Improving bacterial strain classification for more effective surveillance

Most bacterial species have a huge variety of strains, and antibiotic resistance, virulence and potential for transmissibility all vary from one to the next. The precise identification of these different strains is therefore a major public health challenge and is crucial for effective surveillance of infectious agents. But a taxonomy for emerging bacterial strains is still largely lacking, which complicates communication between scientists and public health microbiology actors working on epidemiological surveillance. In a paper published in Molecular Biology and Evolution, scientists from the Institut Pasteur propose a novel broadly applicable genomic classification approach for bacterial strains.

To develop this new system, members of the Biodiversity and Epidemiology of Bacterial Pathogens Unit took as a model Klebsiella pneumoniae, a multiresistant bacterium found in the environment and in food, which represents a major public health challenge as it causes highly antibiotic-resistant infections in hospitals. With the support of the Bioinformatics and Biostatistics Hub, they analyzed more than 7,000 genomic sequences to reconstruct the species' phylogenetic tree and identify natural groupings of strains within current populations. These new classifications are based on a genotyping method which analyzes strains gene by gene to classify them according to their genetic distance. It offers a number of advantages including precision, reproducibility, portability and ease of interpretation.

A technique applicable to multiple bacterial species

The scientists propose a coding system for strains that contains information about their genetic proximity and is simple and practical to use. It combines two types of unique identifier for each strain, to ensure stability of codes over time, while allowing a correspondence to be established between the new system and the "bacterial types" formerly used before the emergence of genomics. The method therefore provides continuity with previously used nomenclatures, while offering much greater precision. In addition to Klebsiella pneumoniae, the new system will be largely applicable to the taxonomy of strains belonging to other bacterial species.

At the Institut Pasteur, this research reflects the 2019-2023 Strategic Plan objective to "Increase the impact of research on health." It is particularly in line with the measure to "Further the process of reflection on the genomic taxonomy of microbial strains," in coordination with the Pasteur International Bioresources Network (PIBnet), which organizes and promotes biological collections (biological strains and samples), both in France in conjunction with the National Reference Centers (CNRs) and in the institutes in the Pasteur Network. Among the scientific community, this study should facilitate communication on the emergence and microevolution of pathogenic bacteria, in the same way as the nomenclature used for strains of SARS-CoV-2, which made it possible to communicate widely on the variants of concern responsible for COVID-19.

This study is part of the priority scientific area Antimicrobial Resistance of the Institut Pasteur's strategic plan for 2019-2023.

Source:

A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains, Molecular Biology and Evolution, June 14, 2022

Melanie Hennart^1,2, Julien Guglielmini³, Sébastien Bridel¹, Martin C.J. Maiden⁴, Keith A. Jolley⁴, Alexis Criscuolo³, Sylvain Brisse¹
1 - Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
2 - Sorbonne Université, Collège Doctoral, Paris, France
3 - Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
4 - Department of Zoology, University of Oxford, Oxford, United Kingdom