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BackgroundViral infections such as influenza have been shown to predispose hosts to increased colonization of the respiratory tract by pathogenic bacteria and secondary bacterial pneumonia. To examine how viral infections and host antiviral immune responses alter the upper respiratory microbiota, we analyzed nasal bacterial composition by 16S ribosomal RNA (rRNA) gene sequencing in healthy adults at baseline and at 1 to 2 weeks and 4 to 6 weeks following instillation of live attenuated influenza vaccine or intranasal sterile saline. A subset of these samples was submitted for microarray host gene expression profiling.ResultsWe found that live attenuated influenza vaccination led to significant changes in microbial community structure, diversity, and core taxonomic membership as well as increases in the relative abundances of Staphylococcus and Bacteroides genera (both p < 0.05). Hypergeometric testing for the enrichment of gene ontology terms in the vaccinated group reflected a robust up-regulation of type I and type II interferon-stimulated genes in the vaccinated group relative to controls. Translational murine studies showed that poly I:C administration did in fact permit greater nasal Staphylococcus aureus persistence, a response absent in interferon alpha/beta receptor deficient mice.ConclusionsCollectively, our findings demonstrate that although the human nasal bacterial community is heterogeneous and typically individually robust, activation of a type I interferon (IFN)-mediated antiviral response may foster the disproportionate emergence of potentially pathogenic species such as S. aureus.Trial registrationThis study was registered with Clinicaltrials.gov on 11/3/15, NCT02597647.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-015-0133-2) contains supplementary material, which is available to authorized users.

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Between 1978 and 1991, 54 patients with metastatic squamous cell or undifferentiated carcinoma to the cervical lymph nodes, with unknown primary mucosal sites, were treated with curative intent at McGill University teaching hospitals. The median age at diagnosis was 58 years with a male:female ratio of 6:1. All patients presented with a painless neck mass. Five patients (9%) presented with N1 disease, 28 (52%) with N2a disease, four (7%) with N2b disease, three (6%) with N2c disease, and 14 (26%) with N3 disease. Twenty-four patients (44%) underwent neck dissection, and 30 (56%) had only excisional lymph node biopsy. Fifty-three patients (98%) were treated with radiotherapy to a median dose of 60 Gy (range 38 to 66 Gy) in 30 fractions. With a median follow-up time of 49 months, the overall actuarial survival was 63% and 59% at 5 and 10 years, respectively. Three patients were found to have a subsequent primary head and neck tumor. The single most important prognostic factor was the N stage, which influences both neck control and long-term survival. There was no statistically significance difference in survival or local neck control rates between patients who had neck dissection or excisional lymph node biopsy (p > 0.05).