Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera

Jh, Kaufman; Terrizzano, Ignacio; Nayar, Gowri; Seabolt, Ed; Agarwal, Akshay; Slizovskiy, Ilya B.; Noyes, Noelle

doi:10.1101/2020.04.07.030320

Cited by 7 publications

(5 citation statements)

References 64 publications

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“…ARGs are other clinically important cargo genes spread by ICEs and GIs ( 76 ). The ARGs identified in E. cecorum confer resistance to tetracycline, macrolides, bacitracin, aminoglycosides, and, much more rarely, glycopeptides.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Laurentie

Loux

Hennequet-Antier

et al. 2023

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Section: Discussionmentioning

confidence: 99%

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Laurentie

Loux

Hennequet-Antier

et al. 2023

mSphere

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show abstract

“…ARGs are other clinically important cargo genes spread by ICEs and GIs (75). The ARGs identified in E. cecorum confer resistance to tetracycline, macrolides, bacitracin, aminoglycosides, and much more rarely to glycopeptides.…”

Section: Discussionmentioning

confidence: 99%

Comparative genome analysis ofEnterococcus cecorumreveals intercontinental spread of a lineage of clinical poultry isolates

Laurentie

Loux

Hennequet-Antier

et al. 2022

Preprint

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Enterococcus cecorumis an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically,E. cecorumis a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones ofE. cecorumcluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones ofE. cecorumbelong mainly to one phylogenetic clade.IMPORTANCEEnterococcus cecorumis an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associatedE. cecorumisolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome ofE. cecorumstrains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden ofE. cecorum-related diseases.

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“…Previous work has identified novel CEs in the human and animal gut microbiomes, but the focus was mainly on ICEs and not on conjugative plasmids [3,18,19]. Identifying conjugative plasmids from a short-read metagenomic assembly is difficult for several reasons.…”

Section: Introductionmentioning

confidence: 99%

Identification of type IV conjugative systems that are systematically excluded from metagenomic bins

Joris¹,

Browne²,

Hamilton³

et al. 2022

Preprint

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BackgroundConjugation enables the exchange of genetic elements throughout environments, including the human gut microbiome. Conjugative elements can carry and transfer clinically relevant metabolic pathways which makes precise identification of these systems in metagenomic samples clinically important. ResultsHere, we outline two related methods to identify conjugative elements in the human gut microbiome. Conjugative systems can effectively be identified from metagenomic assemblies either using a curated sets of profile hidden Markov models or by searching against large-scale databases, such as UniRef90. Both methods were successful at identifying type IV conjugative systems with profile hidden Markov models being faster, but less sensitive than alignment to the UniRef database. Finally, we demonstrate that the majority of assembled conjugative elements are not included within metagenomic bins, and that only a small proportion of the binned conjugative systems are included in "high-quality" metagenomic bins.ConclusionsAnalysis of the human gut microbiome by shotgun metagenomic sequencing has revealed numerous connections to human health outcomes. Our findings emphasize the need to identify and analyze conjugative systems outside of standard metagenomic binning pipelines. We suggest that analysis of type IV conjugative systems should be added to the current metagenomic analysis approaches as they contain much information that could explain differences between cohorts.

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Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera

Cited by 7 publications

References 64 publications

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Comparative genome analysis ofEnterococcus cecorumreveals intercontinental spread of a lineage of clinical poultry isolates

Identification of type IV conjugative systems that are systematically excluded from metagenomic bins

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