Suspected Influenza Infection Control Pathway/Algorithm
The infection control algorithm for suspected influenza implemented during the pre and post POCT testing period of the study are outlined in the supplementary information. In the context of the COVID-19 outbreak the Hospital infection control algorithm for suspected COVID-19 can be accessed at , with entry to the suspected influenza pathway occurring on being ruled out of the COVID-19 pathway.
Matched patient specimens were collected in the medical assessment unit of Bon Secours Hospital, Tralee, Co. Kerry, Ireland, which met the Hospital’s clinical algorithm for suspected influenza between October 2018 and April 2019. A mid turbinate nasal swab (Puritan sterile foam tipped applicator, Ref 25-15061PF) tested within 2 hours of collection was the preferred specimen for the ID NOW POCT device. Nasal and throat specimens for analysis on the GeneXpert were collected using Cepheid Xpert® Nasopharyngeal Sample Collection kit for Viruses (Ref SWAB/B-100) with viral transport medium (VTM). Specimens for testing with the GeneXpert Flu+RSV assay were typically stored at -20 oC for up to 24 h during routine days and up to 72 h at weekends prior to transport to the referral laboratory for testing.
Clinical Implementation and Training
The POCT Co-Ordinator, MAU nursing staff and medical Senior House Officers (SHO’s) were trained by the manufacturer on how to use the ID NOW instrument. Patients who had a positive Influenza result were flagged for standard droplet precautions and isolation by the infection control team.
Patient specimens were analysed on both test systems as per manufacturer’s instructions. Each batch of reagents used in the validation study were quality controlled on receipt. Specimens were tested with the Abbott ID NOW A&B2 assay within 2 h of collection. Analysis of the patient swabs using the GeneXpert platform by the referral laboratory was carried out by mixing an equal volume aliquot of VTM from both the nasal and throat specimens in the test to give an aggregate sample. The GeneXpert method provided a positive result if either the nasal or the throat swab was positive in the pooled sample.
Test Data Collection
The collection details and results for specimens analysed using the ID NOW were manually recorded on an influenza specimen analysis report compiled by the operator which was subsequently filed in the patients medical chart. Specimens for analysis using the GeneXpert were sent to the pathology department. The specimens were registered on the Laboratory Information System (iSOFT) and transferred by courier to the referral laboratory.
Collection of Data on the Management of Influenza-Positive Patients
Data was gathered from the Hospital LIS and Patient Information Management System (PIMS, iSoft) which were retrospectively interrogated using SAP Business Objects (BI Platform 4.1 Version: 18.104.22.1685). Data on all patients who had specimens collected for influenza testing from September 2017 to April 2018 represented the pre POCT testing data set. Data on all patients who had a point-of-care influenza test from September 2018 to April 2019 represented the post POCT implementation data set.
Calculation of Defined Daily Dosing of Antibiotics
The World Health Organisation describes the Defined Daily Dose (DDD) as the assumed average maintenance dose per day for a medicine used for its main indication in adults . The selection criteria included only adult patients who had a confirmed diagnosis of Influenza Type A or B. A multidisciplinary team reviewed medical notes and prescriptions to determine generic antibiotic name, dose, number of doses and cumulative dose of antibiotic administered during inpatient admission for the respective cohort periods. In accordance with WHO Collaborating Centre for Drug Statistics Methodology, antibiotic consumption data were collated and analysed using the 2018 reference values available through the Anatomical Therapeutic Chemical (ATC) classification system . DDDs were calculated for each antimicrobial consumed for every patient suitable for cohort entry.
Suitable statistical analysis was performed using the Microsoft Excel add on XLSTAT. A p-value of < 0.05 was considered to be statistically significant. The Chi-squared test was used for categorical data.