SULM – Schweizerische Union für Labormedizin | Union Suisse de Médecine de Laboratoire | Swiss Union of Laboratory Medicine

Abstracts SGM 2016

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1Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland, 2SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland , 3Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

Amoeba-resisting microorganisms (ARM) such as Nucleocytoplasmic large DNA viruses (NCLDVs) and Chlamydia-related bacteria, evolved to survive and replicate inside amoebae. These ARM are under a strong selection pressure, being in a very adverse environment; the professional phagocyte. However, the evolution rate of their genomes is yet unknown. Therefore, we investigated the mutation rates of two recently discovered ARM: Lausannevirus (346 kb, GC content 42.9%), a large DNA virus and Estrella lausannensis (~ 2.8 Mb, GC content 48.2%), a bacterium belonging to Criblamydiaceae bacterial family. During 1 year (144 passages) both ARM were maintained in coculture within Acanthamoeba castellanii. Each 3 months culture were split in two lineages, for a total of 8 different subcultures at the end of the year. Quantitative real-time PCR allowed the evaluation of viral and bacterial abundance of each subculture. Interestingly, bacterial subcultures showed similar profiles, while major differences in population size among viral subcultures were reported. Sequencing of all subcultures was performed with MiSeq Illumina, viral and bacterial genomes were de novo assembled and Single Nucleotide Polymorphism (SNP) as well as insertion/deletion (INDEL) calling assessed. Analyses showed that both ARM have stable genomes; after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, in Lausannevirus no mutations become fixed, suggesting that mixed populations coexist in the same subculture. While, in E. lausannensis 15% of the mutations reached the fixation (cutoff >= 99%). The presences of different mutations in the endonuclease encoding genes of Lausannevirus were detected in different subcultures, suggesting the importance of this gene product in viral replication. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phospoenolpyruvate-protein phospotransferase (PtsI), implicated in sugar metabolism. Noteworthy, we detected no stable horizontal gene transfer among Lausannevirus and E. lausannensis.


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