Archive for the ‘Uncategorized’ Category


The Schmallenberg Virus and Disease

January 21, 2013

This week in the online journal club #microtwjc we will be discussing this paper titled “Schmallenberg Virus Pathogenesis, Tropis and Interaction with the Innate Immune System of the Host” (Varela M, Schnettler E, Caporale M, Murgia C, Barry G, et al.  (2013) Schmallenberg Virus Pathogenesis, Tropism and Interaction with the Innate Immune System of the Host. PLoS Pathog 9(1):e1003133. doi:10.1371/journal.ppat.1003133).

I’ve written before about Schmallenberg here and here so I will only go into the background briefly before diving in to the paper.


Correct as of November 2012. From

Correct as of November 2012. From

Schmallenberg virus was first discovered in November 2011 so it is still pretty new to scientists.  The virus infects ruminants and whilst it only causes mild disease in adult animals, if an animal is pregnant when she is infected then the baby can end up having both muscle and brain problems and can often be born dead.  The virus now seems to have spread across much of Europe (see the map from The virus itself is in the Bunyaviridae family which means that the virus is surrounded by an envelope and has a genome made up of a single strand of RNA (for reference, our genome is made up of a double strand of DNA).  The virus’ genome is made of of 3 sections named (very imaginatively) small, (S), medium, (M), and large, (L).  The genome codes for 4 proteins that are important in making up the structure of the virus.  Schmallenberg virus is in a smaller subsection of the Bunyaviridae family called the Orthobunyavirus.  Orthobunyavirus members not only have the 4 structural proteins but they also have 2 extra proteins (the NS proteins).  This information will be useful for later…

So on to the paper…

Virus Growth

The first thing the authors wanted to do was to find out how Schmallenberg virus grows in various different cells – this is important because if researchers want to carry out experiments on the viruses they need to know what cells to use.  The researchers tested sheep, cow, human, dog and hamster cells lines from organs including the brain, the aorta and the kidney (all of these are cell lines that were grown in the lab – they are not being tested on live animals).  The virus grew in nearly all the cell lines but particularly well in sheep choroid plexus (part of the brain) cells so the researchers used this type of cell for all of the other experiments.

Virus growth in different cell types.  Taken from the paper.

Virus growth in different cell types. Taken from the paper.

‘Rescuing’ the Virus

The next thing the researchers did was design a system to make more copies of the virus.  (Very) basically they took the S, M and L sequences of the virus genome and put the complementary sequence  into plasmids (circular loops of DNA that are found ‘naturally’ in bacteria). (So if the virus sequence was CCG the plasmid sequence would be GGC.) They then put these plasmids into another cell line and these cells replicated the plasmid genetic sequence, so making more copies of the virus.

Looking for a good animal model

Another thing the authors did was investigate whether mice could be used as an experimental model for Schmallenber virus infection.  They inoculated the virus (or a negative control) into the brains of 2 day old mice.  Those mice that were infected with the virus died within 8 days whereas those that had the negative control survived.  They then looked at other ages, using 10 day old and 18 day old mice.  Infection with the virus also killed most of the animals at these ages.  When the scientists went on to look at the brains of these infected mice they found multiple abnormalities and evidence that the virus was in many of the cells.

The authors also looked at the brains of lambs and calves that had contracted the virus ‘out in the wild’ as it were.  They found the virus in places very similar to where they had seen evidence of the virus in the mice, suggesting that the mice might be a good model.

Which bit of the virus makes it harmful

Couple_of_BacteriaA good way to find out which proteins make a disease agent harmful is to stop the virus/bacteria from producing the protein you suspect.  You then infect this mutant back into your cell lines or animal model and look to see if disease still occurs.  If the disease is no longer seen then you know that protein is vital for the disease (although it is possibly not the only one involved).  If the disease proceeds exactly as it did before you know that you were wrong in your suspicion.

The scientists who wrote this paper did just that – they ‘knocked out’ one of the non-structural (NS) proteins and infected mice with the strain.  All the mice inoculated with the original strain died within 9 days (so very similar to the previous experiment), all the control animals survived.  Of the mice infected with the mutant strain, deaths that occurred happened later than they did in the original strain group and 40-60% survived until the end of the experiment.  These results suggest that the NS protein has an important role to play in the disease caused by the virus, although it is obviously not the only one involved.

To investigate this further the scientists first went back to previously published scientific literature – the NS proteins of other viruses in the same group have been shown to inhibit the making of host immune system proteins called interferon (IFN) alpha and beta.  The scientists speculated that this might also be true for the NS protein that they knocked out. To test this they first infected some cells that can produce IFN with the Schmallenberg virus (either the mutant or the original strain).  They then collected the supernatant (basically the fluid on top of the cells).  If their hypothesis was correct then the fluid from the original strain-infected cells would contain not contain any IFN (because the NS protein inhibits its production) but the fluid from the mutant-infected cells would.  They tested the fluid in a very clever way.  They got another cell line, this time one that could not make IFN.  They added the fluid from the first set of cells.  Then they infected these new cells with a 2nd virus.  This 2nd virus is susceptible to IFN so if the supernatant contained IFN the virus would not be able to properly infect the cells whereas if the supernatant did not contain IFN then the viruses would infect the new cell line.

