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.. Chlamydiifrater

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.

衣原体科（Chlamydiaceae）目前仅包含1个衣原体属（Chlamydia），已获正式确认的物种共11种，其中包括人类致病菌沙眼衣原体（Chlamydia (C.) trachomatis）、肺炎衣原体（C. pneumoniae）与鹦鹉热衣原体（C. psittaci）——后者为一种人畜共患病原体，可引发禽类衣原体病及人类鹦鹉热，该科同时涵盖反刍动物与鸟类中的其他致病菌。2011年，某动物园对15只外观健康的圈养智利红鹳（Phoenicopterus chilensis）开展常规检测时，通过泄殖腔拭子样本的实时荧光定量PCR（real-time PCR）检测到一株非典型衣原体科菌株，未检出其他衣原体类微生物。对16S rRNA基因的序列分析显示，该菌株与此前在鸥类中发现的未分类类衣原体科C122菌株同源性极高。2012年至2015年间，依托法国南部红鹳环志项目的年度采样行动，研究人员采集了更多大红鹳（Phoenicopterus roseus）样本；经PCR检测，在404只1龄以下红鹳中，137只（占比33.9%）呈衣原体科阳性。研究人员从上述阳性样本中成功分离出3株菌株，并在细胞培养体系中完成培养。超微结构分析、16S与23S rRNA基因序列比对、全基因组分析及生物信息学分析（涵盖平均核苷酸同源性（ANI）、四核苷酸频度分析（TETRA）、平均氨基酸同一性（AAI）、保守蛋白质组同一性百分比（POCP）值，以及9个系统发育标记）结果表明，红鹳分离株与衣原体科已确立成员的亲缘关系较远，且这3株菌株分属该科下一个新属中的两个独立物种。据此，我们提议建立新属弗拉比衣原体属（Chlamydiifrater gen. nov.），并将该属的两个新物种分别命名为红鹳弗拉比衣原体（Chlamydiifrater phoenicopteri）与禽弗拉比衣原体（Chlamydiifrater volucris）。