Genome-wide fitness profiling reveals adaptations required by Haemophilus in coinfection with influenza A virus in the murine lung

Abstract

Bacterial coinfection represents a major cause of morbidity and mortality in epidemics of influenza A virus (IAV). The bacterium Haemophilus influenzae typically colonizes the human upper respiratory tract without causing disease, and yet in individuals infected with IAV, it can cause debilitating or lethal secondary pneumonia. Studies in murine models have detected immune components involved in susceptibility and pathology, and yet few studies have examined bacterial factors contributing to coinfection. We conducted genome-wide profiling of the H. influenzae genes that promote its fitness in a murine model of coinfection with IAV. Application of direct, high-throughput sequencing of transposon insertion sites revealed fitness phenotypes of a bank of H. influenzae mutants in viral coinfection in comparison with bacterial infection alone. One set of virulence genes was required in nonvirally infected mice but not in coinfection, consistent with a defect in anti-bacterial defenses during coinfection. Nevertheless, a core set of genes required in both in vivo conditions indicated that many bacterial countermeasures against host defenses remain critical for coinfection. The results also revealed a subset of genes required in coinfection but not in bacterial infection alone, including the iron-sulfur cluster regulator gene, iscR, which was required for oxidative stress resistance. Overexpression of the antioxidant protein Dps in the iscR mutant restored oxidative stress resistance and ability to colonize in coinfection. The results identify bacterial stress and metabolic adaptations required in an IAV coinfection model, revealing potential targets for treatment or prevention of secondary bacterial pneumonia after viral infection.transposon-insertion sequencing | functional genomics

Subjects Hospitalized With the 2009 Pandemic Influenza A (H1N1) Virus in a Respiratory Infection Unit: Clinical Factors Correlating With ICU Admission

“…41,42 This has also been confirmed in numerous preclinical studies. 43,44 Previous reports have shown that radiologically confirmed pneumonia is associated with severe outcomes. 3,4,8,20,32 Although multivariate analysis did not reveal that pneumonia on admission was a significant clinical risk factor for a severe outcome in our study, it is noteworthy that 64% of subjects with 2009 H1N1 had infiltrates on x-rays at admission (92% for ICU subjects) compared with 17% of subjects presenting with an influenzalike illness, underlining its significance in complicating the confirmed cases requiring hospitalization.…”

Tn-Seq Analysis of Vibrio cholerae Intestinal Colonization Reveals a Role for T6SS-Mediated Antibacterial Activity in the Host

“…The recent application of “deep sequencing” to the challenge of tracking the relative abundance of various transposon insertion mutants in multiplex analyses has provided an exciting high-throughput negative selection approach to comprehensively identify genes required for selectable phenotypes (Chao et al, 2013; Dong et al, 2013; Gallagher et al, 2011; van Opijnen and Camilli, 2013; Wong et al, 2013; Zhang et al, 2012). Ordered transposon insertion libraries also can facilitate comprehensive analysis of pathogen-host interactions as well as provide investigators with an opportunity to “cherry pick” mutants for further analysis.…”

What a difference a cluster makes: The multifaceted roles of IscR in gene regulation and DNA recognition

“…Figure prepared with PyMOL (http://www.pymol.org/). influenza A virus [77]. Furthermore, IscR function on Vibrio vulnificus highly impacted its motility and adhesion to host cells, hemolytic activity, and survival under oxidative stress during infection [10].…”