Pan-GWAS of <i>Streptococcus agalactiae</i> highlights lineage-specific genes associated with virulence and niche adaptation

Gori, Andrea; Harrison, Odile; Mlia, Ethwako; Nishihara, Yo; Chinkwita-Phiri, Jacquline; Mallewa, Macpherson; Dube, Queen; Swarthout, Todd D.; Nobbs, Angela H.; Maiden, Martin C. J.; French, Neil; Heyderman, Robert S.

doi:10.1101/574152

Cited by 7 publications

(6 citation statements)

References 79 publications

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“…Microbial GWAS approaches can be particularly powerful, when pan-genomic variation of closely related bacterial strains can be leveraged, as has been shown for e.g. virulence genes [75]. We showed that genetic variation between the strains P1C6b, DSM2003, DSM2343, and DSM3504 (mean ANI = 95.5%) empowered us to pinpoint the TBP ( Figure S1).…”

Section: Microbial Gwas For Host Traits Can Benefit From Strain Levelmentioning

confidence: 58%

Horizontal gene transfer-mediated bacterial strain variation affects host fitness

Wang

Baumdicker

Kuenzel

et al. 2020

Preprint

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How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. We tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS). Leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions, we pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). We suggest that HGT might contribute to microbiome flexibility and speculate that it can also more generally contribute to host adaptation.

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Section: Microbial Gwas For Host Traits Can Benefit From Strain Levelmentioning

confidence: 58%

Horizontal gene transfer-mediated bacterial strain variation affects host fitness

Wang

Baumdicker

Kuenzel

et al. 2020

Preprint

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“…4A). The Pan-GWAS approach helped identify genes unique for each clade which could be considered contributing to virulence and/or niche adaptation (26).…”

Section: Discussionmentioning

confidence: 99%

Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017

Monir

Hossain

Morita

et al. 2021

Preprint

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Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in depth whole genome study of V. cholerae El Tor clinical strains isolated during endemic cholera in Bangladesh (1991 – 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera 2004-2017. Genome wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of the endemic cholera in Bangladesh, with implications for global cholera epidemiology.ImportanceCholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 – 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphylatic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications at a global scale.

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“…Clinically it is useful for identifying outbreak strains, which is a major use of MinION sequencing (error-prone Nanopore reads). In a recent paper [49] the authors worked on almost 2000 samples of Streptococcus agalactiae, characterized by different degrees of virulence and preferred host. However, even if the microbiologists are demanding regarding the distinction of strains, they only distinguish a few dozen different types at most.…”

Section: Discussionmentioning

confidence: 99%

Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

et al. 2021

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This study aimed to provide efficient recognition of bacterial strains on personal computers from MinION (Nanopore) long read data. Thanks to the fall in sequencing costs, the identification of bacteria can now proceed by whole genome sequencing. MinION is a fast, but highly error-prone sequencing device and it is a challenge to successfully identify the strain content of unknown simple or complex microbial samples. It is heavily constrained by memory management and fast access to the read and genome fragments. Our strategy involves three steps: indexing of known genomic sequences for a given or several bacterial species; a request process to assign a read to a strain by matching it to the closest reference genomes; and a final step looking for a minimum set of strains that best explains the observed reads. We have applied our method, called ORI, on 77 strains of Streptococcus thermophilus . We worked on several genomic distances and obtained a detailed classification of the strains, together with a criterion that allows merging of what we termed ‘sibling’ strains, only separated by a few mutations. Overall, isolated strains can be safely recognized from MinION data. For mixtures of several non-sibling strains, results depend on strain abundance.

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Pan-GWAS of Streptococcus agalactiae highlights lineage-specific genes associated with virulence and niche adaptation

Cited by 7 publications

References 79 publications

Horizontal gene transfer-mediated bacterial strain variation affects host fitness

Horizontal gene transfer-mediated bacterial strain variation affects host fitness

Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017

Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

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