The supernatant from the original strain-infected cells must not have had IFN because the 2nd set of cells got infected with the 2nd virus.  In contrast the supernatant from the mutant-infected cells must have had IFN because the cells did NOT get infected with the 2nd virus.  And so this tied in nicely with the scientists’ prediction.

Finally, to confirm this the scientists infected the 2 virus strains into mice that could not respond properly to IFN.  This time 80% of the original strain-infected mice died within 4 days and the rest died within the next 2 days.  ALL of the mutant-infected mice died within 4 days.  This further suggests that an IFN response is vital for protection against disease caused by Schmallenberg virus.

And that’s where this paper ends…

… having covered a lot.  We now know what type of cells we can grow the virus in, we have a proposed animal model of the disease and we know a little (tiny) bit about what the virus needs to cause disease and what can protect the host.  The paper also has the details of 2 different ways a synthetic virus can be produced (see the ‘rescuing’ section) which sounds like it will be of great help to researchers in the future.

I thought it was a very interesting paper and I am looking forward to discussing it with anyone and everyone who joins us at journal club on Tuesday 22nd January 8pm GMT (just follow the hashtag #microtwjc on Twitter).




The map is kindly borrowed from

The ‘When germs go bad’ (one of my favourite microbe pictures) is by Gaspirtz (Own work) (made available under creative commons licence)

The lamb is by Evelyn Simak (made available under creative commons licence)


1.Varela, M., Schnettler, E., Caporale, M., Murgia, C., Barry, G., McFarlane, M., McGregor, E., Piras, I., Shaw, A., Lamm, C., Janowicz, A., Beer, M., Glass, M., Herder, V., Hahn, K., Baumgärtner, W., Kohl, A., & Palmarini, M. (2013). Schmallenberg Virus Pathogenesis, Tropism and Interaction with the Innate Immune System of the Host PLoS Pathogens, 9 (1) DOI: 10.1371/journal.ppat.1003133


Zoonotic diseases – causing more problems than illnesses/deaths alone

July 26, 2012 

@DiseaseMapper recently tweeted a link to a very interesting paper (which happily is also free to access so you can read it too – the link is here )

Why do I think this paper is so interesting?  Firstly, because it is a useful reminder that zoonotic infections (those that pass from animals to man and vice versa) do not just impact on our lives by causing us illness, and in the worst circumstance, death.  They have a massive economic impact as well.  In fact the paper reports that the estimated economic impact of zoonotic diseases from 1995-2008 was over 120 billion dollars.

There are many reasons for the economic burden of these diseases being so high: impact on tourism; impact on international trade agreements; impact on consumer consumption and behaviour; loss of farmed animals.  In many outbreaks the local economy is negatively impacted in multiple ways and obviously in poorer areas this can also secondarily affect people’s health.

The paper also goes on to speculate about why there should be a resurgence of zoonotic infections.  The authors split it into ‘Factors associated with human behaviour’; ‘Factors associated with pathogen characteristics’ and ‘Climate change and zoonotic resurgence’.  So, pinching their titles…

Factors associated with human behaviour

Here the authors split it down further:

Individual human practices – the authors use the example of ecotourism.  “urban citizens of the developed world who visit developing countries or rural areas of the developed world and engage in activities such as forest camping, river rafting, or bat cave exploring, are prone to zoonotic infections such as vector-borne rickettsioses, leptospirosis, and haemorrhagic fevers or lyssavirus-related illness, respectively“.  The authors also talk about how pet ownership, especially the increase in ownership of ‘exotic’ pets like reptiles is increasing people’s exposure to infections that previously they would never have been exposed to.

Socio-economic alterations – with an ever increasing global population there is an ever increasing demand for food, including meat.  It also means that as urban populations are expanding people are moving into previously uninhabited areas and so are being exposed to disease-causing agents that they had never been previously.

Political alterations – the authors talk about some countries with poorer veterinary surveillance or that have focal areas of zoonotic infections that previously were not having a global impact because they had strictly state-controlled economies but are now having a global impact because they have transitioned to allowing free  trade.  They also discuss the role that political disruption and upheaval can have on increasing the spread of zoonotic infections.

Scientific impacts – Part of the reason that we are recognising so many zoonotic infections is that we have got better at detecting them.  Infectious agents that we couldn’t have characterised decades ago can now be identified and classified.  Another scientific impact the authors mention is one that you will recognise if you are a regular reader of this blog: there have been many advances in medicine that allow us to live to an older age, but that have a negative impact on our immune system (for example, chemotherapy drugs can make us immunosuppressed; if you have an organ transplant you have to take immunosuppressing drugs, etc.)  This leaves a section of the population at a much higher risk of contracting any disease and so gives rise to some human infections with agents that would otherwise not normally infect humans.

