CRISPR-cas Subtype I-Fb in Acinetobacter baumannii: Evolution and Utilization for Strain Subtyping

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.

Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

“…Conversely, there were 319 centroids that were found only in the genomes of carbapenem-susceptible A. baumannii isolates compared to carbapenem-resistant A. baumannii isolates (see Table S5b). These centroids include genes involved in type IV secretion systems and CRISPR systems (59), as well as several transcriptional regulatory genes. In addition, 141 (44%) hypothetical genes, one transcriptional regulator, and many phage-related genes are included in this list.…”

“…For example, the identification of the CRISPR genes in the susceptible isolates suggests the loss of these genes was an important step in acquiring genetic elements necessary for carbapenem resistance. CRISPR-cas systems provide bacteria a type of immunity against foreign genetic elements such as plasmids and bacteriophage; therefore, the loss of these genes may allow genetic elements to be acquired more readily (59).…”

Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1

“…Also, two CRISPR-Cas systems have been identified in some strains of A. baumannii (Di Nocera et al, 2011;Hauck et al, 2012). The AYE strain, whose genome is taken in many studies as the basis for GC1 studies (Touchon et al, 2014;Karah et al, 2015), and other A. baumannii clones were identified to harbor the subtype I-Fb, indicating potential interstrain horizontal transfer of this CRISPR-Cas system (Di Nocera et al, 2011;Karah et al, 2015). Based on distinct assortment of spacers harbored by each strain, a CRISPR-based sequence type (Schouls et al, 2003) identified a subclone of A. baumannii GC1 that it is likely it has been originated in Iraq and spread later to the United States and Europe (Karah et al, 2015).…”

Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining

“…Much of this work has focused on CRISPR-Cas9, but there are a large diversity of CRISPR types in bacterial genomes that are less well-characterized (67). The type I-Fa CRISPR-Cas system of A. baylyi is analogous to the type I-Fb CRISPR/Cas system of A. baumanii, except the cas1 gene appears last in the Cas operon (58,60). A. baylyi ADP1 contains three CRISPR arrays: one with 91 spacers adjacent to the Cas operon and two others with 21 and 6 spacers, respectively, located elsewhere in the genome.…”

“…The protospacer adjacent motif (PAM) for type I CRISPR-Cas systems has been reported to be a downstream GG dinucleotide (59), including for the subtype I-F system of Acinetobacter baumanii (60). This is equivalent to a CC located 5' of the spacer sequence on the strand that it matches in the target site DNA sequence.…”