The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Abstract

EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.

BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs

“…Practical applications of these two methods are also greatly facilitated by the existence of structured sequence databases of closely related bacteria such as EnteroBase. Furthermore, visualisation of the genetic relationships among the query hits is also facilitated by the genotyping based on legacy or core genome MLST, which is also provided by EnteroBase [30]. The com-bination of Bifrost, BlastFrost and EnteroBase has the potential to rapidly reveal numerous features of genomic diversity that were previously not readily possible.…”

“…Precision and sensitivity of identifying all query variants in a pangenome. We evaluated the abilities of BlastFrost for detecting sequence variants within a Bifrost graph by querying all 21, 065 orthologs in the whole genome MLST (wgMLST) scheme in EnteroBase [2,30] which were derived from a pan-genome from 537 representative genomes of the genus Salmonella. Bifrost required less than 24 minutes and less than 5GB of memory to create a graph of 926 representative Salmonella strains from EnteroBase [2].…”

“…Recent advances in DNA sequencing technologies have reduced sequencing costs and time, and whole-genome sequencing of bacterial pathogens is being routinely perfomed by public health organizations. The resulting sequence reads and genome assemblies are deposited in the public domain [3,25,30], enabling comparative analysis for 100,000s of genomes [17,31] from individual bacterial genera to investigate their evolutionary history, and their assignment to ongoing or historical epidemiological outbreaks.…”

“…New sequencing data are now routinely uploaded to public databases such as the Sequence Read Archive (SRA [16]), which has resulted in ready access to extensive collections of sequencing data for many bacterial genera. Other databases, including PubMLST [15] and EnteroBase [30], even provide curated collections of genomic assemblies bundled with their metadata for specific bacterial pathogens, as well as dedicated tools for population genomic analyses.…”

“…Speed and memory of BlastFrost for cgMLST genes in comparison to BIGSI (A,B) and minmap2 (C) and as a function of numbers of hits (D). (A, B) Speed and memory with 736 genomes of Yersinia pestis[30] as a function of numbers of queries for BlastFrost with k-mer neighbourhood d = 1 in comparison to both exact and inexact BIGSI queries. C) Speed with subsets of 926 Salmonella genomes[2] as a function of numbers of draft genomes for BlastFrost with k-mer neighbourhood d = 1 in comparison to minimap2.…”