Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus) specimens: Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov.

The family Chlamydiaceae currently comprises a single genus Chlamydia, with 11 accepted species and includes the human pathogens Chlamydia (C.) trachomatis, C. pneumoniae and C. psittaci, a zoonotic agent causing avian chlamydiosis and human psittacosis, as well as other pathogens in ruminants and birds. As part of routine testing of 15 apparently healthy captive flamingos (Phoenicopterus chilensis) in a zoo in 2011, an atypical strain of Chlamydiaceae was detected by real-time PCR of cloacal swab samples. Other chlamydial organisms were absent. Sequence analysis of the 16S rRNA gene revealed high similarity to the non-classified Chlamydiaceae-like C122 strain previously found in gulls. As more samples were collected during annual campaigns of the flamingo ringing program in southern France from 2012 to 2015 (Phoenicopterus roseus), Chlamydiaceae were detected by PCR in 137/404 (33.9%) birds aged less than a year. Three strains were successfully grown in cell culture from these samples. Ultrastructure analysis, comparison of 16S and 23S rRNA gene sequences, as well as whole-genome analysis and bioinformatics (ANI, TETRA, AAI and POCP values, 9 phylogenetic markers) revealed a more distant relatedness of the flamingo isolates to established members of the family Chlamydiaceae and indicated that the three strains belong to two distinct species within a new genus. Therefore, we propose the introduction of Chlamydiifrater gen. nov., as a new genus, and of Chlamydiifrater phoenicopteri and Chlamydiifrater volucris as two new species of the genus.