Genomic characterisation of a novel species of Erysipelothrix associated with mortalities among endangered seabirds

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 spp. has also been sporadically detected from albatrosses on Amsterdam Island and may be contributing to some of the observed mortality. In this study, we genomically characterised 16 Erysipelothrix spp. isolates obtained from three Indian yellow-nosed albatross chick carcasses in 2019. 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 E. 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 hybridisation, these isolates represent a novel Erysipelothrix species, for which we propose the name Erysipelothrix amsterdamensis sp. nov. The type strain is E. amsterdamensis A18Y020dT. The implications of this bacterium for albatross conservation will require further study.

Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis)

“…No. NZ_OW659496) ( Table 2 ; Zhong et al, 2022 ). ANI values >96% and dDDH values >70% indicate the same species ( Auch et al, 2010 ; Meier-Kolthoff et al, 2013 ; Ciufo et al, 2018 ), while ANI values >98% and dDDH values >80% suggest the same subspecies ( Meier-Kolthoff et al, 2014 ; Bannantine et al, 2020 ; Choo et al, 2020 ; Pearce et al, 2021 ).…”

A new multiplexed magnetic capture—Droplet digital PCR tool for monitoring wildlife population health and pathogen surveillance

“…Erysipelothrix amsterdamensis was characterized by Zhong et al. ( 2022 , unpublished) and isolated from deceased albatross chicks on Amsterdam Island and E. poltava from septic swine in the Ukraine (Tarasov et al., 2022 ). With two or fewer mismatches in each of the primer probe regions, both non‐target species are indistinguishable from E. rhusiopathiae in the presented assay.…”

Complete Genome Sequences of Two Pasteurella multocida Isolates from Seabirds

“…Recurrent outbreaks of fowl cholera (FC), caused by Pasteurella multocida , have been associated with mass die-offs; threatening the population of nestling albatrosses on Amsterdam Island, in the southern Indian Ocean ( 1 , 2 , 15 , 16 , and 17 ). Dead birds were necropsied on this island as part of a wildlife health monitoring program conducted since 2013 ( 1 , 3 , 4 ). The fieldwork was approved by the French Regional Animal Experimentation Ethical Committee no.…”