Biodiversity measures to summarize antibiotic resistance

Abstract

Studies of antibiotic resistance frequently focus on resistance to specific antibiotics, or classes of antibiotics, without summarizing the overall resistance for all antibiotics. Biodiversity indices, such as the Shannon-Weiner (SW) index and Bray-Curtis distance, are widely used in ecology to measure overall species abundance and variation within and between regions. We explore the use of biodiversity indices to summarize antibiotic resistance. We illustrate this approach by analyzing data on antibiotic resistance in clinical Salmonella enterica isolates. To understand changes in resistance patterns within and between the provinces of Canada, S. enterica serotypes, and over time, we measure the SW diversity and Bray-Curtis distance and visualize the differences between provinces, serotypes and over time using ordinations. We describe the different types of antibiotic resistance data that are required for measuring alpha and beta diversity and explain the interpretation of biodiversity measures when applied to antibiotic resistance data.