Complete Genome Sequence of Klebsiella oxytoca Strain AHC-6, Isolated from a Patient during Acute Antibiotic-Associated Hemorrhagic Colitis

Dabernig-Heinz, Johanna; Wagner, Gabriel E.; Leitner, Eva; Ruppitsch, Werner; Steinmetz, Ivo; Högenauer, Christoph; Zechner, Ellen L.; Kienesberger, Sabine

doi:10.1128/mra.01350-22

Cited by 1 publication

(1 citation statement)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, all 65 isolates were assessed for the β-lactamase and carbapenemase resistance genes blaOXY , blaKPC, and blaTEM in SeqSphere+ with curated allele libraries from the Institute Pasteur [ https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_klebsiella_seqdef&page=alleleQuery&locus=blaOXY , accessed on 5 March 2023 ( 26 )]. Another query created in SeqSphere+ consists of 12 genes relevant to the functionality of the til gene cluster based on the toxin-producing reference strain K. oxytoca AHC-6 ( CP098757 ) ( 32 ). Results from this genetic analysis were evaluated with results obtained from in vitro toxicity assays.…”

Section: Methodsmentioning

confidence: 99%

Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex

Dabernig-Heinz,

Wagner,

Prior

et al. 2024

J Clin Microbiol

Self Cite

View full text Add to dashboard Cite

The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.

show abstract

Section: Methodsmentioning

confidence: 99%