Postdoctoral Position in Bacterial Genomics and Antibiotic Resistance

We offer a 2-year postdoctoral position in the "Applied Microbial Genomics" Unit (https://www.ibv.csic.es/en/project/applied-microbial-genomics/) at the Institute of Biomedicine of Valencia (IBV-CSIC), Spain. Contact: fcoll (at) ibv.csic.es

We are seeking a postdoctoral scientist with a research background in bioinformatics and microbial genomics and experience in analysing large genomic datasets to work on a recently funded research project entitled “Studying the genetic mechanisms of antibiotic resistance in enterococci”. Enterococciare a leading cause of hospital-acquired infections, especially in patients with underlying health conditions. Enterococci strains resistant to multiple antibiotics, such as vancomycin-resistant enterococci (VRE), are increasing in prevalence globally and are regarded as a high priority pathogen by the WHO.

The successful candidate will work under the supervision of Dr Francesc Coll (https://www.ibv.csic.es/directorio/francesc-coll/) at the IBV-CSIC (https://www.ibv.csic.es/), Spain; and in collaboration with scientists at the University of Cambridge and the Wellcome Sanger Institute (UK).

The research conducted at the Applied Microbial Genomics Unit (https://www.ibv.csic.es/en/project/applied-microbial-genomics/) focuses on the use of whole-genome sequencing as a basic research tool in bacteriology, and its applications in public health and clinical microbiology. We use advanced comparative genomics techniques applied to large genomic datasets to characterize the genetic basis of clinically relevant bacterial traits, such as antibiotic resistance or pathogenicity; as well as to characterize genetic adaptation in bacterial populations. In translational research, we identify genetic markers for microbial genotyping and diagnosis of antibiotic resistance; conduct genomic surveillance studies to study the epidemiology and transmission patterns of infectious bacteria; and develop bioinformatics tools for processing and interpreting bacterial genome data in clinical and public-health contexts. See https://francesccoll.github.io/publications/ for key publications on these topics.

This work would involve the genomic analyses of hundreds of enterococci genomes to establish a complete concordance between phenotypic and genotypic antibiotic resistance in enterococci, building on previous findings, with the goal of enabling accurate antibiotic resistance detection from enterococci genomes for diagnosis and surveillance purposes. See this recent publication (https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00297-5/fulltext) for background on this topic. The successful candidate will also be responsible for presenting and publishing the study results.

The qualified applicant must have a Ph.D. in computational biology, bioinformatics, microbiology, or related discipline. The ideal candidate will have skills in microbial genome analyses; working knowledge of Python, R, and bash scripting; practical skills in executing bioinformatic pipelines; basic knowledge of applied statistical methods (e.g., clustering, regression, machine learning, etc.); data visualisation skills; applied knowledge of population genetics and comparative genomics methods (e.g., phylogenetics, GWAS); and prior knowledge of bacterial genetics. The qualified applicant is expected to meet some but not all these skills. We will also value evidence of good organisation, teamwork, and collaboration skills; as well as evidence of effective written and oral communication skills as demonstrated by first-author publications and oral presentations at scientific conferences.

The successful candidate will be working in "Applied Microbial Genomics" Unit at the Institute of Biomedicine of Valencia (IBV-CSIC), Spain (https://www.ibv.csic.es/). The IBV hosts multiple research groups working on genomics, transcriptomics, and molecular and structural biology applied to the study of pathogenic bacteria. The institute maintains collaborations with other research institutes (FISABIO, IATA, I2SysBio), universities (UV, UPV) and hospitals in the city. Altogether, the IBV is one of the top research institutions in Spain to work in microbiology and microbial genomics.

This job is offered as part of the project CNS2023-144312 funded by the Spanish Ministry of Science (MCIN), Innovation and Universities; and the State Research Agency (AEI) (MCIN/AEI/10.13039/ 501100011033); and by the European Union “NextGenerationEU”/PRTR (Plan de Recuperación, Transformación y Resiliencia).

Application information: Interested candidates should send their CV and a short cover letter to: fcoll (at) ibv.csic.es before the application deadline (extended to 15/05/2024).