| Summary: | During pneumococcal conjugate vaccine (PCV) implementation, studies have shown a reduction in the carriage of serotypes included within the vaccine and differing reports of the indirect effects this reduction has had on other species of the nasopharynx. This study contributes to and expands upon this area of work, focusing on PCV13 implementation, which occurred four years after the introduction of PCV7, and its effects on pneumococcal carriage and other species carried in the upper respiratory tract. Between 2006/07 and 2012/13, PCV13 vaccine serotypes reduced in carriage with a corresponding increase in PCV13 non-vaccine serotypes, and an overall consistent rate of pneumococcal carriage. No change in carriage rate was detected with any of the bacterial species detected at the species level. Carriage of H. influenzae was determined to be predominately non-typeable H. influenzae (NTHi) and demonstrated clonal diversity when typed using MLST. Antibiotic resistance genes were detected in around 10% of pneumococcal and H. influenzae isolates, with ermB and blaTEM genes being most prevalent for each species respectively. Virulence factor profiling resulted in matching gene profiles being ST dependent for S. pneumoniae and H. influenzae. Pneumococcal serotype 15A/ST63 has emerged as being a prevalent strain post-PCV13 with the propensity to contribute to both antibiotic resistance and virulence. This thesis provides information relevant to vaccine policy based on carriage data and expands upon the neglected area of using next generation sequencing and molecular characterisation of carriage isolates.
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