Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Lucy A Weinert; Roy R Chaudhuri; Jinhong Wang; Sarah E Peters; Jukka Corander; Thibaut Jombart; Abiyad Baig; Kate J Howell; Minna Vehkala; Niko Välimäki; David Harris; Tran Thi Bich Chieu; Nguyen Van Vinh Chau; James Campbell; Constance Schultsz; Julian Parkhill; Stephen D Bentley; Paul R Langford; Andrew N Rycroft; Brendan W Wren; Jeremy Farrar; Stephen Baker; Ngo Thi Hoa; Matthew T G Holden; Alexander W Tucker; Duncan J Maskell; BRaDP1T Consortium

doi:10.1038/ncomms7740

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Lucy A Weinert, Roy R Chaudhuri, Jinhong Wang, Sarah E Peters, Jukka Corander, Thibaut Jombart, Abiyad Baig, Kate J Howell, Minna Vehkala, Niko Välimäki, David Harris, Tran Thi Bich Chieu, Nguyen Van Vinh Chau, James Campbell, Constance Schultsz, Julian Parkhill, Stephen D Bentley, Paul R Langford, Andrew N Rycroft, Brendan W WrenJeremy Farrar, Stephen Baker, Ngo Thi Hoa, Matthew T G Holden, Alexander W Tucker, Duncan J Maskell, BRaDP1T Consortium

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Abstract

Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.

Original language	English
Article number	6740
Number of pages	9
Journal	Nature Communications
Volume	6
Early online date	31 Mar 2015
DOIs	https://doi.org/10.1038/ncomms7740
Publication status	Published - May 2015

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weinert2015ncomms6740
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Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (dataset - Genome assemblies)
Weinert, L. A. (Creator), Chaudhuri, R. R. (Creator), Wang, J. (Creator), Peters, S. E. (Creator), Jukka Corander, J. C. (Creator), Jombart, T. (Creator), Baig, A. (Creator), Howell, K. J. (Creator), Vehkala, M. (Creator), Välimäki, N. (Creator), Harris, D. (Creator), Bich Chieu, T. T. (Creator), Campbell, J. (Creator), Schultsz, C. (Creator), Parkhill, J. (Creator), Bentley, S. D. (Creator), Langford, P. R. (Creator), Rycroft, A. N. (Creator), Wren, B. W. (Creator), Farrar, J. (Creator), Baker, S. (Creator), Hoa, N. T. (Creator), Holden, M. T. G. (Creator), Tucker, A. W. (Creator) & Maskell, D. J. (Creator), European Nucleotide Archive (ENA), 13 Feb 2015
http://www.ebi.ac.uk/ena/data/view/ERS655506 and 2 more links, http://www.ebi.ac.uk/ena/data/view/ERS655880, http://www.ebi.ac.uk/ena/data/view/PRJEB8392 (show fewer)
Dataset
Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (dataset - High-Throughput sequencing)
Weinert, L. A. (Creator), Chaudhuri, R. R. (Creator), Wang, J. (Creator), Peters, S. E. (Creator), Corander, J. (Creator), Jombart, T. (Creator), Baig, A. (Creator), Howell, K. J. (Creator), Vehkala, M. (Creator), Välimäki, N. (Creator), Harris, D. (Creator), Bich Chieu, T. T. (Creator), Vinh Chau, N. V. (Creator), Campbell, J. (Creator), Schultsz, C. (Creator), Parkhill, J. (Creator), Bentley, S. D. (Creator), Langford, P. R. (Creator), Rycroft, A. N. (Creator), Wren, B. W. (Creator), Farrar, J. (Creator), Baker, S. (Creator), Hoa, N. T. (Creator), Holden, M. T. G. (Creator), Tucker, A. W. (Creator) & Maskell, D. J. (Creator), National Center for Biotechnology Information, 20 Dec 2012
http://www.ncbi.nlm.nih.gov/sra?term=ERS018463 and 25 more links, http://www.ncbi.nlm.nih.gov/sra?term=ERS132367, http://www.ncbi.nlm.nih.gov/sra?term=ERS132370, http://www.ncbi.nlm.nih.gov/sra?term=ERS132376, http://www.ncbi.nlm.nih.gov/sra?term=ERS132352, http://www.ncbi.nlm.nih.gov/sra?term=ERS132380, http://www.ncbi.nlm.nih.gov/sra?term=ERS132382, http://www.ncbi.nlm.nih.gov/sra?term=ERS132404, http://www.ncbi.nlm.nih.gov/sra?term=ERS132406, http://www.ncbi.nlm.nih.gov/sra?term=ERS132409, http://www.ncbi.nlm.nih.gov/sra?term=ERS132454, http://www.ncbi.nlm.nih.gov/sra?term=ERS132456, http://www.ncbi.nlm.nih.gov/sra?term=ERS132469, http://www.ncbi.nlm.nih.gov/sra?term=ERS132471, http://www.ncbi.nlm.nih.gov/sra?term=ERS132500, http://www.ncbi.nlm.nih.gov/sra?term=ERS132502, http://www.ncbi.nlm.nih.gov/sra?term=ERS132505, http://www.ncbi.nlm.nih.gov/sra?term=ERS132536, http://www.ncbi.nlm.nih.gov/sra?term=ERS132538, http://www.ncbi.nlm.nih.gov/sra?term=ERS132551, http://www.ncbi.nlm.nih.gov/sra?term=ERS156197, http://www.ncbi.nlm.nih.gov/sra?term=ERS156218, http://www.ncbi.nlm.nih.gov/sra?term=ERS156220, http://www.ncbi.nlm.nih.gov/sra?term=ERS156290, http://www.ncbi.nlm.nih.gov/sra?term=ERS156292, http://www.ncbi.nlm.nih.gov/sra?term=ERS156388 (show fewer)
Dataset

