Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

BMC Microbiology
Erin HonsaPhilip M Giffard

Abstract

Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinic...Continue Reading

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Citations

Oct 12, 2010·Journal of Bacteriology·Vartul SangalMark Achtman
Dec 4, 2009·Journal of Clinical Microbiology·Albertine LeonRoland Leclercq
May 26, 2010·Letters in Applied Microbiology·A PetersenH Christensen
Feb 7, 2015·Journal of Paediatrics and Child Health·Danny Wh KoUNKNOWN GBS Study Group
May 25, 2016·Scientific Reports·Jiufeng SunXiaoling Deng
Oct 22, 2016·Emerging Infectious Diseases·Morven S EdwardsImmaculada Margarit
Jul 6, 2014·The Journal of Biological Chemistry·Francesco BertiImmaculada Margarit

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Methods Mentioned

BETA
genotyping
genetic exchange
PCR

Software Mentioned

eBURST
MLST
Minimum SNPs

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