Multilevel population genetic analysis of<i>vanA</i>and<i>vanB Enterococcus faecium</i>causing nosocomial outbreaks in 27 countries (1986–2012)

Freitas, Ana R.; Tedim, Ana P.; Francia, María Victoria; Jensen, Lars; Novais, Carla; Peixe, Luı́sa; Sánchez-Valenzuela, Antonio; Sundsfjord, Arnfinn; Hegstad, Kristin; Werner, Guido; Sadowy, Ewa; Hammerum, Anette M.; Migura-García, Lourdes; Willems, Rob J. L.; Baquero, Fernando; Coque, Teresa M.

doi:10.1093/jac/dkw312

Cited by 138 publications

(141 citation statements)

References 167 publications

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“…The high number of multireplicon plasmids consisting of several combinations of Rip families confirmed the high levels of mosaicism also previously observed for E. faecium plasmids which makes it infeasible to classify Enterococcal plasmids based on Rip-schemes (Freitas et al 2016).…”

Section: Discussionsupporting

confidence: 69%

Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome

Arredondo-Alonso

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et al. 2019

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Enterococcus faecium is a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms. Previous research has suggested that nosocomial strains have multiple zoonotic origins and are only distantly related to those involved in human commensal colonization. Here we present the first comprehensive population-wide joint genomic analysis of hospital, commensal and animal isolates using both short-and long-read sequencing techniques. This enabled us to investigate the population plasmidome, core genome variation and genome architecture in detail, using a combination of machine learning, population genomics and genome-wide co-evolution analysis. We observed a high level of genome plasticity with large-scale inversions and heterogeneous chromosome sizes, collectively painting a high-resolution picture of the adaptive landscape of E. faecium, and identified plasmids as the main indicator for host-specificity. Given the increasing availability of long-read sequencing technologies, our approach could be widely applied to other human and animal pathogen populations to unravel fine-scale mechanisms of their evolution.

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Section: Discussionsupporting

confidence: 69%

Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome

Arredondo-Alonso

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et al. 2019

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“…Plasmid profiling was determined using a modified Barton's method protocol (Barton et al, 1995;Freitas et al, 2016). Plasmid categorization was based on the diversity of genes encoding rep-initiator proteins (rep), relaxases (rel) and toxin-antitoxin (TA) systems of Grampositive plasmids using PCR-typing schemes (Supporting Information Table S4) (Jensen et al, 2010;Wardal et al, 2013;Clewell et al, 2014;Freitas et al, 2016). Characterization of pheromone-responsive plasmids was confirmed by Southern blot hybridization of S1-digested genomic DNA with specific probes for rel, rep and TA genes obtained by PCR using DNA from reference plasmids as positive controls.…”

Section: Characterization Of Plasmidsmentioning

confidence: 99%

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

León‐Sampedro

Campo

Rodríguez-Baños

et al. 2019

Environmental Microbiology

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Summary Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone‐responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.

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“…Plasmids are autonomous extra-chromosomal elements which can act as major drivers of variation and adaptation in bacterial populations (1,2) . Plasmids can also facilitate the dissemination of antimicrobial resistance (AMR) via horizontal transfer of plasmids encoding resistance genes such as plasmid-derived vancomycin resistance in Enterococcus faecium or extended-spectrum beta-lactamase in Enterobacteriaceae isolates (3)(4)(5)(6) . This means that understanding plasmid epidemiology is pivotal to fully understand the introduction and transmission of AMR in bacterial populations (7,8) .…”

Section: Introductionmentioning

confidence: 99%

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Arredondo-Alonso

Rogers

Braat

et al. 2018

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Assembly of bacterial short-read whole genome sequencing (WGS) data frequently results in hundreds of contigs for which the origin, plasmid or chromosome, is unclear. Long-read sequencing has emerged as a solution to resolve plasmid structures and to obtain complete genomes for most bacterial species. This information can be used to generate and label datasets from short-read based contigs as plasmid-or chromosome-derived. We investigated the use of several popular machine learning methods to classify short-read contigs with known plasmid-or chromosome-origin from Enterococcus faecium , Klebsiella pneumoniae and Escherichia coli using pentamer frequencies. Based on resulting F1-scores we selected support-vector machine (SVM) models as best classifier for all three bacterial species (F1-score E. faecium = 0.94, F1-score K. pneumoniae = 0.90, F1-score E. coli = 0.76) , which outperformed other existing plasmid tools using an independent set of isolates (precision E. faecium = 0.92, precision K. pneumoniae = 0.86, precision E. coli = 0.82). We demonstrated the scalability of our model by accurately predicting the plasmidome of a large collection of 1,644 E. faecium isolates with only short-read WGS available using a standard laptop with a single core. A low number of false positive predicted sequences suggests that the assignment of a particular gene of interest as plasmid-or chromosome-encoded by the models is plausible. The SVM classifiers are publicly available as a new R package called 'mlplasmids' at https://gitlab.com/sirarredondo/mlplasmids under the GNU General Public License v3.0. We additionally developed a graphical-user interface using the Shiny package which can be accessed at https://sarredondo.shinyapps.io/mlplasmids/ . Single genomes can easily be predicted by uploading genome assemblies. We anticipate that this tool may significantly facilitate research on the dissemination of plasmids encoding antibiotic resistance and/or contributing to host adaptation.

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Multilevel population genetic analysis ofvanAandvanB Enterococcus faeciumcausing nosocomial outbreaks in 27 countries (1986–2012)

Cited by 138 publications

References 167 publications

Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome

Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

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