Impact of molecular methods in the analysis of the invasiveness of Streptococcus pneumoniae

Abstract

This doctoral thesis proves the necessity of applying molecular techniques in direct sample for a more accurate study of the Invasive Disease Potential (IDP) of Streptococcus pneumoniae and for its epidemiological surveillance. These methods allow a better detection and serotype identification of the pneumococcal population in both Invasive Pneumococcal Disease (IPD) and nasopharyngeal carriers. However, to better understand the behavior of the different serotypes a complete analysis of the clonal types of pneumococci (invasive and carriers) should be also performed.

In the first two studies the IDP of pneumococcal serotypes found in our pediatric population was estimated. In the first study, traditional methods based only in culture were used for both the detection of Streptococcus pneumoniae and the identification of the capsular type; while in the second study, the same estimation was performed but this time adding molecular techniques in direct sample for both the detection and serotyping.

When comparing the results of both studies, the addition of molecular techniques in direct sample doubled the number of pneumococci identified causing IPD, and in the nasopharynx of healthy children. The great increase in the pneumococcus detection revealed a different distribution of the serotypes circulating in the population of the area, when compared with the data that had been obtained only by culture, which was translated in a huge impact in the IDP of these serotypes. In the carrier’s population an important proportion in the increase of serotypes that were able to be identified in carriers was due to the detection of multiple colonies in one sample, with up to four different serotypes distinguished in the same sample. The analysis of the carriers’ population also revealed a rate of co-colonization of 26.4% in the children population of our area.

The better estimation of the ranking order of the most common serotypes in IPD and in the nasopharynx also allowed a more accurate analysis of the effects of PCV7 in the study time period.

The results from the third study provided additional information about the invasive disease potential of serotypes causing IPD in our area due to the clonal study of invasive strains. In addition, it provided information about the evolution of serotypes causing disease after the introduction of PCV13 in 2010, in both children and adults. Although the most common serotypes found in the study were still PCV13 serotypes (with a special concern for the increase of the ST156 serotype 14), probably due to the low vaccine coverage in our area, a significant decrease was observed. In contrast, a significant increase in the proportion of non-PCV13 serotypes was revealed. Worth mentioning, is the increase experienced by serotype 12F (in high association with ST989) and, when analyzed by age groups, the increase of serotype 24F in children less than 2 years old (the major clone being the multi drug resistant ST230).

But most importantly was the data obtained in the serotypes analysis of their clonal composition. Despite the capsule is the most important factor in virulence, strains expressing the same serotype but belonging to different clonal types has been found to present different invasiveness. Certain clonal types may present some characteristics

that are likely to be advantageous for invasiveness, like antibiotic resistance. The study of the genetic population of the serotypes offers a more complete knowledge of the pneumococcal invasiveness, explains temporal trends and differences in geographical areas, and provides useful information for the prediction of which serotypes could be replacing the ones included in the vaccines. For a better interpretation of the pneumococcal behavior, the analysis of the clonal types associated with a serotype should be performed along with the capsular identification.

Aquesta tesis doctoral demostra la necessitat d’aplicar tècniques moleculars en mostra directa per a poder realitzar un estudi més acurat del potencial invasiu de Streptococcus pneumoniae, i per a la seva vigilància epidemiològica. Aquests mètodes permeten una millor detecció i un millor serotipatge de la població pneumocòccica, tant en la malaltia pneumocòccica invasiva (MPI) com en els portadors nasofaringis. Tot i això, per realment entendre millor el comportament dels diferents serotips també s’hauria de realitzar un anàlisi complet dels tipus clonals que presenten els pneumococs (tant en malaltia com en portadors).

Als dos primers estudis es va calcular el potencial invasiu dels serotips pneumocòccics trobats en la població pediàtrica de Catalunya (Espanya). Al primer estudi es van utilitzar mètodes tradicionals basats en el cultiu tant per la detecció de Streptococcus pneumoniae com per la identificació del tipus capsular; mentre que en el segon estudi, es va realitzar el mateix anàlisi però en aquest cas afegint les tècniques moleculars en mostra directa tant per la detecció com pel serotipatge.

Al comparar els resultats d’ambdós estudis, l’addició de les tècniques moleculars en mostra directa va duplicar el número de pneumococs identificats causant MPI i presents a la nasofaringe de nens sans. Aquesta millora en la detecció del pneumococ també es va traduir en un gran impacte en el càlcul del potencial invasiu d’aquest serotips. En la població de portadors la capacitat de detectar múltiples colònies en una mateixa mostra va tenir un paper rellevant en l’increment de serotips que es van poder identificar en el segon estudi.

Els resultats del tercer estudi van aportar informació addicional sobre el potencial invasiu dels serotips causant MPI a la nostra àrea gràcies a l’estudi clonal de les soques invasives. A més, van aportar informació sobre l’evolució dels serotips causant malaltia després de la introducció de la PCV13 al 2010, tant en nens com en adults. L’anàlisi dels tipus clonals sent expressats pels serotips pneumocòccics podria explicar perquè alguns tipus capsulars que es troben normalment colonitzant asimptomàticament han experimentat un canvi en la seva invasivitat convertint-se en les principals causes de la MPI.