Detection of a Transient R292K Mutation in Influenza A/H3N2 Viruses Shed for Several Weeks by an Immunocompromised Patient

Abstract

We describe the case of an immunocompromised patient, positive for influenza A virus (H3N2), in whom the neuraminidase R292K mutation was transiently detected during oseltamivir treatment. The R292K mutation was identified by direct testing in 3 of 11 respiratory specimens collected throughout the patient's illness but in none of the cultures from those specimens. CASE REPORTA 58-year-old male presented to our institution on day 96 following a cord blood allogeneic stem cell transplant for treatment of chemo-refractory chronic lymphocytic leukemia. His symptoms included abdominal pain, weight loss, and increased stool frequency, and he was subsequently readmitted for further management. Despite negative Clostridium difficile PCR tests, colonoscopy revealed mucosal ulceration and exudates throughout the colon and the patient was diagnosed with pseudomembranous colitis. He was started on a course of metronidazole and vancomycin. The patient remained hospitalized with persistent diarrhea, bloody at times, and intermittent human herpesvirus 6 (HHV-6) viremia.On day 133 posttransplantation (21 February 2012), the patient was noted to have a cough consistent with influenza-like illness, and a nasopharyngeal swab (NPS) was collected and submitted for respiratory virus PCR (FilmArray RP; BioFire Diagnostics, Salt Lake City, UT). The sample tested positive for influenza A/H3N2 virus, and a 5-day course of oseltamivir was initiated that day. An NPS collected on 28 February 2012, following completion of the course of oseltamivir, was still positive for influenza A/H3N2 virus. At this time, the patient had no respiratory symptoms, but as a precaution, a second 5-day course of oseltamivir was administered starting on 28 February 2012. Despite the two courses of treatment, repeated NPSs still tested positive for influenza A/H3N2 virus (Table 1). At this point, the patient developed a persistent, nonproductive cough, which continued to worsen. Samples that were positive following several days of antiviral treatment were forwarded for assessment of their antiviral resistance profiles and tested as described below. A chest X ray on 16 March 2014 showed a small pleural effusion, and a follow-up computed tomography (CT) scan revealed new cavitary lesions. A bronchoscopy was performed, and bronchoalveolar lavage (BAL) fluids and bronchial washing specimens (BW) were submitted for viral, bacterial, and fungal cultures. Influenza A virus, adenovirus, and human herpesvirus 6 (HHV-6) were detected in the BAL fluid, with influenza A virus detected by culture in both BAL fluid and BW. The patient was not given any further antiviral treatment and continued to shed the virus for an additional 8 weeks. The first NPS to return a negative result was collected on 4 June 2012, followed by a second negative sample on 11 June 2014. The patient's health continued to deteriorate due to multiple comorbidities, and he expired on 1 July 2012.A FilmArray respiratory panel and viral culture were performed on NPS specimens and BAL fluid/BW, respectively,...

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

“…Guidelines from the Community Network of Reference Laboratories for Human Influenza in Europe suggest that testing for antiviral resistance is typically indicated in the following instances: (i) in patients lacking virological improvement (persistent virus shedding after 5 days of treatment using ab NAAT that "delivers semi-quantitative information" [e.g., a real-time PCR with a C T value]), (ii) in patients treated with antivirals with severe FLU who do not clinically improve (time frame not given), (iii) in fatal cases where an understanding of resistance may influence prophylaxis of contacts, (iv) in cases of FLU developed during or after antiviral prophylaxis, and (v) in contacts of antiviral-treated FLU patients who developed respiratory symptoms or in contacts of FLU patients for whom the presence of resistant virus had been confirmed (323). One group that may benefit from antiviral testing is patients who shed virus for long periods of time and who do not improve after treatment (e.g., highly immunocompromised patients) (324,325).…”

Oseltamivir resistance in an influenza A (H3N2) virus isolated from an immunocompromised patient during the 2014–2015 influenza season in Alberta, Canada

“…9 Immunocompromised patients can shed influenza virus for extended periods of time and this may promote the development of resistant or non-susceptible strains as homogenous or heterogeneous populations over time. 2,3 The R292K mutation has been associated with decreased viral fitness in ferret models and it is possible that reconstitution of the patient's immune system would have at least partly cleared this strain. 10 The phenotypic susceptibility test data also suggest that the isolate from Day +5 post-ASCT would have had normal levels of inhibition if treated with zanamivir.…”

“…We do know from the case description that this R292K mutant was identified during a time range when the patient could be considered highly immunocompromised, with neutropenia . Immunocompromised patients can shed influenza virus for extended periods of time and this may promote the development of resistant or non‐susceptible strains as homogenous or heterogeneous populations over time . The R292K mutation has been associated with decreased viral fitness in ferret models and it is possible that reconstitution of the patient's immune system would have at least partly cleared this strain …”

“…Ideally, if viruses can be isolated in cell culture, a NA phenotypic assay (using a fluorometric or luminescent substrate) should be performed . With the recent dominance of influenza A (H3N2) viruses, there have been several descriptions of A (H3N2) viruses carrying mutation in the NA, especially in immunocompromised patients . This short report describes the identification of an R292K mutation in the NA of a seasonal influenza A (H3N2) virus from an immunocompromised patient.…”

“…1 With the recent dominance of influenza A (H3N2) viruses, there have been several descriptions of A (H3N2) viruses carrying mutation in the NA, especially in immunocompromised patients. 2,3 This short report describes the identification of an R292K mutation in the NA of a seasonal influenza A (H3N2) virus from an immunocompromised patient. This was the only identified oseltamivir-resistant influenza A (H3N2) viral isolate characterized in Canada during the 2014-2015 influenza season.…”