Comparative genome analysis of the recently defined genus Chlamydiifrater

The genus Chlamydiifrater was discovered while examining cloacal swabs taken from flamingos. The samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015. In the past, three Chlamydiifrater strains have been isolated and characterized (Vorimore et al. 2021, https://doi.org/10.1016/j.syapm.2021.126200), and raw sequencing data were deposited at https://www.ebi.ac.uk/ena/browser/view/PRJEB34693. Recently, two more of the cloacal swab samples collected in Etang du Fangassier in 2015 and tested positive for Chlamydiaceae were successfully grown in cell culture. Subsequently, the two samples were subjected to Illumina and Nanopore sequencing (conducted by Fabien Vorimore, ANSES, France). DNA extraction, library preparation, and sequencing via Illumina and Nanopore were conducted as described before (Vorimore et al. 2021, https://doi.org/10.1016/j.syapm.2021.126200). Basecalling of Nanopore data was performed via the superaccurate model (SUP) from Guppy v6.0.0 (Oxford Nanopore Technologies). The sequencing data of all five Chlamydiifrater strains (three from the previous study and the two new strains presented here) were compared with representative genomes from other Chlamydia species.