Chlamydia trachomatis genomic sequence and polypeptides, fragments thereof and uses thereof, in particular for the diagnosis, prevention and treatment of infection

A method for producing a polypeptide, comprising:

• (a) culturing a genetically engineered host cell under conditions suitable to produce a polypeptide encoded by the polynucleotide;
• and
• (b) recovering the polypeptide from the culture;
• said genetically engineered host cell comprising:
• (1) the nucleotide sequence, or a fragment thereof, of SEQ ID NO:
• 1;
• (2) the nucleotide sequence, or a fragment thereof, contained within the Chlamydia trachomatis genomic DNA in ECACC Deposit No. 98112618;
• (3) the nucleotide sequence, or a fragment thereof, contained in a clone insert in ECACC Deposit No. 98112617;
• (4) a nucleotide sequence, or a fragment thereof, exhibiting at least 99.9% identity with the sequence, or a fragment thereof, of SEQ ID NO:
• 1;
• (5) a nucleotide sequence, or a fragment thereof, exhibiting at least 80% homology to SEQ ID NO:
• 1;
• (6) a polynucleotide, or a fragment thereof, which hybridizes to SEQ ID NO:
• 1 or to the Chlamydia trachomatis genomic DNA contained in ECACC Deposit No. 98112618 or to a clone insert in ECACC Deposit No. 98112617 under conditions of high stringency;
• (7) a polynucleotide, or a fragment thereof, which hybridizes to SEQ ID NO:
• 1 or to the Chlamydia trachomatis genomic DNA contained in ECACC Deposit No. 98112618 under conditions of intermediate stringency;
• (8) a polynucleotide, or a fragment thereof, having a nucleotide sequence, an open reading frame (ORF) of a Chlamydia trachomatis genome, comprising:
• (i) a nucleotide sequence, or a fragment thereof, chosen from one of ORF 2 to ORF 1197;
• (ii) a nucleotide sequence, or a fragment thereof, exhibiting at least 99.9% identity with one of ORF 2 to ORF 1197;
• or
• (iii) a nucleotide sequence, or a fragment thereof, exhibiting at least 80% homology to one of ORF 2 to ORF 1197;
• (9) a polynucleotide, or a fragment thereof, which hybridizes to any one of ORF 2 to ORF 1197, or a fragment thereof, under conditions of high stringency;
• (10) a polynucleotide, or a fragment thereof, which hybridizes to any one of ORF 2 to ORF 1197, or a fragment thereof, under conditions of intermediate stringency;
• ( 11) a polynucleotide, or a fragment thereof, which encodes the following polypeptides or fragments thereof:
• (i) a Chlamydia trachomatis transmembrane polypeptide having between 1 and 3 transmembrane domains;
• (ii) a Chlamydia trachomatis transmembrane polypeptide having between 4 and 6 transmembrane domains;
• (iii) a Chlamydia trachomatis transmembrane polypeptide having at least 7 transmembrane domains;
• (iv) a Chlamydia trachomatis polypeptide involved in intermediate metabolism of sugars and/or cofactors;
• (v) a Chlamydia trachomatis polypeptide involved in intermediate metabolism of nucleotides or nucleic acids;
• (vi) a Chlamydia trachomatis polypeptide involved in metabolism of amino acids or polypeptides;
• (vii) a Chlamydia trachomatis polypeptide having involved in metabolism of fatty acids;
• (viii) a Chlamydia trachomatis polypeptide involved in the synthesis of the cell wall;
• (ix) a Chlamydia trachomatis polypeptide involved in transcription, translation, and/or maturation process;
• (x) a Chlamydia trachomatis transport polypeptide;
• (xi) a Chlamydia trachomatis polypeptide involved in the virulence process;
• (xii) a Chlamydia trachomatis polypeptide involved in the secretory system and/or which is secreted;
• (xiii) a Chlamydia trachomatis polypeptide of the cellular envelope or outer cellular envelope of Chlamydia trachomatis;
• (xiv) a Chlamydia trachomatis surface exposed polypeptide;
• (xv) a Chlamydia trachomatis lipoprotein;
• (xvi) a Chlamydia trachomatis polypeptide involved in lipopolysaccharide biosynthesis;
• (xvii) a Chlamydia trachomatis KDO-related polypeptide;
• (xviii) a Chlamydia trachomatis phosphomannomutase-related polypeptide;
• (xix) a Chlamydia trachomatis phosphoglucomutase-related polypeptide;
• (xx) a Chlamydia trachomatis lipid A component-related polypeptide;
• (xxi) a Chlamydia trachomatis polypeptide that contains an RGD sequence;
• (xxii) a Chlamydia trachomatis Type III secreted polypeptide;
• (xxiii) a Chlamydia trachomatis cell wall anchored surface polypeptide;
• (xxiv) a Chlamydia trachomatis polypeptide that is not found in Chlamydia trachomatis;
• (xxv) a polypeptide having at least 80% sequence homology to a polypeptide comprising any one of ORF 2 to ORF 1197, or a fragment thereof;
• or
• (xxvi) a fusion protein comprising any one of ORF 2 to ORF 1197, or a fragment thereof, ligated in frame to a polynucleotide encoding a heterologous polypeptide.

