Population Genetics of Salmonella

Population Genetics of Salmonella

Funding Body (EPA, FP7, etc): SFI

Project type (PhD, post-doc, etc): post-doc

Period (start to end): 01. 2008 – 12. 2010

Researcher: Yajun Song


Project Description 

In ERI, I am working on population genetics of pathogenic bacteria. Population genetics is the study of the allele frequency distribution and change under the influence of evolutionary forces: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. As such, it attempts to explain such phenomena as adaptation and speciation. Population genetics was a vital ingredient in the modern evolutionary synthesis. Here in ERI, we have developed high throughput pipeline for population genetics based on robotics equipments, Luminex technology and genome sequencing. Now I am trying to investigate the population structure of the most common group of Salmonella Typhi group (H58) using the above mentioned pipeline. I am also studying the distribution and spreading of antibiotics resistant related mutations in this group of Typhi strains, which will provide invaluable data for fighting typhi fever.



1.        Cui, Y., Y. Li, O. Gorge, M. E. Platonov, Y. Yan, Z. Guo, C. Pourcel, S. V. Dentovskaya, S. V. Balakhonov, X. Wang, Y. Song, A. P. Anisimov, G. Vergnaud, and R. Yang. 2008. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS ONE. 3:e2652.

2.        Gao, H., D. Zhou, Y. Li, Z. Guo, Y. Han, Y. Song, J. Zhai, Z. Du, X. Wang, J. Lu, and R. Yang. 2008. The iron-responsive Fur regulon in Yersinia pestis. J. Bacteriol. 190:3063-3075.

3.        Han, Y., J. Geng, Y. Qiu, Z. Guo, D. Zhou, Y. Bi, Z. Du, Y. Song, X. Wang, Y. Tan, Z. Zhu, J. Zhai, and R. Yang. 2008. Physiological and regulatory characterization of KatA and KatY in Yersinia pestis. DNA Cell Biol. 27:453-462.

4.        Li, Y., H. Gao, L. Qin, B. Li, Y. Han, Z. Guo, Y. Song, J. Zhai, Z. Du, X. Wang, D. Zhou, and R. Yang. 2008. Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus. BMC Genomics9:143.

5.        Li, Y., E. Dai, Y. Cui, M. Li, Y. Zhang, M. Wu, D. Zhou, Z. Guo, X. Dai, B. Cui, Z. Qi, Z. Wang, H. Wang, X. Dong, Z. Song, J. Zhai, Y. Song, and R. Yang. 2008. Different region analysis for genotyping Yersinia pestis isolates from China. PLoS ONE 3:e2166. (Co-corresponding authors)

6.        Liu, H., H. Wang, J. Qiu, X. Wang, Z. Guo, Y. Qiu, D. Zhou, Y. Han, Z. Du, C. Li, Y. Song, and R. Yang. 2008. Transcriptional profiling of a mice plague model: insights into interaction between Yersinia pestis and its host. J. Basic Microbiol. 48: 1 (Co-corresponding authors)

7.        Chen, C., J. Tang, W. Dong, C. Wang, Y. Feng, J. Wang, F. Zheng, X. Pan, D. Liu, M. Li, Y. Song, X. Zhu, H. Sun, T. Feng, Z. Guo, A. Ju, J. Ge, Y. Dong, W. Sun, Y. Jiang, J. Wang, J. Yan, H. Yang, X. Wang, G. F. Gao, R. Yang, J. Wang, and J. Yu. 2007. A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS ONE.2:e315.

8.        Han, Y., J. Qiu, Z. Guo, H. Gao, Y. Song, D. Zhou, and R. Yang. 2007. Comparative transcriptomics in Yersinia pestis: a global view of environmental modulation of gene expression. BMC. Microbiol. 7:96.

9.        Vergnaud, G., Y. Li, O. Gorge, Y. Cui, Y. Song, D. Zhou, I. Grissa, S. V. Dentovskaya, M. E. Platonov, A. Rakin, S. V. Balakhonov, H. Neubauer, C. Pourcel, A. P. Anisimov, and R. Yang. 2007. Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA. Adv. Exp. Med. Biol. 603:327-338.

10.    Wang, X., Y. Han, Y. Li, Z. Guo, Y. Song, Y. Tan, Z. Du, A. Rakin, D. Zhou, and R. Yang. 2007. Yersinia genome diversity disclosed by Yersinia pestis genome-wide DNA microarray. Can. J. Microbiol. 53:1211-1221.

11.    Wei, H., Y. Zhao, Y. Bi, H. Liu, Z. Guo, Y. Song, J. Zhai, H. Huang, and R. Yang. 2007. Direct detection of Yersinia pestis from the infected animal specimens by a fiber optic biosensor. Sensors and Actuators B-Chemical. 123: 204-210.    

Environmental Research Institute

University College Cork, Lee Road, Cork