During recent decades, the emergence of multidrug-resistant bacteria has become a major concern to public healthcare settings worldwide. Infections caused by drug-resistant bacteria, limiting the available treatment options with a high rate of mortality, morbidity and substantial economic burden. Indeed, drug resistance phenomena occur due to the normal evolutionary process of bacteria, but it accelerates when bacteria gets any external selective pressure such as misuse or overuse of antibiotics. However, in the last decades the problem of antimicrobial-resistance has been increasing due to the growing incidence of infections caused by antibiotic-resistant gram-negative bacteria. Particularly, the prevalence of extended-spectrum beta-lactamase (ESBLs) and carbapenemase-producing E. coli in clinical settings is increasing at an alarming rate. These ESBLs producers are resistant to penicillin, cephalosporin, and monobactam antibiotics and are often associated with urinary tract infections and life-threatening sepsis in immunocompromised hosts.Overall, this thesis demonstrates the genomic characterization and diversity of antimicrobial resistant ESBL-E. coli that were isolated during two nationwide antimicrobial surveillance projects in between 2009 and 2016. Considering the advantages of NGS over the conventional sub genomic typing methods, we used whole genome sequencing to monitor the emergence and spread of antimicrobial resistance. To the best of our knowledge, this is the first study that considered the whole-genome sequence of ESBL-E. coli from humans, animal, environment, and food.
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