Determination of Accessory Gene Patterns Predicts the Same Relatedness among Strains of Streptococcus pneumoniae as Sequencing of Housekeeping Genes Does and Represents a Novel Approach in Molecular Epidemiology

Abstract

Relatedness between isolates of Streptococcus pneumoniae can be determined from sequences of multiple genes belonging to the core genome (multilocus sequence typing [MLST]), but these do not provide information on gene content that may affect the potential of isolates to cause invasive pneumococcal disease. Gene content data, obtained using microarrays, were gathered for 40 clinical isolates of 12 serotypes belonging to 30 multilocus sequence types. We found that sequence variations in housekeeping genes assessed by MLST correlated well with whole-genome microarray analyses identifying the presence/absence of accessory genes/ regions. However, isolates belonging to the same clonal complex, as determined by MLST, may not have identical gene contents, potentially affecting virulence. We found fewer intraclonal (same MLST sequence type) differences associated with pneumococcal serotypes of high invasive disease potential, i.e., serotypes rarely found among carriers compared to serotypes frequently found in carriage. Molecular typing of pneumococci based on the presence/absence of 25 genes localized to accessory regions shows the same relatedness among pneumococcal strains as MLST does. We conclude that molecular typing of pneumococci based on variation in the nucleotide sequences of parts of housekeeping genes (MLST) correlates with the presence/absence of genes in the accessory part of the genome. This covariation is likely due to the fact that both sequence variations and gene content variations are created primarily by recombination events in pneumococci.

Microbiology, Genomics, and Clinical Significance of the Pseudomonas fluorescens Species Complex, an Unappreciated Colonizer of Humans

“…Multilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) utilize the concept of genetic evolution at multiple conserved genes to measure evolutionary distances between species or strains (81-83). These conserved ("housekeeping") genes are required for the basic functions of the cell and must be found in all bacteria in the comparison (84)(85)(86). Examples of housekeeping genes used in classifying Pseudomonas species include rpoD (-subunit of RNA polymerase), rpoB (␤-subunit of RNA polymerase), and gyrB (␤-subunit of gyrase, responsible for negative supercoiling of DNA during replication) (80,87,88).…”

Rapid Determination ofEscherichia coliO157:H7 Lineage Types and Molecular Subtypes by Using Comparative Genomic Fingerprinting

“…A similar methodology has recently been described for typing Streptococcus pneumoniae (11), Campylobacter jejuni (49), and Escherichia coli strains (47), suggesting that this approach is likely to be useful in the development of next-generation genotyping methods. Subsequent iterations of VAP analysis targeting additional loci will be derived from new E. coli O157:H7 sequence data as they become available.…”

The Pneumococcus: Epidemiology, Microbiology, and Pathogenesis

“…PFGE is more discriminatory than MLST and can be used also to study outbreaks. Furthermore, genomic comparisons using whole genome-based microarrays have shown that MLST can be used as a good method to estimate genome content (Dagerhamn et al 2008).…”