An important paper about the interactions between influenza and H. influenzae infection

Wong SM, Bernui M, Shen H, & Akerley BJ (2013). Genome-wide fitness profiling reveals adaptations required by Haemophilus in coinfection with influenza A virus in the murine lung. Proceedings of the National Academy of Sciences of the United States of America, 110 (38), 15413-8 PMID: 24003154

Haemophilus influenzae is a bacterium that causes respiratory tract diseases, but it's often confused with the virus that causes influenza (also a respiratory tract disease).  The modern confusion arises from the similarity of the names, but the name similarity arises from an older confusion about the cause of influenza.

The influenza virus wasn't identified until after the big 'Spanish influenza' pandemic at the end of World War I.   At the time of the epidemic the cause of influenza was still being sought, and a small heme-requiring bacterium informally called 'Pfeiffer's influenza bacillus' (now Haemophilus influenzae) was a likely suspect, since it was found in the lungs of many influenza victims.  We now know that influenza itself is caused by a family of small RNA-genome viruses, and that H. influenzae commonly causes a secondary pneumonia, especially in people whose respiratory tracts have been weakened by other diseases or by old age.

A recent paper from Brian Akerley's group set out to identify the bacterial genes that contribute to this effect.  Their hypothesis was that some H. influenzae functions that are needed for normal infection (in the absence of influenza virus) would not be needed when the virus was present, i.e. that the virus infection allows H. influenzae to take shortcuts.

Their strategy was to infect mouse lungs with a mixed population of H. influenzae mutants carrying transposon insertions in many different genes, and then examine which mutations become lost during the infection.  Cells that have mutations in genes that don't matter during infection will do just fine, but those with mutations in genes needed during infection will be unable to grow and so their DNA will be missing from the final population.  These experiments compared a healthy population of mice with mice that had been lightly infected with influenza A virus 5 days before the H. influenzae infection.  These authors had previously examined genes needed for single infection (Gawronski et al. 2009), and another group (Lee et al. 2010) had shown a few years previously that preinfection of mice with influenza increased the severity of H. influenzae infection, but this new work used a much less virulent strain of H. influenzae.

About 30% of the H. influenzae genes were excluded from the analysis, most because they were either essential or contributed to growth in lab culture medium, and some because they were duplicated or too small to analyze. This left about 1200 genes whose roles in infection and coinfection could be analyzed.

Most of these genes were found to not be important for either type of infection.  (The researchers' criteria for 'important' were quite stringent, so this doesn't mean they make no contribution.)  But 85 genes were required for both types of infection, with another 24 required only in single infection and another 18 required only in the coinfection with influenza virus.

The infection after influenza virus is probably a good model for similar human infections.  But the significance of the simple infection is less clear.  Since the bacteria are quickly cleared from the lung, it's not clear what's being evaluated.  There's also the possibility of chance effects playing a big role here, which might explain why the genes identified by this experiment are not very consistent with those found by a very similar experiment reported by this lab a few years ago (Gawronsky et al 2009).

I went through this paper in the hope that it would give us evidence of the in vivo importance of competence genes, but it doesn't.  None of the competence-inducible (CRP-S regulated) genes are important for the conditions the authors investigated.  In fact, knockouts of quite of few of them are enriched in the recovered lung samples, suggesting that these genes may do more harm than good.

I'll write a separate post considering where my research should be going.