Factors Associated with Pathogen Characteristics

The authors talk about how pathogens (disease causing organisms) that have a high genetic mutation rate (like flu viruses) can help them become zoonotic infections: in the authors’ words ” their enormous mutation rate is essentially a factory producing the species that are most potently pathogenic for humans

The authors also talk about how biodiversity can impact zoonotic disease transmission in this section (although, personally I’m not sure why it came into this section).  They talk about how sometimes wide diversity can reduce the spread of zoonotic agents because (if I am parsing this correctly) if there are many host animals that a vector (like a mosquito) can feed off there is less chance of it coming into contact with an animal that harbours the zoonotic agent – this is called the ‘dilution effect’.

Climate Change and Zoonotic Infection Resurgence

To quote from the paper: “Global warming is an ecological emergency, but its implications for human disease caused by infectious agents remains understudied“.  We do know some of the effects it could have – increases in temperature in previously colder countries leads to the spread of insects like mosquitoes – and the diseases they carry –  into those countries.  Climate change may also affect bird migration patterns and so may affect the exposure of birds to pathogens and also the exposure of us to them via the birds.

Finally the paper finishes with Projections for the Future. The authors point to 4 issues that “need urgent clarification and further attention“.

1) Recognition of the need for pre-emptive studies on the effects of massive or smaller developmental projects on local animal fauna and local zoonotic reservoirs

2) Recognition and enhancement of the health literacy of special populations that are at increased risk for the development of zoonotic infections (meaning that those patients on immunosuppressant drugs or who are immunosuppressed for other reasons should get more information about where they might encounter zoonotic infections and hw to avoid them.

3) Recognition of the major long-term burden induced by certain of these diseases with a chronic phase. There are some diseases that take a long time for any symptoms to show.  If a person has migrated from an area where the disease is relatively common to one where the disease is rare, the clinicians may be less likely to recognise the disease (or may recognise it at a later stage than if they were practicing in a country where the disease is common).  The authors recommend that clinicians “should be prepared to recognize the long history evolving in such patients and the extreme costs, mentioned in the introductory section, that will be passed on to the host countries”

4) Planning any intervention is difficult, for financial and scientific reasons. The burden of many of these diseases remains unrecognized… any zoonosis imposes a threat to the family as a unit—exposure is likely to be common for members of a household, particularly in agricultural settings, and animal loss (owing to the disease or state regulations for sick animals) may have a significant impact on the economy of the household, which is further worsened by the often observed inadequate access to appropriate medical treatment for the human patients themselves (imagine the scenario in any impoverished or conflict-active region of Africa or Asia). … ambitious eradication campaigns are not always feasible when all of the aforementioned issues have not been taken into account, and neither are successful elimination campaigns, as these may have temporary positive results but subsequent surveillance degeneration, leading to zoonotic resurgences, usually with some twists. (So basically we don’t really fully know the burden of most zoonotic diseases and rushing in there with eradication campaigns without considering all the other factors is not necessarily the best move.)

I think sometimes it can be really easy to think of zoonotic diseases as something one human gets from one animal, but this paper was a good reminder that these diseases can have a much broader impact.  It also had a useful discussion about why the number of zoonotic infections seemed to be increasing, but as it said (and as all papers say) there is still more work to be done in this area.

Image credit

All images were released under a creative commons licence (see links for details).  Thanks to Rugby471 for the dollar sign, to Wegmann for the tourist shot and to DROUET for the virus


Cascio A, Bosilkovski M, Rodriguez-Morales AJ, & Pappas G (2011). The socio-ecology of zoonotic infections. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 17 (3), 336-42 PMID: 21175957


Society for General Microbiology Conference ’12: #sgmdub

March 29, 2012
  1. This is the first time I’ve ever used Storify so fingers crossed…
  2. Share
    2 girls, 5 days, 1 piece of checked luggage weighing no more than 15kg… this could be a challenge! #sgmdub
  3. We got into Dublin Sunday night, registered and then went off wandering around the city 🙂
    The next morning the first session I attended was the biocontrol of diseases…
  4. First up was: 
    Novel engineering of attenuated Salmonella enterica serovar Typhi strains for use as live vectors
    Jim Galen (University of Maryland)
  5. Share
    Using salmonella as live vector for vaccination #sgmdub
  6. Share
    Use non-antibiotic selection method to avoid antibiotic resistance genes in vaccine vector strains. #sgmdub
  7. Share
    Live vectors can be used to export antigens. More attenuation means less immune response #sgmdub
  8. Share
    Likely tht delivery of mutiple ags using single plasmid-bearing live vector vaccine will require chromosomal expression of =/>1 ag #sgmdub
  9. Share
    “Attenuated s typhi live vectors represent flexible platform for expression of foreign ags” #sgmdub
  10. Share
    V interesting talk by J Galen #sgmdub
  11. Share
    Genome Atlas – allows you to see secondary structure of your chromosome. #sgmdub
  12. Next up… 
    Vaccination against Clostridium difficile infection
    Simon Cutting (Royal Holloway, University of London)
  13. Share
    Use of bacterial spores as vaccine. Many advantages… #sgmdub
  14. Share
    Cheap, long-lasting, survive well, possibility for oral delivery, heat stable #sgmdub
  15. Share
    Spores also serve as adjuvant and can (?)Adsorb antigens eg viruses. #sgmdub
  16. Share
    C diff infection – 30% of patients develop relapse #sgmdub
  17. Share
    using c diff spores to protect against c diff infection. V interesting talk. #sgmdub
  18. Share
    Oral dosing is better. ?mucosal immunity most important? #sgmdub
  19. The SGM Prize Medal Lecture this year was given by Julian Davies (University of British Columbia)  
    “Molecules, microbes and me” 
    It was a brilliant talk from clearly a brilliant man!

