You are currently browsing Connor’s articles.

Streptococcus_pyogenesThis Tuesday’s paper will be on the consequences of viral/bacterial co-infection in a mouse model, focusing on bacterial transmission and its genetic determinants. As you can imagine, pathogen transmission is a hot-topic right now, especially when viruses such as influenza are involved. So have a read, critique the paper and join us on Tuesday night at 8 pm BST on the 30th of September.

The paper was published recently in PloS pathogens, see link.

For discussion, I think we should focus on these points:

  • what is the model telling us? and is it a good model for this important question?
  • does this paper providing convinving evidence for the role or TLR2-driven inflammation? and what is the role of influenza virus in this?
  • what are the real-world consequences of viral/bacterial co-infection?

TLR2 Signaling Decreases Transmission of Streptococcus pneumoniae by Limiting Bacterial Shedding in an Infant Mouse Influenza A Co-infection Model.

  • Aimee L. Richard,
  • Steven J. Siegel,
  • Jan Erikson,
  • Jeffrey N. Weiser mail


While the importance of transmission of pathogens is widely accepted, there is currently little mechanistic understanding of this process. Nasal carriage of Streptococcus pneumoniae (the pneumococcus) is common in humans, especially in early childhood, and is a prerequisite for the development of disease and transmission among hosts. In this study, we adapted an infant mouse model to elucidate host determinants of transmission of S. pneumoniae from inoculated index mice to uninfected contact mice. In the context of co-infection with influenza A virus, the pneumococcus was transmitted among wildtype littermates, with approximately half of the contact mice acquiring colonization. Mice deficient for TLR2 were colonized to a similar density but transmitted S. pneumoniae more efficiently (100% transmission) than wildtype animals and showed decreased expression of interferon α and higher viral titers. The greater viral burden intlr2−/− mice correlated with heightened inflammation, and was responsible for an increase in bacterial shedding from the mouse nose. The role of TLR2 signaling was confirmed by intranasal treatment of wildtype mice with the agonist Pam3Cys, which decreased inflammation and reduced bacterial shedding and transmission. Taken together, these results suggest that the innate immune response to influenza virus promotes bacterial shedding, allowing the bacteria to transit from host to host. These findings provide insight into the role of host factors in the increased pneumococcal carriage rates seen during flu season and contribute to our overall understanding of pathogen transmission.

Author Summary

In this study, we sought to identify factors contributing to the transmission of the bacterial pathogen Streptococcus pneumoniae (the pneumococcus), a major cause of otitis media, pneumonia, and septicemia. Often found as a co-infection with other bacterial and viral pathogens, the pneumococcus is commonly carried by young children and is spread by close human contact, most likely through large droplet respiratory secretions. The specific determinants of bacterial transmission, however, have not been identified. This report details our use of an infant mouse model of transmission, which includes influenza A co-infection, to elucidate the mechanism of host-to-host transmission. We found that the inflammatory response to influenza, which is aggravated in the context of weakened host defense, promotes transmission by inducing bacterial shedding from the mouse nose. These results show how a bacterial pathogen exploits the host immune response to spread from one host to the next.



Next Tuesday’s #microtwjc paper will be “Total synthesis of a functional designer eukaryotic chromosome“, published last week or so in Science (you may have also seen the accompanying media attention). Apologies for it not being open access but the importance of this paper overshadowed that need. I think. If anyone has any problems accessing it just let me know via this or on twitter.

This paper documents the design, building and biological characterisation of a synthetic yeast chromosome, specifically chromosome III. For a primer on yeast genetics have a look at this. This is the first chromosome to be generated in what has been called the ‘yeast 2.0’ project – an international effort to generate a yeast with a completely synthetic genome (and actually carried out mainly by undergraduates). The paper is important for a number of reasons: 1) yeast is a model organism in its own right, engineering of a complete chromosome (or genome) will aid our understanding of not just yeast biology but of biology in general. 2) yeast are useful in their own right (see this: and this) – S. cerevisiae is my 4th favourite organism, I think. Synthesising the yeast genome will aid our exploitation of this organism, and 3) This is a stepping stone to synthetic ‘higher eukaryotic’ genomes (like us or our domestic animals) – the generation of synthetic higher animals may aid the development of new medical treatments and economic benefits. Remember where we were only a couple of years ago with mycoplasma. Whatever you want to call it. 

The paper is pretty straightforward but has a lot of supplementary data (no surprise there for a Science paper), which actually covers the bulk of this work (biological characterisation) – worth a read to see if there are any downsides to synthetic genomes(!). So have fun reading. Here are a couple of discussion points for you to think about (the usually ‘is this paper written well’ also applies).

