The story behind the paper

We recently published a paper on genomic surveillance of a diarrhoeal pathogen Shigella sonnei across Latin America which represented the culmination of over five years of collaboration, as well as training and development in the region

Graphical abstract

In collaboration with the Wellcome Trust Sanger Institute, the Pan American Health Organisation and PulseNet Latin America and Caribbean (PNLAC), we whole genome sequenced over 400 Shigella sonnei collected from nine countries over two decades. Shigella are the most important bacterial cause of moderate-to-severe childhood diarrhoeal disease in low to middle income nations, and countries in Latin America still experience endemic disease and explosive outbreaks. By sharing information on common pathogen subtypes through public health networks, like PNLAC, pathogens can be traced epidemiologically to facilitate early identification and intervention in disease outbreaks. Whole genome sequencing is transforming surveillance of bacterial pathogens, as it provides the highest resolution of pathogens subtypes and can also be used to explore other genetic factors of interest, like antimicrobial resistance. However, its cost precludes routine use in some areas, which are unfortunately some of those regions where the most Shigella disease is seen.

In this study, we sequenced approximately 50 isolates from nine countries in Latin America and use whole genome phylogenetics to reveal those sublineages that were responsible for most of the disease in the region. We identified a novel global lineage of Shigella sonnei, and by correlating the geography of where isolates came from to their evolutionary relationships, we could see international transmission of some sublineages and what the distribution of different sublineages was across the continent. Visit the microreact page to play with the data yourself.

We were also able to identify key determinants of antimicrobial resistance in the pathogens and how they were distributed among the different sublineages, providing key information for managing this important disease in the region.

In addition to constructing this invaluable regional framework for ongoing surveillance, this project helped build capacity for whole genome sequencing surveillance in the region. Over the course of the collaboration, the World Health Organisation sponsored the establishment of whole genome sequencing facility at the reference laboratory for PNLAC, ANLIS in Buenos Aires, Argentina (see photo). In the paper, we show how locally-generated sequencing data from this facility can be integrated into the regional surveillance framework to determine whether outbreaks were due to locally-circulating lineages or resulted from the importation of new sublineages.

In addition to laboratory capacity building, the collaboration involved training an ANLIS researcher (Josefina Campos – see photo – who now runs the genomics facility there) in bioinformatics, and conducting training courses (in conjunction with Wellcome Trust Advanced Courses) for medical, veterinary and public health professionals in the region, including courses in Argentina, Uruguay and Costa Rica (see picture).

There are 29 authors on our paper and every one of them worked hard on, and cared deeply about, the outcome of the study as well as the training programs and capacity building surrounding it. Every paper has a story behind it, and this one, like so many others, is so much more than it appears.

Photo: Top ANLIS in Buenos Aires, Argentina. Bottom (from right to left) ANLIS collaborator Josefina Campos and co-corresponding author Nicholas Thomson (WTSI) outside the Malbran (ANLIS) Institute; Genomics for Epidemiology and Surveillance of Bacterial Pathogens course instructors and participants held in February 2015 in San Jose, Costa Rica; co-corresponding author Kate Baker with bust of Carlos Gregorio Malbran, the ANLIS institute’s namesake.

Lay summary on Latin America.png

Harambee! Let’s all work together!

36 Maasai elder

An exciting part of the activities of the Mara Herbivore Research project is the work we do with the local communities around Talek in Kenya. For more than a decade we have been running a training course for Kenyans working in the tourist sector. Here we develop the knowledge and skills required to work as a professional tourist guide. The main focus is on making up-to-date scientific knowledge about the African ecosystems and their inhabitants accessible locally. It leads to many stimulating discussions when we are comparing research findings with local ideas about nature: sometimes science is merely confirming what has been long known locally, sometimes the two are at odds and we discuss why this may be.

We also teach on the ecology and conservation of African ecosystems at primary and secondary schools in both Kenya and the UK. Here it is encouraging to experience the connection that kids everywhere have with nature and feel their enthusiasm. We are always hoping that we may inspire some to follow a career in science or conservation later on.

As opportunities arise, we moreover give talks to raise the awareness of the general public on the urgent threats facing Africa’s savannas, particularly from encroaching human populations, intensifying livestock production, poaching and climate change. In doing so, we encourage locals to reflect on the sustainability of some current land-use practices, and we seek to convey to people elsewhere that conservation in developing countries is a global responsibility.

