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Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

Ostria-Hernández ML, Sánchez-Vallejo CJ, Ibarra JA, Castro-Escarpulli G - BMC Res Notes (2015)

Bottom Line: The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different.BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences.The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Bacteriología Médica y, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Delegación Miguel Hidalgo, CP 11340, Mexico, D.F., Mexico. marthal_19@yahoo.com.mx.

ABSTRACT

Background: In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes.

Results: The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

Conclusions: The CRISPR/Cas system is not widely distributed in K. pneumoniae genomes, those present most likely belong to type I-E with few differences from the arrangement of the cse3 gene and most of the spacers have not been are not described yet. Given that the CRISPR/Cas system is scarcely distributed among K. pneumoniae genomes it is not clear whether it is involved in either immunity against foreign genetic material or virulence. We consider that this study represents a first step to understand the role of CRISPR/Cas in K. pneumoniae.

No MeSH data available.


Related in: MedlinePlus

Location of CRISPR/Cas system in the genome of diverse strains of Klebsiella pneumoniae. Alignment generated with Progressive MAUVE of the six genomes that contain CRISPR/Cas. The region was grouped into a single locally collinear block (red). At the ends of the cas operon (empty or blank regions marked by yellow arrows), there is variability, probably due to the presence of CRISPR sequences.
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Fig1: Location of CRISPR/Cas system in the genome of diverse strains of Klebsiella pneumoniae. Alignment generated with Progressive MAUVE of the six genomes that contain CRISPR/Cas. The region was grouped into a single locally collinear block (red). At the ends of the cas operon (empty or blank regions marked by yellow arrows), there is variability, probably due to the presence of CRISPR sequences.

Mentions: In general, based on the MAUVE alignment (for details refer to "Methods" section) it was observed that the region where the cas operon is located in all genomes, only one locally collinear block (LCB) was found. Therefore, this region seems to be shared and syntenic. In the genomes of the strains NTUH-K2044 [GenBank: NC_012731], WGLW2 [GenBank: NZ_JH930419], and WGLW5 [GenBank: NZ_JH930428], this system was found encoded in the complementary strand. In contrast, in the genomes of strains 1084 [GenBank: NC_018522], JHCK1 [GenBank: NZ_ANGH02000012] and RYC492 [GenBank: NZ_APGM01000001], it was found encoded in the plus strand. We also found that upstream and downstream sequences of the cas operon were variable in all cases, which shows the variability of the CRISPR sequences (Fig. 1).Fig. 1


Survey of clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) systems in multiple sequenced strains of Klebsiella pneumoniae.

Ostria-Hernández ML, Sánchez-Vallejo CJ, Ibarra JA, Castro-Escarpulli G - BMC Res Notes (2015)

Location of CRISPR/Cas system in the genome of diverse strains of Klebsiella pneumoniae. Alignment generated with Progressive MAUVE of the six genomes that contain CRISPR/Cas. The region was grouped into a single locally collinear block (red). At the ends of the cas operon (empty or blank regions marked by yellow arrows), there is variability, probably due to the presence of CRISPR sequences.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522967&req=5

Fig1: Location of CRISPR/Cas system in the genome of diverse strains of Klebsiella pneumoniae. Alignment generated with Progressive MAUVE of the six genomes that contain CRISPR/Cas. The region was grouped into a single locally collinear block (red). At the ends of the cas operon (empty or blank regions marked by yellow arrows), there is variability, probably due to the presence of CRISPR sequences.
Mentions: In general, based on the MAUVE alignment (for details refer to "Methods" section) it was observed that the region where the cas operon is located in all genomes, only one locally collinear block (LCB) was found. Therefore, this region seems to be shared and syntenic. In the genomes of the strains NTUH-K2044 [GenBank: NC_012731], WGLW2 [GenBank: NZ_JH930419], and WGLW5 [GenBank: NZ_JH930428], this system was found encoded in the complementary strand. In contrast, in the genomes of strains 1084 [GenBank: NC_018522], JHCK1 [GenBank: NZ_ANGH02000012] and RYC492 [GenBank: NZ_APGM01000001], it was found encoded in the plus strand. We also found that upstream and downstream sequences of the cas operon were variable in all cases, which shows the variability of the CRISPR sequences (Fig. 1).Fig. 1

Bottom Line: The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different.BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences.The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Laboratorio de Bacteriología Médica y, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Delegación Miguel Hidalgo, CP 11340, Mexico, D.F., Mexico. marthal_19@yahoo.com.mx.

ABSTRACT

Background: In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes.

Results: The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in metabolism and resistance to antibiotics.

Conclusions: The CRISPR/Cas system is not widely distributed in K. pneumoniae genomes, those present most likely belong to type I-E with few differences from the arrangement of the cse3 gene and most of the spacers have not been are not described yet. Given that the CRISPR/Cas system is scarcely distributed among K. pneumoniae genomes it is not clear whether it is involved in either immunity against foreign genetic material or virulence. We consider that this study represents a first step to understand the role of CRISPR/Cas in K. pneumoniae.

No MeSH data available.


Related in: MedlinePlus