Senior Laboratory Scientist/ Post-Doctoral Scientist
My Role is a Senior Laboratory Scientist
I perform experiments in the lab to develop and optimise the techniques we use to generate data for our studies. I am involved in projects that take samples (urine or joint fluid, for example) collected from patients with suspected infections and use them to see whether we can diagnose the infection directly from the sample, without needing to try and grow the cause of the infection (usually bacteria) in the lab first. We use a technique called DNA sequencing, which can identify bacteria in the sample and can also sometimes tell us whether the bacteria might be resistant to any antibiotics.
As a senior scientist I oversee some of the lab work performed by our Research Assistants. This can include teaching new skills and lab techniques, and helping to troubleshoot where necessary. MMM is a multidisciplinary team, and my projects involve working alongside doctors, bioinformaticians and other lab scientists. My role also requires me to share the results of my projects with the wider scientific community by writing papers and giving talks at conferences.
To become a Senior Laboratory Scientist I first studied for an undergraduate degree in Biochemistry, and then I studied for a PhD (which is a post-graduate degree where you spend 3 years in a lab working on your own project, which you then write up as a thesis and are examined on). I now have lots of years of experience working in a laboratory.
On my recent project I looked at whether we can use DNA sequencing to identify the cause of infection in patients with suspected prosthetic joint infections. We also tried to look for information about antibiotic resistance in some of the bacteria causing infections, too. I was responsible for collecting the patient samples from the hospital microbiology lab, extracting bacterial DNA from the sample and preparing this DNA for sequencing. Before we could process lots of samples we had to do some experiments in the lab to make sure we were extracting as much bacterial DNA as possible from the samples, and to make sure that the DNA sequencing was as successful as it could be.
My role is a Postdoctoral Research Assistant
I design and develop laboratory based molecular microbiology experiments that help achieve the objectives of each of my projects. I work with bacterial pathogens, those that cause disease or infection to the host, and develop workflows to see if we can diagnose the infection quicker than traditional methods and to investigate if the pathogen is resistant to antibiotics used to treat the infection.
MMM has done a considerable amount of research on bacterial genomics, looking at the genetic instructions provided by DNA from pathogens. To continue and complement this research, I am currently the only member of the lab scientists within the group to research bacterial transcriptomics, which is investigating the gene expression patterns within bacterial pathogens.
I also work with environmental samples from hospital sinks and wastewater that contain more than one kind of pathogen, metagenomic samples, to understand if these pathogens have antimicrobial resistance genes and if there is a link to healthcare-associated infections (infections people get while in healthcare settings such as hospitals whilst receiving treatment for another infection).
To investigate transcriptomics, I extract bacterial RNA from pathogens in the lab, prepare the RNA for RNA sequencing and work very closely with doctors and bioinformaticians to optimise and develop this workflow. I also look at gene expression patterns when the pathogen has been grown in antibiotics and this tells us which genes are switched on or off in response to the antibiotic.
To investigate metagenomics from the environmental samples, I extract the DNA and prepare the DNA for DNA sequencing. Data generated from this project could help to inform ways to prevent the spread of these pathogens in healthcare settings.
To become a Postdoctoral Research Assistant I studied for four years for an honours degree in medical biotechnology, with microbiology being the focus of my final year project. I then completed a PhD, which is three years of lab work on a specific project then writing up the methods and results for publication in the wider scientific field, in both a document called a thesis and journal publications. Since my PhD, I have gained lots of laboratory experience working within different academic research groups here in the UK as well as in industrial settings in countries overseas.
On my project SinkBug, part of National Infection Teams Collaborative for Audit and Research (NITCAR), I help to coordinate a UK-wide survey of sink drains in UK hospitals, using genomics to evaluate the taxonomic and antimicrobial resistance gene distributions in these settings. These findings are compared to hospital infection datasets, as well as the design of sinks and cleaning protocols at each site. I am responsible for preparing samples packs to send to each site who can then take samples from the sink drains. Each site then sends their samples to me and I am responsible for optimising the experiments. To do this I extract the DNA from the metagenomic sink samples, prepare each sample for DNA sequencing and work closely with the bioinformatician who analyses the data.
