Global genomic population structure of <i>Clostridioides difficile</i>

Frentrup, Martinique; Zhou, Zhemin; Steglich, Matthias; Meier‐Kolthoff, Jan P.; Göker, Markus; Riedel, Thomas; Bunk, Boyke; Spröer, Cathrin; Overmann, Jörg; Blaschitz, Marion; Indra, Alexander; Müller, Lutz von; Köhl, Thomas; Niemann, Stefan; Seyboldt, Christian; Klawonn, Frank; Kumar, Nitin; Lawley, Trevor D.; García‐Fernández, Sergio; Campo, R. del; Zimmermann, Ortrud; Groß, Uwe; Achtman, Mark; Nübel, Ulrich

doi:10.1101/727230

Cited by 7 publications

(10 citation statements)

References 47 publications

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“…Thus, cgST HierCC provides a robust approach to analyse population structures at multiple levels of resolution. The identification of closely related genomes using HierCC has been shown to be 89 % consistent between cgMLST and SNPs [34]. Neighbour-joining trees were reconstructed with NINJA – a hierarchical clustering algorithm for inferring phylogenies that is capable of scaling to inputs larger than 100, 000 sequences [35].…”

Section: Methodsmentioning

confidence: 99%

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

et al. 2020

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Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity and antimicrobial resistance in Escherichia coli isolates from four species of non-human primates in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on 11 isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli . The majority of simian isolates belong to phylogroup B2 – characterized by strains that cause human extraintestinal infections – and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and 7 alleles, respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes – indicating novel diversity specific to the primate niche. Our results are of planetary health importance, considering the increasing contact between humans and wild non-human primates.

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Section: Methodsmentioning

confidence: 99%

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

et al. 2020

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“…PEPPA can construct a pan-genome from thousands of genomes with high genetic diversities, and earlier versions of this pipeline were used to generate cgMLST schemes for the genera represented in EnteroBase (Alikhan et al 2018;Frentrup et al 2019;Zhou et al 2020) as well as for ancient DNA analyses (Zhou et al 2018b; Achtman and Zhou 2019). Here we address the genus Streptococcus, which includes very genetically diverse strains and highly significant zoonotic and human pathogens (Gao et al 2014), to demonstrate how to use PEPPA to construct a pan-genome from representative genomes.…”

Section: A Pan-genome For the Genus Streptococcusmentioning

confidence: 99%

“…Similarly, earlier publications indicated fewer and fewer genes within the core-genome as more and more genomes were examined, but this has also not been revisited with the larger datasets. Finally, genetic relationships that are based on single nucleotide polymorphisms are extremely difficult to calculate in real-time with very large datasets, and some large databases focus on core genome Multilocus sequence typing (cgMLST) (Mellmann et al 2011;Moura et al 2016;Alikhan et al 2018;Frentrup et al 2019;Zhou et al 2020) for genotyping and recognizing relationships. cgMLST schemes within public databases calculate the allelic variants within a fixed set of core genes.…”

Section: Introductionmentioning

confidence: 99%

“…In order to create reliable cgMLST schemes for EnteroBase (Frentrup et al 2019;Zhou et al 2020), we have developed PEPPA, a novel pipeline for calculating a pan-genome that deals specifically with the problems described above. Here we describe the algorithms implemented within PEPPA, and show that it outperforms other pan-genome methods with empirical as well as with simulated datasets.…”

Section: Introductionmentioning

confidence: 99%

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Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

Zhou

Charlesworth

Achtman

2020

Preprint

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Bacterial genomes have been shaped by a complex evolutionary history, including extensive homologous recombination, horizontal gene transfer, gene loss, and gene duplications. A pan-genome, consisting of all genes within a defined set of bacterial genomes, can provide the basis for phylogenetic inferences and population studies.Here we introduce PEPPA, a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPA implements a combination of treeand synteny-based approaches to identify and exclude paralogous genes, which facilitates the ready construction of schemes for whole genome multi-locus sequence typing (wgMLST) and core genome MLST. PEPPA also implements similarity-based gene predictions that support consistent annotations of genes and pseudogenes in individual genomes, and which are nearly as accurate as expert manual curation. The PEPPA package includes PEPPA_parser, which calculates trees based on accessory gene content and MLST core genome allelic differences. We also present SimPan, a novel pipeline for simulating the evolution of a bacterial pan-genome. PEPPA was compared with four state-of-the-art pan-genome pipelines on both empirical and simulated datasets. It demonstrated greater accuracy and specificity than any other pipeline, and was almost as fast as any of them at calculating a pan-genome. To demonstrate its abilities, PEPPA was used to construct a Streptococcus pan-genome of >40,000 genes from 3,170 representative genomes spanning at least 80 species. The resulting gene and allelic trees provide an unprecedented overview of the genomic diversity of this genus. Kilian M, Poulsen K, Blomqvist T, Havarstein LS, Bek-Thomsen M, Tettelin H, Sorensen UB. 2008. Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS ONE 3: e2683. Kilian M and Tettelin H. 2019. Identification of virulence-associated properties by comparative genome analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, three S. oralis subspecies, and S. infantis. MBio 10. Konstantinidis KT, Rossello-Mora R, Amann R. 2017. Uncultivated microbes in need of their own taxonomy. ISME J 11: 2399-2406. Koonin EV. 2016. Splendor and misery of adaptation, or the importance of neutral null for understanding evolution. BMC Biol 14: 114.

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“…Thus, cgST HierCC provides a robust approach to analyse population structures at multiple levels of resolution. The identification of closely-related genomes using HierCC has been shown to be 89% consistent between cgMLST and single-nucleotide polymorphisms (42). Neighbour-joining trees were reconstructed with Ninja—a hierarchical clustering algorithm for inferring phylogenies that is capable of scaling to inputs larger than 100,000 sequences (43).…”

Section: Methodsmentioning

confidence: 99%

Genomic diversity ofEscherichia coliisolates from non-human primates in the Gambia

Foster-Nyarko

Alikhan

Ray

et al. 2020

Preprint

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8Increasing contact between humans and non-human primates provides an opportunity for the 1 9 transfer of potential pathogens or antimicrobial resistance between host species. We have 2 0 investigated genomic diversity, and antimicrobial resistance in Escherichia coli isolates from 2 1 four species of non-human primate in the Gambia: Papio papio (n=22), Chlorocebus sabaeus 2 2 (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina 2 3whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read 2 4sequencing on eleven isolates. We identified 43 sequence types (STs) by the Achtman 2 5 scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. 2 6The majority of simian isolates belong to phylogroup B2-characterised by strains that cause 2 7human extraintestinal infections-and encode factors associated with extraintestinal disease. 8A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which 2 9 encodes colibactin, a genotoxin associated with colorectal cancer. We found little 3 0antimicrobial resistance and only one example of multi-drug resistance among the simian 3 1isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are 3 2 closely related to isolates recovered from human clinical cases (differences in 50 and seven 3 3 alleles respectively), suggesting recent exchange between the two host species. Conversely, 3 4 simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five 3 5 simian isolates belong to unique core-genome ST complexes-indicating novel diversity 3 6 specific to the primate niche. Our results are of public health importance, considering the 3 7increasing contact between humans and wild non-human primates. 3 8 3 9

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Global genomic population structure of Clostridioides difficile

Cited by 7 publications

References 47 publications

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

Genomic diversity ofEscherichia coliisolates from non-human primates in the Gambia

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