Limits...
CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping.

Karah N, Samuelsen Ø, Zarrilli R, Sahl JW, Wai SN, Uhlin BE - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden; Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.

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.

Show MeSH

Related in: MedlinePlus

Graphic representation of the arrays of spacers in the CRISPR-cas subtype I-Fb locus of Acinetobacter baumannii.The figure demonstrated the assortment of 74 A. baumannii isolates into 40 CRISPR sequence types (CST) based on the spacer content of their CRISPR arrays. Spacers were represented by red rectangles. Each unique spacer was assigned a number (1–876). Spacers were sequentially aligned in order to facilitate comparison among the CSTs.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4338279&req=5

pone.0118205.g004: Graphic representation of the arrays of spacers in the CRISPR-cas subtype I-Fb locus of Acinetobacter baumannii.The figure demonstrated the assortment of 74 A. baumannii isolates into 40 CRISPR sequence types (CST) based on the spacer content of their CRISPR arrays. Spacers were represented by red rectangles. Each unique spacer was assigned a number (1–876). Spacers were sequentially aligned in order to facilitate comparison among the CSTs.

Mentions: Different assortments of the spacers divided the isolates into 40 CSTs (Fig. 4 and S3 Table). Isolates from CC1 (n = 36) belonged to 13 CSTs, with some CSTs being different from each other only by a duplication or deletion of 1 spacer. CST1 included 18 isolates recovered between 2004 and 2013 from USA (n = 11), Iraq (n = 3), Canada (n = 2), Germany (n = 1), and Sweden (n = 1). Tracking the epidemiological data showed that eight of the isolates were obtained during the military operations in Iraq and Afghanistan [33, 34]. CST1 could be an Iraq-endemic sub-clone of CC1 that was able to spread to USA, Canada, and Europe. A previous study comparing the DNA profiles of A. baumannii isolates from USA and the United Kingdom that were associated with casualties returning from the Iraq conflict has also demonstrated the import of at least one strain responsible for outbreaks of infections in the two countries [35]. Adaptation of CST1 to the pool of phages and plasmids present in a particular geographical site resulted in the acquisition of specific spacers which might be used as a genomic signature of this sub-clone and a biological marker of this particular geographic ecosystem [10, 36]. On the other hand, CST2 included 3 isolates obtained from Czech Republic in 1994 and USA in 2009 and 2010. However, the Czech isolate was not reported to be epidemiologically linked with the two American isolates [37].


CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping.

Karah N, Samuelsen Ø, Zarrilli R, Sahl JW, Wai SN, Uhlin BE - PLoS ONE (2015)

Graphic representation of the arrays of spacers in the CRISPR-cas subtype I-Fb locus of Acinetobacter baumannii.The figure demonstrated the assortment of 74 A. baumannii isolates into 40 CRISPR sequence types (CST) based on the spacer content of their CRISPR arrays. Spacers were represented by red rectangles. Each unique spacer was assigned a number (1–876). Spacers were sequentially aligned in order to facilitate comparison among the CSTs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4338279&req=5

pone.0118205.g004: Graphic representation of the arrays of spacers in the CRISPR-cas subtype I-Fb locus of Acinetobacter baumannii.The figure demonstrated the assortment of 74 A. baumannii isolates into 40 CRISPR sequence types (CST) based on the spacer content of their CRISPR arrays. Spacers were represented by red rectangles. Each unique spacer was assigned a number (1–876). Spacers were sequentially aligned in order to facilitate comparison among the CSTs.
Mentions: Different assortments of the spacers divided the isolates into 40 CSTs (Fig. 4 and S3 Table). Isolates from CC1 (n = 36) belonged to 13 CSTs, with some CSTs being different from each other only by a duplication or deletion of 1 spacer. CST1 included 18 isolates recovered between 2004 and 2013 from USA (n = 11), Iraq (n = 3), Canada (n = 2), Germany (n = 1), and Sweden (n = 1). Tracking the epidemiological data showed that eight of the isolates were obtained during the military operations in Iraq and Afghanistan [33, 34]. CST1 could be an Iraq-endemic sub-clone of CC1 that was able to spread to USA, Canada, and Europe. A previous study comparing the DNA profiles of A. baumannii isolates from USA and the United Kingdom that were associated with casualties returning from the Iraq conflict has also demonstrated the import of at least one strain responsible for outbreaks of infections in the two countries [35]. Adaptation of CST1 to the pool of phages and plasmids present in a particular geographical site resulted in the acquisition of specific spacers which might be used as a genomic signature of this sub-clone and a biological marker of this particular geographic ecosystem [10, 36]. On the other hand, CST2 included 3 isolates obtained from Czech Republic in 1994 and USA in 2009 and 2010. However, the Czech isolate was not reported to be epidemiologically linked with the two American isolates [37].

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden; Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.

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.

Show MeSH
Related in: MedlinePlus