Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis

Wilkinson, David A.; O’Donnell, Andrew J.; Akhter, Rukhshana N.; Fayaz, Ahmed; Mack, Hamish J; Rogers, Lynn; Biggs, Patrick J.; French, Nigel P.; Midwinter, Anne C.

doi:10.1038/s41598-018-20889-x

Cited by 32 publications

(31 citation statements)

References 75 publications

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“…lawsonii could be reclassified as separate species within the genus Campylobacter. Indeed, a more recent study that performed whole-genome sequencing of 18 strains isolated from cattle, sheep, and deer from New Zealand confirmed the previously suggested genomewide plasticity of C. hyointestinalis (78). This work revealed high rates of gene gain/loss across C. hyointestinalis lineages, probably accounting for the effects of horizontal gene transfer.…”

Section: Campylobacter Hyointestinalissupporting

confidence: 71%

“…Together, the observed genomic variability of C. hyointestinalis may indicate a great potential to adapt to different ecological niches, underpinning its capacity to colonize a great variety of mammal species both as a commensal and as a disease-causing agent (78). Further comparisons between commensal and disease-associated strains may provide new insight into the genetic mechanisms underlying C. hyointestinalis pathogenicity.…”

Section: Campylobacter Hyointestinalismentioning

confidence: 99%

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Pathogenomics of EmergingCampylobacterSpecies

2019

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SUMMARY Campylobacter is among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reported Campylobacter infections are caused by Campylobacter jejuni and, to a lesser extent, C. coli; however, the increasing recognition of other emerging Campylobacter pathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has increased the number of whole-genome sequences available to dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such as C. fetus and C. concisus. These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emerging Campylobacter species, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.

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Section: Campylobacter Hyointestinalissupporting

confidence: 71%

Section: Campylobacter Hyointestinalismentioning

confidence: 99%

Pathogenomics of EmergingCampylobacterSpecies

2019

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“…However, infection of children with non-thermophilic Campylobacter spp. (e.g., Campylobacter hyointestinalis, Campylobacter fetus, Campylobacter showae, and Campylobacter concisus) is largely underestimated due to unsuitable culturing methods and their public health risks specifically in EED pathogenesis is not known (19,20).…”

Section: Introductionmentioning

confidence: 99%

Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host Microbiome

Terefe

Deblais

Ghanem

et al. 2020

Front. Public Health

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High Campylobacter prevalence during early childhood has been associated with stunting and environmental enteric dysfunction (EED), especially in low resource settings. This study assessed the prevalence, diversity, abundance, and co-occurrence of Campylobacter spp. in stools from children in a rural area of eastern Ethiopia and their association with microbiome, diarrhea, and EED in children. Stool samples (n = 100) were collected from randomly selected children (age range: 360-498 days) in five kebeles in Haramaya District, Ethiopia. Diarrhea, compromised gut permeability, and gut inflammation were observed in 48, 45, and 57% of children, respectively. Campylobacter prevalence and species diversity were assessed using PCR and meta-total RNA sequencing (MeTRS). The prevalence of Campylobacter spp. in the children's stools was 50% (41-60%) by PCR and 88% (80-93.6%) by MeTRS (P < 0.01). Further, seven Campylobacter species (Campylobacter jejuni, Campylobacter upsaliensis, Campylobacter hyointestinalis, Campylobacter coli, Campylobacter sp. RM6137, uncultured Campylobacter sp., and Campylobacter sp. RM12175) were detected by MeTRS in at least 40% of children stools in high abundance (>1.76-log read per million per positive stool sample). Four clusters of Campylobacter species (5-12 species per cluster) co-occurred in the stool samples, suggesting that Campylobacter colonization of children may have occurred through multiple reservoirs or from a reservoir in which several Campylobacter species may co-inhabit. No associations between Campylobacter spp., EED, and diarrhea were detected in this cross-sectional study; however, characteristic microbiome profiles were identified based on the prevalence of Campylobacter spp., EED severity, and diarrhea. Forty-seven bacterial species were correlated with Campylobacter, and 13 of them also correlated with gut permeability, gut inflammation and/or EED severity. Forty-nine species not correlated with Campylobacter Terefe et al. Campylobacter and Microbiome in Stools were correlated with gut permeability, gut inflammation, EED severity and/or diarrhea. This study demonstrated that (1) in addition to C. jejuni and C. coli, multiple nonthermophilic Campylobacter spp. (i.e., Campylobacter hyointestinalis, Campylobacter fetus, and Campylobacter concisus) were frequently detected in the children's stools and (2) the Campylobacter, gut permeability, gut inflammation, EED severity, and diarrhea were associated with characteristic microbiome composition. Additional spatial and longitudinal studies are needed to identify environmental reservoirs and sources of infection of children with disparate Campylobacter species and to better define their associations with EED in low-income countries.

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“…Recently, the first comparative analysis of multiple C. hyointestinalis strains at whole-genome resolution confirmed the previously observed highly diverse nature of this bacterial species. This study revealed a great level of plasticity between C. hyointestinalis genomes, with high incidence of recombination and accessory gene gain/loss as the main factors contributing to the observed diversity within this species 16 . However, this study was mainly performed using C. hyointestinalis subsp.…”

Section: Discussionmentioning

confidence: 82%

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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Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis

Cited by 32 publications

References 75 publications

Pathogenomics of EmergingCampylobacterSpecies

Pathogenomics of EmergingCampylobacterSpecies

Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host Microbiome

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

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