Classification of Spatiotemporal Data for Epidemic Alert Systems: Monitoring Influenza-Like Illness in France

Voir aussi dépôt du preprint : https://hal.archives-ouvertes.fr/hal-02562668v2International audienceSurveillance data used by epidemic alert systems are typically fully aggregated in space at the national level. However, epidemics may be spatially heterogeneous, undergoing distinct dynamics in distinct regions of the surveillance area. We unveiled this in retrospective analyses by classifying incidence time series. We used Pearson correlation to quantify the similarity between local time series and then classified them using modularity maximization. The surveillance area was thus divided into regions with different incidence patterns. We analyzed 31 years (1985-2016) of data on influenza-like illness from the French Sentinelles system and found spatial heterogeneity in 19 of 31 influenza seasons. However, distinct epidemic regions could be identified only 4-5 weeks after a nationwide alert. The impact of spatial heterogeneity on influenza epidemiology was complex. First, when a nationwide alert was triggered, 32%-41% of the administrative regions of France were experiencing an epidemic, while the others were not. Second, the nationwide alert was timely for the whole surveillance area, but subsequently regions experienced distinct epidemic dynamics. Third, the epidemic dynamics were homogeneous in space. Spatial heterogeneity analyses can provide information on the timing of the peak and end of the epidemic, in various regions, for use in tailoring disease monitoring and control

Host contact dynamics shapes richness and dominance of pathogen strains

International audienceThe interaction among multiple microbial strains affects the spread of infectious diseases and the efficacy of interventions. Genomic tools have made it increasingly easy to observe pathogenic strains diversity, but the best interpretation of such diversity has remained difficult because of relationships with host and environmental factors. Here, we focus on host-to-host contact behavior and study how it changes populations of pathogens in a minimal model of multi-strain interaction. We simulated a population of identical strains competing by mutual exclusion and spreading on a dynamical network of hosts according to a stochastic susceptible-infectious-susceptible model. We computed ecological indicators of diversity and dominance in strain populations for a collection of networks illustrating various properties found in real-world examples. Heterogeneities in the number of contacts among hosts were found to reduce diversity and increase dominance by making the repartition of strains among infected hosts more uneven, while strong community structure among hosts increased strain diversity. We found that the introduction of strains associated with hosts entering and leaving the system led to the highest pathogenic richness at intermediate turnover levels. These results were finally illustrated using the spread of Staphylococcus aureus in a long-term health-care facility where close proximity interactions and strain carriage were collected simultaneously. We found that network structural and temporal properties could account for a large part of the variability observed in strain diversity. These results show how stochasticity and network structure affect the population ecology of pathogens and warn against interpreting observations as unambiguous evidence of epidemiological differences between strains

Bisphosphonate Use and Hospitalization for Hip Fractures in Women: An Observational Population-Based Study in France

International audienceBisphosphonates are widely used in the treatment of women at risk of osteoporotic hip fracture; however, the overall effectiveness of bisphosphonates in the prevention of osteoporotic fractures has not been studied in real life. To investigate whether the use of bisphosphonates in women aged 50 years and over is associated with a decrease in hospitalization for osteoporotic hip fractures, a historical prospective cohort study was conducted between 2009 and 2016 from a permanent representative sample consisting of 1/97 of the French health insurance beneficiaries. Bisphosphonate use was defined according to medication persistence and adherence regarding bisphosphonate dispensations. The primary outcome was the hospitalization rate for osteoporotic hip fracture. Among the 81,268 women included, 2005 were exposed to bisphosphonates. The median time of bisphosphonate exposure was 12 (IQR, 3–29) and 17 (IQR, 5–42) months for the persistence and adherence definitions, respectively. Exposure to bisphosphonates was not associated with a decrease in hospitalization for hip fracture: weighted HRadherence = 0.66 (95% CI, 0.33 to 1.33); HRpersistance = 0.77 (95% CI, 0.38 to 1.57). In real life, bisphosphonate use does not appear to reduce hospitalization for hip fractures, as to date, it is probably prescribed as primary prevention and for a duration too short to be effective

Patients in ICUs Indications of Chest Radiographs for A Web-Based Delphi Study on the Indications of Chest Radiographs for Patients in ICUs*

Detailed feedback for the answers given during the previous round was supplied to each intensivist solicited for updating his answers. Results: Eighty-two intensivists from 32 ICUs completed the study. A consensus emerged that routine CXRs were necessary for eight scenarios and unnecessary for two scenarios. The study also shed light on items without a consensus. In particular, 75% of intensivists (58% on the first round) did not support obtaining daily routine CXRs in intubated patients. Conclusion: The study underlines situations in which intensivists do not support the guidelines and outlines recommendations likely to be followed in clinical practice

Cystic fibrosis gene modifier SLC26A9 modulates airway response to CFTR-directed therapeutics

Cystic fibrosis is realizing the promise of personalized medicine. Recent advances in drug development that target the causal CFTR directly result in lung function improvement, but variability in response is demanding better prediction of outcomes to improve management decisions. The genetic modifier SLC26A9 contributes to disease severity in the CF pancreas and intestine at birth and here we assess its relationship with disease severity and therapeutic response in the airways. SLC26A9 association with lung disease was assessed in individuals from the Canadian and French CF Gene Modifier consortia with CFTR-gating mutations and in those homozygous for the common Phe508del mutation. Variability in response to a CFTRdirected therapy attributed to SLC26A9 genotype was assessed in Canadian patients with gating mutations. A primary airway model system determined if SLC26A9 shows modification of Phe508del CFTR function upon treatment with a CFTR corrector. In those with gating mutations that retain cell surface-localized CFTR we show that SLC26A9 modifies lung function while this is not the case in individuals homozygous for Phe508del where cell surface expression is lacking. Treatment response to ivacaftor, which aims to improve CFTR-channel opening probability in patients with gating mutations, shows substantial variability in response, 28% of which can be explained by rs7512462 in SLC26A9 (P=0.0006). When homozygous Phe508del primary bronchial cells are treated to restore surface CFTR, SLC26A9 likewise modifies treatment response (P=0.02). Our findings indicate that SLC26A9 airway modification requires CFTR at the cell surface, and that a common variant in SLC26A9 may predict response to CFTR-directed therapeutics