Antibiotic resistance in Escherichia coli and Klebsiella pneumoniae: mobile resistance genes and outer membrane porins

Abstract

β-lactam antibiotics are among the most frequently prescribed antimicrobial agents for the treatment of severe infections and the emergence of β-lactam resistance in E. coli and K. pneumoniae (recently described by WHO as critical antibiotic resistant priority pathogens) has become a serious problem world-wide. In this thesis, the β-lactamase genes conferring resistance to third generation cephalosporin in E. coli and K. pneumoniae at a teaching hospital in Ghana were explored (Chapter 2). blaCTX-M-15 was identified as the predominant ESBL gene (n=62/63) in E. coli and K. pneumoniae and this is consistent with global data. In these isolates, blaCTX-M-15 was associated with ISEcp1 and orf477Δ and majority of them also carried additional resistance genes (blaTEM, aac(3)-II, aacA4cr and/or blaOXA-30) conferring resistance to other unrelated antibiotics (Chapter 2). In Chapter 3 of this thesis, the minimal inhibitory concentration (MIC) distributions of selected third-generation cephalosporin and carbapenem antibiotics against E. coli and K. pneumoniae isolates carrying commonly acquired resistance genes including blaCTX-M-15 was explored, to explore variation of the normal distribution of the MIC. It was observed that β-lactam MICs associated with acquired resistance genes are normally distributed and any variation in this normal distribution in K. pneumoniae is predictably linked to changes in the major porin OmpK36. Most clinical isolates of K. pneumoniae lack OmpK35 and therefore cannot compensate for any OmpK36 deficiency, as they normally might. Fitness costs and antimicrobial resistance associated with different outer membrane porin mutations were explored (Chapter 4). The OmpK35 deficient mutant was competitive with the parental strain in high osmolarity nutritious media, where OmpK35 is not normally expressed, which may explain why most ESBL producing K. pneumoniae isolates lack this porin. Among the mutations in the OmpK36 (OmpK36 deletion versus OmpK36134_135dupGD [GD duplication]), the GD duplication had less impact on fitness although both had comparable resistance phenotypes. This suggests that the GD duplication commonly seen in clinical isolate of K. pneumoniae could allow a resistant population to stably co-exist with competing antibiotic-susceptible populations in the absence of antibiotic selection pressure.