Natural Transformation Facilitates Transfer of Transposons, Integrons and Gene Cassettes between Bacterial Species

Sara Domingues,W Florian Fricke,Kaare Magne Nielsen,Klaus Harms,Gabriela J Da Silva,Pål J Johnsen,Michael S Gilmore

doi:10.1371/journal.ppat.1002837

Sara Domingues, W Florian Fricke + Show 5 more

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https://doi.org/10.1371/journal.ppat.1002837

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Abstract

We have investigated to what extent natural transformation acting on free DNA substrates can facilitate transfer of mobile elements including transposons, integrons and/or gene cassettes between bacterial species. Naturally transformable cells of Acinetobacter baylyi were exposed to DNA from integron-carrying strains of the genera Acinetobacter, Citrobacter, Enterobacter, Escherichia, Pseudomonas, and Salmonella to determine the nature and frequency of transfer. Exposure to the various DNA sources resulted in acquisition of antibiotic resistance traits as well as entire integrons and transposons, over a 24 h exposure period. DNA incorporation was not solely dependent on integrase functions or the genetic relatedness between species. DNA sequence analyses revealed that several mechanisms facilitated stable integration in the recipient genome depending on the nature of the donor DNA; homologous or heterologous recombination and various types of transposition (Tn21-like and IS26-like). Both donor strains and transformed isolates were extensively characterized by antimicrobial susceptibility testing, integron- and cassette-specific PCRs, DNA sequencing, pulsed field gel electrophoreses (PFGE), Southern blot hybridizations, and by re-transformation assays. Two transformant strains were also genome-sequenced. Our data demonstrate that natural transformation facilitates interspecies transfer of genetic elements, suggesting that the transient presence of DNA in the cytoplasm may be sufficient for genomic integration to occur. Our study provides a plausible explanation for why sequence-conserved transposons, IS elements and integrons can be found disseminated among bacterial species. Moreover, natural transformation of integron harboring populations of competent bacteria revealed that interspecies exchange of gene cassettes can be highly efficient, and independent on genetic relatedness between donor and recipient. In conclusion, natural transformation provides a much broader capacity for horizontal acquisitions of genetic elements and hence, resistance traits from divergent species than previously assumed.

Highlights

The acquisition and dissemination of antibiotic resistance in Gram-negative bacteria is frequently facilitated by integrons [1,2,3]
We demonstrate that antibiotic resistance determinants present in such genetic elements can spread by natural transformation between species of clinical interest
The integron-carrying bacteria were A. baumannii 064, A. baumannii 65FFC, P. aeruginosa SM, all clinical isolates, S. enterica serovar Rissen 486 and S. enterica serovar Typhimurium 490, both isolated from pork processed food, and C. freundii C16R385, E. cloacae C2R371, E. coli C10R379, and E. fergusonii AS041A2 isolated from food-producing and wild animals (Table 1)

Summary

Introduction

The acquisition and dissemination of antibiotic resistance in Gram-negative bacteria is frequently facilitated by integrons [1,2,3]. Class 1 integrons are the most widely disseminated type in commensals and pathogens of human and animal origins [13,14,15,16,17,18], and have been found in soil and in aquatic ecosystems [19,20,21,22,23] This class of integrons is characterized by two conserved regions, the 59 conserved segment (59-CS), which includes the integrase gene (intI1), the adjacent recombination site (attI1) and the promoter (Pc), and the 39 conserved segment (39CS), which contains the qacED1 gene (encoding an incomplete version of a quaternary ammonium compound resistance), the sulI (encoding resistance to sulfonamides) and the orf5 [2,24]

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