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.

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“Microbes around us” outreach event with Northwood Primary School, 15.03.17

Written by Jo Moran

Last week Mal Horsburgh and I welcomed Northwood Primary School to the IIB, where they undertook activities to teach them about the microbes that surround us all every day.

In the morning, the students used light microscopes to identify different bacteria that they would come across in their everyday lives. In the afternoon session, the students were taught about viruses, and made their own bacteriophage 3D paper model. The students were extremely enthusiastic, and really enjoyed the chance to use scientific equipment. Over lunch, we encouraged the students to ask questions to the scientists who were demonstrating to them. My favourite questions included “how long does it take to become a scientist?”, “how do you know when you’ve really proved something scientifically?” and “what’s the most embarrassing thing that’s ever happened to you in the lab?”

Although the event was run by Jo Moran, Renze Gao, a Biological sciences honours student, designed and developed all of the activities and resources for the day for his honours project. Renze hugely enjoyed working out how to make what he knew about microbes accessible to 10 year olds, and is considering doing something similar in his future career.


IIB PhD student visits Upton Hall School as an inspiring alumnus

This is a guest blog written by Caisey Pulford, a PhD student studying at the Institute for Integrative Biology


On Wednesday 25th January I visited Upton Hall School FCJ to speak with and inspire the next generation of female scientists. I was warmly welcomed to the school with a beautiful, informative and delicious lunch held by the head girls team. I was interested to chat with them informally about their career aspirations and informed them of the many opportunities that University has to offer them.

I then spent an hour presenting a talk to the year 12 students about current topical scientific research being conducted at the University and the impact of scientific research on a global scale. I spent time discussing the invasive Non-Typhoidal Salmonella epidemic in Africa and explained how genome sequencing has revolutionised scientific research. They were fascinated to learn more about “real life research” and about the many different options a career in science could offer them! An informal question time followed were the girls asked many questions about the courses at Liverpool and were keen to find out more about research at the Institute. I was delighted to hear that some students had already taken their first step on the research career ladder by focussing their Extended Project Qualifications (EPQs) on epidemics, viruses and bacteria. I have a feeling we will be seeing quite a few of them leading their own research soon!!!

I would like to extend a huge thank you to the staff and girls at Upton for welcoming me to the school so warmly, for listening so intently and for asking lots of questions! As the Upton Hall School Motto goes “Age quad agis” Whatever you do, do it well! (also have fun, learn lots and make a difference!)

I look forward to returning to Upton over the next few months to speak to the year 10 science students.

You can read more about Caisey’s visit and see the pictures on the Upton Hall School website:

(Microbial) Life in the Institute of Integrative Biology

Guest post by Alex Lowe, Frederick Bennett and Michelle Durrant.
From the 6th– 10th July, A-level students Alex, Frederick and Michelle spent a week with Prof Jay Hinton and PhD student Siân Owen to experience what life is like in a research institute. They did a microbiological survey of the Institute’s kitchen areas; results below!

I had a fantastic week. I gained huge amounts of information; and was able to meet staff from a number of different departments. I saw what research on plants involves, toured the aquariums in the basement, and met Linford: a (non-venomous) California kingsnake, who had previously escaped for three months. The machinery in the genomics and proteomics labs is as impressive as it is expensive. The entire week surpassed all of my expectations. I had a lot of fun, and the knowledge, skills and confidence gained during the week will be incredibly valuable during my degree.

Initially I was feeling slightly nervous about starting as an intern and found the idea of working in a laboratory quite daunting. However, after meeting the other interns and the students and staff who worked at the university, I felt a lot more relaxed and at ease. Looking back, my preconceptions of what working in a laboratory would be like were quite different to how they truly were.  It was a very relaxed and open environment, and meeting some of the other researchers and being able to learn what they were doing was very interesting.

When we were not in the lab (or swabbing the institute’s kitchens) we were on tours throughout the institute to see the amazing facilities and learn more about what other labs were looking at in the university. This showed us all the number of different paths in science. I suggest any aspiring scientist should aim to find experience because it shows you a real life situation, and shows you what an exciting field science is to work in. The week has really motivated me to work harder and keep an open and creative mind. Being in the lab gave me a unique experience and understanding of how scientists work and let me understand lab protocols, which will give me an undeniable advantage in the future.

Thanks to the members of staff who gave up their time to give tours and talk to the students.


Michelle, Frederick, Jay, Alex and Siân in Lab H

The students receiving their Giant Microbe toys after giving a presentation on their findings

The students receiving their Giant Microbe toys after giving a presentation on their findings

The results of the microbial abundance survey of the kitchen areas of IIB.

The results of the microbial abundance survey of the kitchen areas of IIB.

The microbiological survey of the Institute’s kitchen areas found the highest abundance of bacteria in the kitchen area associated with lab E, closely followed by lab G. Labs C, D and F showed a medium abundance, with A, B and H having the lowest.  Altogether, a huge diversity of microbial life was found!

Alex and Michelle hard at work in the Microbiology lab

Alex and Michelle hard at work in the Microbiology lab