For more details about Dr Jakob Bro-Jorgensen‘s work, click on this link: Mara Herbivore Research project

Pint of Science – The evolution of feet, the brain and masturbation

Dr Rebecca Jones board picturefrom the School of Life Sciences recently hosted the Pint of Science event on evolution recently at the Shipping Forecast. Here’s what she had to say:

When I was asked to host a night for the recent Pint of Science event in Liverpool I jumped at the chance. I’d been to a couple already, Manchester and Exeter, and thoroughly enjoyed them. Pint of Science aims to bring science to local pubs where the public can listen to researchers describing their work. There’s normally a theme for each city, with Liverpool covering Our Body, Beautiful Mind and Atoms to Galaxies. As a lecturer in the School of Life Sciences I was hosting the ‘Evolution of feet, the brain and masturbation’ at the Shipping Forecast on the 15th May.

Alongside a team of volunteers (Georgia Drew, Amy Eacock, Chloe Heys and Jo Griffin) and a willing photographer for the evening (Lukasz Lukomski), we had our evening planned. As the public entered the venue, the basement of the Shipping Forecast, they had a chance to fill in the three quizzes set by our three fantastic speakers in the hope of winning some Pint of Science prizes. These included matching the footprint to the nationality, guessing which brain belonged to which animal and pairing animal’s with their penises.


After the welcome and thanking of the sponsors, eLife, we started with our first talk by Dr Kris D’Aout on the evolution of the foot.


Kris discussed his work examining locomotion and the use of shoes in various countries, particularly India. Although it seems Kris struggles with volunteers here in the UK!


He even showed a video of a robot having to meander around some walking humans! Kris was met with a barrage of questions from the audience, including some asking advice on wearing slippers around the house!


Next up we had Dr Tom Butts who spoke on the evolution of the brain and he even managed to rope in some keen volunteers to demonstrate the formation of the spinal cord.




Tom then received some rather tough and philosophical questions about brain development and dinosaurs which got everyone thinking!


We then had a break in which people replenished their drinks but also got to listen to three excellent 2 minute talks from researchers. Jennifer Mitchell, Elinor Chapman and Angela Hackett (L to R) all described their research without the use of props or slides to an enthralled audience who eventually voted Elinor the winner!


Our final talk, and headline act, was Dr Tom Price who spoke about the evolution of masturbation across animal groups.


Tom mostly spoke about sex and masturbation in birds although had some interesting theories on whether masturbation occurred in dinosaurs!! Tom said, “People seemed to enjoy my speculations on solo sexual behaviour in ducks and dinosaurs.” However, he was more surprised that “Some members of the public were surprisingly good at identifying weird animal genitals.”


Following some entertaining questions and prize giving, the conversations moved upstairs where people were keen to find out more about feet, the brain and most importantly, masturbation.

I’d like to say thank you to the speakers and all the volunteers that helped on the night! There was a lot of organising but it made for a memorable event!

College careers talks

by Meriel Jones

Over the years I’ve given many presentations at schools and colleges about what the biological sciences are like at University.  So far this year I’ve been to Xaverian College ( in Manchester and King Edward VI College ( in Stourbridge near Birmingham.

Xaverian College is in central Manchester and has high expectations of its students.  Many continue to higher education and each January the College holds an event with speakers from many universities and subjects areas.  This begins support for the students to decide on their career paths post A-level.  I go along to talk about the biological sciences.  I feel that talking about the subject content is better left to perusal of the websites and prospectuses, and that I should rather include my personal insight from my own experience.  My focus is always on the ways that university differs from school, and what sorts of careers are open to those with biological science degrees.

King Edward VI College is on a (large) traffic island in the centre of Stourbridge near Birmingham.  The college also has great ambitions for its students.  My talk there is at a similar careers event in March that starts the path to UCAS applications and university.  This time my topic is the biomedical sciences, and I explain about the important choice between accredited degrees that are a direct pathway to roles within the NHS and non-vocational degrees that can leave additional career paths more open.  I also talk about the difference between medical and biomedical degrees and careers.

Both colleges have a large and diverse group of students who take these career events very seriously and ask perceptive questions.  Every year, it is a pleasure to see their enthusiasm.  It is also great to answer questions from their teachers, who act as hosts during the events.


Thoughts on #LiveTweeting

As a part of the Centre for Cell Imaging and a member of the Microscopy and BioImage Analysis community, I occasionally get away to conferences like the recent NEUBIAS training school and symposium in Portugal.


Since having joined Twitter last year (@dn_mason), this is the second conference that I’ve been to, and as a result, was the second time I tried (with reasonable success) to Live Tweet at the conference.

