Structural analysis of atypical class 1 integrons in clinical Proteus isolates

Abstract

Objective To analyze the structures of atypical class 1 integrons in clinical Proteus isolates. Methods This study included 26 class 1 integron integrase gene-positive clinical Proteus isolates, from which the variable regions of class 1 integrons could not be amplified.Six isolates were chosen from them to amplify the flanking DNA segments of class 1 integron integrase gene using inverse PCR.The sequences of PCR products were analyzed with BLAST to identify the target homologous sequences as well as their accession numbers in GenBank.Primers for overlap PCR were designed according to the flanking sequences.Then the 26 clinical Proteus isolates were analyzed with overlap PCR and sequencing analysis. Results The variable regions of class 1 integrons in 25 out of the 26 clinical Proteus isolates were completely or partly identified by using inverse PCR, overlap PCR and sequencing analysis.A gene cassette array of estX-psp-aadA2-cmlA1-aadA1a-qacI-tnpA-sul3 was detected in 22 isolates.The variable regions of class 1 integrons in the other three isolates were identified to be estX-psp-aadA2-cmlA1, dfrA14 and IS26, respectively.All of the 25 isolates lacked the 3′ conserved segements in class 1 integron. Conclusion Inverse PCR can be used to analyze the structures of atypical class 1 integrons.Gene cassette psp and gene cassette arrays of estX-psp-aadA2-cmlA1-aadA1a-qacI-tnpA-sul3 and estX-psp-aadA2-cmlA1 in clinical Proteus isolates are reported for the first time. Key words: Integron; Gene cassette; Inverse PCR; Antimicrobial resistance; Proteus