  20. Share
    “Molecules microbes and me” by Julian Davies about to start #sgmdub
  21. Share
    Most expensive hyrolytic reaction in history: betalactamase action. #sgmdub prize lecture
  22. *hydrolytic! 
  23. Share
    #sgmdub cool. In nature, antibiotics may not actually be ANTIbiotics.
  24. Share
    Environmental role of antibs poorly understood V interesting – I’d assumed we knew… #sgmdub
  25. I thought that we knew antibiotics were soil microbes way of protecting themselves from other bugs – apparently we don’t actually know that…
  26. After lunch I ran between the Food Borne Pathogens session and the New Media session.  Sadly I couldn’t be in both places at the same time so I’m sure I missed some great talks but here is what I went to…
  27. Interaction of Salmonella enterica and E. coli pathotypes with edible fruit and vegetables
    Gad Frankel (Imperial College London)
  28. Share
    #sgmdub shift of salmonella transmission: used to be mostly poultry, now vegetables playing larger role
  29. Social media for researchers – maximizing your personal impact
    Alan Cann (University of Leicester)
  30. Share
    “Having online profile no longer an issue of vanity”alan cann #sgmdub
  31. Share
    Build up network of trusted individuals says A Cann in New Media session #sgmdub
  32. Share
    Don’t have time for social media? If you care bout your career you don’t have time not to do it says A cann in New Media session #sgmdub
  33. Share
    Definitely identify with “ploughing lonely furrow” in social media with my dept! #sgmdub
  34. Share
    Back to importance of choosing who is in your network. New Media session at #sgmdub
  35. Share
    “Process of curation never stops”. A Cann. #sgmdub
  36. Scientists and social media
    Alice Bell (Imperial College London)
  37. Share
    Audioboo – like twitter but with sounds according to @alicebell. Anyone know if blackberries can get it as well as iphone? #sgmdub
  38. Share
    Blogging allows parents w/children who can’t go 2conference 2potentially have sane networking opportunity #sgmdub #womeninscience
  39. Share
    Obviously my last tweet shd have read “same networking” rather than “sane”! #womeninscience #sgmdub. May still b applicable!
  40. To be honest I had never really thought of that point before but obviously being a parent will to some extent limit your conference attendance.  I’m hoping that my tweeting from the conference might be interesting to some of those that couldn’t make it this year.
  41. Share
    .@alicebell talk reminding me why I blog – I learn lots and it’s fun. Also great when authors of papers I talk about get in touch #sgmdub
  42. Share
    Excellent talk by @alicebell on scientists and social media #sgmdub
  43. Food from the fire: how the host response feeds Salmonella
    Andreas Baumler (University of California, Davis)
  44. Share
    Hydrogen sulhpide makes food “smell interesting”! Lovely understatement! #sgmdub
  45. Every defeat is a small victory: the what, when, where and how of setting up a microbiology blog
    Benjamin Thompson (Wellcome Trust, London)
  46. Share
    The who what how and why of setting up a micro blog – what shd I have done? Now at #sgmdub
  47. Share
    Make sure ur blog name will come up early on google! #sgmdub
  48. Share
    Scaleabiity is important. Need to balance the rest of ur life and ur blog. #sgmdub
  49. Share
    “Flickr search creative commons = your friend” #sgmdub
  50. Share
    Editing important. Remember short paragraphs for internet posts. #sgmdub
  51. Share
    Get someone to read ur work before u post it. #sgmdub
  52. All of the New Media talks I went to were fantastic.  Sadly I couldn’t make the Twitter Journal Club talk so I don’t know what came out of it – maybe some microbiologist will be setting up a micro twitter journal club soon…
  53. The Peter Wildy Prize for Microbiology Education went to 
    Vincent Racaniello who gave an excellent talk titled
    “Educating the world about microbes”

