Sequence analysis of class 1 integron’s integrase gene and the associated attI1 recombination site

QUIROGA MARÍA PAULA; NARDELLI MAXIMILIANO; RAMÍREZ MARÍA SOLEDAD; CENTRÓN DANIELA

Montevideo

Conferencia; First Latin America Conference of the ISCB; 2010

International Society for Computational Biology (ISCB)

Background Class 1 integrons are genetic elements that contain the components of a site-specific recombination system and they are usually associated to multidrug resistance in clinical isolates. They are composed by the intI1 gene, which encodes the IntI1 recombinase, the attI1 recombination site, and the common promoter region Pc that allows the expression of gene cassettes. Gene cassettes consist in an open reading frame and a recombination site designated as attC, which is recognized by the integron integrase to excise the gene cassette from the integron to be inserted into an attI1 site or into another attC [1, 2, 3, 4]. In our laboratory, we found atypical arrays within the variable region of class 1 and 2 integrons, where the expected attC site was replaced by a deletion of the attI1 or the attI2 recombination sites, yielding unusual gene cassettes [5, 6, 7]. The aim of this study was to evaluate the variability of the intI1 gene and the attI1 site from nosocomial strains and to investigate the dispersion of the attI1 in the bacterial genomes. Materials and methods We used the Blastn algorithm of the Basic Local Alignment Search Tool (BLAST) program from the PubMed website [http://www.ncbi.nlm.nih.gov/pubmed/]. When required, we used the BLAST database of microbes, optimizing the search including only the completed genomes and adjusting the algorithm parameters. Results We found that within the 212 nosocomial samples presenting both the complete intI1 gene and attI1 site in the GenBank database, there are 16 alleles of the intI1 gene, corresponding to point mutations. The attI1 site also showed point mutations but in few cases and not always associated to the same intI1 allele. From the search of the attI1 site in the genomes, we found that in its complete version was always associated to the intI1 gene. We also found deletions, comprising the 13 bp portion of this site that was previously found associated to some unusual gene cassettes and in this study was identified in 115 out of the 696 genomes analyzed. Conclusions While there are a variety of intI1 alleles among the nosocomial samples, the attI1 shows a remarkable stability showing that this association is being selected and is well established. The dispersion in the bacterial genomes from distant bacterial groups, of the attI1 deletions (comprising the portion that was found associated to some unusual gene cassettes), showed that the IntI1 integrase has numerous opportunities in the nature to recombine. Acknowledgements MPQ and MSR are recipients of C.O.N.I.C.E.T. fellowships. MN is receipt of an AGENCIA fellowship. DC is a member of the carrera del Investigador Científico de C.O.N.I.C.E.T. This work was supported by the PICT0690. References 1. Stokes H.W., O´Gorman D.B., Recchia G.D., Parsekhian M., Hall R.M. (1997) Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol Microbiol. 26:731-45. 2. Stokes H.W., Hall R.M. (1989). A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol. 3:1669-83. 3. Hall, R. M., Brookes, D. E., Stokes, H.W. (1991). Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol Microbiol 5, 1941-1959. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 3. Hall, R. M., Brookes, D. E., Stokes, H.W. (1991). Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol Microbiol 5, 1941-1959. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 2. Stokes H.W., Hall R.M. (1989). A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol. 3:1669-83. 3. Hall, R. M., Brookes, D. E., Stokes, H.W. (1991). Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol Microbiol 5, 1941-1959. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 3. Hall, R. M., Brookes, D. E., Stokes, H.W. (1991). Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point. Mol Microbiol 5, 1941-1959. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print]. 4. Collis C.M., Hall R.M. (1992) Gene cassettes from the insert region of integrons are excised as covalently closed circles. Mol Microbiol. 6:2875-85. 5. Centrón D., Roy P.H. (2002). Presence of a group II intron in a multiresistant Serratia marcescens strain that harbors three integrons and a novel gene fusion. Antimicrob Agents Chemother. 46:1402-9. 6. Ramírez M.S., Quiroga C., Centrón D. (2005). Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 49:5179-81. 7. Ramírez M.S., Piñeiro S.; Argentinian Integron Study Group, Centrón D. (2009). Novel insights about class 2 integrons from experimental and genomic epidemiology. Antimicrob Agents Chemother. Nov 16. [Epub ahead of print].