Author Correction: Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species

Grazziotin, Ana Laura; Vidal, Newton Medeiros; Hoepers, Patrícia Giovana; Reis, Thais Fernanda Martins dos; Mesa, Dany; Caron, Luíz Felipe; Ingberman, Max; Beirão, Breno Castello Branco; Zuffo, João Paulo; Fonseca, Belchiolina Beatriz

doi:10.1038/s41598-021-88892-3

Cited by 3 publications

(7 citation statements)

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“…This included 106 genomes: a) the 16 isolates from this study; b) 86 previously sequenced E. rhusiopathiae isolates, representing a diversity of geographic and host origins and spanning the clades described for this species (Clade 1 (n = 7), Clade 2 (n = 14), intermediate clade (n = 8), Clade 3 (n = 57)) [36]; c) two genomes of Erysipelothrix piscisicarius (formerly referred to as E. sp. strain 2) [37,38]: the type strain 15TAL0474 T (GCA_003931795.1) [39], and EsS2-7-Brazil (GCA_016617655.1). E. piscisicarius is the most closely-related species to E. rhusiopathiae currently known; d) a recently deposited Erysipelothrix genome, reported as a new species, Erysipelothrix sp.…”

Section: Methodsmentioning

confidence: 99%

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

Zhong

Medvecký

Tornos

et al. 2022

Preprint

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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.

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Section: Methodsmentioning

confidence: 99%

“…sp. strain 2) [37, 38]: the type strain 15TAL0474 T (GCA_003931795.1) [39], and EsS2-7-Brazil (GCA_016617655.1). E. piscisicarius is the most closely-related species to E. rhusiopathiae currently known; d) a recently deposited Erysipelothrix genome, reported as a new species, Erysipelothrix sp.…”

Section: Methodsmentioning

confidence: 99%

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

Zhong

Medvecký

Tornos

et al. 2022

Preprint

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“…For a more detailed understanding of the phylogenetic relationship of the novel strains among other Erysipelothrix species, the criteria of Pomaranski et al [10,11] and Grazziotin et al [7,8] were considered. Phylogenetic analyses based on the partial nucleotide and amino acid sequences of two representative housekeeping genes, gyrB and rpoB, were performed to also check Table 1.…”

Section: S Rrna Gene Sequence Phylogenymentioning

confidence: 99%

“…[10, 11] and Grazziotin et al . [7, 8] were considered. Phylogenetic analyses based on the partial nucleotide and amino acid sequences of two representative housekeeping genes, gyrB and rpoB , were performed to also check non-synonymous substitutions [26].…”

Section: S Rrna Gene Sequence Phylogenymentioning

confidence: 99%

“…Furthermore, Erysipelothrix inopinata and Erysipelothrix larvae were isolated from vegetable broth and the larval gut of rhinoceros beetle [4,5]. A number of publications present novel species of Erysipelothrix that infect pigs, poultry and fish [2,[6][7][8][9], of which Erysipelothrix piscisicarius has recently been described. Despite its name, this species has proven to cause deadly outbreaks not only in fish, but also in pigs and poultry [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

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Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix

Eisenberg

Mühldorfer

Erhard³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Seven genotypically distinct strains assigned to the genus Erysipelothrix were isolated in different laboratories from several animal sources. Strain D17_0559-3-2-1T and three further strains were isolated from samples of duck, pig and goose. The strains had >99 % 16S rRNA gene sequence similarity to each other and to strain VA92-K48T and two further strains isolated from samples of medical leech and a turtle. The closest related type strains to the seven strains were those of Erysipelothrix inopinata (96.74 %) and Erysipelothrix rhusiopathiae (95.93 %). Average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization results showed that the strains represented two separate novel species. One further phylogenetically distinct strain (165301687T) was isolated from fox urine. The strain had highest 16S rRNA gene sequence similarity to the type strains of Erysipelothrix tonsillarum (95.67 %), followed by Erysipelothrix piscisicarius (95.58 %) and Erysipelothrix larvae (94.22 %) and represented a further novel species. Chemotaxonomic and physiological data of the novel strains were assessed, but failed to unequivocally differentiate the novel species from existing members of the genus. MALDI-TOF MS data proved the discrimination of at least strain 165301687T from all currently described species. Based on the presented phylogenomic and physiological data, we propose three novel species, Erysipelothrix anatis sp. nov. with strain D17_0559-3-2-1T (=DSM 111258T= CIP 111884T=CCM 9044T) as type strain, Erysipelothrix aquatica sp. nov. with strain VA92-K48T (=DSM 106012T=LMG 30351T=CIP 111492T) as type strain and Erysipelothrix urinaevulpis sp. nov. with strain 165301687T (=DSM 106013T= LMG 30352T= CIP 111494T) as type strain.

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

Zhong,

Medvecky,

Tornos

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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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.

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Author Correction: Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Cited by 3 publications

References 0 publications

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

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

Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix

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

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