  54. Share
    V excited about “educating the world about microbes” with Vincent Racaniello #sgmdub
  55. Share
    Blogs give ppl access to scientists – Vincent Racaniello’s talk #sgmdub
  56. Share
    Before my phone battery dies… Fascinating talk by Vincent Racaniello and great day at #sgmdub looking forward to tomorrow!
  57. Share
    Possible to do both research and outreach/education effectively #sgmdub
  58. Food Borne Pathogens again today – not all lectures are covered as some went a little over my head! (There are times when not having done a Microbiology based undergrad degree is a bit of a hindrance!)
  59. The Marjory Stephenson Prize Lecture was given by 
    Yuan Chang & Patrick Moore (University of Pittsburgh Cancer Institute) 
    “Old themes and new variations in human tumor virology”
  60. Share
    Settling down for Marjory Stephenson Prize Lecture being given by Yuan Chang & Patrick Moore #sgmdub
  61. Share
    #sgmdub infections responsible for ~20% of human cancer
  62. Share
    #sgmdub why do some viruses cause cancer when their near relatives don’t? We don’t fully know yet…
  63. Share
    Viral tumours are biological accidents #sgmdub
  64. Share
    #sgmdub kshv innate immune evasion genes = also oncogenic
  65. Share
    #sgmdub “tumour suppression and innate immunity: 2 sides of same coin?”
  66. Share
    #sgmdub mcv almost ubiquitous so why does it only sometimes cause cancers?
  67. Share
    Mcv is replication deficient in mcc #sgmdub
  68. Viral oncology is really not my area but the talk was aimed at a low enough level that even I could keep up – was fascinating 
  69. Intensive broiler chicken production systems and the infection biology of Campylobacter
    Tom Humphrey (University of Liverpool)
  70. Share
    #sgmdub campylobacter is defined as ‘commensal’ in chickens but can cause dz in the birds…
  71. Share
    #sgmdub campylobacter a poorly controlled chicken commensal? Chicken mounts marked response to campy but little to lactobacillus commensal
  72. Share
    #sgmdub antibody response confines bug to chicken gut
  73. Share
    #sgmdub problem with surface contamination- cross contamination. Bigger problem is internal contamination – liver pate outbreaks etc
  74. Share
    #sgmdub can get transient campylobacter bacteraemia in chickens
  75. Effects of co-culture on Campylobacter
    Friederike Hilbert (University of Vienna)
  76. Share
    Campylobacter almost never alone in its natural life cycle #sgmdub
  77. Share
    Campy survives longer in oxygen if cocultured with pseudomonas #sgmdub
  78. Try not to breathe: the role of oxygen in the Campylobacter lifestyle
    Arnoud van Vliet (Institute of Food Research, Norwich)
  79. Share
    Bact. response2stress: parasitism, symbiosis, commensal, sporulation/biofilm, death Gd analogy2managment conflict resolution scheme #sgmdub
  80. Offered paper Campylobacter enteritis; emerging dynamics of human infection
    Susan Bullman (Cork Institute of Technology)
  81. Share
    Campylobacter ureolyticus – an emerging gi pathogen? #sgmdub
  82. Offered paper Bacterial rejuvenation: lag phase is a distinct growth phase that prepares bacteria for exponential growth and involves transient metal accumulation
    Matthew Rolfe (University of Sheffield & Institute of Food Research, Norwich)
  83. Share
    #sgmdub v interesting talk by Matthew Rolfe on bacterial lag phase of growth.
  84. There was a  Hot Topic Lecture given by 
    Richard Elliott 
    “Schmallenberg virus: fact from fiction”

