Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection

Abstract

Secondary bacterial lung infection (SBLI) is a serious complication in patients with H7N9 virus infection, and increases disease severity. The oropharyngeal (OP) microbiome helps prevent colonisation of respiratory pathogens. We aimed to investigate the OP microbiome of H7N9 patients with/without secondary bacterial pneumonia using 16S rRNA gene sequencing. OP swab samples were collected from 51 H7N9 patients (21 with SBLI and 30 without) and 30 matched healthy controls (HCs) and used for comparative composition, diversity and richness analyses of microbial communities. Principal coordinates analysis successfully distinguished between the OP microbiomes of H7N9 patients and healthy subjects, and the OP microbiome diversity of patients with SBLI was significantly increased. There was significant dysbiosis of the OP microbiome in H7N9 patients, with an abundance of Leptotrichia, Oribacterium, Streptococcus, Atopobium, Eubacterium, Solobacterium and Rothia species in patients with SBLI, and Filifactor, Megasphaera and Leptotrichia species in patients without SBLI, when compared with HCs. Importantly, Haemophilus and Bacteroides species were enriched in HCs. These findings revealed dysbiosis of the OP microbiota in H7N9 patients, and identified OP microbial risk indicators of SBLI, suggesting that the OP microbiome could provide novel and non-invasive diagnostic biomarkers for early microbiota-targeted prophylactic therapies for SBLI prevention.

Rapid detection of respiratory organisms with FilmArray respiratory panel and its impact on clinical decisions in Shanghai, China, 2016‐2018

“…It is worth noting that for the commercial FA‐RP used in the present study, identification of Influenza A virus is limited to the H3, H1, and 2009‐H1 subtypes, whereas for other subtypes, such as H7N9, the FA‐RP can only provide the vague result of “not subtyped Influenza A.” However, in mainland China, Influenza A virus H7N9 is one of the epidemic strains associated with UP, and indeed, this strain was particularly prevalent during the winter and spring of 2016‐2017. Compared with other Influenza A infection, H7N9 patients tend to present with a more clinically severe manifestation and require more aggressive treatment.…”

Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia

“…Children with severe influenza showed decreased relative abundance of S. aureus and increased abundance of Prevotella, Streptobacillus, Porphyromonas, Granulicatella, Veillonella, Fusobacterium , and Haemophilus . A recent Chinese study in patients with H7N9 avian influenza demonstrated significantly increased diversity in the oropharyngeal microbiome of H7N9-infected patients compared to healthy controls, particularly H7N9 patients with secondary bacterial pneumonia ( 106 ). Conversely, a French study of nasopharyngeal samples and a South Korean study of oropharyngeal samples from patients with acute respiratory viral infections both displayed decreases in diversity indices during viral infections compared to healthy controls ( 71 , 100 ).…”

Broad neutralizing activity of a human monoclonal antibody against H7N9 strains from 2013 to 2017

“…H7N9 causes severe respiratory distress syndrome in patients and is frequently associated with secondary bacterial pneumonia caused by multidrug-resistant Acinetobacter baumannii and Klebsiella pneumonia 3 . Noticeable dysbiosis of the oropharyngeal microbiome in H7N9 patients has also been observed 4 . During the fifth epidemic alone, 688 human infections were confirmed, making it the largest H7N9 epidemic to date.…”