1) what do you make of the authors design principles? They screwed around a great deal with this chromosome.

2) what do you think of the biological effect of the synthetic chromosome? how much change should be tolerated?

3) what would you do with this system? They mentioned ‘scrambling’ the genome to uncover hidden biology of yeast but what else could you do?

4) how hard would a human chromosome be to generate?



Two papers were recently published in the journal Science providing evidence that mammalian cells can use RNA interference (RNAi) to inhibit the replication of mammalian viruses. Sorry they are not open access by the papers are too interesting to ignore! This has become an important finding because it was widely believed that after we couldn’t find it, it didn’t occur. These papers have not come without their controversy and many do not believe that that 1) they are correct and 2) if they are right, then RNAi is not really important in mammals because we have other defences like interferons, antibodies and other innate and adaptive immune functions. 

The jury is out, so make your own mind up. Here’s a couple of questions to think about:

do you believe the data?

why did they have to use those specific viruses and cells?

do you believe RNAi is important to mammals?

why don’t mammals use RNAi?

Paper 1:

Paper 2:

Two good commentary articles are found in Science: Cell: 

I’ve been meaning to write about this paper for some time…

Viruses continue to cause extensive morbidity, mortality and not to mention economic stress, worldwide by infecting and causing disease in humans, animals and plants. Vaccines have been able to control many of the major viral diseases (smallpox, rinderpest, polio, measles…) but the development of vaccines against all viral pathogens is unrealistic and inefficient with current methods of R and D, testing and production.

When you consider the numbers of currently unknown, uncharacterised viruses replicating in reservoirs of animals or plants that have the potential to jump species (e.g MERS-CoV) and cause outbreaks (ebolavirus), epidemics (nipah) or even pandemics (influenza) then the thinking that generating vaccines against all these viruses becomes even more untenable. Even to generate specific antiviral drugs against them all becomes impossible.

This is why we have a back-up plan. This is why we broad-spectrum antivirals. Broad spectrum antivirals are drugs that will inhibit diverse viruses and are usually based upon targeting a common phenotype linking all the viruses (RNA dependant RNA polymerase, neuraminidase enzyme, RNA genome, RNA dependant DNA polymerase). These drugs tend to suffer from a number of problems 1) they aren’t all that broad spectrum, 2) resistance to antivirals can evolve rapidly and 3) we simply need more broad spectrum options.

This is why I have chosen the following paper for #microtwjc :

A mechanistic paradigm for broad-spectrum antivirals that target virus-cell fusion.

The paper describes an international collaboration between virologists and chemists that resulted in the development of a novel, highly effective, broad spectrum antiviral molecule that has little affect on the functioning of the host cell. The interesting thing is that the molecule inhibits virus – to – cell fusion of the viral envelope with the host cell plasma membrane, i.e one of the most important early steps in the virus (obligate intracellular parasite) lifecycle.

(the drug was originally described here:

Some points on the paper:

1) They know at what point the molecule inhibits (a late stage in virus-to-cell fusion).
2) They know that it leads to the oxidation of fatty acids in all membranes. (but only affects viral ones)
3) They know to do so it has to generate oxygen free radicals in the presence of light
4) Fatty acid oxidation changes membrane properties to prevent fusion of one membrane to another. 
5) They can optimise the molecular to make it even more effective
6) It works to some degree in vivo, but cannot wholly prevent virus-induced disease and death.

And here are some discussion points:

A) do we really need broad-spectrum antivirals? Who is going to have access to these?
B) Is virus envelope fusion a good target? What about non enveloped viruses? What about viruses that can spread via cell-to-cell fusion with limited virus-to-cell?
C) Would these drugs induce viral resistance evolution?
D) Oxidisation of viral lipids sounds a good idea, how come evolution has not come up with this idea already? …Or has it?
E) In vivo it don’t look so good. How come? Can it be made better?

Watch this video to see why this paper is important: .

I picked this paper: Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein by Krzyzaniak et al, in PLoS Pathogens last week because of the depth and detail that they went to in order to determine one of the most basic and important processes in virus infection: cell entry.



How important is it to find out how a virus enters a cell?

Could purification/concentration of the virus particles change how the virus enters?

Did they use the correct cells (not primary respiratory cells) and virus (not a clinical isolate) for their experiments?

Would you target this pathway as an antiviral strategy?

What would you do next?

Read the rest of this entry »