: 12% were taken at home and 27% in partner facilities in the targeted neighbourhoods; 32% were taken from symptomatic patients and 30% in the context of contact tracing; and 40% were positive. Multiple awareness sessions on prevention methods and distributions of personal protection kits and self-diagnostic tests were conducted in the streets, in shelters, in associations or at home. A total of 5,929 doses of COVID-19 vaccine were administered in a walk-in vaccination centre, at temporary street vaccination posts, during operations at partner facilities, or during home-visits to patients with limited autonomy. GLMMs showed that the intervention significantly targeted its testing interventions in neighbourhoods with socioeconomic disadvantage and/or past under-testing (adjusted odds ratio (aOR), 2.75 [1.50-5.00]) and those with high hotspot level (aOR for level-3 versus level-0, 1.83 [1.24-2.71]). Discussion: The pandemic emphasised the potential of health mediation interventions to address health disparities. Building on this, a new program began in July 2022, aiming at enhancing cancer screening and vaccinations in deprived areas of Marseille. Evaluations are ongoing to assess its activities and impact, and provide evidence to future implementation initiatives.

Motivational interview-based health mediator interventions increase intent to vaccinate among disadvantaged individuals.

Coverage for recommended COVID-19 and diphtheria-tetanus-poliomyelitis (DTP) booster shots is often inadequate, especially among disadvantaged populations. To help health mediators (HMs) involved in outreach programs deal with the problems of vaccine hesitancy (VH) in these groups, we trained them in motivational interviewing (MI). We evaluated the effectiveness of this training among HMs on their MI knowledge and skills (objective 1) and among the interviewees on their vaccination readiness (VR) and intention to get vaccinated or accept a booster against COVID-19 and/or DTP (objective 2). Two MI specialists trained 16 HMs in a two-day workshop in May 2022. The validated MISI questionnaire evaluated HMs' acquisition of MI knowledge and skills (objective 1). Trained HMs offered an MI-based intervention on vaccination to people in disadvantaged neighborhoods of Marseille (France). Those who consented completed a questionnaire before and after the interview to measure VR with the 7C scale and intentions regarding vaccination/booster against COVID-19 and DTP (objective 2). The training resulted in HMs acquiring good MI skills (knowledge, application, self-confidence in using it). HMs enrolled 324 interviewees, 96% of whom completed both questionnaires. VR increased by 6%, and intentions to get vaccinated or update COVID-19 and DTP vaccination increased by 74% and 52% respectively. Nearly all interviewees were very satisfied with the interview, although 21% still had questions about vaccination. HMs assimilated MI principles well. MI use in outreach programs appears to show promise in improving vaccine confidence and intentions among disadvantaged people.

'Forest malaria' in Myanmar? Tracking transmission landscapes in a diversity of environments.

BACKGROUND: In the Greater Mekong Subregion, case-control studies and national-level analyses have shown an association between malaria transmission and forest activities. The term 'forest malaria' hides the diversity of ecosystems in the GMS, which likely do not share a uniform malaria risk. To reach malaria elimination goals, it is crucial to document accurately (both spatially and temporally) the influence of environmental factors on malaria to improve resource allocation and policy planning within given areas. The aim of this ecological study is to characterize the association between malaria dynamics and detailed ecological environments determined at village level over a period of several years in Kayin State, Myanmar. METHODS: We characterized malaria incidence profiles at village scale based on intra- and inter-annual variations in amplitude, seasonality, and trend over 4 years (2016-2020). Environment was described independently of village localization by overlaying a 2-km hexagonal grid over the region. Specifically, hierarchical classification on principal components, using remote sensing data of high spatial resolution, was used to assign a landscape and a climate type to each grid cell. We used conditional inference trees and random forests to study the association between the malaria incidence profile of each village, climate and landscape. Finally, we constructed eco-epidemiological zones to stratify and map malaria risk in the region by summarizing incidence and environment association information. RESULTS: We identified a high diversity of landscapes (n = 19) corresponding to a gradient from pristine to highly anthropogenically modified landscapes. Within this diversity of landscapes, only three were associated with malaria-affected profiles. These landscapes were composed of a mosaic of dense and sparse forest fragmented by small agricultural patches. A single climate with moderate rainfall and a temperature range suitable for mosquito presence was also associated with malaria-affected profiles. Based on these environmental associations, we identified three eco-epidemiological zones marked by later persistence of Plasmodium falciparum, high Plasmodium vivax incidence after 2018, or a seasonality pattern in the rainy season. CONCLUSIONS: The term forest malaria covers a multitude of contexts of malaria persistence, dynamics and populations at risk. Intervention planning and surveillance could benefit from consideration of the diversity of landscapes to focus on those specifically associated with malaria transmission.

