Diversity of Chlamydiaceae among native and introduced vertebrate populations from sub-Antarctic islands

Members of the Chlamydiaceae family infect a wide range of vertebrate hosts, yet their diversity and ecology in remote insular ecosystems remain poorly understood. Two previous studies screened 2,274 samples from seabirds and mammals collected across five sub-Antarctic islands in the Southern Indian and Atlantic Oceans between 2017 and 2022. Here, we further characterise 424 Chlamydiaceae positive samples , including members of the Chlamydia and Chlamydiifrater genera. Chlamydiifrater spp. were detected in almost all seabird species, particularly king penguins ( Aptenodytes patagonicus ) and lesser sheathbills ( Chionis minor ), with local prevalence reaching up to 57% and 78%, respectively. In this study, phylogenetic analyses of 16S and 23S rRNA genes revealed a distinct sub-Antarctic lineage structured into three host-associated clusters, likely structured by ecological interactions and spatial segregation. Chlamydia psittaci was detected in a limited number of penguin and sheathbill samples, with omp A- and MLST-based typing revealed at least two novel genotypes. In mammals from Amsterdam Island, C. muridarum -related strains were identified in brown rats ( Rattus norvegicus ), while C. felis -related strains were detected in sub-Antarctic fur seals ( Arctocephalus tropicalis ). This is the first evidence of C. felis in a wild non-feline host, raising the issue of spillover from introduced species (here, cats ( Felis catus )), to native species. These findings demonstrate that Chlamydiaceae are diverse and widespread in sub-Antarctic wildlife, encompassing both endemic and potentially introduced lineages. This emphasizes the need for ongoing surveillance, including whole-genome sequencing, to enhance our understanding of the interactions between hosts, infectious agents and the environment, and to assess potential zoonotic risks to fieldworkers in these sensitive ecosystems. • High diversity of Chlamydiaceae in sub-Antarctic wildlife • High local prevalence of Chlamydiifrater in king penguins and sheathbills • A distinct sub-Antarctic Chlamydiifrater lineage structured by host ecology and spatial segregation • Discovery of novel Chlamydia psittaci genotypes in penguins and sheathbills • First evidence of Chlamydia felis in a non-feline host