Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Salmonella Typhimurium ST34 pandemic strain

Salmonella enterica serovar Typhimurium (S. Typhimurium) comprises a group of closely related human and animal pathogens that account for a large proportion of all Salmonella infections globally. The epidemiological record of S. Typhimurium in Europe is characterized by successive waves of dominant clones, each prevailing for approximately 10–15 years before replacement. Succession of epidemic clones may represent a moving target for interventions aimed at controlling the spread and impact of this pathogen on human and animal health. Here, we investigate the relationship of phage sensitivity and population structure of S. Typhimurium using data from the Anderson phage typing scheme. We observed greater resistance to phage predation of epidemic clones circulating in livestock over the past decades compared to variants with a restricted host range implicating increased resistance to phage in the emergence of epidemic clones of particular importance to human health. Emergence of monophasic S. Typhimurium ST34, the most recent dominant multidrug-resistant clone, was accompanied by increased resistance to phage predation during clonal expansion, in part by the acquisition of the mTmII prophage that may have contributed to the fitness of the strains that replaced ancestors lacking this prophage

Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Salmonella Typhimurium ST34 pandemic strain

Salmonella enterica serovar Typhimurium ( S. Typhimurium) comprises a group of closely related human and animal pathogens that account for a large proportion of all Salmonella infections globally. The epidemiological record of S. Typhimurium in Europe is characterized by successive waves of dominant clones, each prevailing for approximately 10-15 years before replacement. Succession of epidemic clones may represent a moving target for interventions aimed at controlling the spread and impact of this pathogen on human and animal health. Here, we investigate the relationship of phage sensitivity and population structure of S. Typhimurium using data from the Anderson phage typing scheme. We observed greater resistance to phage predation of epidemic clones circulating in livestock over the past decades compared to variants with a restricted host range implicating increased resistance to phage in the emergence of epidemic clones of particular importance to human health. Emergence of monophasic S. Typhimurium ST34, the most recent dominant multidrug-resistant clone, was accompanied by increased resistance to phage predation during clonal expansion, in part by the acquisition of the mTmII prophage that may have contributed to the fitness of the strains that replaced ancestors lacking this prophage

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Requêtes dépendantes de la localisation : Expression, évaluation et optimisation

For a few years, the evolution of handheld devices and wireless and/or mobile networks has implied the development of new services and new applications dedicated to mobile users. Among these applications, we define the proximity applications concept. These applications allow to different users physically close to each other to share and locate available data. These applications are running in a strongly distributed and dynamic context in whic h, the available information is distributed in different participants terminal and is continually modified due to the participants mobility. In this environment, the current localisation services have severe limits. Thus, we have proposed ISLANDS (Information and Services LocalizAtioN and Discovery Service), a localisation service adapted to the data distribution. This service relies on our evaluation model for location dependent queries (LDQ). An example of LDQ is “which is the closest bus stop to me ?”. The proposed evaluation model allows to consider the mobility of users and specially their geographic localization during the query evaluation. This evaluation model has been optimized to be used in constrained environments. The evaluation process of a LDQ relies on several steps : among them, the evaluation of the geographic localization of client who submitted the query. Today, the localization technologies are not always available : for example, GPS which is the most widespread solution, do not always run inside a building, thus, we propose a localization solution based on environment metadata. Our solution allows to locate a user in a approximatively way but sufficient to the location dependent queries evaluation. This solution has been optimised to minimize the resource consumption of nomadic devices and to reduce the communications between participants. A prototype of ISLANDS has been implemented and demonstrated at the french conference : Bases de Données Avancées (BDA'03). This prototype had permit to validate our propositions.Depuis quelques années, l'évolution des terminaux nomades et des réseaux mobiles et/ou sans fil favorise le développement de nouveaux services et de nouvelles applications dédiées aux usagers mobiles. Parmi ces applications, nous définissons le concept d'applications de proximité. Celles-ci permettent à différents usagers physiquement proches les uns des autres de partager certaines de leurs informations et de localiser les données disponibles. Ces applications s'inscrivent dans un contexte fortement distribué et dynamique où l'ensemble de l'information disponible est répartie sur les terminaux des différents participants et subit de fréquentes variations dûes à la mobilité des participants. Dans cet environnement, les services de localisation actuels présentent d'importantes limites. Nous avons donc proposé ISLANDS (Information and Services LocalizAtioN and Discovery Service), un service de localisation adapté à l'environnement des applications de proximité, en particulier à la distribution de l'information. Ce service ISLANDS repose sur notre modèle d'évaluation des requêtes dépendantes de la localisation. Un exemple de requêtes dépendantes de la localisation est « quel est l'arrêt de bus le plus proche de moi ? ». Le modèle d'évaluation proposé permet de considérer la mobilité des utilisateurs et en particulier leur localisation géographique dans l'évaluation des requêtes. Ce modèle d'évaluation a été optimisé afin de pouvoir être pleinement exploité dans un environnement contraint en terme de ressources. Le processus d'évaluation d'une requête dépendante de la localisation s'articule autour de différentes étapes dont l'évaluation de la localisation géographique du client qui émet la requête. Aujourd'hui, les techniques de localisation ne sont pas toujours exploitables : par exemple, le GPS qui est la solution la plus répandue , ne fonctionne généralement pas à l'intérieur d'un bâtiment, nous proposons donc une solution de localisation reposant sur les métadonnées de l'environnement. Notre solution permet de localiser un utilisateur de façon approximative mais avec une précision suffisante pour évaluer des requêtes dépendantes de la localisation. Cette solution a été optimisée de façon à minimiser la consommation des ressources sur les terminaux nomades et à réduire le nombre de communications entre les participants. Un prototype d'ISLANDS a été implémenté et démontré aux 19èmes journées de bases de données avancées (BDA'03) dans le but de valider nos propositions

