Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario
Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2...
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doaj-fa9e141a68e94118b560214ffb29ffbe2020-11-24T23:54:01ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-02-01910.3389/fmicb.2018.00322314029Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak ScenarioLaura Becker0Stephan Fuchs1Yvonne Pfeifer2Torsten Semmler3Tim Eckmanns4Gerit Korr5Gerit Korr6Dagmar Sissolak7Michael Friedrichs8Edith Zill9Mei-Lin Tung10Christian Dohle11Martin Kaase12Sören Gatermann13Holger Rüssmann14Matthias Steglich15Sebastian Haller16Guido Werner17Department of Infectious Diseases, Robert Koch Institute, Berlin, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyPostgraduate Training for Applied Epidemiology, Robert Koch Institute, Affiliated to the European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control (ECDC), Stockholm, SwedenDepartment of Infection Control, Medical Disaster Control and Environmental Health Control, Department of Public Health, Berlin, GermanyMEDIAN Klinik Berlin-Kladow, Berlin, GermanyMedical Care Centre Labor 28 GmbH, Berlin, GermanyMEDIAN Klinik Berlin-Kladow, Berlin, GermanyMEDIAN Klinik Berlin-Kladow, Berlin, GermanyNational Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Berlin, GermanyNational Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Berlin, GermanyImmunology and Laboratory Medicine, Institute for Microbiology, HELIOS Klinikum Emil von Behring, Berlin, GermanyLeibniz Institute DSMZ, German Collection of Microorganisms and Cell Culture, Braunschweig, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyDepartment of Infectious Diseases, Robert Koch Institute, Berlin, GermanyExtended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS. Two independent analysis strategies (reference-based and -free) revealed the same distinct clusters of two CTX-M-15 producing K. pneumoniae clones (ST15, n = 31; ST405, n = 7) and one CTX-M-15 producing Klebsiella quasipneumoniae strain (ST414, n = 8). Additionally, we determined sequence variations associated with antimicrobial resistance phenotypes in single isolates expressing carbapenem and colistin resistance, respectively. For rapid detection of the major K. pneumoniae outbreak clone (ST15), a selective triplex PCR was deduced from WGS data of the major outbreak strain and K. pneumoniae genome data deposited in central databases. Moreover, we introduce two novel open-source applications supporting reference genome selection (refRank; https://gitlab.com/s.fuchs/refRank) and alignment-based SNP-filtering (SNPfilter; https://gitlab.com/s.fuchs/snpfilter) in NGS analyses.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00322/fullESBLoutbreak analysisNGSstrain typingCTX-M-15 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Laura Becker Stephan Fuchs Yvonne Pfeifer Torsten Semmler Tim Eckmanns Gerit Korr Gerit Korr Dagmar Sissolak Michael Friedrichs Edith Zill Mei-Lin Tung Christian Dohle Martin Kaase Sören Gatermann Holger Rüssmann Matthias Steglich Sebastian Haller Guido Werner |
spellingShingle |
Laura Becker Stephan Fuchs Yvonne Pfeifer Torsten Semmler Tim Eckmanns Gerit Korr Gerit Korr Dagmar Sissolak Michael Friedrichs Edith Zill Mei-Lin Tung Christian Dohle Martin Kaase Sören Gatermann Holger Rüssmann Matthias Steglich Sebastian Haller Guido Werner Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario Frontiers in Microbiology ESBL outbreak analysis NGS strain typing CTX-M-15 |
author_facet |
Laura Becker Stephan Fuchs Yvonne Pfeifer Torsten Semmler Tim Eckmanns Gerit Korr Gerit Korr Dagmar Sissolak Michael Friedrichs Edith Zill Mei-Lin Tung Christian Dohle Martin Kaase Sören Gatermann Holger Rüssmann Matthias Steglich Sebastian Haller Guido Werner |
author_sort |
Laura Becker |
title |
Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario |
title_short |
Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario |
title_full |
Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario |
title_fullStr |
Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario |
title_full_unstemmed |
Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario |
title_sort |
whole genome sequence analysis of ctx-m-15 producing klebsiella isolates allowed dissecting a polyclonal outbreak scenario |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2018-02-01 |
description |
Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS. Two independent analysis strategies (reference-based and -free) revealed the same distinct clusters of two CTX-M-15 producing K. pneumoniae clones (ST15, n = 31; ST405, n = 7) and one CTX-M-15 producing Klebsiella quasipneumoniae strain (ST414, n = 8). Additionally, we determined sequence variations associated with antimicrobial resistance phenotypes in single isolates expressing carbapenem and colistin resistance, respectively. For rapid detection of the major K. pneumoniae outbreak clone (ST15), a selective triplex PCR was deduced from WGS data of the major outbreak strain and K. pneumoniae genome data deposited in central databases. Moreover, we introduce two novel open-source applications supporting reference genome selection (refRank; https://gitlab.com/s.fuchs/refRank) and alignment-based SNP-filtering (SNPfilter; https://gitlab.com/s.fuchs/snpfilter) in NGS analyses. |
topic |
ESBL outbreak analysis NGS strain typing CTX-M-15 |
url |
http://journal.frontiersin.org/article/10.3389/fmicb.2018.00322/full |
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