Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures
Vishnu Raghuram, Jessica J. Gunoskey, Katrina S. Hofstetter, Natasia F Jacko, Margot J. Shumaker, Yi‐Juan Hu, Timothy D. Read, Michael David
Abstract
skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to those for the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of intra-clonal polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.