Hypoparathyroidism-related health care utilization and expenditure during the first postoperative year after total thyroidectomy for cancer: a comprehensive national cohort study.

Objectives: Hypoparathyroidism is the most common complication of total thyroidectomy for cancer, and requires calcium and/or vitamin D supplementation for an unpredictable period of time. The additional cost associated with this complication has not hitherto been assessed. The aim of this study was to assess the economic burden of postoperative hypoparathyroidism after total thyroidectomy for cancer in France. Methods: Based on the French national cancer cohort, which extracts data from the French National Health Data System (SNDS), all adult patients who underwent a total thyroidectomy for cancer in France between 2011 and 2015 were identified, and their healthcare resource use during the first postoperative year was compared according to whether they were treated postoperatively with calcium and/or vitamin D or not. Univariate and multivariate cost analyses were performed with the non-parametric Wilcoxon test and generalized linear model (gamma distribution and log link), respectively. Results: Among the 31,175 patients analyzed (75% female, median age: 52y), 13,247 (42%) started calcium and/or vitamin D supplementation within the first postoperative month, and 2,855 patients (9.1%) were still treated at 1 year. Over the first postoperative year, mean overall and specific health expenditures were significantly higher for treated patients than for untreated patients: €7,233 vs €6,934 per patient (p<0.0001) and €478.6 vs €332.7 per patient (p<0.0001), respectively. After adjusting for age, gender, Charlson Comorbidity index, ecological deprivation index, types of thyroid resection, lymph node dissection and complications, year and region, the incremental cost of overall health care utilization was €142 (p<0.004). Conclusion: Our study found a significant additional cost in respect of health expenditures for patients who had hypoparathyroidism after thyroidectomy for cancer, over the first postoperative year. Five-year follow-up is planned to assess the impact of more severe long-term complications on costs.

Social deprivation and SARS-CoV-2 testing: a population-based analysis in a highly contrasted southern France region.

Background: Testing was the cornerstone of the COVID-19 epidemic response in most countries until vaccination became available for the general population. Social inequalities generally affect access to healthcare and health behaviors, and COVID-19 was rapidly shown to impact deprived population more drastically. In support of the regional health agency in Provence-Alpes-Côte d'Azur (PACA) in South-Eastern France, we analyzed the relationship between testing rate and socio-demographic characteristics of the population, to identify gaps in testing coverage and improve targeting of response strategies. Methods: We conducted an ecological analysis of SARS-CoV-2/COVID-19 testing rate in the PACA region, based on data aggregated at the finest spatial resolution available in France (IRIS) and by periods defined by public health implemented measures and major epidemiological changes. Using general census data, population density, and specific deprivation indices, we used principal component analysis followed by hierarchical clustering to define profiles describing local socio-demographic characteristics. We analyzed the association between these profiles and testing rates in a generalized additive multilevel model, adjusting for access to healthcare, presence of a retirement home, and the age profile of the population. Results: We identified 6 socio-demographic profiles across the 2,306 analyzed IRIS spatial units: privileged, remote, intermediate, downtown, deprived, and very deprived (ordered by increasing social deprivation index). Profiles also ranged from rural (remote) to high density urban areas (downtown, very deprived). From July 2020 to December 2021, we analyzed SARS-CoV-2/COVID-19 testing rate over 10 periods. Testing rates fluctuated strongly but were highest in privileged and downtown areas, and lowest in very deprived ones. The lowest adjusted testing rate ratios (aTRR) between privileged (reference) and other profiles occurred after implementation of a mandatory healthpass for many leisure activities in July 2021. Periods of contextual testing near Christmas displayed the largest aTRR, especially during the last periods of 2021 after the end of free convenience testing for unvaccinated individuals. Conclusion: We characterized in-depth local heterogeneity and temporal trends in testing rates and identified areas and circumstances associated with low testing rates, which the regional health agency targeted specifically for the deployment of health mediation activities.

Anti-spike protein to determine SARS-CoV-2 antibody levels: Is there a specific threshold conferring protection in immunocompromised patients?

