Dataset Information

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

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.

SUBMITTER: Roy S

PROVIDER: S-EPMC6821348 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Publications

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

Roy Sunando S Hartley John J Dunn Helen H Williams Rachel R Williams Charlotte A CA Breuer Judith J

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20191001 10

<h4>Background</h4>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.<h4>Me ...[more]

PMID: 30993315

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Project description:Background: Nosocomial infections (NIs) are among the main preventable healthcare adverse events. Like all countries, Canada and its provinces are affected by NIs. In 2004, Ministry of Health and Social Services (MSSS) of Quebec instituted a mandatory surveillance NI program for the prevention and control (NIPC) in the hospitals of the province. One target of the MSSS 2015-2020 action plan is to assess the implementation, costs, effects, and return on investment of NIPC measures. This project goes in the same way and is one of the first major studies in Canada to evaluate the efficiency of the NIPC measures. Three objectives will be pursued: evaluate the cost of implementing clinical best practices (CBPs) for infection control; evaluate the economic burden attributable to NIs; and examine the cost-effectiveness of the NIPC by comparing the costs of CBPs against those of NIs. Methods: This project is based on an infection control intervention framework that includes four CBPs: hand hygiene; hygiene and sanitation; screening; and additional precautions. Four medical and surgical units in two hospitals (nonUniversity, University) in the province of Quebec will be studied. The project has four components. Component 1 will construct and content validate an observation grid for measuring the costs of CBPs. Component 2 will estimate CBP costs via 2-week prospective observations of health workers, conducted every 2 months over a 1-year period. Component 3 will evaluate, through a matched case-control study, the economic burden of the four most monitored NIs in Quebec (C-difficile, MRSA, VRE, and CPGNB). Archival patient data will be collected retrospectively. Component 4 will determine the optimal breakeven point for CBPs associated with NIPC. Discussion: This project will produce evidence of the economic analysis of NIPC and give health stakeholders an overview of NIPC cost-effectiveness. It will meet the objectives of the Canadian Patient Safety Institute and the MSSS action plan to analyze the efficiency of NIPC preventive measures. To our knowledge, this is the first such exercise in Quebec and Canada. It will provide governments with a decision support tool through a major empirical study that could be replicated nationally to capture the financial benefits of NIPC.

Dataset Information

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

Background

Methods

Results

Conclusions

Publications

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

Similar Datasets

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