  85. Share
    Looking forward to “Schmallenberg virus: fact from fiction” with Richard Elliott #sgmdub
  86. Share
    #sgmdub orthobunyavirus genus – >170 named viruses – now includes schmallenberg
  87. Share
    “It is unlikely that this virus can cause dz in humans but it cannot be completely excluded at this stage” #sgmdub
  88. Share
    #schmallenberg #sgmdub been detected in france, germany, uk, italy, spain, jersey
  89. Share
    #schmallenberg #sgmdub adult animals show little to no dz but congenital abnormalities in offspring. Healthy newborns not viraemic
  90. Share
    #sgmdub #schmallenberg by december ’11 getting congenital defects in lambs and calves positive for sbv
  91. Share
    #sgmdub #schmallenberg is not a notifiable dz. Are we missing cases?
  92. Share
    #sgmdub likely that sbv was in midges blown across channel
  93. Share
    #sgmdub I can’t help but think is pretty impressive that from 1st known cases2virus isolation2now ppl have managed2learn so much bout virus
  94. Share
    #sgmdub need to look in midge head to find evidence cd transmit to animal.virus cd b in gut purely because fed on infected animal recently
  95. Share
    #sgmdub with akabane (related virus) get waves of immunity in livestock
  96. It was an absolutely fantastic lecture bringing us all up to date on the latest on the virus
  97. Campylobacter jejuniexploits host cell processes 
    Michael Konkel (Washington State University)
  98. Share
    #sgmdub seeing increase in c jejuni isolates resistant to antib’s
  99. Share
    #sgmdub c jejuni binds to fibronectin – 37kDa OMP exhibits fn-binding activity
  100. Share
    #sgmdub anti-flaA chick maternal antibodies can inhibit motility. Can we use maternal antibodies to show poss vaccine targets?
  101. Share
    V interesting talk by M Konkel – looks like promising approach to vaccine development #sgmdub
  102. At this point I nipped across to the phylogeography session…
    Global spread of multidrug resistant Salmonella Typhi
    Kathryn Holt (University of Melbourne) 
  103. Share
    #sgmdub v interesting to see how different drug regimes may have affected resistance profile of S typhi
  104. Clonal evolution and spread of a transmissible cancer lineage in Tasmanian devils 
    Elizabeth Murchison (Wellcome Trust Sanger Institute, Cambridge)
  105. Share
    #sgmdub shd we consider transmissible cancers to be microbes?
  106. Share
    #sgmdub horizontal transmission of living cancer cells – wow
  107. This was one of my favourite talks of the whole conference – very clearly explained and an interesting topic.
  108. Fleming Prize Lecture
    Plagues and populations – patterns of pathogen evolution 
    Bill Hanage (Harvard School of Public Health, Boston, Massachusetts)
  109. Share
    #sgmdub Plagues and Populations: patterns of pathogen evolution with Bill Hanage
  110. Share
    #sgmdub 3 E coli isolates (therefore supposedly same species) – only 39% genes present in all 3 strains (Weich et al 2002)
  111. Share
    #sgmdub Are bacteria bags of genes brought together for transient benefit? Interesting question
  112. The lecture was brilliant (and I think someone compared Bill Hanage to House!)
  113. Offered paper Out of the environment and into the host; mapping the path to pathogenicity across the genus Yersinia
    Thomas Connor (Wellcome Trust Sanger Institute, Cambridge)
  114. Share
    #sgmdub if we only consider pathogenic Yersinia we are missing most of diversity in the genus
  115. Offered paper Assessing Bartonella henselae diversity using whole-genome sequencing and single-nucleotide polymorphism analysis
    Gemma Chaloner (University of Liverpool)
  116. Share
    Bartonella henselae – a few uncommon STs responsible for most human infections (vets beware!) #sgmdub #zoonosis
  117. Offered paper Assessing the diversity of antimicrobial resistance in animal and human Salmonella Typhimurium DT104 using phenotypic and genotypic data
    Alison Mather (Wellcome Trust Sanger Institute, Cambridge)
  118. Share
    V interesting talk on antimicrobial resistance by Alison Mather #sgmdub #zoonosis
  119. Offered paper The transcriptional architecture of Salmonella Typhimurium SL1344
    Jay Hinton (Trinity College Dublin)
  120. Share
    V clear description of RNAseq results from Jay Hinton. #sgmdub
  121. Share
  122. Offered paper Non-O157 verocytotoxigenic Escherichia coli (VTEC) on bovine farms
    Declan Bolton (Teagasc Food Research Centre, Ashtown)
  123. Share
    Non-O157 STEC/VTEC – shdnt forget this grp of E coli #sgmdub #zoonosis
  124. Share
    Only 1 more #sgmdub event left for me 😦 But it is “Stopping the Spread of Superbugs” which I’m really looking forward to 🙂
  125. Share
    Fab description of how and why infection with MRSA in diff places causes diff symptoms #sgmdub
  126. Share
    Dogs, cats, pigs all been found with MRSA – another gd reason to wash ur hands after playing with ur pet. #sgmdub #zoonosis
  127. I loved this session – I thought it was a great way to approach public engagement.  It didn’t feel like microbiologists were just telling stuff to the audience – (IMO anyway) it felt like the audience’s opinions were valued.
  128. Overall the conference was a brilliant experience (and I really need to get a thesaurus – sorry!) I met many friendly people and learnt a lot.  Thanks to the poster presenters, the speakers, the exhibitors, the CCD staff and everyone at the SGM who organised the event – you did a stunning job 🙂

Quick note

January 3, 2012

I hope that you have all had a good holiday season.

I’m just updating quickly with a shameless plug for the January edition of the Molecular Biology Carnival which I’m thrilled to be in – there are some fantastic posts linked so it’s well worth checking out.

For anyone going to the American Society for Microbiology conference in 2012 – have you come across this website where you can submit topics for presentation at the conference and the top 5 voted topics get to present?  There’s some great topics there so do check it out and PLEASE vote for your favourites.

Research blogging to resume asap…



Image By MZMcBride and released into the public domain.  Available here


Using a parasite as a vaccine…

December 6, 2011

A group of researchers (see reference below) have been looking at a very interesting new method of vaccine delivery: using trypanosomes.

T. (megatrypanum) theileri  is found infecting cattle worldwide.  It is transmitted by flies and gains entry to the animal either through broken skin or via mucous membranes and once the animal is infected it tends to carry low numbers (~100 organisms/ml) of trypanosomes for the rest of its life. Although there is some evidence suggesting that infection with this organism has the potential to cause a drop in milk yield in some cattle the authors state that the “ubiquity of infection with this organism in cattle herds suggests that it has no significant impact on health or productivity in healthy animals”. 

Because of this apparent lack of pathogenicity and because the parasites persist for such a long time in the host the researchers thought they could potentially use the trypanosome to deliver antigens (molecules that will trigger an immune response) from other, more pathogenic organisms to the cattle, so effectively using it like a vaccine.

