Genetic diversity of class 2 integrons among Escherichia coli isolates from food, animal and human sources. Detection of a novel arrangement in ST57 E. coli clones from Mexico

ALONSO, CA; CORTÉS-CORTÉS G; MAAMAR E; MASSÓ MG; ROCHA-GRACIA RC; TORRES C; CENTRÓN D; QUIROGA MARÍA PAULA

Viena

Congreso; 27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID); 2017

Background: Class 1 and 2 integrons are associated with multidrug-resistancedue to their capability to mobilize and express multiple gene cassettes (GC).Class 2 integrons usually carry in the variable region (VR) the dfrA1-sat2-aadA1 array, followedby a putativeGC called orfX (ybeA, unknownfunction) and three additional genes (ybfA,ybfB, ybgA), embedded in the Tn7transposition module (TnsEDCBA). The intI2is frequently interrupted by a premature stop codon, rendering a non-functionalintegrase. Here, we characterized the genetic location and organization ofclass 2 integrons carried by E. coliisolates from Spain, Tunisia and Mexico.Material/methods: Class 2 integrons of 34 E. coli isolates from different origins (15 poultry meat, 6 chickens,4 wild animals, 5 pets, 5 humans) were fully characterized. E. coli from wild animals (gull, stork,genet, deer), pets (dogs, turtles) and chickens were recovered from faeces.Human-source strains were isolated from hemocultures (n=2) and healthy donors?faeces (n=3). PCR cartography was performed with different primer combinationsto determine the VR and the presence of tnsgenes. In integrons lacking ybeA-ybfA-ybfB-ybgA and transposition module, the 3?ends of classic and unusual class 1 integrons were screened. Newly designedprimers were used to determine novel arrangements. Integron?s location at Tn7 transposon and its chromosomal insertion was confirmed by PCR. The intI2 gene was sequenced in integronsshowing structures different to the classical one. Clonal relatedness wasdetermined by MLST and/or OD-PCR.Results: Diversity of the VR among the studied integronsincluded: a) The classical GC arrangement (dfrA1-sat2-aadA1-ybeA-ybfA-ybfB-ybgA)(n=27), b) Excisions/substitutions of common GCs (sat2-aadA1-ybeA-ybfA-ybfB-ybgA,n=1; estX-sat2-aadA1-ybeA-ybfA-ybfB-ybgA,n=2), c) IS-element insertions (IS10-dfrA1-sat2-∆aadA1-ybeA-ybfA-ybfB-ybgA, n=1; dfrA1-sat2-aadA1-ybeA-ISSen4-ybfA-ybfB-ybgA, n=2), d) Absence of the ybeA-ybfA-ybfB-ybgAmodule (dfrA1-sat2-aadA1). Another feature of this last integron,detected in turtle?s faeces, was the lack of tns genes. Although novel rearrangements and the occurrence ofhybrid class2/class1 integrons were tested, none of the PCRs were successful.Among integrons harboring the classical arrangement, mosaic structures of the tns module were detected. The integroncontaining an ISSen4-element (IS3 family), frequently identified next toblaNDM-1/blaKPC genes, has been firstdescribed here. It was found in two E.coli from Mexico, assigned to ST57 and showing indistinguishableOD-PCR-pattern, but from distinct sources (dog/meat). Ninety-one percent of theintegrons were embedded in Tn7transposons chromosomally located adjacent to glmS gene.Conclusions:Genetic background of class 2 integrons is highlyconserved among E. coli fromdifferent ecosystems, being novel arrangements mainly driven by the insertionof IS-elements or the activity of a functional integrase. We described a novelclass 2 integron carrying an ISSen4 intwo ST57 E. coli from Mexico. Reportedstructures evidence how class 2 integrons have evolved by the activity ofintegron integrases and the invasion of a variety of insertion elements.