Thomas Bénet’s research while affiliated with Santé Publique France and other places

Introduction Following its emergence in January 2020, SARS-CoV-2 diffusion occurred for a year with only non-pharmaceutical interventions (NPIs) available as mitigation tools. We aimed to assess the predictive capability of census-based indicators on the infection risk by SARS-CoV-2 in the French Auvergne-Rhône-Alpes region to assist NPIs allocation at the neighbourhood level. Methods We aggregated all counts of biologically confirmed cases of SARS-CoV-2 infection at the neighbourhood level between May 2020 and February 2021. 10 census-based ecological covariates were evaluated as predictors of case incidence using a Poisson regression with conditional autoregressive (CAR) spatial effects. Benefits of CAR effects and covariates on model fit were evaluated using pseudo-R² and Moran’s I statistics. Results 438,992 infection cases over 5,410 neighbourhoods among 7,917,997 inhabitants were analysed. The association between covariates and case incidence was inconstant across time and space. Spatial correlation was estimated at high levels. Spatial CAR effects were necessary to improve on the pseudo-R ² and the Moran’s I statistics compared to the null model (intercept only). Conclusion The ecological covariates assessed were insufficient to adequately model the distribution of cases at the neighbourhood level. Excess incidence was found mainly in metropolitan areas before the epidemic wave peak.

Objectives: Quantify the effects of characteristics of nursing homes and their surroundings on the spread of COVID-19 outbreaks and assess the changes in resident protection between the first 2 waves (March 1 to July 31 and August 1 to December 31, 2020). Design: An observational study was carried out on data on COVID-19 outbreaks extracted from a database that monitored the spread of the virus in nursing homes. Setting and participants: The study concerned all 937 nursing homes with >10 beds in Auvergne-Rhône-Alpes region, France. Methods: The rate of nursing homes with at least 1 outbreak and the cumulative number of deaths were modeled for each wave. Results: During the second (vs the first wave), the proportion of nursing homes that reported at least 1 outbreak was higher (70% vs 56%) and the cumulative number of deaths more than twofold (3348 vs 1590). The outbreak rate was significantly lower in public hospital-associated nursing homes than in private for-profit ones. During the second wave, it was lower in public and private not-for-profit nursing homes than in private for-profit ones. During the first wave, the probability of outbreak and the mean number of deaths increased with the number of beds (P < .001). During the second wave, the probability of outbreak remained stable in >80-bed institutions and, under proportionality assumption, the mean number of deaths was less than expected in >100-bed institutions. The outbreak rate and the cumulative number of deaths increased significantly with the increase in the incidence of hospitalization for COVID-19 in the surrounding populations. Conclusions and implications: The outbreak in the nursing homes was stronger during the second than the first wave despite better preparedness and higher availabilities of tests and protective equipment. Solutions for insufficient staffing, inadequate rooming, and suboptimal functioning should be found before future epidemics.

Background Exposure to infected healthcare workers (HCWs) is a source of hospital-acquired (HA) influenza. We estimated the risk of HA influenza for hospitalized patients by rate of influenza vaccine coverage (IVC) of HCWs. Methods A case–case negative control study nested in a prospective cohort was conducted in 2 French university hospitals during 2 influenza seasons. Each inpatient with influenza-like illness (ILI) provided a nasal swab sample that was systematically analyzed for influenza virus by polymerase chain reaction (PCR) testing. An HA influenza case was a patient with a virological confirmation of influenza with onset of symptoms ≥72 hours after admission to the ward. The IVC rate of HCWs in each participating ward was calculated from the data provided by the occupational health departments. A mixed-effect logistic regression was performed with adjustments on patient sex, age, the presence of a potential source of influenza on the ward in the 5 days prior to the start of the ILI, type of ward and influenza season. Results The overall HA influenza attack rate was 1.9 per 1,000 hospitalized patients. In total, 24 confirmed HA influenza cases and 141 controls were included. The crude odds ratio (OR) of HA influenza decreased from 0.52 (95% confidence interval [CI], 0.21–1.29) to 0.14 (95% CI, 0.03–0.63) when the IVC of HCWs increased from 20% to 40%. After adjustment, IVC ≥40% was associated with a risk reduction of HA influenza (aOR, 0.07; 95% CI, 0.01–0.78). Conclusions Considering a limited sample size, influenza vaccination of HCWs is highly suggestive of HA flu prevention among hospitalized patients. Trial Registration: clinicaltrials.gov identifier: NCT02198638.

