Innuendo Whole Genome And Core Genome Mlst Schemas And Datasets For Campylobacter Jejuni

Rossi, Mirko; Silva, Mickael Santos Da; Ribeiro-Gonçalves, Bruno; Silva, Diogo N.; Machado, Miguel P.; Oleastro, Mónica; Borges, Vítor; Isidro, Joana; Viera, Luis; Barker, Dillon Or; Llarena, Ann-Katrin; Halkilahti, Jani; Jaakkonen, Anniina; Kivistö, Rauni; Kovanen, Sara; Nieminen, Tea; Hänninen, Marja‐Liisa; Salmenlinna, Saara; Hakkinen, Marjaana; Garaizar, Javier; Bikandi, Joseba; Hilbert, Friederike; Taboada, Eduardo; Carriço, João André

doi:10.5281/zenodo.1322564

Cited by 10 publications

(3 citation statements)

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“…The C. jejuni genomes were clustered in a phylogenetic tree based on a 678 gene core genome (cg)MLST scheme [ 44 ], which grouped the genomes mostly according to clonal complexes of the seven-gene MLST for C. jejuni ( Fig. 3 ) and the different C. coli clades ( Fig.…”

Section: Resultsmentioning

confidence: 99%

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A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

2021

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Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli . CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli . CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C . jejuni genomes and 92/1347 (6.8 %) C . coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter .

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Section: Resultsmentioning

confidence: 99%

“… jejuni and 1347 C . coli genomes using a 678 gene set described previously [ 44 ]. Allele calling was performed using chewBBACA version 2.6 [ 45 ] using default settings.…”

Section: Methodsmentioning

confidence: 99%

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

2021

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“…Three sources of reference sequences were utilized for the preparation of the strainEST database: PubMLST isolate genomes, genomes utilized in generation of the innuendo wgMLST typing scheme [ 39 ], and isolates genomes assembled in this study ( Supplementary Data S1 ). Genomes were reannotated to obtain 9MLST profiles with the mlst tool ( , accessed on 30 December 2022) using a custom scheme generated from the sequences downloaded for the KMA step.…”

Section: Methodsmentioning

confidence: 99%

Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds

et al. 2023

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As the world’s leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution.

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Genotyping of Campylobacter jejuni and prediction tools of its antimicrobial resistance

Strakova,

Michova,

Shagieva

et al. 2023

Folia Microbiol

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Although Campylobacter jejuni is the pathogen responsible for the most common foodborne illness, tracing of the infection source remains challenging due to its highly variable genome. Therefore, one of the aim of the study was to compare three genotyping methods (MLST, PFGE, and mP-BIT) to determine the most effective genotyping tool. C. jejuni strains were divided into 4 clusters based on strain similarity in the cgMLST dendrogram. Subsequently, the dendrograms of the 3 tested methods were compared to determine the accuracy of each method compared to the reference cgMLST method. Moreover, a cost-benefit analysis has showed that MLST had the highest inverse discrimination index (97%) and required less workflow, time, fewer consumables, and low bacterial sample quantity. PFGE was shown to be obsolete both because of its low discriminatory power and the complexity of the procedure. Similarly, mP‑BIT showed low separation results, which was compensated by its high availability. Therefore, our data showed that MLST is the optimal tool for genotyping C. jejuni. Another aim was to compare the antimicrobial resistance to ciprofloxacin, erythromycin, and tetracycline in C. jejuni strains isolated from human, water, air, food, and animal samples by two gene sequence-based prediction methods and to compare them with the actual susceptibility of C. jejuni strains using the disc diffusion method. Both tools, ResFinder and RGI, synchronously predict the antimicrobial susceptibility of C. jejuni and either can be used.

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Innuendo Whole Genome And Core Genome Mlst Schemas And Datasets For Campylobacter Jejuni

Cited by 10 publications

References 0 publications

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?

Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds

Genotyping of Campylobacter jejuni and prediction tools of its antimicrobial resistance

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