TY - JOUR
T1 - Single nucleotide polymorphism (SNP)-based differentiation of Shigella isolates by pyrosequencing
AU - Hayford, Alice E.
AU - Mammel, Mark K.
AU - Lacher, David W.
AU - Brown, Eric W.
N1 - Funding Information:
We thank the National Bioforensics Analysis Center of the Department of Homeland Security, the Centers for Disease Control and Prevention, and the Navy Environmental and Preventive Medicine Unit for providing some of the Shigella isolates used in this study. We acknowledge the Department of Homeland Security ( IAG 224-04-2806 ) for supporting this work.
PY - 2011/10
Y1 - 2011/10
N2 - Analysis of single nucleotide polymorphisms (SNPs) is an important genetic tool that provides molecular markers for rapid differentiation of closely related strains. We have applied SNP discovery and analysis for distinguishing each of the four Shigella serogroups (Boydii, Dysenteriae, Flexneri, and Sonnei) and for discriminating individual strains within the same serogroup by using 24 SNPs selected from nine genes. Five SNPs were identified from sequence analysis of two housekeeping genes (gapA and thrB) used previously in our lab to differentiate Shigella isolates into distinct lineages. The remaining 19 SNPs were identified by in silico analyses of eight Shigella genomes and are within the genes lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, and ynhA. A total of 118 Shigella strains comprising 20 Boydii, 29 Dysenteriae, 42 Flexneri, and 27 Sonnei isolates were analyzed using the SNP typing scheme reported here. The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups and also provided some discriminatory resolution among individual strains within the same serogroup. The SNPs presented here should prove useful in identifying Shigella using PCR amplification and rapid sequence typing strategies.
AB - Analysis of single nucleotide polymorphisms (SNPs) is an important genetic tool that provides molecular markers for rapid differentiation of closely related strains. We have applied SNP discovery and analysis for distinguishing each of the four Shigella serogroups (Boydii, Dysenteriae, Flexneri, and Sonnei) and for discriminating individual strains within the same serogroup by using 24 SNPs selected from nine genes. Five SNPs were identified from sequence analysis of two housekeeping genes (gapA and thrB) used previously in our lab to differentiate Shigella isolates into distinct lineages. The remaining 19 SNPs were identified by in silico analyses of eight Shigella genomes and are within the genes lpxC, sanA, yaaH, ybaP, ygaZ, yhbO, and ynhA. A total of 118 Shigella strains comprising 20 Boydii, 29 Dysenteriae, 42 Flexneri, and 27 Sonnei isolates were analyzed using the SNP typing scheme reported here. The combination of the 24 SNPs resulted in the identification of 26 SNP genotypes among the four Shigella serogroups and also provided some discriminatory resolution among individual strains within the same serogroup. The SNPs presented here should prove useful in identifying Shigella using PCR amplification and rapid sequence typing strategies.
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U2 - 10.1016/j.meegid.2011.07.015
DO - 10.1016/j.meegid.2011.07.015
M3 - Article
C2 - 21839856
AN - SCOPUS:80053561448
SN - 1567-1348
VL - 11
SP - 1761
EP - 1768
JO - Infection, Genetics and Evolution
JF - Infection, Genetics and Evolution
IS - 7
ER -