Cite this

Weinert, L. A., Chaudhuri, R. R., Wang, J., Peters, S. E., Corander, J., Jombart, T., Baig, A., Howell, K. J., Vehkala, M., Välimäki, N., Harris, D., Chieu, T. T. B., Van Vinh Chau, N., Campbell, J., Schultsz, C., Parkhill, J., Bentley, S. D., Langford, P. R., Rycroft, A. N., ... BRaDP1T Consortium (2015). Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 6, Article 6740. https://doi.org/10.1038/ncomms7740

@article{3f61c0b959684304bc0979d47b910daa,

title = "Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis",

abstract = "Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.",

author = "Weinert, {Lucy A} and Chaudhuri, {Roy R} and Jinhong Wang and Peters, {Sarah E} and Jukka Corander and Thibaut Jombart and Abiyad Baig and Howell, {Kate J} and Minna Vehkala and Niko V{\"a}lim{\"a}ki and David Harris and Chieu, {Tran Thi Bich} and {Van Vinh Chau}, Nguyen and James Campbell and Constance Schultsz and Julian Parkhill and Bentley, {Stephen D} and Langford, {Paul R} and Rycroft, {Andrew N} and Wren, {Brendan W} and Jeremy Farrar and Stephen Baker and Hoa, {Ngo Thi} and Holden, {Matthew T G} and Tucker, {Alexander W} and Maskell, {Duncan J} and {BRaDP1T Consortium}",

note = "This work was supported by a Longer and Larger (LoLa) grant from the Biotechnology and Biological Sciences Research Council (grant numbers BB/G020744/1, BB/G019177/1, BB/G019274/1 and BB/G003203/1), the UK Department for Environment, Food and Rural Affairs and Zoetis, awarded to the Bacterial Respiratory Diseases of Pigs: 1 Technology (BRaDP1T) consortium. Part of this work was supported by The Wellcome Trust Overseas Programme in Vietnam (2010–2015) (089276/Z/09/Z) and the Vietnam Initiative on Zoonotic Infections (VIZIONS) award (WT/093724/Z/10/Z). S.D.B. is partly funded by the NIHR Cambridge BRC. ",

year = "2015",

month = may,

doi = "10.1038/ncomms7740",

language = "English",

volume = "6",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature publishing group",

}

Weinert, LA, Chaudhuri, RR, Wang, J, Peters, SE, Corander, J, Jombart, T, Baig, A, Howell, KJ, Vehkala, M, Välimäki, N, Harris, D, Chieu, TTB, Van Vinh Chau, N, Campbell, J, Schultsz, C, Parkhill, J, Bentley, SD, Langford, PR, Rycroft, AN, Wren, BW, Farrar, J, Baker, S, Hoa, NT, Holden, MTG, Tucker, AW, Maskell, DJ & BRaDP1T Consortium 2015, 'Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis', Nature Communications, vol. 6, 6740. https://doi.org/10.1038/ncomms7740

TY - JOUR

T1 - Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

AU - Weinert, Lucy A

AU - Chaudhuri, Roy R

AU - Wang, Jinhong

AU - Peters, Sarah E

AU - Corander, Jukka

AU - Jombart, Thibaut

AU - Baig, Abiyad

AU - Howell, Kate J

AU - Vehkala, Minna

AU - Välimäki, Niko

AU - Harris, David

AU - Chieu, Tran Thi Bich

AU - Van Vinh Chau, Nguyen

AU - Campbell, James

AU - Schultsz, Constance

AU - Parkhill, Julian

AU - Bentley, Stephen D

AU - Langford, Paul R

AU - Rycroft, Andrew N

AU - Wren, Brendan W

AU - Farrar, Jeremy

AU - Baker, Stephen

AU - Hoa, Ngo Thi

AU - Holden, Matthew T G

AU - Tucker, Alexander W

AU - Maskell, Duncan J

AU - BRaDP1T Consortium

N1 - This work was supported by a Longer and Larger (LoLa) grant from the Biotechnology and Biological Sciences Research Council (grant numbers BB/G020744/1, BB/G019177/1, BB/G019274/1 and BB/G003203/1), the UK Department for Environment, Food and Rural Affairs and Zoetis, awarded to the Bacterial Respiratory Diseases of Pigs: 1 Technology (BRaDP1T) consortium. Part of this work was supported by The Wellcome Trust Overseas Programme in Vietnam (2010–2015) (089276/Z/09/Z) and the Vietnam Initiative on Zoonotic Infections (VIZIONS) award (WT/093724/Z/10/Z). S.D.B. is partly funded by the NIHR Cambridge BRC.

PY - 2015/5

Y1 - 2015/5

N2 - Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.

AB - Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.

U2 - 10.1038/ncomms7740

DO - 10.1038/ncomms7740

M3 - Article

C2 - 25824154

SN - 2041-1723

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 6740

ER -

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Abstract

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Datasets

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (dataset - Genome assemblies)

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (dataset - High-Throughput sequencing)

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