Intraspecific diversity of Staphylococcus aureus populations isolated from cystic fibrosis respiratory infections

Long-term associations within an individual host allow bacterial populations to diversify over time, sometimes resulting in the coexistence of multiple species or variants of the same species. Traditional methods for identifying infective agents generally involve isolating a single pathogen and potentially even a single colony from a given sample. While screening samples for virulent or difficult-to-treat pathogens is an important part of informing clinical treatment and correlative research, these reductive methods alone do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population. In this study, we begin to address this limitation by comparing the phenotypic and genotypic diversity of single colonies and pooled isolates of Staphylococcus aureus taken from fresh sputum samples from three patients with cystic fibrosis. Additionally, we compare the results collected in our research laboratory to those processed by the Emory Clinical Microbiology Laboratory with the identical sputum samples. We identified unrelated coexisting lineages in two out of three sputum samples, as well as clinically relevant population structures that were not apparent from studying single-colony isolates alone. Altogether, our observations presented here demonstrate that the true nature and phenotype of a clinically isolated pathogen can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices. IMPORTANCE When obtaining bacterial isolates from infections, it is important to consider the ecological biases introduced by methods used for collection and processing. In this study, we demonstrate how reductive sampling and processing methods traditionally used by clinical microbiology labs often do not adequately capture complex and clinically relevant traits present in diverse pathogen populations. When treating or studying bacteria like Staphylococcus aureus that can maintain multiple variants within a population over a long period of time, it may be more effective and informative to employ sampling methods that account for the potential diversity within a population, as outlined in our approach presented here.