Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.
BACKGROUND
While the pneumococcal protein conjugate vaccines reduce the incidence in invasive pneumococcal disease (IPD), serotype replacement remains a major concern. Thus, serotype-independent protection with vaccines targeting virulence genes, such as PspA, have been pursued. PspA is comprised of diverse clades that arose through recombination. Therefore, multi-locus sequence typing (MLST)-defined clones could conceivably include strains from multiple PspA clades. As a result, a method is needed which can both monitor the long-term epidemiology of the pneumococcus among a large number of isolates, and analyze vaccine-candidate genes, such as pspA, for mutations and recombination events that could result in 'vaccine escape' strains.


METHODS
We developed a resequencing array consisting of five conserved and six variable genes to characterize 72 pneumococcal strains. The phylogenetic analysis of the 11 concatenated genes was performed with the MrBayes program, the single nucleotide polymorphism (SNP) analysis with the DNA Sequence Polymorphism program (DnaSP), and the recombination event analysis with the recombination detection package (RDP).


RESULTS
The phylogenetic analysis correlated with MLST, and identified clonal strains with unique PspA clades. The DnaSP analysis correlated with the serotype-specific diversity detected using MLST. Serotypes associated with more than one ST complex had a larger degree of sequence polymorphism than a serotype associated with one ST complex. The RDP analysis confirmed the high frequency of recombination events in the pspA gene.


CONCLUSIONS
The phylogenetic tree correlated with MLST, and detected multiple PspA clades among clonal strains. The genetic diversity of the strains and the frequency of recombination events in the mosaic gene, pspA were accurately assessed using the DnaSP and RDP programs, respectively. These data provide proof-of-concept that resequencing arrays could play an important role within research and clinical laboratories in both monitoring the molecular epidemiology of the pneumococcus and detecting 'vaccine escape' strains among vaccine-candidate genes.
Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America.
Gagan A
GA
Pandya
M Catherine
MC
McEllistrem
Pratap
P
Venepally
Michael H
MH
Holmes
Behnam
B
Jarrahi
Ravi
R
Sanka
Jia
J
Liu
Svetlana A
SA
Karamycheva
Yun
Y
Bai
Robert D
RD
Fleischmann
Scott N
SN
Peterson
D001426:Bacterial Proteins / Q000235:genetics; D006360:Heat-Shock Proteins / Q000235:genetics; D057131:Immune Evasion; D017720:Molecular Epidemiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012984:Software; D013296:Streptococcus pneumoniae / Q000235:genetics* / Q000276:immunology; D014612:Vaccines / Q000494:pharmacology
D001426:Bacterial Proteins; D006360:Heat-Shock Proteins; D014612:Vaccines; C069816:phage shock protein, Bacteria
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