BACKGROUND: Identifying a specific threshold level of SARS-CoV-2 antibodies that confers protection in immunocompromised patients has been very challenging. The aim was to assess the threshold of 264 binding antibody units (BAU)/ml using four different SARS-CoV-2 antibody assays (Abbott, Beckman, Roche, and Siemens) and to establish a new optimal threshold of protection for each of the four antibody assays. METHODS: This study was performed on data retrieved from 69 individuals, who received at least one dose of the Pfizer/BioNTech BNT162b2 or Moderna COVID-19 vaccine (Spikevax) at the Alphabio Laboratory in Marseille, France (European Hospital, Alphabio-Biogroup). The results were compared to the percent inhibition calculated using a functional surrogate of a standardized virus neutralization test (Genscript). RESULTS: Samples from 69 patients were analyzed. For a reference cutoff of 264 BAU/ml, assays showed moderate to good overall concordance with Genscript: 87% concordance for Abbott, 78% for Beckman, 75% for Roche, and 88% for Siemens. Overall concordance increased consistently after applying new thresholds, i.e., 148 BAU/ml (Abbott), 48 (Beckman), 559 (Roche), and 270 (Siemens). CONCLUSION: We suggest specific adjusted thresholds (BAU/ml) for the four commercial antibody assays that are used to assess pre-exposure prophylaxis in immunocompromised patients.

Malaria temporal dynamic clustering for surveillance and intervention planning.

BACKGROUND: Targeting interventions where most needed and effective is crucial for public health. Malaria control and elimination strategies increasingly rely on stratification to guide surveillance, to allocate vector control campaigns, and to prioritize access to community-based early diagnosis and treatment (EDT). We developed an original approach of dynamic clustering to improve local discrimination between heterogeneous malaria transmission settings. METHODS: We analysed weekly malaria incidence records obtained from community-based EDT (malaria posts) in Karen/Kayin state, Myanmar. We smoothed longitudinal incidence series over multiple seasons using functional transformation. We regrouped village incidence series into clusters using a dynamic time warping clustering and compared them to the standard, 5-category annual incidence standard stratification. RESULTS: We included 1115 villages from 2016 to 2020. We identified eleven P. falciparum and P. vivax incidence clusters which differed by amplitude, trends and seasonality. Specifically the 124 villages classified as "high transmission area" in the standard P. falciparum stratification belonged to the 11 distinct groups when accounting to inter-annual trends and intra-annual variations. Likewise for P. vivax, 399 "high transmission" villages actually corresponded to the 11 distinct dynamics. CONCLUSION: Our temporal dynamic clustering methodology is easy to implement and extracts more information than standard malaria stratification. Our method exploits longitudinal surveillance data to distinguish local dynamics, such as increasing inter-annual trends or seasonal differences, providing key information for decision-making. It is relevant to malaria strategies in other settings and to other diseases, especially when many countries deploy health information systems and collect increasing amounts of health outcome data. FUNDING: The Bill & Melinda Gates Foundation, The Global Fund against AIDS, Tuberculosis and Malaria (the Regional Artemisinin Initiative) and the Wellcome Trust funded the METF program.

Concerted and multidisciplinary management of COVID-19 drug therapies during the first two epidemic waves in a tertiary hospital in Marseille, France: Results of the PHARMA-COVID study.

OBJECTIVES: To evaluate the impact of local therapeutic recommendation updates made by the COVID multidisciplinary consultation meeting (RCP) at the Hôpital Européen Marseille (HEM) through the description of the drug prescriptions for COVID-19 during the first two waves of the epidemic. METHODS: This retrospective observational study analysed data from the hospital's pharmaceutical file. We included all patients hospitalized for COVID-19 between February 1, 2020 and January 21, 2021 and extracted specific anti-COVID-19 therapies (ST) from computerized patient record, as well as patients' demographic characteristics, comorbidities and outcome. The evolution of ST prescriptions during the study period was described and put into perspective with the updates of local recommendations made during the first (V1, from 2/24/2020 to 7/27/2020), and second (V2, from 7/28/2020 to 1/21/2021) epidemic waves. RESULTS: A total of 607 COVID-19 hospitalized patients, 197 during V1 and 410 during V2. Their mean age was 65 years-old, and they presented frequent comorbidities. In total, 93% of hospitalized patients received ST: anticoagulants (90%), glucocorticoids (39%) mainly during V2 (49% vs 17%, P<0.001), and azithromycin (30%) mainly during V1 (71% vs 10%, P<0.001). Lopinavir/ritonavir and hydroxychloroquine were prescribed to 17 and 7 inpatients, respectively, and only during V1. Remdesivir was never administered. A total of 22 inpatients were enrolled into clinical trials. CONCLUSIONS: The effective dissemination of evidence-based and concerted recommendations seems to have allowed an optimized management of COVID-19 drug therapies in the context of this emerging infection with rapidly evolving therapeutic questions.

