Genomic Characterisation of Extra-intestinal Pathogenic Escherichia coli from Human Infection

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Tracking resistance genes based on specific structural features of class 1 integrons is an integral part of clinical epidemiology. A class 1 integron is a gene capture and expression unit, most frequently found in Gram-negative bacteria. They are known to be one of the greatest contributors to the spread of multi-drug resistance genes within clinical isolates. Recent studies indicate that certain insertion elements target specific regions of class 1 integrons creating unique structures. Consequently, the resistance pool in such integrons goes unnoticed in standard molecular screening methodologies, although they are equally efficient in expressing and disseminating resistance genes. Examples of such class 1 integrons with atypical structures, now realised to have widely disseminated within human and animal 𝘌. 𝘤𝘰𝘭𝘪 populations worldwide, were generated by the insertion of a genetic element known as IS26. This project aimed to determine the presence of such structures, as well as characterise the diverse complex resistance loci (CRL) and virulence cargo of extraintestinal pathogenic 𝘌. 𝘤𝘰𝘭𝘪 samples in a specific Sydney hospital. This was achieved by identifying the virulence-associated and antimicrobial resistance gene pool harboured by these strains with a particular focus on insertion or deleterious molecular events, discerning the locations of CRL within genome or plasmid where possible and observing trends within clonal groups. Targeted PCR, Sanger sequencing and next generation short and long read genome sequencing techniques in conjunction with bioinformatic analyses were used to characterise clinical 𝘌. 𝘤𝘰𝘭𝘪 samples from Sydney Adventist Hospital isolated between 2009 and 2011. Our data suggests that antibiotic resistance is readily transferring between host populations via lateral gene transfer of mobile elements in Sydney through the observation of unique molecular signatures. Clonal groups were identified in the cohort which share virulence and antimicrobial resistance traits, in some cases at seemingly differing stages of evolution. Large scale studies such as this provide insight to the mechanisms and forces driving the dissemination of antimicrobial resistance.
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