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

Zhong, J., Medvecky, M., Tornos, J., Clessin, A., Le Net, R., Gantelet, H., Gamble, A. , Forde, T. L. and Boulinier, T. (2024) Erysipelothrix amsterdamensis sp. nov., associated with mortalities among endangered seabirds. International Journal of Systematic and Evolutionary Microbiology, 74(2), 006264. (doi: 10.1099/ijsem.0.006264) (PMID:38359084)

Abstract

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 A18Y020dT (=CIP 112216T=DSM 115297T). The implications of this bacterium for albatross conservation will require further study.

• Item Type: Articles
• Additional Information: JT received support from CEVA and ANRT for a CIFRE PhD fellowship and project France relance TVACALBA. AG was supported by the US National Science Foundation (DEB-1557022) and the Strategic Environmental Research and Development Program (RC2635). The research was also supported by the French Polar Institute (IPEV ECOPATH-1151), ANR ECOPATHS (ANR-21-CE35-0016), Zone Atelier Antarctique et Terres Australes (ZATA) and OSU OREME ECOPOP.
• Keywords: Erysipelothrix spp., yellow-nosed albatross, comparative genomics, conservation.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Medvecky, Dr Matej and Clessin, Mr Augustin and Gamble, Dr Amandine and Forde, Dr Taya

Creator Roles

Medvecky, M.: Formal analysis, Methodology, Supervision, Visualization, Writing – review and editing
Clessin, A.: Investigation, Methodology, Writing – review and editing
Gamble, A.: Investigation, Writing – review and editing
Forde, T.: Investigation, Supervision, Writing – original draft, Writing – review and editing

• Authors: Zhong, J., Medvecky, M., Tornos, J., Clessin, A., Le Net, R., Gantelet, H., Gamble, A., Forde, T. L., and Boulinier, T.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: International Journal of Systematic and Evolutionary Microbiology
• Publisher: Microbiology Society
• ISSN: 1466-5026
• ISSN (Online): 1466-5034
• Copyright Holders: Copyright: © 2024 The Authors
• First Published: First published in International Journal of Systematic and Evolutionary Microbiology 74(2): 006264
• Publisher Policy: Reproduced under a Creative Commons licence