Live What Now?

Going right back to basics, Twitter is a platform for broadcasting small messages (of ~140 characters). Some describe it as micro-blogging. To many, the brevity of each tweet is both it’s greatest strength and also one of the most frustrating features.

Live tweeting, is basically the act of providing a running commentary of a seminar, event or even a whole conference. All of the tweets associated with such an event can be tied together using a text-tag called a #hashtag (which starts with a hash like that last one).

You can always go back through the twitter website (or app) and see all of the tweets associated with a hashtag. For example, check out all the #NEUBIAS tweets.

OK, I get it, but why bother?

I find myself being asked this question quite a bit. So here are my three main reasons for live tweeting (in no particular order):

  1. OPEN NOTEBOOKS: Like most people these days, I have way too much paperwork. Between manuscripts, notes and admin, the last thing I need is more paper on my desk. By live tweeting, I can keep track of who presented what, and when (and, what I or the audience thought of that in the question periods/breaks). Once you get the hang of it, you can check and record links to papers and websites on the fly so you know that you’ve not made a mistake in writing down the the URL (especially important if your handwriting is less than clear). Everything is time-stamped and fully searchable so it’s easy to find that note you took six months ago (can you say the same about your regular notebooks?).
  2. ACCESSIBILITY: Plain and simple, live tweeting, gives people who aren’t at the event access to some of the ideas, thoughts and opinions that are expressed there (see endnote #1). Perhaps you’re off at another conference but want to stay abreast of the latest research, or maybe your budget doesn’t stretch to a trans-atlantic flight. Furthermore, this taps into the idea of open science. By sharing your ‘notes’ via Twitter, everyone gets interactive access to them and the community can start a conversation around them.
  3. NETWORKING: This might be a slightly broader point, but a lot of scientists use Twitter. By becoming part of the twitter ecosystem surrounding an event, you will probably find it easier to get yourself and your work known. You’re also becoming a bigger part of the community and getting involved with discussions to which you would otherwise be oblivious.

Tips for Tweeters

I am by no means a twitter expert (a twexpert?) least of all regarding live tweeting, but below are a few tips that might help you to get started:

1) Ditch the default website


At least 3% of your screen here is taken up by beard.

The twitter homepage (above) may look nice but it’s really inefficient on space. Once you move to Tweetdeck, you will never look back. Tweetdeck is a very customisable app built into twitter. Compare the image above with the one below. Left to right, I have my home feed (tweets from people I follow), my notifications (people talking directly to me or interacting with my tweets) and the #NEUBIAS hashtag, all on one page.


You can add as many columns as you want, so you can follow individual people, hashtags or direct messages, tailoring exactly what you see in each column (likes, retweets, follows &c)

2) Tabbed browsing

It’s fairly obvious that Twitter is a web application (see endnote #2). So you probably already have a web browser open. Learn how to use and manage tabbed browsing, so you can quickly search for websites (IE the speaker’s homepage), papers (PubMed or your equivalent repository), or relevant links that you might want to come back to later. Learn shortcuts to quickly switch between and close tabs.

3) Links and Hashtag

Does the speaker use twitter? If it’s not on their title slide, a quick search is a good way to find out:


Assuming you don’t have a ridiculously common name…

If they do, include it in your tweet. It lets them know that people are discussing their work and opens up another avenue for discussion (once they’re off the stage).

This also helps with the visibility and networking mentioned above. Same idea goes for hashtags. If the event has a tag, use it in every tweet. Also, try to hashtag topics that will expose your tweet to others who might find the content interesting. #Don’t #over #do #it #though.

4) Harness the power of images

A tweet with an attached image is more visible and easier for you and others to find later when scrolling down a timeline. I try to add images at least once per logical break, even if they’re screen grabs from a website or company logos.

2017-02-18-tweets1Get to know how to screengrab, crop, save and upload an image quickly on your platform. Most browsers can open PDFs directly so you don’t need to download and open in an external application to screen grab an interesting figure or notable schematic from a paper. Make sure you include a link (a DOI or URL) so people can put the image in context.

5) Get to know the tweeps!

As I said before, a lot of scientists use Twitter. Try to figure out who are the people tweeting at a conference and make sure to follow them to see what they’re talking about. You may find extra insight or perhaps an interesting discussion point in which you can get involved (on or off-line).

