title: Genetic antigen diversity and gene flux among meningitic and bacteraemia-associated pneumococci from Malawi
Creators: name: Kulohoma, Benard
Publisher: name: University of Liverpool Repository
Year: 2013

description: Streptococcus pneumoniae (pneumococcus) is among the commensal bacteria species that asymptomatically colonise the human nasopharynx. However, this species may occasionally invade the host’s sterile sites (lungs, blood, middle of the ear and cerebral spinal fluid) and cause severe life-threatening disease, such as pneumonia, meningitis, acute otitis media and bacteraemia (bloodstream infection). Invasive pneumococcal disease (IPD) is especially common among children under the age of five, the elderly (&gt;65 years) and among individuals with compromised immunity, such as asplenia and among individuals with immunosuppressive illness, particularly those infected with HIV. Each year, IPD accounts for one fifth of these deaths and more than 150 million episodes of pneumococcal pneumonia in children under five years, most of which occur in sub-Saharan Africa (SSA). Although the population genetics and evolutionary biology of pneumococci is well understood, it still remains unclear why some pneumococci strains are associated with meningitis more than others, and whether there are virulence factors that are associated with the tendency to cause meningitis. This thesis explores the differences in genetic diversity among meningitis and bacteraemia associated (blood sepsis) pneumococci to establish whether such differences exist among invasive pneumococcal isolates collected from Malawian patients. It also examines the differences in likelihood and direction of genetic flux (gene acquisition or loss), which mainly occurs by recombination, among meningitisassociated and bacteraemia-associated pneumococcal isolates. Furthermore, the prevalence of the pneumococcal pilus, which greatly enhances initial pneumococcal adhesion at the V nasopharynx, thereby providing a colonisation advantage; and has been identified as a highly immunogenic potential vaccine candidate was examined for the period prior to the 13-valent pneumococcal conjugate vaccine (PCV13) introduction into the childhood immunisation programme of Malawi, in order assess the impact of PCV13 introduction on pilus prevalence. Various innovative, robust and high-throughput bioinformatics techniques, some of which were newly developed, were used to interrogate the genome sequences of these invasive pneumococcal disease isolates. Here, by comparing the differences in the composition of genomic antigen diversity among isolates associated with bacteraemia and meningitis, I provide some evidence from human disease that meningitis causing pneumococci have a distinct “core genome”, which encodes for both known and previously undescribed proteins that are likely to be essential for meningeal invasion and survival. Furthermore, I present evidence suggesting that meningitisassociated pneumococci undergo less genetic flux and have a more conserved genome than those associated with bacteraemia. I also show for the first time in SSA that there is a low prevalence of invasive piliated pneumococci (16.43%), and that these piliated pneumococci are all covered by the PCV13. Interestingly, it was noted that most of the piliated pneumococci were resistant to cotrimoxazole. However, this antibiotic resistance can also be attributed to the widespread use of sulphadoxine pyrimethamine (Fansidar TM), an antimalarial drug that also has the same targets as cotrimoxazole (that is the dihydrofolate reductase and dihydropteroate synthase genes) that has resulted in drug resistance conferring mutations in Plasmodium falciparum, and more conclusive studies that include carriage isolate datasets are required.