title: Roadmap to resistance: antimicrobial resistance in Malawian pneumococci
Creators: name: Cornick, Jen
Publisher: name: University of Liverpool Repository
Year: 2013

description: Multi-drug resistant (MDR) Streptococcus pneumoniae are a major public health concern worldwide. In Malawi a resource poor country, even the simplest antimicrobials remain a precious commodity. Given the limited number of antimicrobials available for the management of MDR invasive pneumococcal disease (IPD) measures need to be implemented to limit the spread of resistance. In order to design such measures it is essential that we gain a better understanding of the evolution of antimicrobial resistance in this setting. The purpose of this thesis was to assess the molecular basis and mode of dissemination of antimicrobial resistance in S. pneumoniae with the aim of identifying a biomarker of antimicrobial resistance that could be used to design a diagnostic PCR to assist epidemiological surveillance of antimicrobial resistance and inform treatment policy. Malawi introduced the 13-valent pneumococcal conjugate vaccine (PCV13) in 2011. To provide baseline data to assess the impact of PCV13 all invasive pneumococci isolated from children admitted to Queen Elizabeth Central Hospital, Malawi 2004-2006 were serotyped and subjected to antimicrobial susceptibility testing. The data suggested PCV13 will not provide protection against 61% of penicillin resistant pneumococci and if serotype replacement occurs following the introduction of PCV13, the incidence of penicillin resistant IPD could therefore increase Over 130 resistant and susceptible pneumococcal isolates from carriage and invasive disease were subjected to whole genome sequencing. The employment of an in vitro and in silco analytical approach established that S. pneumoniae employs a diverse array of antimicrobial resistance mechanisms, the dissemination of which is likely to be driven by high antimicrobial consumption. A relatively high incidence of antimicrobial resistant was observed in serotype 1 pneumococci, the most common cause of IPD in Malawi. This serotype is not usually associated with resistance in other geographic locations, the short duration of serotype 1 carriage is assumed to limit the chance it has to acquire resistance mechanisms via recombination. Interestingly the resistance mechanisms employed by serotype 1 had been acquired through multiple recombination events. Recombination was evidenced to contribute to &gt;90% of the variation in the serotype 1 genomes. To allow the identification of resistance biomarkers free from any preconceptions about which genes are involved in resistance, multiple antimicrobial resistant lineages were generated in vitro. Isolates were sequenced at several time points as resistance developed. Comparison of the resistant isolates to the wild type isolates identified single nucleotide polymorphisms in 46 genes, 40 of these genes have not previously been implicated in antimicrobial resistance. The role of these genes in resistance warrants further investigation. The analysis suggests that rather than a single biomarker future research needs to identify multiple biomarkers; the dynamic nature of this organism means that it can adopt one of many routes to antimicrobial resistance.