scholarly journals Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A

2019 ◽  
Vol 69 (10) ◽  
pp. 1649-1656 ◽  
Author(s):  
Sunando Roy ◽  
John Hartley ◽  
Helen Dunn ◽  
Rachel Williams ◽  
Charlotte A Williams ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Prevention And Control ◽  
Influenza A ◽  
Infection Prevention ◽  
Team Work ◽  
Infection Prevention And Control ◽  
Whole Genome ◽  
Street Hospital ◽  
And Control

Abstract Background Influenza A virus causes annual epidemics in humans and is associated with significant morbidity and mortality. Haemagglutinin (HA) and neuraminidase (NA) gene sequencing have traditionally been used to identify the virus genotype, although their utility in detecting outbreak clusters is still unclear. The objective of this study was to determine the utility, if any, of whole-genome sequencing over HA/NA sequencing for infection prevention and control (IPC) in hospitals. Methods We obtained all clinical samples from influenza (H1N1)-positive patients at the Great Ormond Street Hospital between January and March 2016. Samples were sequenced using targeted enrichment on an Illumina MiSeq sequencer. Maximum likelihood trees were computed for both whole genomes and concatenated HA/NA sequences. Epidemiological data was taken from routine IPC team activity during the period. Results Complete genomes were obtained for 65/80 samples from 38 patients. Conventional IPC analysis recognized 1 outbreak, involving 3 children, and identified another potential cluster in the haemato-oncology ward. Whole-genome and HA/NA phylogeny both accurately identified the previously known outbreak cluster. However, HA/NA sequencing additionally identified unrelated strains as part of this outbreak cluster. A whole-genome analysis identified a further cluster of 2 infections that had been previously missed and refuted suspicions of transmission in the haemato-oncology wards. Conclusions Whole-genome sequencing is better at identifying outbreak clusters in a hospital setting than HA/NA sequencing. Whole-genome sequencing could provide a faster and more reliable method for outbreak monitoring and supplement routine IPC team work to allow the prevention of transmission.

scholarly journals NovelblaKPC-carrying species identified in the hospital environment

2016 ◽  
Author(s):  
Hang T.T. Phan ◽  
Zoie Aiken ◽  
Oluwafemi Akinremi ◽  
Julie Cawthorne ◽  
Andrew Dodgson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Prevention And Control ◽  
Infection Prevention ◽  
Diagnostic Methods ◽  
Hospital Environment ◽  
Infection Prevention And Control ◽  
Clinical Implications ◽  
Whole Genome ◽  
And Control

AbstractblaKPC, encoding one of five dominant global carbapenemase families, is increasingly identified in environmental species difficult to characterize using routine diagnostic methods, with epidemiological and clinical implications. During environmental hospital infection prevention and control investigations (Manchester, UK) we used whole genome sequencing to confirm species identification for isolates infrequently associated withblaKPCand/or difficult to classify by MALDI-ToF. Four previously undescribedblaKPC-carrying species were identified from the hospital environment, including a putative, novelEnterobacterspecies.

scholarly journals Considering the Potential Application of Whole Genome Sequencing to Gonorrhea Prevention and Control

2018 ◽  
Vol 45 (6) ◽  
pp. e29-e32 ◽  
Author(s):  
Robert D. Kirkcaldy ◽  
Katy Town ◽  
Kim M. Gernert ◽  
Virginia B. Bowen ◽  
Elizabeth A. Torrone ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Potential Application ◽  
Prevention And Control ◽  
Whole Genome ◽  
And Control

Case 34

2020 ◽  
pp. 233-240
Author(s):  
Hilary Humphreys
Keyword(s):  
Genome Sequencing ◽  
Prevention And Control ◽  
Infection Prevention And Control ◽  
Whole Genome ◽  
Third Generation ◽  
Gram Negative ◽  
First Choice ◽  
Phenotypic Tests ◽  
And Control ◽  
Third Generation Cephalosporins

Multi-drug-resistant Enterobacteriales are an increasing problem and include those mediated by extended-spectrum β‎-lactamases (ESBLs) and carpapenemase production (CPE). Third-generation cephalosporins are inactivated by ESBLs but for CPEs there are much fewer options for treatment. The challenge in detection, management, and treatment is compounded by CPEs occurring amongst such a broad category of Gram-negative bacilli and because the genetic elements are very mobile, often being quickly and widely disseminated through plasmids. Phenotypic tests for identification have their limitations and there is increasing emphasis on PCR with microarrays and whole genome sequencing being available in specialist centres. Colistin is often the drug of first choice for CPE infections but is usually combined with another agent such as an aminoglycoside. Aggressive infection prevention and control precautions are mandatory given the propensity to spread, the reduced options for treatment, and a lack of insight to patterns and duration of carriage.

scholarly journals Clostridioides difficile Whole-genome Sequencing Differentiates Relapse With the Same Strain From Reinfection With a New Strain

2020 ◽  
Author(s):  
Janice Cho ◽  
Scott Cunningham ◽  
Meng Pu ◽  
Ryan J Lennon ◽  
Jennifer Dens Higano ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Data ◽  
Infection Prevention And Control ◽  
Whole Genome ◽  
Clostridioides Difficile ◽  
Allelic Differences ◽  
Clostridioides Difficile Infection ◽  
And Control ◽  
Zip Code

Abstract Background Current approaches in tracking Clostridioides difficile infection (CDI) and individualizing patient management are incompletely defined. Methods We recruited 468 subjects with CDI at Mayo Clinic Rochester between May and December 2016 and performed whole-genome sequencing (WGS) on C. difficile isolates from 397. WGS was also performed on isolates from a subset of the subjects at the time of a recurrence of infection. The sequence data were analyzed by determining core genome multilocus sequence type (cgMLST), with isolates grouped by allelic differences and the predicted ribotype. Results There were no correlations between C. difficile isolates based either on cgMLST or ribotype groupings and CDI outcome. An epidemiologic assessment of hospitalized subjects harboring C. difficile isolates with ≤2 allelic differences, based on standard infection prevention and control assessment, revealed no evidence of person-to-person transmission. Interestingly, community-acquired CDI subjects in 40% of groups with ≤2 allelic differences resided within the same zip code. Among 18 subjects clinically classified as having recurrent CDI, WGS revealed 14 with initial and subsequent isolates differing by ≤2 allelic differences, suggesting a relapse of infection with the same initial strain, and 4 with isolates differing by >50 allelic differences, suggesting reinfection. Among the 5 subjects classified as having a reinfection based on the timing of recurrence, 3 had isolates with ≤2 allelic differences between them, suggesting a relapse, and 2 had isolates differing by >50 allelic differences, suggesting reinfection. Conclusions Our findings point to potential transmission of C. difficile in the community. WGS better differentiates relapse from reinfection than do definitions based on the timing of recurrence.

Sign in / Sign up

Export Citation Format

Share Document