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Abstract
Discussion Forum (0)
Abstract number: 4180

Session Type: ePosters

Session Title: ePosters

Authors(s): M. Maatallah (1), A.M. Örmälä-Odegrip (2), R. Mzoughi (1), C. G. Giske (2, 3)

Authors Affiliations(s): (1) Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP : LR01ES16), Faculté de pharmacie de Monastir, Université de Monastir, Tunisie., Tunisia, (2) Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden., Sweden, (3) Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden., Sweden

Background:

This study aimed at exploring the resistome, virulome, plasmid replicon typing, serotyping, CRISPR-Cas system, prophage prediction of CP-KP, and establishing their phylogenetic relatedness based on core genome MLST (cgMLST694) and whole genome SNP (wgSNP).

Methods:

A total of 29 strains of (CP-KP) with diverse STs from five countries: Sweden, UK, Greece, India and USA were analyzed by whole genome sequencing (WGS); HiSeq (Illumina, San Diego, USA). The antimicrobial resistance genes (ARG) and plasmid replicons were identified using Resfinder4.1 and Plasmidfinder2.1. CRISPRCasFinder was used to identify CRISPR-Cas systems. The database BIGSdb was used to predict virulence genes and to retrieve the allele numbers of standard MLST and cgMLST694. Prophages were predicted using PHASTER and the capsular serotypes (K-types) were identified using Kaptive V 0.7.0. The allelic profiles of cgMLST694 were used to create a Minimum Spanning Tree implemented in BioNumerics7.6.3. Maximum Likelihood Tree based on concatenated wgSNP was created using CSI phylogeny1.4.

Results:

The 29 isolates yielded 16 distinct STs and most of isolates were classified in these clonal groups: CG258 (n=7), CG14 (n=6), CG147 (n=5) and CG17 (n= 2). A total of 16 different K-types were found with a relative association between STs and K-types. A wide range of ARG was detected in our strains conferring resistance to diverse class of antibiotics. Resfinder analysis identified 9 isolates as KPC, 8 isolates as VIM and 7 isolates as NDM. The CRISPR-Cas system was detected in 12 isolates with an equal occurrence of CRISPR-Cas type IE and type IE*. The type IV CRISPR-Cas system, which is localized on plasmids, was found in 7 isolates. Three to 8 replicons types were found per strain. Two virulome categories were retrieved and the hypervirulent isolates were notified among diverse STs. Our analysis showed that all strains had at least 4 prophages. The cgMLST694 and wgSNP both provided good resolution for strain subtyping particularly within closely related isolates.

Conclusions:

This study broadens our reflections of how high-risk clones of CP-KP diversify at clonal levels. This emphasizes the importance of implementing real-time bacterial genomics to hinder the silent appearance of high-risk clones of CP-KP in clinical settings.  

Keyword(s): carbapenemase-producing Klebsiella pneumoniae, resistome, CRISPR-Cas

Abstract number: 4180

Session Type: ePosters

Session Title: ePosters

Authors(s): M. Maatallah (1), A.M. Örmälä-Odegrip (2), R. Mzoughi (1), C. G. Giske (2, 3)

Authors Affiliations(s): (1) Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP : LR01ES16), Faculté de pharmacie de Monastir, Université de Monastir, Tunisie., Tunisia, (2) Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden., Sweden, (3) Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden., Sweden

Background:

This study aimed at exploring the resistome, virulome, plasmid replicon typing, serotyping, CRISPR-Cas system, prophage prediction of CP-KP, and establishing their phylogenetic relatedness based on core genome MLST (cgMLST694) and whole genome SNP (wgSNP).

