Mycoplasma anserisalpingitidis törzsek vizsgálata a maggenomot célzó multilókusz szekvenciatipizáló módszerrel
Kovács, Áron Botond
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Background: Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, and can cause significant economic losses. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one emerging methodology is the core genome Multi-Locus Sequence Typing (cgMLST). The core genome contains a high percentage of the coding DNA sequence (CDS) set of the tested strains. Objectives: The aim of this study was to set up a precise and robust cgMLST schema for the genotyping of M. anserisalpingitidis strains. Materials and Methods: In this study, Illumina short reads of 107 M. anserisalpingitidis strains were used along with 3 complete genomes from the NCBI database, including samples from Hungary, Poland, Vietnam, and China (110 samples overall). Draft genomes were assembled with the SPAdes software and analyzed with chewBBACA program. The threshold of the presence of CDS in the strains was set to 95%, resulting in the most accurate and robust schema. Five hundred forty CDSs constituted our cgMLST schema (representing 68.87% of the whole CDS set of M. anserisalpingitidis ATCC BAA-2147), and a Neighbor joining tree was created using the allelic profiles. Result and Discussion: The phylogenetic tree from the cgMLST schema resembled the real-life relationships of the strains. The schema allowed to differentiate between strains from different integrations and managed to group the strains by geographical origin and isolation date and even strains from the same animal.