Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of < i > Francisella tularensis < /i >

by Anne Busch, Timo Homeier-Bachmann, Mostafa Y. Abdel-Glil, Anja Hackbart, Helmut Hotzel, Herbert Tomaso By combining a reference-independent SNP analysis and average nucleotide identity (ANI) with affinity propagation clustering (APC), we developed a significantly improved methodology allowing resolving phylogenetic relationships, based on objective criteria. These bioinformatics tools can be used a s a general ruler to determine phylogenetic relationships and clustering of bacteria, exemplary done withFrancisella (F.)tularensis. Molecular epidemiology ofF.tularensis is currently assessed mostly based on laboratory methods and molecular analysis. The high evolutionary stability and the clonal nature makesFrancisella ideal for subtyping with single nucleotide polymorphisms (SNPs). Sequencing and real-time PCR can be used to validate the SNP analysis. We investigate whole-genome sequences of 155F.tularensis subsp.holarctica isolates. Phylogenetic testing was based on SNPs and average nucleotide identity (ANI) as reference independent, alignment-free methods taking small-scale and large-scale differences within the genomes into account. Especially the whole genome SNP analysis with kSNP3.0 allowed deciphering quite subtle signals of systematic differences in molecular variation. Affinity propagation clustering (APC) resulted in three clusters showing the known clades B.4, B.6, and B.12. These data correlated with the results of real ‐time PCR assays targeting canSNPs loci. ...
Source: PLoS Neglected Tropical Diseases - Category: Tropical Medicine Authors: Source Type: research