The researchers tested this by genetically modifying the trypanosome to produce Bd37 – an antigen from Babesia divergens (which causes a disease called “redwater fever” in cattle).  They engineered 3 different groups of trypanosomes.  The first expressed the Bd37 within themselves (intracellularly), the second expressed the Bd37 on their surface (extracellularly) and the third actively pumped out the Bd37 (secretory).  They then infected cattle with the trypanosomes.  After inoculation they took blood samples at regular timepoints to look for any antibody response.

All of the cattle became infected with the trypanosomes and they stayed infected for the entirety of the 12 week period of the trial.  The number of cattle that started to produce antibodies against Bd37 after infection were:

Intracellular group: 4/6

Extracellular group: 3/6

Secretory group: 5/5

The researchers also showed that those in the secretory group had significantly higher antibody levels than the other two groups.  The antibody levels of all animals that produced them continued to increase for 60 days and remained high for at least another 24 days (which was as long as they were measured for).

Finally the researchers compared the antibody levels achieved with the trypanosome method of delivery with a traditional vaccine delivery and they found that the antibody levels were “equivalent”.  (So this trypanosome delivery method is effectively providing as much protection as the traditional vaccine.)

If this method does not produce better antibody production than a standard vaccine why would you go to the bother of engineering these trypanosomes?  Well the researchers say that this method of delivery has several advantages:

  1. As trypanosomes can cross mucous membranes there is the possibility for vaccine delivery
  2. As the trypanosomes infect the host for a very long time, potentially for the rest of its life, they could potentially stimulate an immune response against a target antigen for this length of time, so providing immunity for a longer period than a traditional vaccine

Another advantage is that T. theileri is already non-disease causing in cattle.  Some vaccine delivery systems use attenuated bacteria such as Salmonella but these bacteria have the potential to revert to being disease-causing.  As T. theileri doesn’t cause disease this isn’t something the researchers need to worry about.

So all of this research is very promising and suggests that with more research trypanosomes could be used in the future to protect cattle from disease.

But I’ve tagged this as a ‘zoonosis’ post and so far only talked about cattle diseases.  What relevance does this have to human health? 

Blood smear from patient with African trypanosomiasis. Image taken by the US Centre for Disease Control and Prevention.

Human African Trypanosomiasis, also known as sleeping sickness is a fatal disease that occurs in sub-Saharan Africa.  It is caused by the trypanosomes Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense.  These trypanosomes are spread from person to person by the tsetse fly (it bites infected Person A, takes a blood meal which contains trypanosomes, flies off and then bites uninfected Person B, infecting them as it does so).  The main reservoir for T. brucei gambiense is the human population however cattle are an extremely important reservoir for T. brucei rhodesiense.

T. brucei rhodesiense (as you can tell by the name) is closely related to another trypanosome that infects cattle T. brucei brucei.  This trypanosome only infects cattle – it can’t infect humans because a substance called ApoL1 found in human serum kills it.

The researchers speculate (and it is currently only speculation) that if T. theileri was used to deliver a modified form of ApoL1 that killed T. brucei rhodesiense  this vaccine system could be used to dramatically reduce the cattle reservoir of this dangerous parasite.  There is a HUGE amount of work that needs to be done before this can even be trialled but it has the potential to make a great impact on human health. 

Watch this space!


The trypanosome image came from the paper (see below).

The blood smear image is available on Wikimedia Commons here

Further Reading

WHO information on Human African Trypanosomiasis

Mott, G., Wilson, R., Fernando, A., Robinson, A., MacGregor, P., Kennedy, D., Schaap, D., Matthews, J., & Matthews, K. (2011). Targeting Cattle-Borne Zoonoses and Cattle Pathogens Using a Novel Trypanosomatid-Based Delivery System PLoS Pathogens, 7 (10) DOI: 10.1371/journal.ppat.1002340



How do we know what causes an infectious disease? Part 2

November 18, 2011

So in Part 1 I discussed the set of guidelines, or postulates, designed by Robert Koch (and his colleagues) that helps scientists get the evidence they need to establish that a specific infectious agent causes a specific infectious disease.

1) Establish association of the organism with the disease.

2) Isolate the organism and grow in pure culture.

3) Put the organism into a healthy host and show the host gets diseased.

4) Reisolate the organism from the now healthy host and show it is the same now as when you put it in.

I also discussed the main limitations of the guidelines:

Asymptomatic carriers – not every host infected will show signs of diseases.

Organisms that are difficult to culture – these include organisms for which we just don’t know the right culture conditions as well as viruses which need to be in a cell in order to multiply and so by definition cannot be grown in the “pure culture” that the postulates require.

Another limitation which I didn’t discuss in my previous post: the type of healthy host that you need to use for 3).  Say chocolatitis is only found in humans and that Chocolobacter has no harmful effect on other species – what would I do then?  It wouldn’t be ethical to use a human host for 3).

