Pathogen Genomics and Evolution Group Members

I’m currently a doctoral candidate in the Institute for Microbiology and Epizootics at the Freie Universität Berlin and am doing my project in collaboration with the Pathogen Genomics and Evolution Group of the University of Cambridge. My main focus is on Streptococcus canis, an emerging pathogen which mainly affects dogs by causing skin infection. I am currently working on population genetics for S.canis where we will identify particularly interesting groups which we will then test for new virulence factors. This will be done with Transposon Directed Insertion-site Sequencing (TraDIS) in the context of blood and skin invasions. Before this, I received my Master’s degree in Microbiology from the Université de Clermont-Ferrand after having submitted my thesis on Salmonella typhimurium bacterial persistence in the context of macrophage invasion.

I am a senior research associate with an interest in microbial functional genomics, in particular Klebsiella pneumoniae and other Enterobacteriaceae species (Salmonella Typhimurium, Enterobacter cloacae). After graduating from the Technical University of Braunschweig/Germany, I joined to lab of Susanne Häussler at the Helmholtz Centre for Infection Research. During my PhD I used deep transcriptomic sequencing (RNA-seq) to study Antimicrobial Resistance in Pseudomonas aeruginosa and Klebsiella pneumoniae. Following a short post-doc in the same group where I developed rapid molecular diagnostics to detect hospital outbreaks and antibiotic resistance in several different bacterial species (mainly, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli and Clostridium difficile). In 2017, I took up a post as a postdoctoral fellow in the Parkhill group at the Wellcome Sanger Institute using Functional Genomics (RNA-sequencing and transposon-directed insertion site sequencing, TraDIS) to understand the antimicrobial stress response in the Enterobacteriaceae species Klebsiella, Salmonella and Enterobacter. In my current work at the Department of Veterinary Medicine I am using different sequencing-based methods to understand how the human pathogen Klebsiella pneumoniae interacts with the immune system, in particular macrophages.

I am a PhD student focusing on Burkholderia pseudomallei, an environmental bacterium and the causative agent of a deadly infectious disease called ‘Melioidosis’, which is endemic in many low- and middle-incomes countries. This bacterium is an intrinsically drug resistant pathogen and potential bioweapon. The antibiotic treatment options for melioidosis are limited and the mortality rate from acute melioidosis remains high at about 40% in Thailand. I am co-supervised by Claire Chewapreecha, a Wellcome International Intermediate Fellow at MORU (Thailand), and Prof. Julian Parkhill at Department of Veterinary Medicine. For my PhD, I will focus on the evolution of antibiotic resistance mechanisms in B. pseudomallei, including their prevalence, dissemination, adaptive strategies across laboratory, environmental and clinical settings.

I am a post-doctoral researcher interested in understanding how evolutionary processes shape microbial genomes. My work focuses more on method than microbe, aiming to develop statistical approaches and computational tools for the analysis of genetic data in multiple species. After graduating with a BA&Sc in Molecular Biology and Political Science from McGill University in 2012, I moved from Canada to the UK to complete the MPH at Imperial College in 2013. I earned my PhD at Imperial College in 2020, under the supervision of Dr. Xavier Didelot and Dr. Christophe Fraser, for developing methods to perform genome-wide association studies in clonal and recombining organisms. My PhD research culminated in the release of treeWAS: the first phylogenetic method for microbial GWAS. As a postdoc in the Parkhill group, my aim is to develop approaches to incorporate non-SNP genetic variation into phylogenetic inference methods in bacteria. In mapping recombination and gene gain/loss events across the clonal frame, we hope to determine whether rates of change in these genetic elements can be reliably estimated. We aim to use these inferences to improve the resolution and temporal calibration of phylogenetic trees in partially-recombinant organisms.

I am a research associate with an interest in pathogen genomics, especially foodborne pathogens such as E. coli and S. enterica. I graduated with a BSc in Biology from the Aristotle University of Thessaloniki in 2015. The following academic year I joined the PalaeoBARN lab, at the University of Oxford, as an Erasmus exchange student and started my training in ancient DNA wet lab techniques and bioinformatic analyses. This position transitioned into a DPhil in Archaeological Science focusing on ancient DNA metagenomics and zoonotic pathogen evolution. Following the completion of my DPhil in 2021, I took up a post as a postdoctoral research associate in the Parkhill group at the Vet School in the University of Cambridge working on E. coli, and other foodborne pathogens, transmission dynamics and evolution.