Methods:

A total of 29 strains of (CP-KP) with diverse STs from five countries: Sweden, UK, Greece, India and USA were analyzed by whole genome sequencing (WGS); HiSeq (Illumina, San Diego, USA). The antimicrobial resistance genes (ARG) and plasmid replicons were identified using Resfinder4.1 and Plasmidfinder2.1. CRISPRCasFinder was used to identify CRISPR-Cas systems. The database BIGSdb was used to predict virulence genes and to retrieve the allele numbers of standard MLST and cgMLST694. Prophages were predicted using PHASTER and the capsular serotypes (K-types) were identified using Kaptive V 0.7.0. The allelic profiles of cgMLST694 were used to create a Minimum Spanning Tree implemented in BioNumerics7.6.3. Maximum Likelihood Tree based on concatenated wgSNP was created using CSI phylogeny1.4.

Results:

The 29 isolates yielded 16 distinct STs and most of isolates were classified in these clonal groups: CG258 (n=7), CG14 (n=6), CG147 (n=5) and CG17 (n= 2). A total of 16 different K-types were found with a relative association between STs and K-types. A wide range of ARG was detected in our strains conferring resistance to diverse class of antibiotics. Resfinder analysis identified 9 isolates as KPC, 8 isolates as VIM and 7 isolates as NDM. The CRISPR-Cas system was detected in 12 isolates with an equal occurrence of CRISPR-Cas type IE and type IE*. The type IV CRISPR-Cas system, which is localized on plasmids, was found in 7 isolates. Three to 8 replicons types were found per strain. Two virulome categories were retrieved and the hypervirulent isolates were notified among diverse STs. Our analysis showed that all strains had at least 4 prophages. The cgMLST694 and wgSNP both provided good resolution for strain subtyping particularly within closely related isolates.

Conclusions:

This study broadens our reflections of how high-risk clones of CP-KP diversify at clonal levels. This emphasizes the importance of implementing real-time bacterial genomics to hinder the silent appearance of high-risk clones of CP-KP in clinical settings.  

Keyword(s): carbapenemase-producing Klebsiella pneumoniae, resistome, CRISPR-Cas

Genome typing and in silico analysis of diverse sequence types of extremely drug-resistant (XDR) carbapenemase-producing Klebsiella pneumoniae (CP-KP)
Dr. Makaoui Maatallah
Dr. Makaoui Maatallah
ESCMID eAcademy. Maatallah M. 07/09/2021; 329763; 4180
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Dr. Makaoui Maatallah
Abstract
Discussion Forum (0)
Abstract number: 4180

Session Type: ePosters

Session Title: ePosters

Authors(s): M. Maatallah (1), A.M. Örmälä-Odegrip (2), R. Mzoughi (1), C. G. Giske (2, 3)

Authors Affiliations(s): (1) Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP : LR01ES16), Faculté de pharmacie de Monastir, Université de Monastir, Tunisie., Tunisia, (2) Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden., Sweden, (3) Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden., Sweden

Background:

This study aimed at exploring the resistome, virulome, plasmid replicon typing, serotyping, CRISPR-Cas system, prophage prediction of CP-KP, and establishing their phylogenetic relatedness based on core genome MLST (cgMLST694) and whole genome SNP (wgSNP).

Methods:

A total of 29 strains of (CP-KP) with diverse STs from five countries: Sweden, UK, Greece, India and USA were analyzed by whole genome sequencing (WGS); HiSeq (Illumina, San Diego, USA). The antimicrobial resistance genes (ARG) and plasmid replicons were identified using Resfinder4.1 and Plasmidfinder2.1. CRISPRCasFinder was used to identify CRISPR-Cas systems. The database BIGSdb was used to predict virulence genes and to retrieve the allele numbers of standard MLST and cgMLST694. Prophages were predicted using PHASTER and the capsular serotypes (K-types) were identified using Kaptive V 0.7.0. The allelic profiles of cgMLST694 were used to create a Minimum Spanning Tree implemented in BioNumerics7.6.3. Maximum Likelihood Tree based on concatenated wgSNP was created using CSI phylogeny1.4.

