AUTHOR=Becker Laura , Fuchs Stephan , Pfeifer Yvonne , Semmler Torsten , Eckmanns Tim , Korr Gerit , Sissolak Dagmar , Friedrichs Michael , Zill Edith , Tung Mei-Lin , Dohle Christian , Kaase Martin , Gatermann Sören , Rüssmann Holger , Steglich Matthias , Haller Sebastian , Werner Guido 

TITLE=Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.00322

DOI=10.3389/fmicb.2018.00322

ISSN=1664-302X

ABSTRACT=<p>Extended-spectrum β-lactamase (ESBL) producing <italic>Klebsiella pneumoniae</italic> pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant <italic>K. pneumoniae</italic> 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 <italic>K. pneumoniae</italic> clones (ST15, <italic>n</italic> = 31; ST405, <italic>n</italic> = 7) and one CTX-M-15 producing <italic>Klebsiella quasipneumoniae</italic> strain (ST414, <italic>n</italic> = 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 <italic>K. pneumoniae</italic> outbreak clone (ST15), a selective triplex PCR was deduced from WGS data of the major outbreak strain and <italic>K. pneumoniae</italic> genome data deposited in central databases. Moreover, we introduce two novel open-source applications supporting reference genome selection (<italic>refRank</italic>; <ext-link ext-link-type="uri" xlink:href="https://gitlab.com/s.fuchs/refRank" xmlns:xlink="http://www.w3.org/1999/xlink">https://gitlab.com/s.fuchs/refRank</ext-link>) and alignment-based SNP-filtering (<italic>SNPfilter</italic>; <ext-link ext-link-type="uri" xlink:href="https://gitlab.com/s.fuchs/snpfilter" xmlns:xlink="http://www.w3.org/1999/xlink">https://gitlab.com/s.fuchs/snpfilter</ext-link>) in NGS analyses.</p>