Long-term neuromuscular consequences of SARS-Cov-2 and their similarities with myalgic encephalomyelitis/chronic fatigue syndrome: results of the retrospective CoLGEM study.

BACKGROUND: Patients with long-COVID often complain of continuous fatigue, myalgia, sleep problems, cognitive dysfunction, and post-exertional malaise. No data are available on EMG recording of evoked myopotentials (M-waves) or exercise-induced alterations in long-COVID patients, providing evidence of muscle membrane fatigue. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) develops in more than half of patients after an infectious disease, particularly viral diseases. A large proportion (around 70%) of these patients have neuromuscular disorders with M-wave alterations during and after exercise. Our hypothesis was that M-wave alterations would be also found in long-COVID patients, in association with neuromuscular symptoms, similar to ME/CFS. METHODS: This retrospective observational ColGEM (Covid LonG Encéphalomyelite Myalgique) study compared 59 patients with long-COVID and 55 ME/CFS patients with a history of severe infection who presented before the COVID pandemic. All of these patients underwent the same protocol consisting of a questionnaire focusing on neural and neuromuscular disorders and M-wave recording in the rectus femoris muscle before, during, and 10 min after a progressive cycling exercise. Maximal handgrip strength (MHGS) and maximal exercise power were also measured. The frequency of symptoms and magnitude of M-wave changes in the two groups were compared using non-parametric and parametric tests. RESULTS: The frequency of fatigue, myalgia, sleep problems, cognitive dysfunction, and post-exertional malaise as well as the magnitude of exercise-induced M-wave alterations were the same in the two groups. By contrast, digestive problems were less present in long-COVID. M-wave alterations were greater in ME/CFS patients as in those with long-COVID when the highest muscle strength and highest exercise performance were measured. CONCLUSIONS: These high clinical and biological similarities between long-COVID and ME/CFS support the hypothesis that SARS-Cov-2 infection can cause ME/CFS symptoms. Trial registration Registered retrospectively.

Cholera in Haiti.

The cholera epidemic that hit Haiti from October 2010 to February 2019 was the world's deadliest of the last 25 years. Officially, the successive waves caused 9789 deaths, although numerous additional casualties could not be recorded. The origin of this epidemic has been the subject of a controversy involving two opposing theories. The first hypothesis, put forward by renowned American academics, was that the cholera epidemic originated from the environment, due to the proliferation and transmission of aquatic Vibrio cholerae bacteria driven by a confluence of circumstances, i.e., the earthquake followed by a hot summer and, ultimately, heavy rainfall and flooding. The alternative hypothesis, which was subsequently confirmed by epidemiological and genomic studies, attributed the epidemic to the recent importation of cholera by UN peacekeepers recently arrived from Nepal, and to a river polluted with sewage. In late 2016, the Secretary General of the United Nations finally begged the Haitian people for forgiveness. This implicit recognition of the role of the UN in the cholera epidemic helped to fund the ongoing fight against it. Case-area targeted interventions aimed at interrupting cholera transmission were reinforced, which resulted in the extinction of the epidemic within two years. In the meantime, several phylogenetic studies on Vibrio cholerae during the seventh cholera pandemic demonstrated that local environmental and global epidemic Vibrio populations were distinct. These studies also showed that epidemics arose when the bacterium had diversified and that it had spread during transmission events associated with human travel.

Un modèle innovant d'intervention, de dépistage et de prise en charge mobile de la COVID-19 chez les personnes sans-abri à Marseille.

INTRODUCTION: Homeless people are particularly at risk of becoming infected with COVID-19 because their precarious living conditions make prevention measure difficult. OBJECTIVE: We describe an innovative approach with the aim of implementing testing and monitoring adapted to the needs of the homeless people of Marseille (inhabitants of slums, squats or those living on the street). RESULTS: The intervention included 1) the coordination of 18 support organizations for homeless people, 2) the training and the provision of rapid serological and antigenic tests, 3) a mobile outreach team with community mediators in order to provide tests, including COVID-19 PCR on point of care, prevention and monitoring of positive cases. Acceptability of the intervention by participants, field organization was good. The lack of adapted places of accommodation was an important restricting factor for optimal care and support. CONCLUSION: The emergence of COVID-19 has highlighted discontinuities in health care among homeless people. Specific mobile outreach teams could limit the impact on this high-risk population.