The last word…

Live tweeting is not for everyone, but hopefully I’ve given you some reasons why you might at least want to follow a conference hashtag, even if you don’t contribute. Like any community however, the more people that get involved, the more everyone benefits.



#1: There is a really interesting discussion around this point, which extends to recording and/or streaming a conference. The argument goes that if people can “be at a conference” from their computer why would they ever pay the flight/hotel/conference fee to go to a conference in person? To me, this argument is patently ridiculous. Attending (most) conferences is about being part of a community, and this is a 2-way interaction. Some of the most interesting discussions happen over drinks or at meals, not necessarily during the talks and question periods. I’m fully for recording and streaming talks at conferences, and I seriously doubt that this would impact attendance.

#2: Many people use Twitter on their smart phones. The one and only time I do this is if I want to take a photo and tweet it directly. Otherwise, it’s just too slow and lacking in the editing / lookup tools (eg. good tabbed browsing) and screen real-estate to make the most of tweetdeck. If you can, always use a laptop or maybe (if you’re really good with it) a tablet.

Endosymbiont talk at Loreto College, Manchester


Department of Evolution, ecology and behaviour student Louise Reynolds recently gave a talk on endosymbionts and here is what she had to say:


‘On Thursday 21st April I visited Loreto College, Manchester to give a talk to around 60 Upper Sixth biology students about endosymbionts. Biology is a very popular option at the college, which has 1000 students taking the subject at A-level.

Endosymbionts, such as Wolbachia are commonly found in insects and other arthropods. They live within the cells of their host and are inherited through females. During my talk I spoke about different aspects of Wolbachia biology.

Wolbachia is able to manipulate the sex determination system of its host, for instance some strains of Wolbachia cause the male offspring of infected females to die. Wolbachia is currently being trialed as a form of biological pest control to halt diseases that are spread by the mosquito Aedes aegypti, such as Dengue Fever, Zika, and Chikungunya. I also spoke about my own research investigating the genetics of rapid evolutionary change in the blue moon butterfly. This butterfly is infected with a strain of Wolbachia that causes male offspring of infected female butterflies to die. The blue moon butterfly has evolved the ability to suppress male-killing so that infected butterflies are able to produce both male and female offspring.

After the talk I had some sandwiches and juice, and spoke to students interested in studying biology at university.’

Talking rodents at Liverpool Light Night and PubhD

Guest post by Nicola Davidson, PhD student in the Institute of Integrative Biology at the University of Liverpool

I recently took part in two, quite different, public engagement events. The first was PubhD on 12th May. PubhD is a new event for Liverpool organised by Kat Ford. PubhD takes place in The Vines pub near Lime Street station and runs for about an hour and a half once a month. There are three speakers each night talking on a variety of topics. Apart from my talk on rodent control there was a talk from IIB’s Rebecca Donnelly on mathematical biology and Samuel Mercer on social and political science. Each speaker is given 10 minutes to present their PhD without any slides, followed by 20 minutes of questions. I really enjoyed talking without having to rely on PowerPoint. It made me really think about how to get my research across to a non-academic audience. The question session afterwards was really interesting. As my PhD is on trying to solve a practical problem (stopping non-target rodents from getting poisoned by rat poison), there were lots of ideas on how the problem could be solved. I think PubhD could be a good forum to get some fresh ideas and perspective for your research. The audience was small (~15) as the weather was too good to tempt many people indoors. However, this gave the event a nice intimate feel and I think encouraged more people to ask questions. I would highly recommend this event, especially for PhD students who want to practice communicating the premise of their thesis. You can contact Kat on or have a look at the twitter page @PubhD_Liverpool.

The second event I took part in (on 13th May) was Liverpool Light Night. This was a much bigger event and was directed more towards families. Light Night is a one-night arts & culture festival. The University opened several venues for this event, and I was stationed in the Guild. The event ran from 5pm to 9pm. There were around 150 people coming through the Guild in that time. I was in charge of a stand based on my research group’s work on rodent control. I had two posters: one on rodent control and the other on rodent species in the UK. I also had videos of some wild rodents, a demonstration of a rat bait station and a make your own mouse book mark for children. I made plenty of bookmarks with children, and some adults too! As well as learning about rodents from my stand, attendees could visit other stands where they could have an ice cream made from liquid nitrogen, power a solar car with a lamp and learn how to fight cancer. It was a really good opportunity to talk to people about the realities of rodent control and try to convince them that rats aren’t that bad. Overall I really enjoyed taking part in this event, especially getting the chance to inspire children with the kind of research we are doing at Liverpool.