Characteristics of adults with influenza A virus pneumonia and co-infections identified by mNGS in Jilin, China during 2024–2025

TL;DR

This study examines IAV pneumonia and co-infections in hospitalized patients in China using mNGS, finding that mNGS is more sensitive than traditional tests and that severe cases are linked to chronic conditions and co-infections.

Contribution

The study demonstrates the superior sensitivity of mNGS over conventional methods for detecting IAV and identifies risk factors for severe disease and co-infections.

Findings

mNGS detected IAV with 100% sensitivity compared to 60% with nucleic acid tests.

H1N1 and H3N2 were the most common IAV subtypes, with H3N2 linked to more severe illness.

Severe/critical patients had higher D-dimer levels and lower lymphocyte counts, and were more likely to have bacterial and fungal co-infections.

Abstract

Influenza A virus (IAV) was included in the World Health Organization priority pathogen list for 2024 owing to its pandemic potential. We aimed to investigate the characteristics of IAV pneumonia and co-infection identified using metagenomic next-generation sequencing (mNGS) in hospitalized patients in Jilin, China, during 2024–2025.

This retrospective study included patients hospitalized for IAV pneumonia. All patients underwent mNGS testing using sputum or bronchoalveolar lavage fluid. Patients were categorized into mild-to-moderate (MM) and severe-to-critical (SC) groups, depending on their disease severity. We analyzed demographic data, clinical manifestations, laboratory findings, and imaging results, and compared the two groups.

Of the 73 patients included, 45 were in the MM group and 28 were in the SC group. Compared with nucleic acid tests of throat swabs, mNGS has higher sensitivity for detecting IAV (60% vs 100%). H1N1 and H3N2 were the predominant IAV subtypes. Underlying conditions, especially asthma and chronic obstructive pulmonary disease, were associated with an increased risk of severe illness. The D-dimer levels were higher, and lymphocyte counts were lower in patients in the SC group than in those in the MM group. Of the 73 patients, 63 (86.3%) had secondary infections, with bacterial infections being more prevalent (mild/moderate: 26 [58%] and severe/critical: 24 [86%]) than fungal infections (23 [51%] and 23 [82%], respectively).

mNGS is a sensitive method for detecting IAV co-infections, effectively identifying co-infection with pathogenic bacterial strains. Hospitalized patients with IAV pneumonia, especially those with H3N2 infection and chronic airway disease, showed a high prevalence of severe and critical illness [total: 8 [11%], severe/critical: 7 [25%]). Fungal infections were frequent regardless of the presence of underlying comorbidities, and patients with SC disease were more likely to develop gram-negative bacterial and fungal infections. These findings may assist clinicians in the early identification of critically ill patients and the provision of appropriate empirical treatment.

Figures