Respiratory Infectious Disease

Identifying Nosocomial Influenza A: Whole-Genome vs Hemagglutinin/Neuraminidase Sequencing

Sweta Gupta
|
Although sensitivity is an important consideration when deciding among HIV tests, there are other factors to consider, such as test invasiveness, available resources, need for additional studies, and patient adherence.6 Serum- and plasma-based HIV testing is the most invasive and requires the most resources, such as access to a skilled clinician or phlebotomist and access to special equipment (eg, needles, biohazard containers, laboratory). Whole blood testing can be performed by venipuncture or finger-stick. When blood-based tests yield a sufficient specimen sample using venipuncture, additional studies can be undertaken, such as HIV subtyping and assessment for coinfections, including hepatitis or syphilis. In contrast, oral fluid tests do not require special equipment and can be performed in any setting, including at home, providing results in minutes. These tests also eliminate safety and biohazard concerns, such as needlestick injuries and sharps disposal.

Although sensitivity is an important consideration when deciding among HIV tests, there are other factors to consider, such as test invasiveness, available resources, need for additional studies, and patient adherence.6


Serum- and plasma-based HIV testing is the most invasive and requires the most resources, such as access to a skilled clinician or phlebotomist and access to special equipment (eg, needles, biohazard containers, laboratory).


Whole blood testing can be performed by venipuncture or finger-stick. When blood-based tests yield a sufficient specimen sample using venipuncture, additional studies can be undertaken, such as HIV subtyping and assessment for coinfections, including hepatitis or syphilis. In contrast, oral fluid tests do not require special equipment and can be performed in any setting, including at home, providing results in minutes. These tests also eliminate safety and biohazard concerns, such as needlestick injuries and sharps disposal.

Whole-genome sequencing was better at identifying nosocomial influenza A outbreak clusters than hemagglutinin (HA)/neuraminidase (NA) gene sequencing.

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.

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.

Related Content

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.

Reference

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

Related Articles

This article originally appeared on Infectious Disease Advisor

  • Latest News Your top articles for Tuesday

  • Haymarket Medical NetworkTop Picks

  • Loading...

    Continuing Medical Education (CME/CE) Courses

    Show More