Abstract
BackgroundStreptococcus 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.ResultsIt was found that a SNP set derived from the MLST database on the basis of maximisation 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 clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates.ConclusionA five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.
Highlights
Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, of newborns
We investigated the population biology of GBS using the well-established GBS multilocus sequence typing (MLST) database [3,4,21], and used this analysis to guide our approach to the selection of a five member single nucleotide polymorphism (SNP) set for identifying GBS clonal complexes and ensuring high sensitivity for CC17
We assessed the utility of the D-maximisation SNP selection method that, in the case of S. aureus, yielded a SNP set with good resolving power and good correlation between SNP profile and clonal complex structure
Summary
Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, of newborns. 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. There is a strong association between a serotype III subtype (designated (msst) III-2 in our genotyping system) and late onset neonatal sepsis [6], and these subtypes are likely to be members of CC17 This subtype can be distinguished from the most common serotype III subtype (III-1) and other less common subtypes on the basis of the presence or absence of two specific single nucleotide polymorphisms (SNPs) in the cps gene cluster (between the 3' end of cpsE-cpsF and 5' end of cpsG) [7]
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