I am interested in genetic, antimicrobial resistance of zoonotic pathogens and potential interventions for reducing zoonotic infections. I am co-supervised by Assoc. Prof. Ngo Thi Hoa from Oxford University Clinical Research Unit (OUCRU-Vietnam) and Prof. Julian Parkhill at the Department of Veterinary Medicine. My DPhil will focus on the zoonotic transmission and persistent colonisation with colistin-resistant bacteria in different chicken farming systems in Vietnam

I am a PhD Student focussing on Campylobacter genomics; I have a strong interest in population genomics, microbiology and bioinformatic/statistical approaches to sequence data. I obtained my undergraduate degree in Biomedical Science at The University of Manchester; during my degree, I completed a placement year at QIAGEN, focussing mainly on qPCR development. I then undertook a role as a Data Analyst within Prof. Brown’s aDNA laboratory at the Manchester Institute of Biotechnology investigating the domestication and origins of tetraploid wheat using GBS data. I obtained my MPhil at the University of Manchester in Biostatistics in early 2020 working on Bayesian statistics and different approaches to Mendelian randomization. After graduating, I then worked within the Maiden Group at the University of Oxford investigating and characterizing the population structuring of Neisseria gonnorrhoeae, focussing mainly on PorB.

I am a PhD student with a strong interest in machine learning and its use in identifying novel antibiotic resistance mechanisms in the bacterium Klebsiella pneumoniae. My research project is co-supervised by Professor Tim Walsh from the University of Oxford. I have previously completed my MSci degree at University College London, where I carried out research under the supervision of Dr. Lucy Van Dorp. My thesis focused on characterising the genetic determinants of antibiotic resistance in the bacteria Acinetobacter baumannii. I later joined the research group of Dr. Moritz Treek at The Francis Crick Institute. As a part of my project, I also applied machine learning techniques to the analysis of Perturb-seq data of the parasite Toxoplasma gondii and infected human cells to understand host-pathogen interaction. A key aspect of the project was the functional annotation of previously uncharacterised parasite effector proteins.

Noemie’s work focuses on the integration of genetic and spatial data to better understand the spread, maintenance, and control of pathogens. She is co-supervised by Henrik Salje at the Department of Genetics and Julian Parkhill at the Department of Veterinary Medicine. She is working with datasets of Bordetella pertussis genomes from throughout France as well as other European countries in a collaborative project with the national reference center for Pertussis in France. She also works with Listeria monocytogenes, Streptococcus pneumoniae and dengue virus.

I am a Research Assistant interested in bacterial pathogenesis and antimicrobial resistance. In 2012 I graduated from the University of Portsmouth with a BSc (Hons) in Applied Biomedical Science, which included a training placement as a Biomedical Scientist in the NHS. Subsequently, I held the roles of Senior Scientist and Laboratory Manager in a clinical pathology laboratory within a specialist veterinary referral centre, working principally in the microbiology department. During this time, I oversaw the implementation of automated identification and sensitivity testing of bacterial pathogens, developed AST protocols and enjoyed being a member of the infection control committee. Meanwhile, I also completed a part-time MSc in Clinical Microbiology, graduating from the University of Nottingham in 2021. I joined the Department of Veterinary Medicine in December 2021 to work on a research project that aims to understand how Klebsiella pneumoniae interacts with macrophages. I am looking forward to expanding my knowledge of microbial genomics throughout this project.

The research of my group focusses on the evolution of bacterial pathogens; their origin, transmission and adaptation to selective pressure. I primarily use genomic and phylogenetic approaches to address these, and over the last few years my group has used large-scale population genomics to identify the global origin and routes of spread of many human and animal pathogens. Overlaid on the phylogeny, we look for signatures of adaptation to the host, to antibiotics and to vaccine pressure, most recently developing bacterial genome-wide association approaches to identify genetic determinants responsible for this adaptation. In addition to informatics approaches, we develop and apply genome-wide experimental tools, studying interaction with the host and antimicrobial resistance mechanisms. We have an interest in metagenomics, currently studying the microbiota in the gut, the lung, the nasopharynx and the placenta (which doesn’t have one). We often work at an international level, with many collaborations in Low- and Middle-Income countries. Our work has clear translational benefits for tracking transmission at the hospital level and more broadly. To enable this translation, we have been collaborating with local hospitals, and national and international health-protection agencies, as well as the commercial sector.

