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Background  The connection structure of class 1 integron and insertion sequence common region 1 (IS CR1 ) is called “complex class 1 integrons” or “complex  sul1 -type integrons”, which is also known to be associated with many resistance genes. This structure is a powerful gene-capturing tool kit that can mobilize antibiotic resistance genes. In order to look for and study the structure among clinical multidrug-resistant (MDR) Gram-negative isolates, 63 isolates simultaneously harbored class 1 integron and IS CR1 -linked resistance genes were isolated from 2309 clinical non-redundant MDR Gram-negative isolates in Nanfang Hospital in 2008–2013. The connecting regions between the class 1 integrons and IS CR1  were examined using PCR and DNA sequencing to determine the structures in these isolates.    Result  The two elements (the variable regions of the class 1 integron structures and the IS CR1 -linked resistance genes) are connected in series among 63 isolates according to long-extension PCR and DNA sequencing. According to the kinds and permutations of resistance genes in the structure, 12 distinct types were identified, including 8 types that have never been described in any species. Several types of these structures are similar with the structures of other reports, but not entirely same.    Conclusion  This study is the first to determine the structure simultaneously harboring class 1 integron and IS CR1- linked resistance genes by detecting the region connecting class 1 integrons and IS CR1  in a large number of MDR bacteria. These structures carrying various resistance genes were closely associated with multidrug resistance bacteria in Southern China.

New structures simultaneously harboring class 1 integron and ISCR1-linked resistance genes in multidrug-resistant Gram-negative bacteria