相关论文: Does Antibiotic Resistance Evolve in Hospitals?
Antimicrobial resistance (AMR) poses a mounting global health crisis, requiring rapid and reliable prediction frameworks that capture its complex evolutionary dynamics. Traditional antimicrobial susceptibility testing (AST), while accurate,…
Fitness landscapes are central in analyzing evolution, in particular for drug resistance mutations for bacteria and virus. We show that the fitness landscapes associated with antibiotic resistance are not compatible with any of the…
Within many bacterial colonies, persister cells exist as a subpopulation that is tolerant to antibiotics and other stressors, yet not genetically distinct from the rest of the colony. A recent study has proposed epigenetic inheritance as a…
How adaptive evolution to one environmental stress improves or suppresses adaptation to another is an important problem in evolutionary biology. For instance, in microbiology, the evolution of bacteria to be resistant to different…
The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence…
There has been interest in the interactions between infectious disease dynamics and behaviour for most of the history of mathematical epidemiology. This has included consideration of which mathematical models best capture each phenomenon,…
Antimicrobial resistance is a threat to public health with millions of deaths linked to drug resistant infections every year. To mitigate resistance, common strategies that are used are combination therapies and therapy switching. However,…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
Antigenic escape constitutes the main mechanism allowing rapidly evolving viruses to achieve endemicity. Beyond granting immune escape, empirical evidence also suggests that mutations of viruses might increase their inter-host…
A model describing the dynamics related to the spreading of non-lethal infectious diseases in a fixed-size population is proposed. The model consists of a non-linear delay-differential equation describing the time evolution of the increment…
Antibiotic resistance constitutes a major health threat. Predicting bacterial causes of infections is key to reducing antibiotic misuse, a leading driver of antibiotic resistance. We train a machine learning algorithm on administrative and…
Compartmental epidemiological models categorize individuals based on their disease status, such as the SEIRD model (Susceptible-Exposed-Infected-Recovered-Dead). These models determine the parameters that influence the magnitude of an…
Some microbial organisms are known to randomly slip into and out of hibernation, irrespective of environmental conditions [1]. In a (genetically) uniform population a typically very small subpopulation becomes metabolically inactive whereas…
Mycobacterium tuberculosis infection can involve all immune system components and can result in different disease outcomes. The antibiotic TB drugs require strict adherence to prevent both disease relapse and mutation of drug- and…
Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways to reliably predict…
Multidrug-resistant Enterobacteriaceae (MDR-E) have become a major public health threat in many European countries. While traditional infection control strategies primarily target the containment of intra-hospital transmission, there is…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
Detecting anomalies in irregularly sampled multi-variate time-series is challenging, especially in data-scarce settings. Here we introduce an anomaly detection framework for irregularly sampled time-series that leverages neural jump…
Infectious diseases outbreaks are often characterized by a spatial component induced by hosts' distribution, mobility, and interactions. Spatial models that incorporate hosts' movements are being used to describe these processes, to…