Intraoperative Mapping Angiograms of the Parathyroid Glands Using Indocyanine Green During Thyroid Surgery: Results of the Fluogreen Study.

BACKGROUND: During thyroid surgery, preservation of parathyroid gland (PG) feeding vessels is often impossible. The aim of the Fluogreen study was to determine the feasibility of using indocyanine green (ICG)-based intraoperative mapping angiograms of the PG (iMAP) to improve vascular preservation. STUDY DESIGN: This prospective study enrolled all patients undergoing thyroid lobectomy or total thyroidectomy at the Hôpital Européen Marseille between September and December 2018. After exploring the thyroid lobe by autofluorescence to locate the PGs, ICG solution was injected intravenously to locate the PG feeding vessels and guide dissection. A second ICG injection was administered at the end of the lobectomy to assess perfusion of the PGs. The primary outcome was the quality of the angiogram, scaled as iMAP 0 (not informative), iMAP 1 (general vascular pattern visible but no clear vascular pedicle flowing into the PG), or iMAP 2 (clear vascular pedicle flowing into the PG). The secondary outcome was the PG perfusion score at the end of surgery, scaled from ICG 0 (no perfusion) to ICG 2 (intense uptake). RESULTS: A total of 47 adult patients were analyzed, including 34 total thyroidectomies and 13 lobectomies. ICG angiography assessed 76 PGs, which were scored as iMAP 2 in 24 cases (31.6%), iMAP 1 in 46 (60.5%) and iMAP 0 in six (7.9%). At the end of dissection, the ICG perfusion score was significantly better for the PGs with informative angiography (iMAP 1 or 2), than for the PGs with uninformative angiography (iMAP 0), or the PGs not evaluated by vascular angiography (p < 0.05). CONCLUSION: iMAP is feasible and provides direct vascular information in one-third of the cases. Further improvements to this technology are necessary, and the influence of this technique on patient outcomes during thyroidectomy will need to be further evaluated.

Toward Cholera Elimination, Haiti.

This study describes the apparent discontinuation of cholera transmission in Haiti since February 2019. Because vulnerabilities persist and vaccination remains limited, our findings suggest that case-area targeted interventions conducted by rapid response teams played a key role. We question the presence of environmental reservoirs in Haiti and discuss progress toward elimination.

Cold and dry winter conditions are associated with greater SARS-CoV-2 transmission at regional level in western countries during the first epidemic wave.

Higher transmissibility of SARS-CoV-2 in cold and dry weather conditions has been hypothesized since the onset of the COVID-19 pandemic but the level of epidemiological evidence remains low. During the first wave of the pandemic, Spain, Italy, France, Portugal, Canada and USA presented an early spread, a heavy COVID-19 burden, and low initial public health response until lockdowns. In a context when testing was limited, we calculated the basic reproduction number (R0) in 63 regions from the growth in regional death counts. After adjusting for population density, early spread of the epidemic, and age structure, temperature and humidity were negatively associated with SARS-CoV-2 transmissibility. A reduction of mean absolute humidity by 1 g/m3 was associated with a 0.15-unit increase of R0. Below 10 °C, a temperature reduction of 1 °C was associated with a 0.16-unit increase of R0. Our results confirm a dependency of SARS-CoV-2 transmissibility to weather conditions in the absence of control measures during the first wave. The transition from summer to winter, corresponding to drop in temperature associated with an overall decrease in absolute humidity, likely contributed to the intensification of the second wave in north-west hemisphere countries. Non-pharmaceutical interventions must be adjusted to account for increased transmissibility in winter conditions.

Factors associated with the spatial heterogeneity of the first wave of COVID-19 in France: a nationwide geo-epidemiological study.

