Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth,
            <i>Mammuthus primigenius</i>

Гончаров, А. Е.; Grigorjev, Semyon; Karaseva, Alena; Колоджиева, В. В.; Azarov, Daniil; Akhremenko, Yana A.; Tarasova, Lidia; Tikhonov, Alexei; Masharskiy, Alexey E.; Зуева, Л П; Suvorov, Alexander

doi:10.1128/genomea.01706-15

Cited by 11 publications

(11 citation statements)

References 8 publications

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“…It has been estimated that the Enterococcus as a genus arose around 500 million years ago 44 and ancient isolates of E. faecium have been found in permafrost over 20,000 y.a. 45 , supporting our findings that a more ancient branching between Clade A and B could have occurred.…”

Section: Discussionsupporting

confidence: 89%

Genomic epidemiology of vancomycin resistantEnterococcus faecium(VREfm) in Latin America: Revisiting the global VRE population structure

Ríos

Reyes

Carvajal

et al. 2019

Preprint

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42The prevalence of vancomycin-resistant Enterococcus faecium varies across 43 geographical regions yet little is known about its population structure in Latin 44 America. Here, we provide a complete genomic characterization of 55 45 representative Latin American VREfm recovered from 1998-2015 in 5 countries. 46 We found that VREfm population in the region is structured into two main clinical 47 clades without geographical clustering. To place our regional findings in context, 48 we reconstructed the global population structure of VREfm by including 285 49 genomes from 36 countries from 1946-2017. Our results differ from previous 50 studies showing an early branching of animal related isolates and a further split of 51 clinical isolates into two sub-clades, all within clade A. The overall phylogenomic 52 structure was highly dependent on recombination (54% of the genome) and the 53 split between clades A and B is estimated to have occurred more than 3585 years 54 BP. Furthermore, while the branching of animal isolates and clinical clades was 55 predicted to have occur ~894 years BP, our molecular clock calculations suggest 56 that the split within the clinical clade occurred around ~371 years BP. By including 57 isolates from Latin America, we present novel insights into the population structure 58 of VREfm and revisit the evolution of this pathogen. 59 60 61 62 63 64 Enterococci are predominantly non-pathogenic gastrointestinal commensal 65 bacteria that occasionally cause human infections. Among them, Enterococcus 66 faecalis and Enterococcus faecium represent the species that account for most 67 clinically relevant infections. In particular, E. faecium has been able to adapt to the 68 hospital environment, emerging during the last few decades as a leading cause of 69 health-care infections worldwide, and becoming the most challenging species to 70 treat 1,2 . 71 Genome plasticity, the presence of multiple antibiotic resistance determinants, and 72 the lack of therapeutic options have contributed to the adaptation of E. faecium to 73 hospital environments 3,4 . Moreover, high recombination rates and the acquisition of 74 mobile elements in the genome of E. faecium also have driven this evolutionary 75 process 5 . In addition, the enrichment of virulence determinants, such as surface 76 proteins and phosphotransferase systems (particularly PTS clin , a putative factor 77 found to contribute to the intestinal colonization in a murine model) seems to 78 provide an advantage to the hospital adaptive process 3,6 . Furthermore, functional 79 gene groups, such as those involved in galactosamine metabolism, bile hydrolysis 80 and phosphorus utilization, are also abundant in E. faecium clinical strains 81 compared to non-clinical isolates, suggesting that specific metabolic factors have 82 also facilitated adaptation 7 .83In terms of antibiotic resistance, one of the most relevant antibiotic resistance traits 84 acquired by enterococci is resistance to vancomycin due to the van gene clusters 8 . 85Furthermor...

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Section: Discussionsupporting

confidence: 89%

Genomic epidemiology of vancomycin resistantEnterococcus faecium(VREfm) in Latin America: Revisiting the global VRE population structure

Ríos

Reyes

Carvajal

et al. 2019

Preprint

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“…LGAN00000000 and LGAO00000000. The characteristics of the genome of Enterococcus faecium 58m, including the presence of genes associated with pathogenic potential, were discussed by Goncharov et al (2016). Also Carnobacterium maltaromaticum was isolated from the mammoth's bowel.…”

Section: Microbiologymentioning

confidence: 99%

A woolly mammoth ( Mammuthus primigenius ) carcass from Maly Lyakhovsky Island (New Siberian Islands, Russian Federation)

Grigoriev

Fisher

Obadă

et al. 2017

Quaternary International

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A partial carcass of an adult woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island presents a new opportunity to retrieve associated anatomical, morphological, and life history data on this important component of Pleistocene biotas. In addition, we address hematological, histological, and microbiological issues that relate directly to quality of preservation. Recovered by staff from North-Eastern Federal University in Yakutsk, this individual is a relatively old female preserving soft tissue of the anteroventral portion of the head, most of both fore-quarters, and the ventral aspect of much of the rest of the body. Both tusks were recovered and subjected to computed tomographic analysis in which annual dentin increments were revealed as cycles of variation in X-ray attenuation. Measurements of annual increment areas (in longitudinal section) display a pulsed pattern of tusk growth showing cycles of growth rate variation over periods of 3e5 years. These intervals are interpreted as calving cycles reflecting regular shifts in calcium and phosphate demand for tusk growth vs. fetal ossification and lactation. Brown liquid associated with the frozen carcass turned out to include remains of hemolyzed blood, and blood samples examined microscopically included white blood cells with preserved nuclei. Muscle tissue from the trunk was unusually well preserved, even at the histological level. Intestinal contents and tissue samples were investigated microbiologically, and several strains of lacticacid bacteria (e.g., Enterococcus faecium, Enterococcus hirae) that are widely distributed as commensal organisms in the intestines of herbivores were isolated.

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“…In the recent publication “Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius ” in Genome Announcements ( 1 ), Goncharov et al claim to have isolated and grown in pure culture a 28,000-year-old Enterococcus faecium strain. However, the authors ignored a breadth of literature about the authentication of ancient DNA, failed to adhere to recommended guidelines ( 2 ), and did not provide the appropriate experimental controls and analyses required to substantiate such a claim.…”

Section: Lettermentioning

confidence: 99%

Isolating Viable Ancient Bacteria: What You Put In Is What You Get Out

2016

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Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius

Cited by 11 publications

References 8 publications

Genomic epidemiology of vancomycin resistantEnterococcus faecium(VREfm) in Latin America: Revisiting the global VRE population structure

Genomic epidemiology of vancomycin resistantEnterococcus faecium(VREfm) in Latin America: Revisiting the global VRE population structure

A woolly mammoth ( Mammuthus primigenius ) carcass from Maly Lyakhovsky Island (New Siberian Islands, Russian Federation)

Isolating Viable Ancient Bacteria: What You Put In Is What You Get Out

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