Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis

• Published in: Forensic science international : genetics Vol. 45; p. 102230
• Main Authors: Dwibedi, Chinmay, Larsson, Pär, Ahlinder, Jon, Lindgren, Petter, Myrtennäs, Kerstin, Granberg, Malin, Larsson, Eva, Öhrman, Caroline, Sjödin, Andreas, Stenberg, Per, Forsman, Mats, Johansson, Anders
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01-03-2020
• Subjects: Bacteriological Techniques; DNA, Bacterial - genetics; Francisella tularensis; Francisella tularensis - genetics; Genetic variation; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Microbial forensics; Molecular evolution; Monomorphic bacteria; Mutation; Polymorphism, Single Nucleotide; Source attribution; Microbial forensics; Molecular evolution; Source attribution; Genetic variation; Monomorphic bacteria; Francisella tularensis
• ISSN: 1872-4973; 1878-0326; 1878-0326
• DOI: 10.1016/j.fsigen.2019.102230

•Mutations accumulate in specific genes during laboratory culture.•The mutational profile of a laboratory cultured strain is different from wild strain.•Low frequency mutations are amplified by serial passaging in the laboratory.•Biological enrichment of mutations can link bacterial culture to its source.•Highly similar bacteria can be resolved by low frequency variants in the population.
Challenges of investigating a suspected bio attack include establishing if microorganisms have been cultured to produce attack material and to identify their source. Addressing both issues, we have investigated genetic variations that emerge during laboratory culturing of the bacterial pathogen Francisella tularensis. Key aims were to identify genetic variations that are characteristic of laboratory culturing and explore the possibility of using biological amplification to identify genetic variation present at exceedingly low frequencies in a source sample. We used parallel serial passage experiments and high-throughput sequencing of F. tularensis to explore the genetic variation. We found that during early laboratory culture passages of F. tularensis, gene duplications emerged in the pathogen genome followed by single-nucleotide polymorphisms in genes for bacterial capsule synthesis. Based on a biological enrichment scheme and the use of high-throughput sequencing, we identified genetic variation that likely pre-existed in a source sample. The results support that capsule synthesis gene mutations are common during laboratory culture, and that a biological amplification strategy is useful for linking a F. tularensis sample to a specific laboratory variant among many highly similar variants.