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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

E. faecalisST40 genome comparison against the D32 reference genome. Generated by BRIG (http://brig.sourceforge.net/ [last access 16.07.2014] [56]), the circular map illustrates the whole genome comparison of D32 against the other 14 sequenced ST40 isolates and the probiotic isolate Symbioflor 1 Clone DSM 16431. The outer cycle (dark grey) represents the complete genome of the reference strain D32. The shade of color is geared to similarities in origin of the strains (green: isolate from bovine mastitis; blue: animal and human commensals; violet: isolates from human infections; red: human blood culture isolates; turquoise: strain Symbiolfor 1). The inner cycle illustrates the GC content of D32. Location of the PAI is illustrated by a blue colored box, while the red box indicates the presence of an uncharacterized and large genomic island (GI; 138 kb). Additionally, black labels highlighted four identified prophages of D32; A, animal; B, blood culture; C, colonizer; E, endocarditis; H, human; M, bovine mastitis; U, urine.
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Fig3: E. faecalisST40 genome comparison against the D32 reference genome. Generated by BRIG (http://brig.sourceforge.net/ [last access 16.07.2014] [56]), the circular map illustrates the whole genome comparison of D32 against the other 14 sequenced ST40 isolates and the probiotic isolate Symbioflor 1 Clone DSM 16431. The outer cycle (dark grey) represents the complete genome of the reference strain D32. The shade of color is geared to similarities in origin of the strains (green: isolate from bovine mastitis; blue: animal and human commensals; violet: isolates from human infections; red: human blood culture isolates; turquoise: strain Symbiolfor 1). The inner cycle illustrates the GC content of D32. Location of the PAI is illustrated by a blue colored box, while the red box indicates the presence of an uncharacterized and large genomic island (GI; 138 kb). Additionally, black labels highlighted four identified prophages of D32; A, animal; B, blood culture; C, colonizer; E, endocarditis; H, human; M, bovine mastitis; U, urine.

Mentions: De novo sequences, generated by both 454 pyrosequencing and Illumina/Solexa sequencing, were hybrid assembled. This combined sequencing and assembly approach resulted in satisfactory analysis parameters since it improved overall coverage and read length, slightly increased the genome size (2.928 - 3.33 Mbp) and reduced the number of genomic contigs (<100; Table 5). Mapping of the 14 ST40 draft genomes against the D32 reference genome suggested a high level of genomic similarity irrespective of the geographical, host, temporal or clinical/non-clinical origin of the isolates (Figure 3). Differences between the strains were minor and corresponded to (1) a different composition of the E. faecalis PAI, (2) differences in phage content and (3) a putative genomic island first described in D32 which is absent in all other ST40 strains except for another animal isolate, UW7729. This genomic island was located at a putative hot spot for integration in the E. faecalis chromosome, since strain V583 contained the vanB operon at this site whereas OG1RF harboured the myo-inositol operon (which D32 lacks).Table 5


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)

E. faecalisST40 genome comparison against the D32 reference genome. Generated by BRIG (http://brig.sourceforge.net/ [last access 16.07.2014] [56]), the circular map illustrates the whole genome comparison of D32 against the other 14 sequenced ST40 isolates and the probiotic isolate Symbioflor 1 Clone DSM 16431. The outer cycle (dark grey) represents the complete genome of the reference strain D32. The shade of color is geared to similarities in origin of the strains (green: isolate from bovine mastitis; blue: animal and human commensals; violet: isolates from human infections; red: human blood culture isolates; turquoise: strain Symbiolfor 1). The inner cycle illustrates the GC content of D32. Location of the PAI is illustrated by a blue colored box, while the red box indicates the presence of an uncharacterized and large genomic island (GI; 138 kb). Additionally, black labels highlighted four identified prophages of D32; A, animal; B, blood culture; C, colonizer; E, endocarditis; H, human; M, bovine mastitis; U, urine.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: E. faecalisST40 genome comparison against the D32 reference genome. Generated by BRIG (http://brig.sourceforge.net/ [last access 16.07.2014] [56]), the circular map illustrates the whole genome comparison of D32 against the other 14 sequenced ST40 isolates and the probiotic isolate Symbioflor 1 Clone DSM 16431. The outer cycle (dark grey) represents the complete genome of the reference strain D32. The shade of color is geared to similarities in origin of the strains (green: isolate from bovine mastitis; blue: animal and human commensals; violet: isolates from human infections; red: human blood culture isolates; turquoise: strain Symbiolfor 1). The inner cycle illustrates the GC content of D32. Location of the PAI is illustrated by a blue colored box, while the red box indicates the presence of an uncharacterized and large genomic island (GI; 138 kb). Additionally, black labels highlighted four identified prophages of D32; A, animal; B, blood culture; C, colonizer; E, endocarditis; H, human; M, bovine mastitis; U, urine.
Mentions: De novo sequences, generated by both 454 pyrosequencing and Illumina/Solexa sequencing, were hybrid assembled. This combined sequencing and assembly approach resulted in satisfactory analysis parameters since it improved overall coverage and read length, slightly increased the genome size (2.928 - 3.33 Mbp) and reduced the number of genomic contigs (<100; Table 5). Mapping of the 14 ST40 draft genomes against the D32 reference genome suggested a high level of genomic similarity irrespective of the geographical, host, temporal or clinical/non-clinical origin of the isolates (Figure 3). Differences between the strains were minor and corresponded to (1) a different composition of the E. faecalis PAI, (2) differences in phage content and (3) a putative genomic island first described in D32 which is absent in all other ST40 strains except for another animal isolate, UW7729. This genomic island was located at a putative hot spot for integration in the E. faecalis chromosome, since strain V583 contained the vanB operon at this site whereas OG1RF harboured the myo-inositol operon (which D32 lacks).Table 5

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