Erysipelothrix amsterdamensis sp. nov., associated with mortalities among endangered seabirds

• Published in: International Journal of Systematic and Evolutionary Microbiology
• Main Authors: Zhong, Jiadong, Medvecky, Matej, Tornos, Jérémy, Clessin, Augustin, Le Net, Rozenn, Gantelet, Hubert, Gamble, Amandine, Forde, Taya, Boulinier, Thierry
• Other Authors: Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences Glasgow, University of Glasgow-University of Glasgow, University of Glasgow, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Vet Diagnostics, CEVA- BIOVAC, Cornell University New York
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2024
• Subjects: [SDV]Life Sciences [q-bio]; Amsterdam Island
• Online Access: https://hal.science/hal-04496590; https://hal.science/hal-04496590/document; https://hal.science/hal-04496590/file/ijsem006264.pdf; https://doi.org/10.1099/ijsem.0.006264

International audience Infectious diseases threaten endangered species, particularly in small isolated populations. Seabird populations on the remote Amsterdam Island in the Indian Ocean have been in decline for the past three decades, with avian cholera caused by Pasteurella multocida proposed as the primary driver. However, Erysipelothrix species have also been sporadically detected from albatrosses on Amsterdam Island and may be contributing to some of the observed mortality. In this study, we genomically characterized 16 Erysipelothrix species isolates obtained from three Indian yellow-nosed albatross ( Thalassarche carteri ) chick carcasses in 2019. Histological analyses suggest that they died of bacterial septicaemia. Two isolates were sequenced using both Illumina short-read and MinION long-read approaches, which – following hybrid assembly – resulted in closed circular genomes. Mapping of Illumina reads from the remaining isolates to one of these new reference genomes revealed that all 16 isolates were closely related, with a maximum of 13 nucleotide differences distinguishing any pair of isolates. The nucleotide diversity of isolates obtained from the same or different carcasses was similar, suggesting all three chicks were likely infected from a common source. These genomes were compared with a global collection of genomes from Erysipelothrix rhusiopathiae and other species from the same genus. The isolates from albatrosses were phylogenetically distinct, sharing a most recent common ancestor with E. rhusiopathiae . Based on phylogenomic analysis and standard thresholds for average nucleotide identity and digital DNA–DNA hybridization, these isolates represent a novel Erysipelothrix species, for which we propose the name Erysipelothrix amsterdamensis sp. nov. The type strain is A18Y020d T (=CIP 112216 T =DSM 115297 T ). The implications of this bacterium for albatross conservation will require further study.