I am a research associate interested in using genetic sequences to understand pathogen transmission. During my PhD at University College London, I worked to understand the factors that drive norovirus pandemics. Since joining the labs of Andres Floto and Julian Parkhill in Cambridge, my research has focussed on understanding the pathways of Mycobacterium abscessus transmission. Through this work, I developed a novel method to reconstruct pathogen mutational spectra and I am currently investigating what we can learn about pathogen ecology, transmission and biology from mutational spectra.

I am a Research Assistant working primarily on bacterial genomics and the microbiome of the respiratory tract. While studying part time at the London School of Hygiene and Tropical Medicine in 2007, I started working in the Sequencing Production team at the Wellcome Sanger Institute. I did my final research project there on the identification of mixed genotype Plasmodium falciparum infections using the newly developed Illumina sequencing platform, under the supervision of Professor Dominic Kwiatkowski. In 2008 I took a Research Assistant position with Professor Julian Parkhill on the Pathogen Genomics team, where I went on to focus on novel capsule biosynthesis genes in Streptococcus pneumoniae, the human microbiota, and mitigating contamination in low biomass samples. I joined the Department of Veterinary Medicine in 2019.

I am a research associate with an interest in pathogen genomics, in particular Mycobacterium bovis and non-tuberculous Mycobacteria (NTM). I graduated with a BSc (Hons) in Biology and a MRes in Bioinformatics from the University of York in 2006 and 2007 respectively. Following three years working as a genome analyst at the Wellcome Sanger Institute, I moved to the University of Oxford as a research assistant in the Brueggemann lab in the Department of Zoology. This position transitioned into a DPhil in Clinical Medicine focusing on pneumococcal genomics and evolution. Following my graduation in 2017, I took up a post as a postdoctoral fellow in the Parkhill group at the Wellcome Sanger Institute working on Mycobacterium bovis transmission dynamics and evolution, and non-tuberculous mycobacteria in cystic fibrosis and bronchiectasis patients. In June 2019, the Parkhill group moved to the Department of Veterinary Medicine where I’m currently based.

I’m a research associate in the Molecular Immunity Unit at the Laboratory of Molecular Biology and the Cambridge Vet School co-supervised by Professor Andres Floto. Before coming to Cambridge, I worked at the Helmholtz Centre for Infection Research on using machine learning to predict antimicrobial resistance from multi-omics data. In my research I combine the analysis of high-throughput phenotypic and transcriptomic screens of large knockout libraries e.g., using scRNAseq and TraDIS, with bacterial genomics and phylodynamics to learn about the biology of bacterial pathogens. Where I find that appropriate methods are missing, I’m eager to develop novel approaches which has resulted in a method for bacterial trait prediction called Traitar and the pan-genome analysis tool Panaroo. I enjoy the interaction with the wet lab and am always keen to engage in stimulating collaborations around the world. My current focus is on the frequently drug resistant bacteria Pseudomonas aeruginosa a major cause of hospital acquired infections and lung infections in people suffering from cystic fibrosis (CF) significantly contributing to mortality and morbidity. My projects are to: 1) Derive a systems level understanding of Pseudomonas behaviour in the CF lungs 2) Investigate the transmission, spread and pathoadaptation of Pseudomonas aeruginosa across the globe

I am a PhD student with a strong interest in genomic epidemiology and phylogenetics. My work is focussed on the genomic epidemiology of ESBL-E. coli. My research is based on a ‘One Health’ concept and I will be investigating the transmission of resistant strains between humans, animals and the environment using phylogenetics and genomic epidemiology. I recently joined the Parkhill group as a PhD Student in the Department of Veterinary Medicine. I’m a veterinarian by profession and before joining the group I was working as a Lecturer in the Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Pakistan. I’m also looking forward to working with genomic epidemiology as a tool to help investigate disease outbreaks in animals in the future.