Background Worldwide, COVID-19 outbreaks in nursing homes have often been sudden and massive. The study investigated the role SARS-CoV-2 virus spread in nearby population plays in introducing the disease in nursing homes. Material and methods This was carried out through modelling the occurrences of first cases in each of 943 nursing homes of Auvergne-Rhône-Alpes French Region over the first epidemic wave (March-July, 2020). The cumulative probabilities of COVID-19 outbreak in the nursing homes and those of hospitalization for the disease in the population were modelled in each of the twelve Départements of the Region over period March-July 2020. This allowed estimating the duration of the active outbreak period, the dates and heights of the peaks of outbreak probabilities in nursing homes, and the dates and heights of the peaks of hospitalization probabilities in the population. Spearman coefficient estimated the correlation between the two peak series. Results The cumulative proportion of nursing homes with COVID-19 outbreaks was 52% (490/943; range: 22–70% acc. Département). The active outbreak period in the nursing homes lasted 11 to 21 days (acc. Département) and ended before lockdown end. Spearman correlation between outbreak probability peaks in nursing homes and hospitalization probability peaks in the population (surrogate of the incidence peaks) was estimated at 0.71 (95% CI: [0.66; 0.78]). Conclusion The modelling highlighted a strong correlation between the outbreak in nursing homes and the external pressure of the disease. It indicated that avoiding disease outbreaks in nursing homes requires a tight control of virus spread in the surrounding populations.

In France, measures including curfew and lockdown were implemented to control the COVID-19 pandemic second wave in 2020. This study descriptively assesses their possible effects, also relative to their timing. A considerable decrease in incidence of COVID-19 cases and hospital admissions was observed 7 to 10 days after mitigation measures were put in place, occurring earlier in metropolitan areas which had implemented these first. This temporal coincidence suggests the measures’ positive impact, consistent with international experiences.

Background Hospital-acquired influenza potentially leads to significant morbidity and mortality in already vulnerable patients, but its overall burden is not fully understood. We undertook this study to estimate the incidence and trends of hospital-acquired laboratory-confirmed influenza among adults, and to compare clinical characteristics between hospital-acquired and community-acquired influenza cases. Methods This was a prospective surveillance study over 11 years of adults with influenza-like-illness (ILI) hospitalized in surgery, medicine and geriatric wards in a tertiary acute-care hospital in Lyon, France. Nasal swabs were systematically collected from those with ILI and tested for influenza by reverse transcriptase-polymerase chain reaction at the national influenza reference laboratory (Lyon, France). Results Influenza was laboratory confirmed at a rate of 1 in 13 patients who developed ILI during their hospitalization. Having an underlying disease was an important characteristic of hospital-acquired ILI cases. Cardiovascular disease was the most frequent underlying condition in both influenza-positive and influenza-negative patients. Complications were more frequent for influenza-positive than influenza-negative patients. The influenza incidence rate was highest in the geriatric ward and increased over the study period. Conclusions Hospital-acquired influenza poses a significant risk to already vulnerable patients. Longitudinal surveillance data are essential to support better recognition and monitoring of viral infections in hospitals.

Background: Influenza is an important cause of viral hospital-acquired infection involving patients, healthcare workers (HCW), and visitors. The frequency of asymptomatic influenza among HCW with possible subsequent transmission is poorly described. The objective is to determine the cumulative incidence of asymptomatic, pauci-symptomatic and symptomatic influenza among HCW. Method: A multicenter prospective cohort study was done in 5 French university hospitals, including 289 HCW during the 2016-2017 influenza season. HCW had 3 physical examinations (Time [T] 0, before epidemic onset; T.1, before epidemic peak; T.2, T.3 after epidemic peak). A blood sample was taken each time for influenza serology and a nasal swab was collected at T1 and T2 for influenza detection by PCR. Positive influenza was defined as either a positive influenza PCR, and/or virus-specific seroconversion against influenza A, the only circulating virus, with no vaccination record during follow-up. Symptoms were self-reported daily between T1 and T2. Cumulative incidence of influenza was stratified by clinical presentation per 100 HCW. Findings: Of the 289 HCW included, 278 (96%) completed the entire follow-up. Overall, 62 HCW had evidence of influenza of whom 46·8% were asymptomatic, 41·9% were pauci-symptomatic, and 11·3% were symptomatic. Cumulative influenza incidence was 22·3% (95%CI:17·4%-27·2%). Cumulative incidence of asymptomatic influenza was 5·8% (95%CI: 3·3%-9·2%), 13·7% (95%CI:9·9%-18·2%) for pauci-symptomatic influenza, and 2·9% (95%CI:1·3%-5·5%) for symptomatic influenza. Interpretation: Asymptomatic and pauci-symptomatic influenza were frequent among HCW, representing 47% and 42% of the influenza burden respectively. These findings highlight the importance of systematic implementation of infection control measures among HCW regardless of respiratory symptoms from preventing nosocomial transmission of influenza. Trial registration: clinicaltrials.gov identifier: NCT02868658.