scholarly journals Genomic characterization of vancomycin-resistant Enterococcus faecium transmission in hospital by whole genome sequencing

2021 ◽  
Vol 58 ◽  
pp. 21004027
Author(s):  
Hye Mee Kim ◽  
Doo Ryeon Chung ◽  
Kyungmin Huh ◽  
Cheol-In Kang ◽  
Kyong Ran Peck
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterococcus Faecium ◽  
Whole Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Genomic Characterization ◽  
Vancomycin Resistant

scholarly journals Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

2017 ◽  
Author(s):  
Kimon Lemonidis ◽  
Talal S. Salih ◽  
Stephanie J. Dancer ◽  
Iain S. Hunter ◽  
Nicholas P. Tucker
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterococcus Faecium ◽  
Sequence Type ◽  
Whole Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Phylogenetic Comparison ◽  
Vancomycin Resistant ◽  
The Uk ◽  
Increased Susceptibility

AbstractMulti-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two closely located hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains across both hospitals, while the fifth was of a multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested VanA-type pstS-null VREfm strains (5 English and 18 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.

scholarly journals Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole-genome Sequencing-based Surveillance

2019 ◽  
Vol 70 (11) ◽  
pp. 2336-2343 ◽  
Author(s):  
Alexander J Sundermann ◽  
Ahmed Babiker ◽  
Jane W Marsh ◽  
Kathleen A Shutt ◽  
Mustapha M Mustapha ◽  
...  
Keyword(s):  
Interventional Radiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterococcus Faecium ◽  
Whole Genome ◽  
Training Video ◽  
Prevention Interventions ◽  
Vancomycin Resistant ◽  
Record Review ◽  
Hospital Acquired

Abstract Background Vancomycin-resistant enterococci (VRE) are a major cause of hospital-acquired infections. The risk of infection from interventional radiology (IR) procedures is not well documented. Whole-genome sequencing (WGS) surveillance of clinical bacterial isolates among hospitalized patients can identify previously unrecognized outbreaks. Methods We analyzed WGS surveillance data from November 2016 to November 2017 for evidence of VRE transmission. A previously unrecognized cluster of 10 genetically related VRE (Enterococcus faecium) infections was discovered. Electronic health record review identified IR procedures as a potential source. An outbreak investigation was conducted. Results Of the 10 outbreak patients, 9 had undergone an IR procedure with intravenous (IV) contrast ≤22 days before infection. In a matched case-control study, preceding IR procedure and IR procedure with contrast were associated with VRE infection (matched odds ratio [MOR], 16.72; 95% confidence interval [CI], 2.01 to 138.73; P = .009 and MOR, 39.35; 95% CI, 7.85 to infinity; P < .001, respectively). Investigation of IR practices and review of the manufacturer’s training video revealed sterility breaches in contrast preparation. Our investigation also supported possible transmission from an IR technician. Infection prevention interventions were implemented, and no further IR-associated VRE transmissions have been observed. Conclusions A prolonged outbreak of VRE infections related to IR procedures with IV contrast resulted from nonsterile preparation of injectable contrast. The fact that our VRE outbreak was discovered through WGS surveillance and the manufacturer’s training video that demonstrated nonsterile technique raise the possibility that infections following invasive IR procedures may be more common than previously recognized.

scholarly journals Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2637
Author(s):  
Jolien D’aes ◽  
Marie-Alice Fraiture ◽  
Bert Bogaerts ◽  
Sigrid C. J. De Keersmaecker ◽  
Nancy H. C. Roosens ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetically Modified ◽  
Added Value ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
Genomic Characterization

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

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