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.
journal_name
Front Microbioljournal_title
Frontiers in microbiologyauthors
Becker L,Fuchs S,Pfeifer Y,Semmler T,Eckmanns T,Korr G,Sissolak D,Friedrichs M,Zill E,Tung ML,Dohle C,Kaase M,Gatermann S,Rüssmann H,Steglich M,Haller S,Werner Gdoi
10.3389/fmicb.2018.00322subject
Has Abstractpub_date
2018-02-23 00:00:00pages
322issn
1664-302Xjournal_volume
9pub_type
杂志文章abstract::Our perspective on nature has changed throughout history and at the same time has affected directly or indirectly our perception of biological processes. In that sense, the "fluxus" of information in a viral population arises a result of a much more complex process than the encoding of a protein by a gene, but as the ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.02625
更新日期:2017-12-22 00:00:00
abstract::Bacteroides is among the most abundant microorganism inhabiting the human intestine. They are saccharolytic bacteria able to use dietary or host-derived glycans as energy sources. Some Bacteroides fragilis strains contribute to the maturation of the immune system but it is also an opportunistic pathogen. The intestine...
journal_title:Frontiers in microbiology
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journal_title:Frontiers in microbiology
pub_type: 杂志文章
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journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2015.00269
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abstract::A better understanding of global ruminal microbiota and metabolites under extensive feeding conditions is a prerequisite for optimizing rumen function and improving ruminant feed efficiency. Furthermore, the gap between the information on the ruminal microbiota and metabolites needs to be bridged. The aim of this stud...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.02206
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abstract::Microbial eukaryotes can play prominent roles in the Arctic marine ecosystem, but their diversity and variability is not well known in the ice-covered ecosystems. We determined the community composition of microbial eukaryotes in an Arctic under-ice spring bloom north of Svalbard using metabarcoding of DNA and RNA fro...
journal_title:Frontiers in microbiology
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pub_type: 杂志文章
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journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
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pub_type: 杂志文章,评审
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journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.579916
更新日期:2020-10-06 00:00:00
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journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01195
更新日期:2017-06-28 00:00:00
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journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.590683
更新日期:2020-12-15 00:00:00
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journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.01324
更新日期:2018-06-19 00:00:00
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pub_type: 杂志文章
doi:10.3389/fmicb.2020.599756
更新日期:2020-12-01 00:00:00
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pub_type: 杂志文章
doi:10.3389/fmicb.2020.01231
更新日期:2020-06-09 00:00:00
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journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.01489
更新日期:2019-07-02 00:00:00
abstract::[This corrects the article DOI: 10.3389/fmicb.2019.01752.]. ...
journal_title:Frontiers in microbiology
pub_type: 已发布勘误
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更新日期:2019-09-24 00:00:00
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pub_type: 杂志文章
doi:10.3389/fmicb.2019.00585
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