Abstract
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.
Highlights
Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae are important nosocomial pathogens (Gupta et al, 2003)
During April and May 2015 ESBL-producing K. pneumoniae were detected in nine different patients who just came from the intensive care unit of the neurorehabilitation clinic with overall 202 beds
ESBL-producing K. pneumoniae isolates have been detected in 52 patients of whom 20 developed a clinical infection
Summary
Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae are important nosocomial pathogens (Gupta et al, 2003). WGS-based analysis of an ongoing detection of ESBL-producing K. pneumoniae revealed prevalence of the outbreak strain over a period of several months while extensive infection control measures have been performed. WGS analysis allowed identification of the origin of the outbreak years before the first clinical and supposed index case was notified (Haller et al, 2015). Most of these studies were performed retrospectively. Real-time WGS analysis during nosocomial outbreaks is, in principle, a realistic scenario nowadays, limitations in terms of costs, quick access to relevant techniques and qualified personnel and other factors exist in practice. Simple but reliable and specific tests such as PCR-based assays using WGS data would be one of the possible solutions to existing restrictions
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