Whole-genome sequencing was better at identifying nosocomial influenza A outbreak clusters than hemagglutinin (HA)/neuraminidase (NA) gene sequencing, according to a study published in Clinical Infectious Diseases.

To determine the utility of whole-genome sequencing over HA/NA sequencing for infection prevention and control in hospitals, researchers collected 80 residual nasopharyngeal aspirate samples from 38 children who tested positive for influenza A (H1N1) at Great Ormond Street Hospital, London, England, from January to March 2016. All samples were phylogenetically distinct from the H1N1 vaccine strain used in the seasonal vaccine formulation and were of the H1N1 genetic subtype 6B.1.

Of the 80 samples, 65 were successfully sequenced. Conventional infection prevention and control analysis recognized 1 outbreak involving 3 children. Infection prevention and control data also identified another potential cluster comprising 11 patients from the hematology/oncology ward, who shared some services and were suspected to have cross-infections, but the connection was inconclusive.

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A phylogenetic analysis of HA/NA sequences alone generated a poorly supported tree, which identified both cluster outbreaks but demonstrated low bootstrap values. The tree failed to adequately discriminate directly transmitted strains from other co-circulating strains in the same hospital. In addition, HA/NA sequencing identified unrelated strains as part of this outbreak cluster.

In addition to the 1 cluster involving 3 children, whole-genome analysis identified another cluster comprising 2 patients, which was missed by infection prevention and control. Phylogenetic and pairwise analyses of whole-genome sequencing supported the second cluster as directly linked cases. Moreover, phylogenetic data refuted suspicions of cryptogenic nosocomial transmission in patients from the hematology/oncology ward, which was supported by pairwise genetic distances between them.

As turnaround times and per sample costs continue to decline, “whole-genome sequencing could provide a faster and more reliable method for outbreak monitoring and supplement routine [infection prevention and control] team work to allow the prevention of transmission,” concluded the researchers.


Roy S, Hartley J, Dunn H, Williams R, Williams CA, Breuer J. Whole-genome sequencing provides data for stratifying infection prevention and control management of nosocomial influenza A [published online April 17, 2019]. Clin Infect Dis. doi:10.1093/cid/ciz020

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This article originally appeared on Infectious Disease Advisor