Allelic variation contributes to bacterial host specificity

Min Yue; Xiangan Han; Leon De Masi; Chunhong Zhu; Xun Ma; Junjie Zhang; Renwei Wu; Robert Schmieder; Radhey S. Kaushik; George P. Fraser; Shaohua Zhao; Patrick F. McDermott; François Xavier Weill; Jacques G. Mainil; Cesar Arze; W. Florian Fricke; Robert A. Edwards; Dustin Brisson; Nancy R. Zhang; Shelley C. Rankin; Dieter M. Schifferli

doi:10.1038/ncomms9754

Allelic variation contributes to bacterial host specificity

Min Yue, Xiangan Han, Leon De Masi, Chunhong Zhu, Xun Ma, Junjie Zhang, Renwei Wu, Robert Schmieder, Radhey S. Kaushik, George P. Fraser, Shaohua Zhao, Patrick F. McDermott, François Xavier Weill, Jacques G. Mainil, Cesar Arze, W. Florian Fricke, Robert A. Edwards, Dustin Brisson, Nancy R. Zhang, Shelley C. RankinDieter M. Schifferli

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Abstract

Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

Original language	English
Article number	8754
Number of pages	11
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms9754
Publication status	Published - 30 Oct 2015
Externally published	Yes

Bibliographical note

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Keywords

microbial pathotype diversity
cross-species transmission
pathoadaptive nonsynonymous single-nucleotide polymorphisms
Allelic variation

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

Yue, M., Han, X., Masi, L. D., Zhu, C., Ma, X., Zhang, J., Wu, R., Schmieder, R., Kaushik, R. S., Fraser, G. P., Zhao, S., McDermott, P. F., Weill, F. X., Mainil, J. G., Arze, C., Fricke, W. F., Edwards, R. A., Brisson, D., Zhang, N. R., ... Schifferli, D. M. (2015). Allelic variation contributes to bacterial host specificity. Nature Communications, 6, Article 8754. https://doi.org/10.1038/ncomms9754

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abstract = "Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.",

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AU - Schifferli, Dieter M.

N1 - This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

PY - 2015/10/30

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N2 - Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

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Allelic variation contributes to bacterial host specificity

Abstract

Bibliographical note

Keywords

UN SDGs

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