The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

Abstract

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR.Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors.Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.

Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics

“…The 20 EIEC genomes and 37 E. coli and Shigella reference genomes were compared by large-scale BLAST score ratio (LS-BSR) analysis as previously described (29,34,35). Briefly, the predicted protein-encoding genes of each genome that had Ն90% nucleotide sequence identity to each other were assigned to gene clusters with uclust (36).…”

“…The 57 E. coli and Shigella genomes included in the phylogenomic analysis were also compared by LS-BSR analysis, which is a de novo method used to determine gene-based similarity in groups of genomes (34,47) (Table 2). There were 16,418 total gene clusters that were identified in the 57 genomes, which included 1,628 gene clusters with significant similarity (LS-BSR, Ն0.9) that were present in all of the genomes (Table 2).…”

Defining the Phylogenomics of Shigella Species: a Pathway to Diagnostics

“…This difference may be indicative of the large number of environments where E. coli can be isolated, in contrast to Shigella species, which are primarily identified as pathogens of humans. The numbers and compositions of genes were also compared using BLAST score ratio (BSR) analysis (40,45). The core genome of E. coli, based on an analysis of 69 genomes, is ϳ2,155 genes (BSR Ն 0.80 in 100% of the genomes).…”

“…To identify genes differentially distributed between the E. coli and Shigella genomes, a large-scale BSR (LS-BSR) analysis was performed on 69 E. coli and 69 Shigella genomes (45). The results demonstrate that several genes, primarily associated with metabolism, are conserved in E. coli isolates and largely absent (n Ͻ 2) in Shigella isolates (Table 2); this stands in contrast to a recent study which suggested that no genes could be used to distinguish the two groups (47).…”

Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains

“…The genes of pB171_90 were predicted and annotated using an in-house annotation pipeline (73). These genes were then detected in a collection of 4,798 E. coli genome assemblies available in GenBank as of November 2016, using large-scale BLAST score ratio (LS-BSR) analysis as previously described (74,75). The pB171_90 protein-coding genes were compared to each genome listed in Table S1 using TBLASTN (76) with composition-based adjustment turned off.…”