On my second project, for the Health Protection Research Unit Sequencing and Contexts themes, I have a couple of roles. One is to investigate bacterial transcriptomics, which I have explained above. The second role is to work closely with the UK Health Security Agency (UKHSA) to perform DNA sequencing on metagenomic samples collected by UKHSA. We then work together to write up the methods and findings to publish in relevant journals.
What do you do
I work as a molecular microbiologist in a team developing new, rapid methods to identify and understand bugs that make patients ill. Our goal is to help patients receive a fast and accurate diagnosis, and appropriate treatment.
How do you do it
To do this, we start with clinical samples, such as sputum, blood and urine. We avoid the traditional, time consuming process of growing or culturing bugs in a lab. Instead, we concentrate the bugs (bacteria or viruses) and sequence their genomes directly from clinical samples. This is a key aim of our laboratory work.
On my project, [‘TB direct from sample’] I am responsible for developing methods to obtain and concentrate DNA of tuberculosis bacteria, directly from patients’ sputum samples. The development of a recipe for a special solution, in which sputum samples are heated, provided a recent breakthrough. During heating in the solution, the tuberculosis DNA is both protected, and concentrated. Consequently, we can sequence tuberculosis genomes directly from clinical samples*. We are now developing methods to increase the amount of tuberculosis DNA we get from samples containing very low numbers of these bacteria.
To become a molecular microbiologist you need to study science subjects at A’ level, especially biology and chemistry, then you need a degree in microbiology or a related subject. Getting summer jobs in labs during summer vacations of your degree is great experience; to obtain these, it’s a good idea to write ‘on spec’ to government and academic labs, and biotech companies you’re interested in. Summer jobs can help you decide if you like lab work, the area you might want to go in to, and whether you want to study for a research degree like a masters, or PhD.
*J. Clin Micro paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7512152/
- What you do?
I am developing new ways to identify which bacteria are making you ill and how we can treat them. When patients come into the hospital we will be able to take a sample from them and say what is causing the infection and what is the correct antibiotic to use to treat it. At the moment this process can take days to get a result, but we are working to get this down to hours.
- How you do it? (using simple examples if needed)
I use powerful microscopes to look for bacteria in patient samples. I add different coloured tags to the sample and use computers to tell us what the bacteria is by checking which of the tags lights up. I also expose the bacteria to different antibiotics to see which ones work to kill it.
- How to become a postdoctoral scientist
I studied science at university and then for four years I researched a bacteria that causes food poisoning to obtain a PhD in microbiology. I used my PhD qualification to get a job as a postdoctoral scientist.
Dr. Justine Rudkin
I am a Molecular Microbiologist who studies bacteria to figure out how they make us sick. I mostly work on the hospital superbug MRSA, trying to find out how it changes from being a harmless resident in your nose to causing deadly diseases. I do this by comparing bacteria which have been collected from healthy people’s noses to bacteria which have been collected from people with blood infections. I compare the content of their DNA to look for differences, and I compare how they grow and interact with parts of the human immune system. Day-to-day that means working in a lab (yes, I do wear a lab coat) and doing lots of experiments.
To do this job I needed to get an undergraduate degree in biology followed by a PhD. Some people also have a masters degree! That is a lot of university time, but there are other lab based jobs that don’t require a PhD, such as research assistant and technician posts, and jobs in industry and biomedical labs.
My three projects are;
Bugbank- prospective sampling of bacterial infection isolates from UK Biobank participants, with a view to doing joint human-pathogen GWAS studies. http://www.bugbank.uk/index.html
S. aureus trios project– Genomic, transcriptomic, and proteomic assessment of matched pairs of S. aureus nasal and bloodstream infection isolates from the same patient, coupled with genetically related healthy population controls, to uncover the mechanisms of the commensal to pathogen switch.
Chasing GWAS– Verifying GWAS identified mediators of antibiotic resistance in E. coli
My role in these projects is to lead the lab based aspects of the research, generating large data sets about bacterial biology to understand how and why bacteria cause severe disease in some people but not others.