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

Laurentie, Jeanne; Loux, Valentin; Hennequet-Antier, Christelle; Chambellon, Émilie; Deschamps, Julien; Trotereau, Angélina; Furlan, Sylviane; Darrigo, Claire; Kempf, Florent; Lao, Julie; Milhes, Marine; Roques, Céline; Quinquis, Benoît; Vandecasteele, Céline; Boyer, Roxane; Bouchez, Olivier; Repoila, Francis; Guennec, Jean Le; Chiapello, Hélène; Briandet, Romain; Helloin, Emmanuelle; Schouler, Catherine; Kempf, Isabelle; Serror, Pascale

doi:10.1128/msphere.00495-22

Cited by 9 publications

(6 citation statements)

References 105 publications

(141 reference statements)

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“…We interpret all of the phylogenomic data as most consistent with pathogenic isolates arising from non-pathogenic isolates and that sepsis isolates are closely related to BCO isolates. Our conclusions contrast with those from previous analyses of smaller collections of genomes that suggested distinct lineages for commensal and pathogenic isolates of E. cecorum [ 13 , 16 , 37 ].…”

Section: Resultscontrasting

confidence: 99%

“…Our analyses of all publicly available genomes of E. cecorum support a polyphyletic origin of pathogenicity in chickens as well as the recent outbreaks of early on-set sepsis in broiler flocks. This contrasts with previous works suggesting a common lineage in chicken pathogenesis [ 16 ]. Our analysis of the pangenome of E. cecorum identified no gene or gene clusters essential for the switch from chicken commensal to chicken pathogen or for chicken sepsis isolates.…”

Section: Discussioncontrasting

confidence: 99%

“…The tree contained 100 genomes from isolates collected from 16 poultry farms in France between 2007 and 2017. Some of these genomes were from probable sepsis cases (red circles), with many representing pericarditis isolates [ 16 ]. These isolates appeared throughout the tree, with clusters including BCO and probable sepsis virulence phenotypes.…”

Section: Resultsmentioning

confidence: 99%

“…Our Prokka–Roary analysis of 227 genomes suggests that the core + pan-genome of this species contains 14,728 genes with 878 genes in the strict-core genome (99% ≤ strains ≤ 100%), 335 genes in the soft-core genome (95% ≤ strains < 99%), 1689 genes in the shell genome (15% ≤ strains < 95%), and 11,826 cloud genes (strains < 15%). Prior analysis of 140 genomes suggested a pangenome of 8523 gene clusters with 1207 genes in the strict-core genome, 4664 genes in the accessory genome, and a unique genome of 2652 [ 16 ]. Thus, our results appear to expand the pangenome by over 6000 genes with similar gene content for the sum of the strict-core and soft-core to the previous numbers for a strict-core genome.…”

Section: Resultsmentioning

confidence: 99%

“…The evolution of pathogenesis and drug resistance in E. faecalis and E. faecium has been associated with mobile elements and the acquisition of capsular gene clusters [ 14 , 15 ]. Phylogenomic analysis of more than 100 genomes of E. cecorum isolates from French broilers suggested that a specific lineage of pathogenic isolates is infecting broilers in Europe and the United States [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers

Rhoads,

Pummill,

Alrubaye

2024

Microorganisms

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Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggest a polyphyletic origin, likely arising from core genome mutations rather than gene acquisition. This species is a normal intestinal flora of avian species with particular isolates associated with osteomyelitis. More recently, this species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post-hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate genomes. Pangenome analyses detect no gene acquisitions that distinguish all the sepsis isolates. Core genome single nucleotide polymorphism analyses have identified a number of mutations, affecting the protein-coding sequences, that are enriched in sepsis isolates. The analysis of the protein substitutions supports the mutational origins of sepsis isolates.

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Section: Resultscontrasting

confidence: 99%

Section: Discussioncontrasting

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers

Rhoads,

Pummill,

Alrubaye

2024

Microorganisms

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A rare case of invasive Enterococcus cecorum infection and related diagnostic difficulties

Szymanski,

Skiba,

Piasecka

et al. 2024

Clinical Case Reports

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Key Clinical MessageThis report presents a rare case of invasive infection caused by Enterococcus cecorum. There are no specific guidelines regarding antibiotic therapy for this infection. Based on this case, it can be concluded that linezolid demonstrates in vivo activity against Enterococcus cecorum and can be successfully used in therapy.AbstractEnterococcus cecorum is an extremely rare pathogen in humans. Since 1984, when the microorganism was first described, only a dozen cases of invasive infections in humans have been reported in the literature. The diagnostic pathway may involve difficulties in correctly identifying this microorganism. Based on the case described, it can be thought that Enterococcus cecorum is a more challenging bacterium than the much more common Enterococcus faecium or Enterococcus faecalis. The described case underscores the importance of medical vigilance in clinical practice. It seems that due to increasingly advanced techniques in molecular biology, we will more frequently detect pathogens that were previously encountered only sporadically. Since not every center has access to modern and advanced microbiological diagnostic methods, publications that practically combine classical microbiological diagnostic methods with those less accessible but more modern are exceptionally valuable. In the case described, it is also worth noting that classical methods still play a significant and crucial role in conducting microbiological diagnostics. In the era of rapid diagnostic tool development, it is important to emphasize the necessity of combining different methods rather than replacing one with another.

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Serological monitoring of Enterococcus cecorum specific antibodies in chickens

Silberborth,

Schnug,

Rautenschlein

et al. 2024

Veterinary Immunology and Immunopathology

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

Abstract: Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers.

Cited by 9 publications

References 105 publications

Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers

Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers

A rare case of invasive Enterococcus cecorum infection and related diagnostic difficulties

Serological monitoring of Enterococcus cecorum specific antibodies in chickens

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