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Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40.

Zischka M, Künne CT, Blom J, Wobser D, Sakιnç T, Schmidt-Hohagen K, Dabrowski PW, Nitsche A, Hübner J, Hain T, Chakraborty T, Linke B, Goesmann A, Voget S, Daniel R, Schomburg D, Hauck R, Hafez HM, Tielen P, Jahn D, Solheim M, Sadowy E, Larsen J, Jensen LB, Ruiz-Garbajosa P, Quiñones Pérez D, Mikalsen T, Bender J, Steglich M, Nübel U, Witte W, Werner G - BMC Genomics (2015)

Bottom Line: Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source.D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

View Article: PubMed Central - PubMed

Affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany. melanie.zischka@googlemail.com.

ABSTRACT

Background: Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type.

Results: We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).

Conclusion: Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

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Related in: MedlinePlus

Comparative analysis of the finished and publicly availableE. faecalisgenomes. EDGAR generated Venn diagram facilitates visualizing core and strain-specific (“unique”) genes. This comparative analysis only exploits CDS of the chromosomes without considering of plasmid genes, whereby all strains shared 2173 CDS; 1, E. faecalis strain 62 (CP002491); 2, E. faecalis strain OG1RF (CP002621); 3, E. faecalis V583 (NC_004668); 4, E. faecalis probiotic strain Symbioflor 1 Clone DSM 16431 (NC_019770); 5, E. faecalis strain D32 (CP003726).
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Fig2: Comparative analysis of the finished and publicly availableE. faecalisgenomes. EDGAR generated Venn diagram facilitates visualizing core and strain-specific (“unique”) genes. This comparative analysis only exploits CDS of the chromosomes without considering of plasmid genes, whereby all strains shared 2173 CDS; 1, E. faecalis strain 62 (CP002491); 2, E. faecalis strain OG1RF (CP002621); 3, E. faecalis V583 (NC_004668); 4, E. faecalis probiotic strain Symbioflor 1 Clone DSM 16431 (NC_019770); 5, E. faecalis strain D32 (CP003726).

Mentions: We used a Venn diagram presentation generated by the web application EDGAR to illustrate homologies and differences between the finished and publicly available E. faecalis genomes. It illustrated a common gene pool of 2173 CDS, present in all of the finished E. faecalis genomes (Figure 2). This analysis also revealed that the number of unique CDS of the clinical strain V583 was approximately twice that of the counts of the commensal isolates 62 and our ST40 isolate D32 as well as the probiotic Symbioflor 1 strain. As a derivate of the commensal isolate, the OG1RF strain carried the minimal number of 140 unique CDS. The commensal strains 62 and D32 both shared significantly more CDS with the V583 chromosome, whereas the Symbioflor 1 and OG1RF chromosomes overlapped less with the V583 core genome.Figure 2


Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40.

Zischka M, Künne CT, Blom J, Wobser D, Sakιnç T, Schmidt-Hohagen K, Dabrowski PW, Nitsche A, Hübner J, Hain T, Chakraborty T, Linke B, Goesmann A, Voget S, Daniel R, Schomburg D, Hauck R, Hafez HM, Tielen P, Jahn D, Solheim M, Sadowy E, Larsen J, Jensen LB, Ruiz-Garbajosa P, Quiñones Pérez D, Mikalsen T, Bender J, Steglich M, Nübel U, Witte W, Werner G - BMC Genomics (2015)

Comparative analysis of the finished and publicly availableE. faecalisgenomes. EDGAR generated Venn diagram facilitates visualizing core and strain-specific (“unique”) genes. This comparative analysis only exploits CDS of the chromosomes without considering of plasmid genes, whereby all strains shared 2173 CDS; 1, E. faecalis strain 62 (CP002491); 2, E. faecalis strain OG1RF (CP002621); 3, E. faecalis V583 (NC_004668); 4, E. faecalis probiotic strain Symbioflor 1 Clone DSM 16431 (NC_019770); 5, E. faecalis strain D32 (CP003726).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4374294&req=5

Fig2: Comparative analysis of the finished and publicly availableE. faecalisgenomes. EDGAR generated Venn diagram facilitates visualizing core and strain-specific (“unique”) genes. This comparative analysis only exploits CDS of the chromosomes without considering of plasmid genes, whereby all strains shared 2173 CDS; 1, E. faecalis strain 62 (CP002491); 2, E. faecalis strain OG1RF (CP002621); 3, E. faecalis V583 (NC_004668); 4, E. faecalis probiotic strain Symbioflor 1 Clone DSM 16431 (NC_019770); 5, E. faecalis strain D32 (CP003726).
Mentions: We used a Venn diagram presentation generated by the web application EDGAR to illustrate homologies and differences between the finished and publicly available E. faecalis genomes. It illustrated a common gene pool of 2173 CDS, present in all of the finished E. faecalis genomes (Figure 2). This analysis also revealed that the number of unique CDS of the clinical strain V583 was approximately twice that of the counts of the commensal isolates 62 and our ST40 isolate D32 as well as the probiotic Symbioflor 1 strain. As a derivate of the commensal isolate, the OG1RF strain carried the minimal number of 140 unique CDS. The commensal strains 62 and D32 both shared significantly more CDS with the V583 chromosome, whereas the Symbioflor 1 and OG1RF chromosomes overlapped less with the V583 core genome.Figure 2

Bottom Line: Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source.D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

View Article: PubMed Central - PubMed

Affiliation: Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany. melanie.zischka@googlemail.com.

ABSTRACT

Background: Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type.

Results: We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).

Conclusion: Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.

Show MeSH
Related in: MedlinePlus