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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.

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Genetic structure of the CRISPR-cas subtype I-Fb locus in Acinetobacter baumannii.A) The CRISPR-cas subtype I-Fb locus in A. baumannii strain AYE (GenBank accession number: CU459141, located at position 1,057,691 to 1,069,768). The locus consisted of two CRISPR–associated genes (cas1 and cas3/cas2), four Cas system-associated genes (csy1, csy2, csy3, and csy4), and an array of spacers. The map was created using Artemis (http://www.sanger.ac.uk/resources/software/artemis/). B) Nucleotide sequence of the array of spacers in A. baumannii strain AYE. The array included 59 spacers surrounded by 60 direct repeats (marked in green). Some repeats, mainly at the trailer end of the array, included degenerated nucleotides (marked in yellow). C) Comparative analysis of the genetic surroundings. The comparison was performed between the locus-positive strain AYE which belonged to sequence type (ST1) and the locus-negative strains TYTH-1, AB4857, and OIFC099 which belonged to ST2, ST3, and ST32, respectively. Homologous sequences shared by all the isolates were indicated by gray zones.
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pone.0118205.g001: Genetic structure of the CRISPR-cas subtype I-Fb locus in Acinetobacter baumannii.A) The CRISPR-cas subtype I-Fb locus in A. baumannii strain AYE (GenBank accession number: CU459141, located at position 1,057,691 to 1,069,768). The locus consisted of two CRISPR–associated genes (cas1 and cas3/cas2), four Cas system-associated genes (csy1, csy2, csy3, and csy4), and an array of spacers. The map was created using Artemis (http://www.sanger.ac.uk/resources/software/artemis/). B) Nucleotide sequence of the array of spacers in A. baumannii strain AYE. The array included 59 spacers surrounded by 60 direct repeats (marked in green). Some repeats, mainly at the trailer end of the array, included degenerated nucleotides (marked in yellow). C) Comparative analysis of the genetic surroundings. The comparison was performed between the locus-positive strain AYE which belonged to sequence type (ST1) and the locus-negative strains TYTH-1, AB4857, and OIFC099 which belonged to ST2, ST3, and ST32, respectively. Homologous sequences shared by all the isolates were indicated by gray zones.

Mentions: The CRISPR-cas subtype I-Fb locus, located at position 1,057,691 to 1,069,768 of the genome of A. baumannii strain AYE (GenBank accession number: CU459141), consisted of six genes consecutively encoding the Cas1 endonuclease, Cas3/cas2 helicase/RNAse, and four Csy proteins (Fig. 1A and B). csy4 (cas6f) was followed by a short non-coding TA-rich leader sequence. Then, the locus enclosed an array of spacers, where each spacer was flanked by two DRs. The spacers had variable sequences and a common length of 32 bp, whereas the DRs had the 5′-GTTCATGGCGGCATACGCCATTTAGAAA-3′ consensus sequence and were 28 bp long. Similarly to the CRISPR-Cas subtype I-F systems in other genera, the consensus sequence belonged to the DR cluster 4, showing a nucleotide similarity of 65–75% with those of Escherichia coli, Pseudomonas aeruginosa, Yersinia pestis, Shewanella spp., and Pectobacterium atrosepticum [3, 5, 29, 30]. Overall, 876 distinct A. baumannii-spacers (Ab-1 to-876) were identified (S2 Table). The size of the arrays was remarkably different among the isolates, ranging from 148 bp (2 spacers) up to 7354 bp (122 spacers).


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)

Genetic structure of the CRISPR-cas subtype I-Fb locus in Acinetobacter baumannii.A) The CRISPR-cas subtype I-Fb locus in A. baumannii strain AYE (GenBank accession number: CU459141, located at position 1,057,691 to 1,069,768). The locus consisted of two CRISPR–associated genes (cas1 and cas3/cas2), four Cas system-associated genes (csy1, csy2, csy3, and csy4), and an array of spacers. The map was created using Artemis (http://www.sanger.ac.uk/resources/software/artemis/). B) Nucleotide sequence of the array of spacers in A. baumannii strain AYE. The array included 59 spacers surrounded by 60 direct repeats (marked in green). Some repeats, mainly at the trailer end of the array, included degenerated nucleotides (marked in yellow). C) Comparative analysis of the genetic surroundings. The comparison was performed between the locus-positive strain AYE which belonged to sequence type (ST1) and the locus-negative strains TYTH-1, AB4857, and OIFC099 which belonged to ST2, ST3, and ST32, respectively. Homologous sequences shared by all the isolates were indicated by gray zones.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0118205.g001: Genetic structure of the CRISPR-cas subtype I-Fb locus in Acinetobacter baumannii.A) The CRISPR-cas subtype I-Fb locus in A. baumannii strain AYE (GenBank accession number: CU459141, located at position 1,057,691 to 1,069,768). The locus consisted of two CRISPR–associated genes (cas1 and cas3/cas2), four Cas system-associated genes (csy1, csy2, csy3, and csy4), and an array of spacers. The map was created using Artemis (http://www.sanger.ac.uk/resources/software/artemis/). B) Nucleotide sequence of the array of spacers in A. baumannii strain AYE. The array included 59 spacers surrounded by 60 direct repeats (marked in green). Some repeats, mainly at the trailer end of the array, included degenerated nucleotides (marked in yellow). C) Comparative analysis of the genetic surroundings. The comparison was performed between the locus-positive strain AYE which belonged to sequence type (ST1) and the locus-negative strains TYTH-1, AB4857, and OIFC099 which belonged to ST2, ST3, and ST32, respectively. Homologous sequences shared by all the isolates were indicated by gray zones.
Mentions: The CRISPR-cas subtype I-Fb locus, located at position 1,057,691 to 1,069,768 of the genome of A. baumannii strain AYE (GenBank accession number: CU459141), consisted of six genes consecutively encoding the Cas1 endonuclease, Cas3/cas2 helicase/RNAse, and four Csy proteins (Fig. 1A and B). csy4 (cas6f) was followed by a short non-coding TA-rich leader sequence. Then, the locus enclosed an array of spacers, where each spacer was flanked by two DRs. The spacers had variable sequences and a common length of 32 bp, whereas the DRs had the 5′-GTTCATGGCGGCATACGCCATTTAGAAA-3′ consensus sequence and were 28 bp long. Similarly to the CRISPR-Cas subtype I-F systems in other genera, the consensus sequence belonged to the DR cluster 4, showing a nucleotide similarity of 65–75% with those of Escherichia coli, Pseudomonas aeruginosa, Yersinia pestis, Shewanella spp., and Pectobacterium atrosepticum [3, 5, 29, 30]. Overall, 876 distinct A. baumannii-spacers (Ab-1 to-876) were identified (S2 Table). The size of the arrays was remarkably different among the isolates, ranging from 148 bp (2 spacers) up to 7354 bp (122 spacers).

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