Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are polymorphic elements found in the genome of some or all strains of particular bacterial species, providing them with a system of acquired immunity against invading bacteriophages and plasmids. Two CRISPR-Cas systems have been identified in Acinetobacter baumannii, an opportunistic pathogen with a remarkable capacity for clonal dissemination. In this study, we investigated the mode of evolution and diversity of spacers of the CRISPR-cas subtype I-Fb locus in a global collection of 76 isolates of A. baumannii obtained from 14 countries and 4 continents. The locus has basically evolved from a common ancestor following two main lineages and several pathways of vertical descent. However, this vertical passage has been interrupted by occasional events of horizontal transfer of the whole locus between distinct isolates. The isolates were assigned into 40 CRISPR-based sequence types (CST). CST1 and CST23-24 comprised 18 and 9 isolates, representing two main sub-clones of international clones CC1 and CC25, respectively. Epidemiological data showed that some of the CST1 isolates were acquired or imported from Iraq, where it has probably been endemic for more than one decade and occasionally been able to spread to USA, Canada, and Europe. CST23-24 has shown a remarkable ability to cause national outbreaks of infections in Sweden, Argentina, UAE, and USA. The three isolates of CST19 were independently imported from Thailand to Sweden and Norway, raising a concern about the prevalence of CST19 in Thailand. Our study highlights the dynamic nature of the CRISPR-cas subtype I-Fb locus in A. baumannii, and demonstrates the possibility of using a CRISPR-based approach for subtyping a significant part of the global population of A. baumannii.
Highlights
Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA elements present in the genome of 1176 out of 2612 fully sequenced bacterial strains
The aim of this study was to investigate the evolutionary history of CRISPR-cas subtype I-Fb in A. baumannii and to determine the genetic relatedness among a collection of CRISPR-positive clinical isolates of A. baumannii, based on comparative sequence analysis of the arrays of spacers located in their CRISPR-cas subtype I-Fb locus
The locus enclosed an array of spacers, where each spacer was flanked by two direct repeat (DR)
Summary
Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA elements present in the genome of 1176 out of 2612 fully sequenced bacterial strains (http://crispr.u-psud.fr/ crispr/, last accessed December 2014). These elements together with neighboring genes, called cas for “CRISPR-associated”, provide bacteria with an adaptive immunity system against invading genetic elements, such as bacteriophages and plasmids [1]. Upon the entry of an invading element, the Cas machinery takes up a short sequence(s), a proto-spacer, from the invasive DNA and integrates it into the CRISPR array, where the adjacent direct repeat (DR) is duplicated and the integrated sequence becomes a new spacer. PAMs, representing the recognition sites for the CRISPR-Cas machinery, play an important role in the adaptation and interference steps [3]
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