scholarly journals Whole Genome Sequencing for Investigation of a Hospital Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)–Producing Klebsiella pneumoniae (KPN) Linked with an Index Case of Community-Acquired KPC-Producing KPN Infection

2016 ◽  
Vol 3 (suppl_1) ◽  
Author(s):  
Je Eun Song ◽  
Young Soun Lim ◽  
Eunjin Ha ◽  
Hyunsoo Kim ◽  
Moo Hyun Kim ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Index Case ◽  
Whole Genome ◽  
Klebsiella Pneumoniae Carbapenemase ◽  
Hospital Outbreak

scholarly journals Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

2015 ◽  
Vol 21 (11) ◽  
pp. 1001-1007 ◽  
Author(s):  
Y. Jiang ◽  
Z. Wei ◽  
Y. Wang ◽  
X. Hua ◽  
Y. Feng ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Hospital Outbreak

scholarly journals Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

2015 ◽  
Vol 59 (3) ◽  
pp. 1656-1663 ◽  
Author(s):  
Amy J. Mathers ◽  
Nicole Stoesser ◽  
Anna E. Sheppard ◽  
Louise Pankhurst ◽  
Adam Giess ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Single Institution ◽  
Content Type ◽  
Klebsiella Pneumoniae Carbapenemase ◽  
Distinct Sequence ◽  
Sequence Types

ABSTRACTThe global emergence ofKlebsiella pneumoniaecarbapenemase-producingK. pneumoniae(KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258K. pneumoniaein the setting of an outbreak mediated by an endemic plasmid. We describe the interplay ofblaKPCplasmids andK. pneumoniaestrains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kpclinical isolates collected from a single institution over 5 years following the introduction ofblaKPCin August 2007, as well as two plasmid transformants. KPC-Kpfrom 37 patients yielded 16 distinct sequence types (STs). Two novel conjugativeblaKPCplasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence ofblaKPCin 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kpstrain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal ofblaKPCto many non-ST258 lineages in a hospital through spread of at least two novelblaKPCplasmids. In contrast, ST258 KPC-Kpwas imported into the institution on numerous occasions, with otherblaKPCplasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kpstrain, ST941, became associated with both novelblaKPCplasmids and spread locally, making it a future candidate for clinical persistence and dissemination.

scholarly journals Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

2012 ◽  
Vol 4 (148) ◽  
pp. 148ra116-148ra116 ◽  
Author(s):  
E. S. Snitkin ◽  
A. M. Zelazny ◽  
P. J. Thomas ◽  
F. Stock ◽  
D. K. Henderson ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Hospital Outbreak ◽  
Carbapenem Resistant

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

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