Requêtes dépendantes de la localisation en environnements mobiles (expression, évaluation et optimisation)

Depuis quelques années, l évolution des terminaux nomades et des réseaux mobiles et/ou sans fil favorise le développement de nouveaux services et de nouvelles applications dédiées aux usagers mobiles. Parmi ces applications, nous définissons le concept d applications de proximité. Ces applications s'inscrivent dans un contexte fortement distribué et dynamique où l ensemble de l information disponible est répartie sur les terminaux des différents participants et subit de fréquentes variations dues à la mobilité des participants. Dans cet environnement, les services de localisation actuels présentent d importantes limites. Nous avons donc proposé ISLANDS (Information and Services LocalizAtioN and Discovery Service), un service de localisation adapté à l environnement des applications de proximité, en particulier à la répartition de l information. Ce service ISLANDS repose sur notre modèle d évaluation des requêtes dépendantes de la localisation (LDQ) telles que quel est l arrêt de bus le plus proche de moi ? . Ces requêtes permettent de considérer la mobilité des utilisateurs et en particulier leur localisation géographique. Le modèle d évaluation proposé a été optimisé afin de minimiser les ressources des terminaux nomades et le temps d évaluation. Il repose sur différentes étapes dont l évaluation de la localisation géographique du client qui émet la requête. Pour pallier aux limites des solutions actuelles telles que le GPS, nous avons proposé une solution de localisation optimisée pour les environnements contraints et reposant sur les métadonnées de l environnement. Un prototype d ISLANDS a été implémenté dans le but de valider nos propositions.For a few years, the evolution of handheld devices and wireless and/or mobile networks has implied the development of new services and new applications dedicated to mobile users. Among these applications, we define the proximity applications concept. These applications allow to different users physically close to each other to share and locate available data. These applications are running in a strongly distributed and dynamic context in which, the available information is distributed in different participants terminal and is continually modified due to the participants mobility. In this environment, the current localisation services have severe limits. Thus, we have proposed ISLANDS (Information and Services LocalizAtioN and Discovery Service), a localisation service adapted to the data distribution. This service relies on our evaluation model of location dependent queries (LDQ) such as which is the closest bus stop to me ? . These queries allow to consider the users mobility and especially their geographic localization. The proposed evaluation model has been optimized to minimize the handheld devices resources and the evaluation time. The model relies on several steps : among them, the evaluation of the geographic localization of client. The current solutions such as GPS present different limits, thus, we have proposed a localiszation solution based on metadata environments and optimisated to constrained environements. A prototype of ISLANDS has been implemented to validate our propositions.VALENCIENNES-BU Sciences Lettres (596062101) / SudocSudocFranceF

Location-based Mobile Querying in Peer-to-Peer Networks

Peer-to-peer (P2P) networks are receiving increasing attention in a variety of current applications. In this paper, we concentrate on applications where a mobile user queries peers to find either data (e.g., a list of restaurants) or services (e.g., a reservation service). We classify location-based queries in categories depending on parameters such as the user's velocity, the nature of the desired information, and the anticipated proximity of this information. We then propose query routing strategies to ensure the distributed query evaluation on different peers in the application while optimizing the device and network energy consumption