Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni)

Piccirillo, Alessandra; Niero, Giulia; Calleros, Lucía; Pérez, Ruben; Naya, Hugo; Iraola, Gregorio

doi:10.1099/ijsem.0.001219

Cited by 43 publications

(22 citation statements)

References 44 publications

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“…Genomes were estimated to be less than 10% contaminated, with all but eight under 5% (Supplementary Table S1). The taxonomic annotation of the type strain Campylobacter geochelonis (GCA_900063025.1) was manually modified as the NCBI record for this genome incorrectly labels it as C. fetus (Piccirillo et al, 2016). Thirty-three draft population genomes (median completeness 93.8%, contamination 1.1%) belonging to the Epsilonproteobacteria were recovered from publicly available metagenomic data sets as part of a larger study (Parks et al, submitted) and included in our analysis.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

et al. 2017

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The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.

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Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

et al. 2017

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“…Of the most recently added species, few have been associated with disease in the host. Most have been incidental findings in surveys of primates, sea mammals, captive reptiles or wild birds (Caceres, Munoz, Iraola, Diaz‐Viraque, & Collado, ; Debruyne et al, ; Gilbert, Kik, Miller, Duim, & Wagenaar, ; Gilbert et al, ; Kaur et al, ; Koziel et al, ; Piccirillo et al, ). In contrast, C. hepaticus was isolated from clinical disease (SLD) in laying hens and has been confirmed as the cause of SLD (Van, Elshagmani, et al, ).…”

Section: The Significance Of C Hepaticusmentioning

confidence: 99%

A review of the novel thermophilicCampylobacter,Campylobacter hepaticus,a pathogen of poultry

Crawshaw

2019

Transbound Emerg Dis

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In 2015, a novel thermophilic Campylobacter was isolated from cases of spotty liver disease in laying hens in the UK. In 2016, it was isolated from laying hens in Australia where it was formally named Campylobacter hepaticus and confirmed as the cause of spotty liver disease. It has also been isolated from laying hens in America. It is fastidious, grows slowly on first isolation and does not grow on media used to routinely isolate Campylobacter. Spotty liver disease is an acute, randomly distributed, focal, necrotic hepatitis causing mortality in up to 10% of a flock and a 10%–15% fall in egg production. It occurs mainly in free‐range hens or hens reared on the ground at around the time of peak lay. The incidence of the disease has increased in countries where there is an increase in keeping free‐range laying hens. It is similar to the condition avian vibrionic hepatitis which was reported in America, Europe and Australasia in the 1950s to 1970s and the agent isolated from cases of avian vibrionic hepatitis and C. hepaticus appear to be very similar. It is not known if C. hepaticus is zoonotic but whole genome sequencing shows that it is most closely related to the known zoonotic campylobacters Campylobacter jejuni and Campylobacter coli. Human exposure to C. hepaticus is likely through similar exposure routes. Analysis of the whole genome showed a reduction in the genes for iron metabolism compared to C. jejuni. A requirement for iron was confirmed as it showed reduced growth in an iron depletion assay and this may explain its tissue tropism. With a move towards free‐range egg production in many countries, the incidence of C. hepaticus hepatitis is likely to increase, but the identification of the causal agent will provide opportunities for the development of control methods.

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“…Resulting contigs were annotated using Prokka 27 . Species membership was checked by calculating the Average Nucleotide Identity (ANI) index as previously described 28 . Available genomic data at the time of designing this work consisted in 19 C. hyointestinalis subsp.…”

Section: Methodsmentioning

confidence: 99%

Pangenome analysis reveals genetic isolation inCampylobacter hyointestinalissubspecies adapted to different mammalian hosts

Costa

Lévesque²,

Kumar

et al. 2019

Preprint

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Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. 40 hyointestinalis subsp. lawsonii which is restricted to pigs, and C. hyointestinalis subsp. hyointestinalis which can 41 be found in a much wider range of mammalian hosts. Despite C. hyointestinalis has been reported as an 42 emerging pathogen, its evolutionary and host-associated diversification patterns are still vastly unexplored. For 43 this reason, we whole-genome sequenced 13 C. hyointestinalis subsp. hyointestinalis strains and performed a 44 comprehensive comparative analysis including publicly available genomes of C. hyointestinalis subsp.45 hyointestinalis and C. hyointestinalis subsp. lawsonii to gain insight into the genomic variation of these 46 differentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present a barrier to 47 homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns 48 that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a 49 bigger and more diverse accessory genome, which probably reflects its capacity to colonize different mammalian 50 hosts unlike C. hyointestinalis subsp. lawsonii that is host-restricted. This greater plasticity in the accessory 51 genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide 52 recombination events, that may be the underlying mechanism driving its diversification. Concordantly, both 53 subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-54 associated proteins and restriction-modification systems. Together, our results provide an overview of the 55 genetic mechanisms shaping the genomes of C. hyointestinalis subspecies, contributing to understand the 56 biology of Campylobacter species that are increasingly found as emerging pathogens.

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Campylobacter geochelonis sp. nov. isolated from the western Hermann's tortoise (Testudo hermanni hermanni)

Cited by 43 publications

References 44 publications

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

A review of the novel thermophilicCampylobacter,Campylobacter hepaticus,a pathogen of poultry

Pangenome analysis reveals genetic isolation inCampylobacter hyointestinalissubspecies adapted to different mammalian hosts

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