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 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 Whole Genome Sequencing of Vancomycin Resistant Enterococcus faecium Isolated from Saudi Arabia

2018 ◽  
Vol 15 (4) ◽  
pp. 791-797
Author(s):  
Mushtaq Ahmad Khan ◽  
Fauwaz Al-Rashid ◽  
Mamdoh Meqdam ◽  
Hisham Al-Ajlan ◽  
Mohammed Al-Mogbel
Keyword(s):  
Saudi Arabia ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterococcus Faecium ◽  
Gene Cassette ◽  
Multidrug Resistant ◽  
Maternity Hospital ◽  
Whole Genome ◽  
Healthcare Facilities ◽  
Vancomycin Resistant

Enterococcus faecium are one of the most prevalent species cultured from humans and they have become increasingly common cause of infections in the hospital settings globally. The objective of current study was to characterize 26 E. faecium isolates collected from different patients attending Maternity Hospital in Ha’il, Saudi Arabia. The bacterial isolates were identified by MALDI-TOF-MS and the antibiotic susceptibility was performed by Microscan. Whole genome sequencing of a single vancomycin resistant E. faecium (VRE) was performed using MiSeq. The results of antimicrobial susceptibility revealed that, 99%, 90%, 83% and 73% of isolates were resistant to Clindamycin, Gentamicin, Oxacillin and Tetracycline respectively. One (3%) among 26 E. faecium isolates was found to produce resistance to vancomycin. The WGS analysis of VRE showed that it belonged to ST280 and was found to harbor vanB gene cassette. This is the first report of VRE from the Ha’il region of Saudi Arabia. VRE may act as a reservoir for multidrug resistant genes and other important virulence factors that favor the dissemination of antimicrobial resistance. Therefore, the surveillance studies to prevent dissemination of VRE shall be implemented in the healthcare facilities all across Saudi Arabia.

scholarly journals Whole-Genome Sequencing for Bacterial Strain Typing Using the iSeq100 Platform

2020 ◽  
Vol 41 (S1) ◽  
pp. s434-s434
Author(s):  
Grant Vestal ◽  
Steven Bruzek ◽  
Amanda Lasher ◽  
Amorce Lima ◽  
Suzane Silbert
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outbreak Detection ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Dna Libraries ◽  
Patient Health ◽  
Hospital Acquired ◽  
Reference Genomes

Background: Hospital-acquired infections pose a significant threat to patient health. Laboratories are starting to consider whole-genome sequencing (WGS) as a molecular method for outbreak detection and epidemiological surveillance. The objective of this study was to assess the use of the iSeq100 platform (Illumina, San Diego, CA) for accurate sequencing and WGS-based outbreak detection using the bioMérieux EPISEQ CS, a novel cloud-based software for sequence assembly and data analysis. Methods: In total, 25 isolates, including 19 MRSA isolates and 6 ATCC strains were evaluated in this study: A. baumannii ATCC 19606, B. cepacia ATCC 25416, E. faecalis ATCC 29212, E. coli ATCC 25922, P. aeruginosa ATCC 27853 and S. aureus ATCC 25923. DNA extraction of all isolates was performed on the QIAcube (Qiagen, Hilden, Germany) using the DNEasy Ultra Clean Microbial kit extraction protocol. DNA libraries were prepared for WGS using the Nextera DNA Flex Library Prep Kit (Illumina) and sequenced at 2×150-bp on the iSeq100 according to the manufacturer’s instructions. The 19 MRSA isolates were previously characterized by the DiversiLab system (bioMérieux, France). Upon validation of the iSeq100 platform, a new outbreak analysis was performed using WGS analysis using EPISEQ CS. ATCC sequences were compared to assembled reference genomes from the NCBI GenBank to assess the accuracy of the iSeq100 platform. The FASTQ files were aligned via BowTie2 version 2.2.6 software, using default parameters, and FreeBayes version 1.1.0.46-0 was used to call homozygous single-nucleotide polymorphisms (SNPs) with a minimum coverage of 5 and an allele frequency of 0.87 using default parameters. ATCC sequences were analyzed using ResFinder version 3.2 and were compared in silico to the reference genome. Results: EPISEQ CS classified 8 MRSA isolates as unrelated and grouped 11 isolates into 2 separate clusters: cluster A (5 isolates) and cluster B (6 isolates) with similarity scores of ≥99.63% and ≥99.50%, respectively. This finding contrasted with the previous characterization by DiversiLab, which identified 3 clusters of 2, 8, and 11 isolates, respectively. The EPISEQ CS resistome data detected the mecA gene in 18 of 19 MRSA isolates. Comparative analysis of the ATCCsequences to the reference genomes showed 99.9986% concordance of SNPs and 100.00% concordance between the resistance genes present. Conclusions: The iSeq100 platform accurately sequenced the bacterial isolates and could be an affordable alternative in conjunction with EPISEQ CS for epidemiological surveillance analysis and infection prevention.Funding: NoneDisclosures: None

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