Whole-Genome Sequencing of a Clinically Isolated Antibiotic-Resistant Enterococcus faecium EntfacYE

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.

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Whole-genome sequencing and characterization of an antibiotic resistant Neisseria meningitidis B isolate from a military unit in Vietnam

Annals of Clinical Microbiology and Antimicrobials ◽

10.1186/s12941-019-0315-z ◽

2019 ◽

Vol 18 (1) ◽

Cited By ~ 3

Author(s):

Thach Xuan Tran ◽

Trang Thu Le ◽

Long Phi Trieu ◽

Christopher M. Austin ◽

Dong Van Quyen ◽

...

Keyword(s):

Neisseria Meningitidis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Antibiotic Resistant ◽

Military Unit

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Successful containment of two vancomycin-resistant Enterococcus faecium (VRE) outbreaks in a Dutch teaching hospital using environmental sampling and whole genome sequencing

Journal of Hospital Infection ◽

10.1016/j.jhin.2021.02.007 ◽

2021 ◽

Author(s):

K.B. Gast ◽

A.J.G. van Oudheusden ◽

J.L. Murk ◽

J.J.J.M. Stohr ◽

A.G. Buiting ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Teaching Hospital ◽

Enterococcus Faecium ◽

Environmental Sampling ◽

Whole Genome ◽

Vancomycin Resistant Enterococcus ◽

Vancomycin Resistant

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Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3

Genome Announcements ◽

10.1128/genomea.01275-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 5

Author(s):

Jennifer K. Bender ◽

Stefan Fiedler ◽

Ingo Klare ◽

Guido Werner

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Enterococcus Faecium ◽

Complete Genome ◽

Laboratory Strain ◽

Whole Genome ◽

Coding Sequences

The genome sequence of the commensal and widely used laboratory strain Enterococcus faecium 64/3 was resolved by means of PacificBioscience and Illumina whole-genome sequencing. The genome comprises 2,575,333 bp with 2,382 coding sequences as assigned by NCBI.

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Virulence and resistance pattern of a novel sequence type of linezolid-resistant Enterococcus faecium identified by whole-genome sequencing

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2016.02.002 ◽

2016 ◽

Vol 6 ◽

pp. 27-31 ◽

Cited By ~ 5

Author(s):

Gladys Villas Boas do Prado ◽

Ana Paula Marchi ◽

Luisa Zanolli Moreno ◽

Camila Rizek ◽

Ulisses Amigo ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Sequence Type ◽

Resistance Pattern ◽

Whole Genome

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Application of combined genomic and transfer analyses to identify factors mediating regional spread of antibiotic resistant bacterial lineages

10.1101/2020.03.03.20029447 ◽

2020 ◽

Author(s):

Joyce Wang ◽

Betsy Foxman ◽

Ali Pirani ◽

Zena Lapp ◽

Lona Mody ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Analysis ◽

Patient Characteristics ◽

Patient Transfer ◽

Whole Genome ◽

Nursing Facilities ◽

Antibiotic Resistant ◽

Patient Level ◽

Healthcare Associated

ABSTRACTBackgroundPatients entering nursing facilities (NFs) are frequently colonized with antibiotic resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission we applied whole-genome sequencing to track the spread of four ARO species across regional NFs and evaluated patient-level characteristics and transfer acute-care hospitals (ACHs) as risk factors for colonization.Methods584 patients from six NFs were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm) and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined using multivariable regression models.ResultsThe majority of ARO isolates across study sites belonged to major healthcare-associated lineages: MRSA (ST5;N=89/117); VREfc (ST6;N=68/75); CipREc (ST131; N=58/64), and VREfm (clade A; N=129/129). While the genomic similarity of strains between NF pairs was associated with overlap in their feeder ACHs (Spearman’s rho=0.44-0.75, p<0.05 for MRSA, VREfc and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status (adjusted odds ratio [aOR]>1 for all four AROs) and recent exposure to glycopeptides (aOR>2 for VREfm, VREfc and MRSA) or 3rd/4th-generation cephalosporins (aOR>2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only one ARO/ACH pair (VREfm/ACH19, aOR=2.48[1.06-5.83]).ConclusionIn this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.SummaryUsing a combination of whole-genome sequencing, patient transfer and clinical data, we discerned the dissemination of four high-priority antibiotic-resistant organisms (ARO) in the regional healthcare network, and epidemiolocal drivers underlying the high ARO importation rate into regional nursing facilities.

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

10.1101/236786 ◽

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.

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