Results:

The 29 isolates yielded 16 distinct STs and most of isolates were classified in these clonal groups: CG258 (n=7), CG14 (n=6), CG147 (n=5) and CG17 (n= 2). A total of 16 different K-types were found with a relative association between STs and K-types. A wide range of ARG was detected in our strains conferring resistance to diverse class of antibiotics. Resfinder analysis identified 9 isolates as KPC, 8 isolates as VIM and 7 isolates as NDM. The CRISPR-Cas system was detected in 12 isolates with an equal occurrence of CRISPR-Cas type IE and type IE*. The type IV CRISPR-Cas system, which is localized on plasmids, was found in 7 isolates. Three to 8 replicons types were found per strain. Two virulome categories were retrieved and the hypervirulent isolates were notified among diverse STs. Our analysis showed that all strains had at least 4 prophages. The cgMLST694 and wgSNP both provided good resolution for strain subtyping particularly within closely related isolates.

Conclusions:

This study broadens our reflections of how high-risk clones of CP-KP diversify at clonal levels. This emphasizes the importance of implementing real-time bacterial genomics to hinder the silent appearance of high-risk clones of CP-KP in clinical settings.  

Keyword(s): carbapenemase-producing Klebsiella pneumoniae, resistome, CRISPR-Cas

Abstract number: 4180

Session Type: ePosters

Session Title: ePosters

Authors(s): M. Maatallah (1), A.M. Örmälä-Odegrip (2), R. Mzoughi (1), C. G. Giske (2, 3)

Authors Affiliations(s): (1) Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP : LR01ES16), Faculté de pharmacie de Monastir, Université de Monastir, Tunisie., Tunisia, (2) Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden., Sweden, (3) Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden., Sweden

Background:

This study aimed at exploring the resistome, virulome, plasmid replicon typing, serotyping, CRISPR-Cas system, prophage prediction of CP-KP, and establishing their phylogenetic relatedness based on core genome MLST (cgMLST694) and whole genome SNP (wgSNP).

Methods:

A total of 29 strains of (CP-KP) with diverse STs from five countries: Sweden, UK, Greece, India and USA were analyzed by whole genome sequencing (WGS); HiSeq (Illumina, San Diego, USA). The antimicrobial resistance genes (ARG) and plasmid replicons were identified using Resfinder4.1 and Plasmidfinder2.1. CRISPRCasFinder was used to identify CRISPR-Cas systems. The database BIGSdb was used to predict virulence genes and to retrieve the allele numbers of standard MLST and cgMLST694. Prophages were predicted using PHASTER and the capsular serotypes (K-types) were identified using Kaptive V 0.7.0. The allelic profiles of cgMLST694 were used to create a Minimum Spanning Tree implemented in BioNumerics7.6.3. Maximum Likelihood Tree based on concatenated wgSNP was created using CSI phylogeny1.4.

Results:

The 29 isolates yielded 16 distinct STs and most of isolates were classified in these clonal groups: CG258 (n=7), CG14 (n=6), CG147 (n=5) and CG17 (n= 2). A total of 16 different K-types were found with a relative association between STs and K-types. A wide range of ARG was detected in our strains conferring resistance to diverse class of antibiotics. Resfinder analysis identified 9 isolates as KPC, 8 isolates as VIM and 7 isolates as NDM. The CRISPR-Cas system was detected in 12 isolates with an equal occurrence of CRISPR-Cas type IE and type IE*. The type IV CRISPR-Cas system, which is localized on plasmids, was found in 7 isolates. Three to 8 replicons types were found per strain. Two virulome categories were retrieved and the hypervirulent isolates were notified among diverse STs. Our analysis showed that all strains had at least 4 prophages. The cgMLST694 and wgSNP both provided good resolution for strain subtyping particularly within closely related isolates.

Conclusions:

This study broadens our reflections of how high-risk clones of CP-KP diversify at clonal levels. This emphasizes the importance of implementing real-time bacterial genomics to hinder the silent appearance of high-risk clones of CP-KP in clinical settings.  

Keyword(s): carbapenemase-producing Klebsiella pneumoniae, resistome, CRISPR-Cas

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