Genotyping and high flux sequencing of the bacterial pathogenic elements - integrons

Regarded as a common genetic element responsible for horizontal gene transfer and wide spread of antimicrobial resistance among a large variety of bacteria, integrons are commonly distributed and considered as a determinant in the acquisition and evolution of virulence and antibiotic resistance. To date, the surveillances of integrons have been widely conducted in clinic, community even husbandry. For exact and accurate integron screening, as well as resistant cassettes, reliable monitoring methods is need. Current methods applied on integron screening are mainly conducted by the screening of integrases, followed by the detection of various gene cassettes inserted into integrons. PCR and PCR-related methods (such as RFLP) are mainly employed under such circumstances. Matured LAMP and Sequencing technology have lowered cost and dramatically increased throughput in integron screening and possessed the advantages in similarity analysis of mutated resistant cassettes. This review focused on the classification and characterization of integrons, antimicrobial resistance of integron and genotyping methods for integrons. In methodology, PCR, LAMP and Sequencing technology were mainly introduced for the screening of various classes' integrons and the detection of resistant gene cassettes. Staphylococcus, Pseudomonas and Enterococcus were selected as typical integron-positive clinical and environmental pathogens screened with three methods mentioned above. With the surveillance of the occurrence of integron and resistance gene cassettes conducted in South China, the review also summarized the occurrence, pathogenicity and virulence mediated by integrons.