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

Luhmann, Nina; Holley, Guillaume; Achtman, Mark

doi:10.1186/s13059-020-02237-3

Cited by 23 publications

(19 citation statements)

References 39 publications

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“…Clade-C contains 2 nalidixic acid-resistant, but ciprofloxacin-susceptible ST198 isolates, whereas clade-D contains 2 ciprofloxacin-resistant ST198 isolates (Figure 1) and these clades correlate with PFGE cluster-A2 (Supplementary Figure 1). These results suggest that the population of Flu R S. Kentucky ST198 is comprised of multiple genetically divergent lineages, which corroborates with published reports (Sukhnanand et al, 2005;Timme et al, 2013;Haley et al, 2016;Tasmin et al, 2017;Luhmann et al, 2021). Epidemiologic source tracing revealed that 11 out of 15 (73%) Flu R S. Kentucky clinical isolates within PFGE cluster-A2 originated from patients with a history of travel to different international destinations before the onset of illness (Table 1).…”

Section: International Travelsupporting

confidence: 90%

“…Comparative genomics analysis of a large collection of S. Kentucky isolates in this study also confirmed that ST152 and ST198 form two distinct genetic lineages. While others have reported that ST152 and ST198 are genetically distinct (Sukhnanand et al, 2005;Timme et al, 2013;Haley et al, 2016;Tasmin et al, 2017;Luhmann et al, 2021), lineage-specific genetic polymorphisms that clearly distinguish these two lineages have not been identified and described well. Thus, we aimed 2).…”

Section: International Travelmentioning

confidence: 99%

“…S. Kentucky shows unique ecological and epidemiological characteristics. Unlike most other NTS serovars, comparative whole genomic and MLST analysis has revealed that S. Kentucky is polyphyletic and the two predominant sequence types (STs), ST198 and ST152 represent the two distinct genetic lineages (Sukhnanand et al, 2005;Timme et al, 2013;Haley et al, 2016;Tasmin et al, 2017;Luhmann et al, 2021). Globally, ST198 and ST152 are also among the most predominant STs isolated from a variety of poultry sources and people (Le Hello et al, 2011;Haley et al, 2016;Tasmin et al, 2017;Xiong et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

Soltys

Sakomoto

Oltean

et al. 2021

Front. Sustain. Food Syst.

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Non-typhoidal Salmonella (NTS) is a major cause of foodborne illness globally. Salmonella Kentucky is a polyphyletic NTS serovar comprised of two predominant multilocus sequence types (STs): ST152 and ST198. Epidemiological studies have revealed that ST152 is most prevalent in US poultry whereas ST198 is more prevalent in international poultry. Interestingly, ST152 is sporadically associated with human illness, whereas ST198 is more commonly associated with human disease. The goal of this study was to develop a better understanding of the epidemiology of ST198 and ST152 in WA State. We compared the antimicrobial resistance phenotypes and genetic relationship, using pulsed-field gel electrophoresis, of 26 clinical strains of S. Kentucky isolated in Washington State between 2004 and 2014, and 140 poultry-associated strains of S. Kentucky mostly recovered from the northwestern USA between 2004 and 2014. We also sequenced whole genomes of representative human clinical and poultry isolates from the northwestern USA. Genome sequences of these isolates were compared with a global database of S. Kentucky genomes representing 400 ST198 and 50 ST152 strains. The results of the phenotypic, genotypic, and case report data on food consumption and travel show that human infections caused by fluoroquinolone-resistant (FluR) S. Kentucky ST198 in WA State originated from outside of North America. In contrast, fluoroquinolone-susceptible (FluS) S. Kentucky ST198 and S. Kentucky ST152 infection have a likely domestic origin, with domestic cattle and poultry being the potential sources. We also identified lineage-specific non-synonymous single nucleotide polymorphisms (SNPs) that distinguish ST198 and ST152. These SNPs may provide good targets for further investigations on lineage-specific traits such as variation in virulence, metabolic adaptation to different environments, and potential for the development of intervention strategies to improve the safety of food.

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Section: International Travelsupporting

confidence: 90%

Section: International Travelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

Soltys

Sakomoto

Oltean

et al. 2021

Front. Sustain. Food Syst.

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“…A total of 2632, 1158 and 1379 fully assembled genomes were downloaded from NCBI Reference Sequence Database 33 , 60 (RefSeq; accessed on 15 April 2021), NCBI’s GenBank 34 (accessed on 15 April 2021), and EnteroBase (accessed on 27 April 2021) 35 , respectively. The EnteroBase repository was screened for bla NDM using BlastFrost (v1.0.0) 61 allowing for one mismatch. In addition, we used the Bitsliced Genomic Signature Index (BIGSI) tool (v0.3) 62 to identify all SRA unassembled reads that carry the bla NDM gene.…”

Section: Methodsmentioning

confidence: 99%

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

et al. 2022

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The mobile resistance gene blaNDM encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. The blaNDM gene is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within highly recombining and transposon-rich genomic regions, which leads to the dynamics underlying the global dissemination of blaNDM to remain poorly resolved. Here, we compile a dataset of over 6000 bacterial genomes harbouring the blaNDM gene, including 104 newly generated PacBio hybrid assemblies from clinical and livestock-associated isolates across China. We develop a computational approach to track structural variants surrounding blaNDM, which allows us to identify prevalent genomic contexts, mobile genetic elements, and likely events in the gene’s global spread. We estimate that blaNDM emerged on a Tn125 transposon before 1985, but only reached global prevalence around a decade after its first recorded observation in 2005. The Tn125 transposon seems to have played an important role in early plasmid-mediated jumps of blaNDM, but was overtaken in recent years by other elements including IS26-flanked pseudo-composite transposons and Tn3000. We found a strong association between blaNDM-carrying plasmid backbones and the sampling location of isolates. This observation suggests that the global dissemination of the blaNDM gene was primarily driven by successive between-plasmid transposon jumps, with far more restricted subsequent plasmid exchange, possibly due to adaptation of plasmids to their specific bacterial hosts.

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“…Others exclusively focus on protein alignment ( Buchfink et al , 2015 ; Suzuki et al , 2015 ; Vaser et al , 2016 ; Zhao et al , 2012 ). Recently, the tool BlastFrost ( Luhmann et al , 2021 ) appeared, which enables sequence queries on a pangenome graph. However, it does not calculate alignments.…”

Section: Introductionmentioning

confidence: 99%

Detecting high-scoring local alignments in pangenome graphs

et al. 2021

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Motivation Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet. Results We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome. Availability Source code and test data are available from https://gitlab.ub.uni-bielefeld.de/gi/plast. Supplementary information Supplementary data are available at Bioinformatics online.

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

Cited by 23 publications

References 39 publications

High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

High-Resolution Comparative Genomics of Salmonella Kentucky Aids Source Tracing and Detection of ST198 and ST152 Lineage-Specific Mutations

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Detecting high-scoring local alignments in pangenome graphs

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