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

Honsa, Erin, Fricke, Thomas, Stephens, Alex J., Ko, Danny, Kong, Fanrong, Gilbert, Gwendolyn, Huygens, Flavia, & Giffard, Philip M. (2008) Assignment of streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms. BMC Microbiology, 8, pp. 1-10.

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Abstract

Background: 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 -- Results: It 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 -- Conclusion: A 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.

Impact and interest:

10 citations in Scopus
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7 citations in Web of Science®

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110 since deposited on 03 Feb 2009
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ID Code: 17308
Item Type: Journal Article
Additional Information: The contents of this journal can be freely accessed online via the journal’s web page (see hypertext link).
Keywords: Streptococcus, agalactiae, single, nucleotide, polymorphisms
DOI: 10.1186/1471-2180-8-140
ISSN: 1471-2180
Subjects: Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > CLINICAL SCIENCES (110300) > Clinical Microbiology (110303)
Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > CLINICAL SCIENCES (110300) > Infectious Diseases (110309)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > MICROBIOLOGY (060500) > Infectious Agents (060502)
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Past > Schools > School of Life Sciences
Copyright Owner: Copyright 2008 [please consult the authors]
Deposited On: 03 Feb 2009 12:59
Last Modified: 29 Feb 2012 23:45

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