Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

Kaas, Rolf Sommer; Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller; Lund, Ole

doi:10.1371/journal.pone.0104984

Cited by 643 publications

(524 citation statements)

References 26 publications

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“…In order to explore the genetic diversity between the 95 strains analysed, a whole genome Single-Nucleotide Polymorphisms (SNPs) analysis was performed using the online software CSI Phylogeny 1.0a [32]. Here, the analysis focuses upon all the genes shared in common by the strains and the number and location of the single nucleotide differences within those common genes.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics of European avian pathogenic E. Coli (APEC)

Cordoni

Woodward

et al. 2016

BMC Genomics

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BackgroundAvian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were characterised using multiplex polymerase chain reactions (PCRs) targeting 22 equally weighted factors covering virulence genes, R-type and phylogroup. Following these analysis, 95 of the selected strains were further analysed using Whole Genome Sequencing (WGS).ResultsThe most prevalent phylogroups were B2 (47%) and A1 (22%), although there were national differences with Germany presenting group B2 (35.3%), Italy presenting group A1 (53.3%) and UK presenting group B2 (56.1%) as the most prevalent. R-type R1 was the most frequent type (55%) among APEC, but multiple R-types were also frequent (26.8%). Following compilation of all the PCR data which covered a total of 15 virulence genes, it was possible to build a similarity tree using each PCR result unweighted to produce 9 distinct groups. The average number of virulence genes was 6–8 per isolate, but no positive association was found between phylogroup and number or type of virulence genes. A total of 95 isolates representing each of these 9 groupings were genome sequenced and analysed for in silico serotype, Multilocus Sequence Typing (MLST), and antimicrobial resistance (AMR). The UK isolates showed the greatest variability in terms of serotype and MLST compared with German and Italian isolates, whereas the lowest prevalence of AMR was found for German isolates. Similarity trees were compiled using sequencing data and notably single nucleotide polymorphism data generated ten distinct geno-groups. The frequency of geno-groups across Europe comprised 26.3% belonging to Group 8 representing serogroups O2, O4, O18 and MLST types ST95, ST140, ST141, ST428, ST1618 and others, 18.9% belonging to Group 1 (serogroups O78 and MLST types ST23, ST2230), 15.8% belonging to Group 10 (serogroups O8, O45, O91, O125ab and variable MLST types), 14.7% belonging to Group 7 (serogroups O4, O24, O35, O53, O161 and MLST type ST117) and 13.7% belonging to Group 9 (serogroups O1, O16, O181 and others and MLST types ST10, ST48 and others). The other groups (2, 3, 4, 5 and 6) each contained relatively few strains.However, for some of the genogroups (e.g. groups 6 and 7) partial overlap with SNPs grouping and PCR grouping (matching PCR groups 8 (13 isolates on 22) and 1 (14 isolates on 16) were observable). However, it was not possible to obtain a clear correlation between genogroups and unweighted PCR groupings. This may be due to the genome plasticity of E. coli that enables strains to carry the same virulence factors even if the overall genotype is substantially different.ConclusionsThe conclusion to be drawn from the lack of correlations is that firstly, APEC are very diverse and secondly, it is not possible to rely on any one or more basic molecular or phenotypic tests t...

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Section: Methodsmentioning

confidence: 99%

Comparative genomics of European avian pathogenic E. Coli (APEC)

Cordoni

Woodward

et al. 2016

BMC Genomics

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“…The version described in this paper is version XXXX01000000. Genomic analyses (MultiLocus Sequences Typing-MLST and virulence factors) were performed using the Center for Genomic Epidemiology website platform Zankari et al, 2012;Joensen et al, 2014;Kaas et al, 2014).…”

Section: Genomes Sequencingmentioning

confidence: 99%

Existence of two groups of Staphylococcus aureus strains isolated from bovine mastitis based on biofilm formation, intracellular survival, capsular profile and agr-typing

Bardiau

Caplin

Detilleux

et al. 2016

Veterinary Microbiology

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A B S T R A C TStaphylococcus (S.) aureus is recognised worldwide as an important pathogen causing contagious acute and chronic bovine mastitis. Chronic mastitis account for a significant part of all bovine cases and represent an important economic problem for dairy producers. Several properties (biofilm formation, intracellular survival, capsular expression and group agr) are thought to be associated with this chronic status. In a previous study, we found the existence of two groups of strains based on the association of these features. The aim of the present work was to confirm on a large international and non-related collection of strains the existence of these clusters and to associate them with case history records. In addition, the genomes of eight strains were sequenced to study the genomic differences between strains of each cluster. The results confirmed the existence of both groups based on capsular typing, intracellular survival and agr-typing: strains cap8-positive, belonging to agr group II, showing a low invasion rate and strains cap5-positive, belonging to agr group I, showing a high invasion rate. None of the two clusters were associated with the chronic status of the cow. When comparing the genomes of strains belonging to both clusters, the genes specific to the group "cap5-agrI" would suggest that these strains are better adapted to live in hostile environment. The existence of these two groups is highly important as they may represent two clusters that are adapted differently to the host and/or the surrounding environment.

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“…A single-nucleotide polymorphism (SNP) based phylogeny tree, using strain EGD-e as the reference genome, was inferred by CSI Phylogeny 1.4. [19] using the default parameters. Briefly, SNPs were called by mapping the genomes of the studied strains to that of the reference.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food

2016

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Background Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia.ResultsThe genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains.ConclusionsWhole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

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Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

Cited by 643 publications

References 26 publications

Comparative genomics of European avian pathogenic E. Coli (APEC)

Comparative genomics of European avian pathogenic E. Coli (APEC)

Existence of two groups of Staphylococcus aureus strains isolated from bovine mastitis based on biofilm formation, intracellular survival, capsular profile and agr-typing

Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food

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