Streptococcus pneumoniae has remained one of the major causative agents of potentially life threatening human disease in our era. Nevertheless, introduction of antibiotics (penicillin) and ? more recently ? the conjugate vaccine provoked major evolutionary changes in the structure of natural populations of this pathogen. The purpose of this research proposal is to combine the power of whole genome sequencing (WGS) and epidemiology to obtain insights into the mechanisms by which antibiotic resistant and non-vaccine type pneumococcal lineages emerged in the in vivo environment. The studies will have three foci of concentration. Project I. Three highly penicillin resistant pneumococcal (PRPn) clones: ST-1, ST-2 and ST-3, each with a unique sequence type (MLST) and capsular type have achieved pandemic spread and appear to remain stable over long times and distant geographic sites of isolation. Such genetic stability in a highly recombinogenic pathogen is unusual and it contrasts with the well documented diversity of penicillin susceptible pneumococci. The purpose of this project is to use whole genome sequencing (WGS) to better document and understand the nature and mechanisms of genetic stability in these three PenR clones. Project II. An outbreak investigation in an AIDS hospice identified members of the PenR clone ST-1 as causative agents of the disease. All but two of the 11 single patient isolates expressed capsular polysaccharide 23F typical of this clone. However, 2 isolates produced capsular type 3 which was associated with a tremendous (106 fold) increase in virulence measured in mouse IP models. The purpose of these studies is to use WGS ? in combination with the appropriate in vitro complementation experiments ? to identify genetic determinants of virulence produced ? in vivo ? in such a spontaneous ?experiment of nature?. Project III. Pneumococcal strains expressing the non-vaccine type (NVT) capsular polysaccharides, such as 11A, 6A or 19A have been identified as minority components of the nasopharyngeal flora of children attending Day Care Centers ? even before the introduction of the conjugate vaccine. WGS will be used to test if the emergence of these strains from minority to majority status in the nasopharynx and from colonizers to disease causing strains ? is accompanied by changes in genetic makeup

Public Health Relevance

Streptococcus pneumoniae (Sp) is a cause of many human diseases including ear infections, pneumonia, meningitis (infection of the tissue lining the brain), sepsis, and infectious arthritis, moreover it is the cause of over one million deaths per year world- wide. In this application we propose to study the genetics of several penicillin-resistant (penR) clonal lineages that have spread around the world and appear, surprisingly in the context of what we have observed with most other Sp strains, to have to have remained nearly immutable over several decades and across multiple continents. One possible reason for their genetic isolation is that their penR fundamentally alters their cell surface which could limit their interactions with other strains. Importantly two of the isolates of one of these clonal lineages display very different disease profiles and thus, since the number of genetic differences between them is small, we propose to use genetic engineering to learn which of these genes are responsible for the more severe disease. The introduction a few years ago of a vaccine against some types of Sp was successful in reducing the incidence of those types, unfortunately other nonvaccine types have arisen to take their place. We will also study the genetics of these replacement types to see if they possess most of the genes of the clonal lineages that have just hidden in new outer coats (what the vaccine is directed against) or whether these escape strains are truly new with respect to their entire genetics.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Clinical Research and Field Studies of Infectious Diseases Study Section (CRFS)
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Khambaty, Farukh M
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Allegheny-Singer Research Institute
United States
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