Carolina Nodari ▮

Ongoing projects

ESGEM-AMR working group / AMRrules – Organism-specific interpretation of AMR genotypes. 2024-present.

The overall purpose of the group is to capture expert knowledge on the relationship between antimicrobial resistance (AMR) genotypes and antimicrobial susceptibility testing (AST) phenotypes in bacterial pathogens. The initial focus of the ESGEM-AMR working group will be expert curation of interpretive standards for AMR genotypes in the AMRrules format.

  • Project supported by ESCMID and EUCAST.
  • Role: Collaborating investigator, member of the E. coli/Shigella subgroup. Group leader: Kat Holt and Natacha Couto. E. coli/Shigella subgroup leader: Kate Baker.
  • More information: https://github.com/katholt/AMRrules

Evaluation of the potential use of intimin and flagellar antigen types as molecular markers for the diversity of enteropathogenic Escherichia coli (EPEC) populations. 2024-present.

The present project aims to extensively explore the global EPEC population diversity, allowing the identification of “rare” or less characterized clones. The algorithm resulting from our data analysis has the potential to replace sero-agglutination without the need of WGS-based molecular typing. By targeting only two genes, which include the genomic marker of EPEC, this affordable new tool can be used both as a diagnostic test as well as a marker for local and global epidemiology of this enteric pathogen. Additionally, it has the potential to identify emerging EPEC clones. The expansion of knowledge about the EPEC population structure can also guide the future development of testing panels that could be explored by amplification-based sequencing using portable high-throughput platforms.

Development and improvement of genomic typing tools for Shigella spp. and enteric E. coli populations. 2023-present.

Since the implementation of WGS as the first intention method for molecular typing and surveillance purposes at the French National Reference Center for Escherichia coli, Shigella, and Salmonella (CNR-ESS), in 2018, several initiatives to create and/or improve existing tools have been proposed by the Enteric Bacterial Pathogens Unit at the Institut Pasteur, which hosts the CNR-ESS, many of which are done in collaboration with other international experts in these pathogens. Some of the focuses of these projects include the implementation and curation of cgMLST schemes, of genomic frameworks for stable clade nomenclature schemes, and in silico serotype prediction.

Surveillance of emerging extremely drug resistant (XDR) populations of Shigella spp.. 2023-present.

As part of the epidemiological surveillance activities of the French National Reference Center for Escherichia coli, Shigella, and Salmonella (CNR-ESS), we characterize antimicrobial-resistance populations of Shigella spp. by both genotypic (WGS) and phenotypic (AST) methods, in order to identify in real-time emerging populations of this pathogen and potential risk factors associated with infections caused by them. A special focus is given to clones resistant to third-generation cephalosporins, ciprofloxacin, and/or azithromycin, the main drugs used for the treatment of shigellosis.

Evolution of enteropathogenic and enterohemorrhagic populations of E. coli in Europe and emergence of antimicrobial resistance among these pathotypes. 2020-present.

Profiting from one of the largest collections of diarrheagenic E. coli, dating back to the 1950s, we aim to expand the knowledge on the different EPEC and EHEC clones circulating in Europe in the last 70 years and increase the understanding on how some of the EPEC clades evolved into EHEC by the acquisition of the phage-encoded stx genes, as well as the potential reasons for their permanence and clonal expansion until recent times. In addition, we explore the AMR mechanisms present in historical and contemporary strains belonging to these pathotypes and mobile genetic elements associated to their emergence.

Previous projects