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Class 1 integrons lacking qacEΔ1 and sul1 genes in Escherichia coli isolates of food, animal and human origins

Sáenz, Y., Vinué, L., Ruiz, E., Somalo, S., Martínez, S., Rojo-Bezares, B., Zarazaga, M., Torres, C.
Veterinary microbiology 2010 v.144 no.3-4 pp. 493-497
Escherichia coli, animal pathogenic bacteria, food pathogens, bacterial proteins, strain differences, nucleotide sequences, amino acid sequences, polymerase chain reaction, genes, sequence analysis, genetic techniques and protocols, plasmids, microbial genetics
Objectives: To study the frequency and diversity of class 1 integrons lacking the 3′-conserved segment (CS) in intI1-positive Escherichia coli isolates of different origins. Methods: The presence of intI1 was previously detected in 84 E. coli isolates of food (21 isolates), animal (32) and healthy-human volunteer (31) origins. The qacEΔ1-sul1 genes were analyzed by PCR and those isolates that lacked these genes were included in this work. The genetic structure of class 1 integrons was determined, using the PCR and sequencing primer-walking strategy. Isolates and plasmids were typed. Results: Class 1 integrons lacking the 3′-CS were found in 13 of the 84 intI1-positive E. coli isolates (15.5%) of food, animal, and human origins. All 13 isolates showed unrelated patterns by REP-PCR. The following gene cassette arrangements were identified inside the class 1 integrons of these 13 strains: dfrA1; dfrA5; dfrA12-orfF-aadA2-cmlA1-aadA1-qacH-IS440-sul3; dfrA12-orfF-aadA2-cmlA1-aadA1-IS440-sul3; estX-psp-aadA2-cmlA1-aadA1-qacH-IS440-sul3; and a new arrangement estX-psp-aadA2-cmlA1Δ-IS1294-ΔcmlA1-aadA1-qacH-IS440-sul3 that contain the IS1294 into the cmlA1 gene (included in GenBank, number EU704128). Complete or truncated mef(B) gene was detected upstream of sul3 gene in this type of integrons. Plasmids were identified in four of the studied strains by PCR-replicon-typing, detecting different combinations of IncY, I1, FIC, FII, FIB plasmids. Non-classic integrons were located into plasmids of 100-150kb in four studied strains. Conclusions: Occurrence and diversity of class 1 integrons lacking 3′-CS among the studied intI1-positive E. coli isolates of different origins were relatively high. The sul3 gene was detected in most of class 1 integrons lacking 3′-CS.