Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak

Abstract

Traditional epidemiological investigation of nosocomial transmission of influenza involves the identification of patients who have the same influenza virus type and who have overlapped in time and place. This method may misidentify transmission where it has not occurred or miss transmission when it has. We used influenza virus whole-genome sequencing (WGS) to investigate an outbreak of influenza A virus infection in a hematology/oncology ward and identified 2 separate introductions, one of which resulted in 5 additional infections and 79 bed-days lost. Results from WGS are becoming rapidly available and may supplement traditional infection control procedures in the investigation and management of nosocomial outbreaks.

Figure 1.

Map of the ward. Rectangles are side rooms, and squares indicate bays with 4 beds. Letters indicate patients and are colored green or purple according to whether influenza virus sequences are considered part of the same transmission cluster. Patient D is colored black since the genome coverage was considered of sufficient depth. ^aPatient G was asymptomatic but tested positive for influenza virus A on day 4.

Figure 2.

Maximum-likelihood tree derived from a genomic alignment of sequences generated during the influenza outbreak on ward 1. Tips are colored according to location within the hospital and whether the patients are considered part of the same transmission cluster (green, ward 1, linked; blue, ward 1, unlinked; red, elsewhere in the same hospital, unlinked). Tips in black indicate insufficient genome coverage (only the sequence for NS-1 was available). Bootstrap support percentages from 1000 replicates are shown for each node. A and E, Accident and Emergency Department; OPD, Out Patient Department.