BACKGROUND: The objective of this study was to better understand the factors associated with the heterogeneity of in-hospital COVID-19 morbidity and mortality across France, one of the countries most affected by COVID-19 in the early months of the pandemic. METHODS: This geo-epidemiological analysis was based on data publicly available on government and administration websites for the 96 administrative departments of metropolitan France between March 19 and May 11, 2020, including Public Health France, the Regional Health Agencies, the French national statistics institute, and the Ministry of Health. Using hierarchical ascendant classification on principal component analysis of multidimensional variables, and multivariate analyses with generalised additive models, we assessed the associations between several factors (spatiotemporal spread of the epidemic between Feb 7 and March 17, 2020, the national lockdown, demographic population structure, baseline intensive care capacities, baseline population health and health-care services, new chloroquine and hydroxychloroquine dispensations, economic indicators, degree of urbanisation, and climate profile) and in-hospital COVID-19 incidence, mortality, and case fatality rates. Incidence rate was defined as the cumulative number of in-hospital COVID-19 cases per 100 000 inhabitants, mortality rate as the cumulative number of in-hospital COVID-19 deaths per 100 000, and case fatality rate as the cumulative number of in-hospital COVID-19 deaths per cumulative number of in-hospital COVID-19 cases. FINDINGS: From March 19 to May 11, 2020, hospitals in metropolitan France notified a total of 100 988 COVID-19 cases, including 16 597 people who were admitted to intensive care and 17 062 deaths. There was an overall cumulative in-hospital incidence rate of 155·6 cases per 100 000 inhabitants (range 19·4-489·5), in-hospital mortality rate of 26·3 deaths per 100 000 (1·1-119·2), and in-hospital case fatality rate of 16·9% (4·8-26·2). We found clear spatial heterogeneity of in-hospital COVID-19 incidence and mortality rates, following the spread of the epidemic. After multivariate adjustment, the delay between the first COVID-19-associated death and the onset of the national lockdown was positively associated with in-hospital incidence (adjusted standardised incidence ratio 1·02, 95% CI 1·01-1·04), mortality (adjusted standardised mortality ratio 1·04, 1·02-1·06), and case fatality rates (adjusted standardised fatality ratio 1·01, 1·01-1·02). Mortality and case fatality rates were higher in departments with older populations (adjusted standardised ratio for populations with a high proportion older than aged >85 years 2·17 [95% CI 1·20-3·90] for mortality and 1·43 [1·08-1·88] for case fatality rate). Mortality rate was also associated with incidence rate (1·0004, 1·0002-1·001), but mortality and case fatality rates did not appear to be associated with baseline intensive care capacities. We found no association between climate and in-hospital COVID-19 incidence, or between economic indicators and in-hospital COVID-19 incidence or mortality rates. INTERPRETATION: This ecological study highlights the impact of the epidemic spread, national lockdown, and reactive adaptation of intensive care capacities on the spatial distribution of COVID-19 morbidity and mortality. It provides information for future geo-epidemiological analyses and has implications for preparedness and response policies to current and future epidemic waves in France and elsewhere. FUNDING: None.

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.

Impact of patron saint festivities on cholera in three communes in Haiti.

BACKGROUND: Religious pilgrimages are among the anthropogenic factors known to be associated with the transmission of diarrheal diseases, such as cholera. This ecological study aimed to describe the evolution of cholera and assess the relationship between the implementation of the 'coup de poing' strategy during the patron saint festivities and the incidence of cholera in the three communes of Cabaret, Carrefour, and Croix-des-Bouquets in Haiti in 2017. METHODS: An epidemiological curve was produced to illustrate the evolution of cholera at the communal level. Generalized linear models assuming a Poisson distribution were used to weight the annual cholera incidence of communal sections against variables such as the number of patronal festivities, population density and annual precipitation rates. The number of cases in the week of the festivity as well as one and 2 weeks later was weighted against patronal festivities and weekly precipitation rates. RESULTS: In total, 3633 suspected cholera cases were continuously reported in three communes in Haiti (Cabaret, Carrefour, Croix-des-bouquets) during the 52-epidemiological week period in 2017. After controlling for rainfall and population density, the implementation of the 'coup de poing' strategy during the patron saint festivities was associated with a significant reduction in cholera incidence of 57.23% [PR = 0.4277 (97.5% CI: 0.2798-0.6193), p = 0.0000244]. The implementation of the strategy was associated with a reduction in cholera incidence of 25.41% 1 week following patronal festivities. CONCLUSION: This study showed a continuous presence of cholera in three communes in Haiti in 2017 and an association between the implementation of the 'coup de poing' strategy during patronal festivities and a reduction in cholera incidence. The findings imply that the multi-partner 'coup de poing' strategy may have contributed to the reduced cholera incidence following patron saint festivities and in Ouest department in Haiti in 2017.