Evolution of Clusters Transmission Patterns in France during the Last Decade

Background: The recent transmission clusters (RTCs) identified through phylogenetic approaches allow to describe the main transmission networks. This render possible to describe potential shifts among HIV transmission routes and populations and, in some cases, to specifically target prevention measures. Here we describe the evolution of RTCs over the last decade in a specialized laboratory serving centers from the entire French territory. Method(s): We extracted all the HIV reverse transcriptase sequences available between 01/01/2013 and 31/08/2022. The sequences dataset was studied overall and divided into three equal time periods: 2013-15, 2016-18, 2019-2021. The first sequences available for each patient were aligned and the trees were reconstructed by maximum likelihood using IQtree software. Clusters, defined by a maximum genetic distance < 4.5% and a branch support >90%, were extracted using ClusterPicker. Result(s): Overall, 8591 sequences were included. Among them, 950 RTCs were identified including 2492 sequences (29%) and 68 large RTCs ( >4 sequences) with 475 (5.6%) sequences. The mean duration of large RTCs (from the first to the last sequences) was 5.1 years [IQR: 4.1-7.1] and 34 were still active (including at least one sequence during the last year of the study period). 3640, 2897 and 2157 sequences were included for the 2013-15, 2016-18 and 2019-2021 periods, respectively. We identified 298 RTCs (19.5% of sequences), 249 (20.4%) and 226 (27.5%) among those periods, respectively. While the number of sequence pairs decreased from 2013-15 to 2019-21, the number of large RTCs increased steadily (see Table 1). During the period 2019-21, including the largest clusters, patients belonging to a RTC were more often male (68 vs 58%, p< 0.001) and younger (average age: 39 vs 44 years, p< 0.001) than non-RTC patients. This observation was even more marked for very large RTCs (see Table 2). It should be noted that the largest cluster (14 patients) was mainly composed of women and located in French overseas territories. Conclusion(s): This study shows an evolution of the structure of HIV sequence clusters over time with a decreasing number of small RTCs but an increasing number of large RTCs. These trends can be explained by a better global control of transmission, due in part to TasP, but not preventing some super-transmitters networks, despite PrEP use and not only including MSM is some settings. The COVID period does not seem to have strongly prevented such large transmission networks.

Diagnostic des pneumonies aiguës communautaires aux urgences et distinction entre étiologie virale ou bactérienne

La pandémie actuelle liée à l'émergence du SARSCoV-2 en 2019 a considérablement modifié la perception des médecins de l'impact des virus respiratoires et de leur rôle dans les pneumonies aiguës communautaires (PAC). Alors que plus de 25 % des tableaux de PAC chez l'adulte étaient d'origine virale, les virus respiratoires étaient souvent perçus comme des agents pathogènes peu graves. Devant le défi que représente encore à nos jours la documentation microbiologique d'une PAC, l'instauration d'un traitement empirique par antibiotiques est souvent réalisée aux urgences. La pandémie de COVID-19 a surtout mis en exergue le rôle déterminant de la biologie moléculaire et du scanner thoracique dans l'algorithme diagnostique de la PAC. En effet, un diagnostic rapide et fiable est la clé pour améliorer les mesures de précaution et réduire la prescription inutile d'antibiotiques. Du fait de prises en charges très différentes, il est nécessaire de distinguer l'étiologie virale de la bactérienne d'une PAC.Alternate : The current pandemic linked to the emergence of SARS-CoV-2 in 2019 has considerably changed the perception of doctors of the impact of respiratory viruses and their role in community-acquired acute pneumonia (CAP). While more than 25% of CAP in adults were of viral origin, respiratory viruses were often perceived as harmless pathogens. Faced with the challenge that the microbiological documentation of a CAP still represents today, the establishment of empirical antibiotic treatment is often carried out in the emergency room. The COVID-19 pandemic has primarily highlighted the decisive role of molecular biology and chest CT in the diagnostic algorithm of CAP. Indeed, a rapid and reliable diagnosis is the key to improve isolation decisions and reducing the unnecessary prescription of antibiotics. Due to significantly different treatments, it is necessary to distinguish the viral etiology from the bacterial of a CAP.

Diagnosis of community-acquired acute pneumonia in the emergency room and distinction between viral or bacterial etiology.

The current pandemic linked to the emergence of SARS-CoV-2 in 2019 has considerably changed the perception of doctors of the impact of respiratory viruses and their role in community-acquired acute pneumonia (CAP). While more than 25% of CAP in adults were of viral origin, respiratory viruses were often perceived as harmless pathogens. Faced with the challenge that the microbiological documentation of a CAP still represents today, the establishment of empirical antibiotic treatment is often carried out in the emergency room. The COVID-19 pandemic has primarily highlighted the decisive role of molecular biology and chest CT in the diagnostic algorithm of CAP. Indeed, a rapid and reliable diagnosis is the key to improve isolation decisions and reducing the unnecessary prescription of antibiotics. Due to significantly different treatments, it is necessary to distinguish the viral etiology from the bacterial of a CAP. Copyright © 2022 Lavoisier. All rights reserved.

Plainte cognitive post-COVID-19 : profil et déterminants

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