These limitations mean that sometimes Koch’s postulates are an inappropriate set of guidelines to try to use.  If a microbe fulfills all of Koch’s postulates it is most likely the cause of the disease you’re looking at.  If a microbe doesn’t fulfill all of them it might still be the cause but it might instead be there coincidentally.

But is there anything else scientists can do to provide more evidence for whether or not microbes that don’t fulfill the postulates are the cause of the disease?

Over the years since Koch first published his postulates scientists have adapted them in various ways to help them identify disease-causing microbes.  Now that we have the ability to isolate, amplify and study nucleic acid sequences (those that make up DNA or RNA) a new set of guidelines has been proposed(1).

And so we return once more to chocolatitis, and the agent I suspect is causing it – Chocolobacter.  It turns out that Chocolobacter is very difficult to isolate alive and culture but I have managed to sequence at least some of its genome.  So although this means that I can’t easily use Koch’s postulates to help me establish Chocolobacter‘s guilt, I can use these ones (I’ve quoted the guidelines as they are written in the paper in bold and then explained it in the non-bold font):

1) “A nucleic acid sequence belonging to a putative pathogen should be present in most cases of an infectious disease.”  To fulfil this I need to find my Chocolobacter genome sequence in the diseased host, preferably in the brain (which I’m assuming is the organ most severely affected in this infection) and I need to find it in most cases of the disease.

2) “Fewer, or no, copy numbers of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease.” So the Chocolobacter sequence must not be found (or be only rarely found) in healthy hosts and preferably, even in diseased hosts it shouldn’t be found in organs unaffected by the disease.

3) “With resolution of disease (for example with clinically effective treatment), the copy number of pathogen-associated nucleic acid sequences should decrease or become undetectable.” So if my diseased host gets better, I should no longer find any Chocolobacter sequences (or at least there should be fewer) in their brain.  (I know my host has now apparently had several brain biopsies – this is totally fine in my imaginary world!)  If my host then gets ill again the sequences should also return.

4) “When sequence detection predates disease, or sequence copy number correlates with severity of disease or pathology, the sequence-disease association is more likely to be a causal relationship.”  If either I could detect the Chocolobacter sequences before the host started to show any symptoms, or if the host getting sicker corresponded to an increase in the number of sequences detected, this would strongly suggest that Chocolobacter was the cause.

5) “The nature of the microorganism inferred from the available sequence should be consistent with the known biological characteristics of that group of organisms.”  What this is saying is that first, I need to identify other organisms that are related to Chocolobacter (I can use the genome sequence to help me with this).  Let’s say it’s related to Spinachobacter (infection with this causes people to eat lots of spinach – I’m so imaginative…) and Coffeobacter (guess what this does…).  To fulfil this guideline the behaviour of Chocolobacter and the characteristics of the disease it causes should be similar to its relatives Spinachobacter and Coffeobacter.

6) “Tissue-sequence correlates should be sought at the cellular level.” Ideally I should be able to make a nucleic acid sequence that will bind to the Chocolobacter sequence, and I should label my sequence with a fluorescent dye.  Using tissue samples (for example on a slide) my sequence should bind to regions with the Chocolobacter sequence and should fluoresce.  This can then be looked at for example by using a microscope.  (This is a type of in situ hybridisation.) The areas of fluorescence should correspond to either visible Chocolobacters or to areas which I presume to be affected by Chocolobacter.

7) “These sequence-based forms of evidence for microbial causation should be reproducible.”  I can’t just fulfil the above six guidelines once.  I have to do it lots of times to be sure.

No doubt as the technology we have available improves the guidelines will once again be adapted and adjusted as we find new ways of detecting microbes but in a way this is irrelevant. 

What really matters is that, regardless of the set of guidelines we as scientists use to prove the cause of a disease, the process should be logical.  I can’t just conclude that Chocolobacter causes chocolatitis just because it happened to be present in a few chocolatitis cases and I’m strongly suspicious of it.  But if I follow a logical set of steps, whether the original ones published by Koch or a newly designed set of my own, I should be able to generate enough evidence to prove whether or not Chocolobacter causes chocolatitis. 


References/where to find more info

(1) Fredericks DN, & Relman DA (1996). Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clinical microbiology reviews, 9 (1), 18-33 PMID: 8665474

(2) Inglis, T. (2007). Principia aetiologica: taking causality beyond Koch’s postulates Journal of Medical Microbiology, 56 (11), 1419-1422 DOI: 10.1099/jmm.0.47179-0



September 28, 2011

At last my desk has gone from this:




I have handed in my first year report, got through my first year viva/presentation thingy, presented a poster at an international conference and got the next set of experiments pretty much ready to go so I can finally get back to looking at zoonoses. 

Watch this space! (Or just use the RSS feed/sign up by email options 😉 )

In the mean time there’s a great blog post by James Byrne over at Disease Prone on Hendra virus – a potentially deadly zoonotic virus that infects horses and fruit bats and sometimes us.  Go have a look.



The busy desk image is by MZMcBride and was released into the public domain (for more details see here)

The less busy desk is a derivative image of the first by Train2104 and was released into the public domain (for more details see here)