Characterization of ecotin homologs from Campylobacter rectus and Campylobacter showae

Thomas, Cody; Nothaft, Harald; Yadav, Ruchi; Fodor, Christopher; Alemka, Abofu; Oni, Oluwadamilola; Bell, Michael A.; Rada, Balázs; Szymanski, Christine M.

doi:10.1371/journal.pone.0244031

Cited by 6 publications

(6 citation statements)

References 86 publications

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“…C. upsaliensis and C. helveticus grouped together which is consistent with Stanley et al ( 41 ). C. showae and C. rectus grouped together which is consistent with Thomas et al( 42 ). Several species that occupy unique ecological niches were distantly related to other members of the genus on the phylogenetic tree.…”

Section: Resultssupporting

confidence: 91%

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Wu,

Payne,

Zhang

et al. 2024

mSystems

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Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes ( n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future. IMPORTANCE In recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter .

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Section: Resultssupporting

confidence: 91%

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Wu,

Payne,

Zhang

et al. 2024

mSystems

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“…Here we found that Ecotin is important for STm to survive against both PMN killing mechanisms, granules content and NETs. Similar results were found for ecotin from Campylobacter rectus and Campylobacter showae [34]. We also found that the addition of rEcotin to the NETs prior to the incubation with the Δ eco strain reverted the phenotype to WT levels.…”

Section: Discussionsupporting

confidence: 89%

Ecotin protectsSalmonellaTyphimurium against the microbicidal activity of host proteases

Saposnik,

Coria,

Bruno

et al. 2024

Preprint

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Salmonella entericaserovar Typhimurium causes acute diarrhea upon oral infection in humans. The harsh and proteolytic environment found in the gastrointestinal tract is the first obstacle that these bacteria face after infection. However, the mechanisms that allowSalmonellato survive the hostile conditions of the gut are poorly understood. Theecotingene is found in an extensive range of known phyla of bacteria and it encodes a protein that has been shown to inhibit serine proteases. Thus, in the present work we studied the role ofecotinofSalmonellaTyphimurium in host-pathogen interactions. We found thatSalmonellaTyphimurium Δecotinstrain exhibited lower inflammation in a murine model ofSalmonellainduced colitis. The Δecotinmutant was more susceptible to the action of pancreatin and purified pancreatic elastase. In addition, the lack ofecotinled to impaired adhesion to Caco-2 and HT-29 cell lines, related to the proteolytic activity of brush border enzymes. Besides, Δecotinshowed higher susceptibility to lysosomal proteolytic content and intracellular replication defects in macrophages. In addition, we found Ecotin to have a crucial role inSalmonellaagainst the microbicide action of granules released and neutrophil extracellular traps from human polymorphonuclear leukocytes. Thus, the work presented here highlights the importance ofecotininSalmonellaas countermeasures against the host proteolytic defense system.

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“…Campylobacter showae (2.40%) was found in nine cases (90%) of PTAP, which has not been found in other countries. It is implicated in the development and progression of periodontal disease (Thomas et al, 2020), and it may play a role in post-treatment endodontic disease. Olsenella uli (2.30%) was detected in 6/10 patients with PTAP, which was also detected in symptomatic endodontic infections of studies in Brazil (Prada et al, 2019;.…”

Section: Discussionmentioning

confidence: 99%

Potential relationship between clinical symptoms and the root canal microbiomes of root filled teeth based on the next‐generation sequencing

et al. 2021

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Aim: To determine the microorganism in root canal systems of root filled teeth with periapical disease and their relationship with clinical symptoms using nextgeneration sequencing. Methodology:The roots of 10 extracted teeth were collected from 10 patients who presented with post-treatment apical periodontitis (PTAP; six with symptoms and four without symptoms). Each root was divided horizontally into two parts (apical and coronal segments) and cryo-pulverized. Microbial communities were detected using 16S rDNA hypervariable V3-V4 region. The diversity, principal coordinate analysis and linear discriminant analysis effect size were performed in the symptomatic and asymptomatic groups (apical and coronal parts respectively). A Mann-Whitney test and an analysis of similarities were applied for intergroup analysis, at a significance level of 5%.Results: A total of 23 phyla, 257 genera and 425 species were detected. Firmicutes was the most abundant phylum in all samples. Three phyla (Fusobacteria, Synergistetes and unidentified_Bacteria) and seven genera (Fusobacterium, Porphyromonas, Phocaeicola, Olsenella, Campylobacter, Tannerella and Fretibacterium) were significantly more abundant in the symptomatic patients (p < .05), whereas asymptomatic patients had more Sphingomonas. The species more significantly abundant in the symptomatic samples were Porphyromonas gingivalis, Phocaeicola abscessus, Campylobacter showae, Tannerella forsythia and Olsenella uli (p < .05).Conclusions: A greater microbial diversity was observed in root filled teeth with PTAP compared to earlier reports. Several genera and species in root canal systems might be associated with clinical symptoms of PTAP.

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Characterization of ecotin homologs from Campylobacter rectus and Campylobacter showae

Cited by 6 publications

References 86 publications

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Ecotin protectsSalmonellaTyphimurium against the microbicidal activity of host proteases

Potential relationship between clinical symptoms and the root canal microbiomes of root filled teeth based on the next‐generation sequencing

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