Origin, adaptation and biogeography of the inti1 gene

ÁLVAREZ VE ; CHAMOSA L; NARDELLI M; POWER P; QUIROGA MP; CENTRÓN D

Córdoba

Congreso; XI Congreso Argentino de Microbiología General (SAMIGE 2015; 2015

Universidad Nacional de Córdoba

Class 1 integrons are the most successful mechanism associated to Lateral Antimicrobial Resistance Genetic Transfer amongGram-Negative clinical isolates. Recent studies showed they can be found in different habitats; however, a detailed study hasnot been conducted yet. The aim of this work was to identify the origin and the variability of circulating alleles of intI1 type genefrom class 1 integrons. IntI1 gene sequences from GenBank running a BLASTn query using AF313471 as reference (April 2015)were analyzed for its origin according to the degree of human impact, the continent where they had been firstly isolated, thepresence of Tn402 platform and the type of site attI1associated. AWK and Bioperl scripts, ClustalW algorithm in MEGA v6.0,phylogenetic trees using the Neighbor Joining and Maximum Likelihood algorithms and Jalview v2.8.2 were used in order tostudy circulating alleles. Seventy one alleles of intI1 belonging to the environment (n = 36), clinic (n = 29) and 6 shared by bothhabitats were detected. Within the latter category, 4 alleles had a frequency higher than 20% and they were spread over the 4continents evaluated. Furthermore, 81.7% were unique alleles. Only 1.72% of the intI1 genes (11/640) were inserted into thecomplete Tn402 transposon. We detected several variants of the attI1 site linked to intI1. Although we identified 116 attI1variants, one prevalent was detected in 83.1% of the intI1 alleles, while the second in frequency was detected in 9.86% ofthem. Mutations over the entire intI1 gene were identified, some with a low rate of preservation of the physical and chemicalproperties of amino acids. Moreover, other mutations which led to the generation of pseudogenes were seen. RHRY conservedtetrad characteristic of tyrosine integrase recombinases was analyzed. This tetrad is specifically related to the orientation ofDNA in the proper conformation needed for the site-specific recombination. We confirmed that even at very low frequencies, theresidue H was the only mutated in the tetrad, replaced in one allele by an amino acid that has the same physicochemicalproperties. These studies evidenced an active flow of intI1 alleles, both within the clinic and the environment. Although a smallnumber of alleles flowed in both habitats, they corresponded to the 90.93% of the strains, suggesting the generalist intrinsicnature of this gene, which is functional in different niches. The hypothesis of this two-way flow was also supported by theidentification of unique clinical intI1 alleles which have emerged recently, whose class 1 integron 3? ends are different from theknown 3?-CS. These results suggest a scenario in which the first intI1 alleles that started to circulate among clinical strains, havedisseminated all around the world, with sporadic and continue captures of novel alleles from the open environment.