Choisy, M. | Search bioRxiv

bioRxiv2020

Evolution of virulence in emerging epidemics: inference from an evolution experiment

Inference using mathematical models of infectious disease dynamics is a powerful tool to analyse epidemiological data and elucidate pathogen life cycles. Key epidemiological parameters can be estimated from demographic time series by computing the likelihood of alternative models of pathogen transmission. Here we use this inference approach to analyze data from an evolution experiment in which we monitored both the epidemiology and the evolution of the temperate bacteriophage{lambda} during an epidemic. We estimate parameter values for all the life-history traits of two distinct strains of the virus. In particular, we estimate the ability of the two virus strains to modulate plastically the rate of lysogenization with the multiplicity of infection. Our work illustrates how inference from experimental evolution data can feedback on the development of models aiming to predict the epidemiology and evolution of infectious diseases.

evolutionary biology↗

bioRxiv2020

Effects of prophylactic and therapeutic antimicrobial uses in small-scale chicken flocks

SynopsisO_ST_ABSBackgroundC_ST_ABSAntimicrobials are extensively used both prophylactically and therapeutically in poultry production. Despite this, there are little data on the effect of antimicrobial use (AMU) on disease incidence and mortality rate. ObjectiveWe investigated the relationships between AMU and disease and between AMU and mortality using data from a large (n=322 flocks) cohort of small-scale chicken flocks in the Mekong Delta, Vietnam, that were followed longitudinally from day-old to slaughter (5,566 observation weeks). MethodsWe developed a parameterized algorithm to categorize the observation weeks into non-AMU, prophylactic AMU and therapeutic AMU. To evaluate the prophylactic AMU effect, we compared the frequencies of clinical signs in non-AMU and prophylactic AMU periods. To analyse therapeutic AMU, we compared mortality rates between the weeks of disease episodes before and after AMU. Analyses were stratified by clinical signs (4) and antimicrobial classes (13). ResultsProphylactic AMU never reduced the probability of disease, some antimicrobial classes such as lincosamides, amphenicols and penicillins increased the risk. The risk of diarrhoea consistently increased with prophylactic AMU. Therapeutic AMU often had an effect on mortality but the pattern was inconsistent across the combinations of antimicrobial classes and clinical signs with 14/29 decreasing and 11/29 increasing the mortality rate. Lincosamides, methenamines and cephalosporins were the only three antimicrobial classes that always decreased the mortality rate when used therapeutically. Results were robust respective to the parameters values of the weeks categorization algorithm. ConclusionThis information should help support policy efforts and interventions aiming at reducing AMU in animal production.

pharmacology and toxicology↗