A method for the detection and/or identification of Chlamydia trachomatis in a biological sample, comprising:

• (a) contacting the sample with a polynucleotide primer in the presence of a polymerase enzyme and nucleotides under conditions which permit primer extension or contacting a sample with a polynucleotide probe under conditions which permit hybridization of complementary base pairs;
• and
• (b) detecting the presence of primer extension products in the sample in which the detection of primer extension products indicates the presence of Chlamydia trachomatis in the sample or detecting the presence of hybridization complexes in the sample in which the detection of hybridization complexes indicates the presence of Chlamydia trachomatis in the sample;
• wherein said probe or primer detects:
• (1) the nucleotide sequence, or a fragment thereof, of SEQ ID NO:
• 1;
• (2) the nucleotide sequence, or a fragment thereof, contained within the Chlamydia trachomatis genomic DNA in ECACC Deposit No. 98112618;
• (3) the nucleotide sequence, or a fragment thereof, contained in a clone insert in ECACC Deposit No. 98112617;
• (4) a nucleotide sequence, or a fragment thereof, exhibiting at least 99.9% identity with the sequence, or a fragment thereof, of SEQ ID NO:
• 1;
• (5) a nucleotide sequence, or a fragment thereof, exhibiting at least 80% homology to SEQ ID NO:
• 1;
• (6) a polynucleotide, or a fragment thereof, which hybridizes to SEQ ID NO:
• 1 or to the Chlamydia trachomatis genomic DNA contained in ECACC Deposit No. 98112618 or to a clone insert in ECACC Deposit No. 98112617 under conditions of high stringency;
• (7) a polynucleotide, or a fragment thereof, which hybridizes to SEQ ID NO:
• 1 or to the Chlamydia trachomatis genomic DNA contained in ECACC Deposit No. 98112618 under conditions of intermediate stringency;
• (8) a polynucleotide, or a fragment thereof, having a nucleotide sequence, of an open reading frame (ORF) of a Chlamydia trachomatis genome, comprising:
• (i) a nucleotide sequence, or a fragment thereof, chosen from one of ORF 2 to ORF 1197;
• (ii) a nucleotide sequence, or a fragment thereof, exhibiting at least 99.9% identity with one of ORF 2 to ORF 1197;
• or
• (iii) a nucleotide sequence, or a fragment thereof, exhibiting at least 80% homology to one of ORF 2 to ORF 1197;
• (9) a polynucleotide, or a fragment thereof, which hybridizes to any one of ORF 2 to ORF 1197, or a fragment thereof, under conditions of high stringency;
• (10) a polynucleotide, or a fragment thereof, which hybridizes to any one of ORF 2 to ORF 1197, or a fragment thereof, under conditions of intermediate stringency;
• (11) a polynucleotide, or a fragment thereof, which encodes the following polypeptides or fragments thereof:
• (i) a Chlamydia trachomatis transmembrane polypeptide having between 1 and 3 transmembrane domains;
• (ii) a Chlamydia trachomatis transmembrane polypeptide having between 4 and 6 transmembrane domains;
• (iii) a Chlamydia trachomatis transmembrane polypeptide having at least 7 transmembrane domains;
• (iv) a Chlamydia trachomatis polypeptide involved in intermediate metabolism of sugars and/or cofactors;
• (v) a Chlamydia trachomatis polypeptide involved in intermediate metabolism of nucleotides or nucleic acids;
• (vi) a Chlamydia trachomatis polypeptide involved in metabolism of amino acids or polypeptides;
• (vii) a Chlamydia trachomatis polypeptide having involved in metabolism of fatty acids;
• (viii) a Chlamydia trachomatis polypeptide involved in the synthesis of the cell wall;
• (ix) a Chlamydia trachomatis polypeptide involved in transcription, translation, and/or maturation process;
• (x) a Chlamydia trachomatis transport polypeptide;
• (xi) a Chlamydia trachomatis polypeptide involved in the virulence process;
• (xii) a Chlamydia trachomatis polypeptide involved in the secretory system and/or which is secreted;
• (xiii) a Chlamydia trachomatis polypeptide of the cellular envelope or outer cellular envelope of Chlamydia trachomatis;
• (xiv) a Chlamydia trachomatis surface exposed polypeptide;
• (xv) a Chlamydia trachomatis lipoprotein;
• (xvi) a Chlamydia trachomatis polypeptide involved in lipopolysaccharide biosynthesis;
• (xvii) a Chlamydia trachomatis KDO-related polypeptide;
• (xviii) a Chlamydia trachomatis phosphomannomutase-related polypeptide;
• (xix) a Chlamydia trachomatis phosphoglucomutase-related polypeptide;
• (xx) a Chlamydia trachomatis lipid A component-related polypeptide;
• (xxi) a Chlamydia trachomatis polypeptide that contains an RGD sequence;
• (xxii) a Chlamydia trachomatis Type III secreted polypeptide;
• (xxiii) a Chlamydia trachomatis cell wall anchored surface polypeptide;
• (xxiv) a Chlamydia trachomatis polypeptide that is not found in Chlamydia trachomatis;
• (xxv) a polypeptide having at least 80% sequence homology to a polypeptide comprising any one of ORF 2 to ORF 1197, or a fragment thereof;
• (xxvi) a fusion protein comprising any one of ORF 2 to ORF 1197, or a fragment thereof, ligated in frame to a polynucleotide encoding a heterologous polypeptide;
• or
• (xxvii) a polypeptide, or fragment thereof, comprising any one of ORF 2 to ORF 1197.

A method for the detection and/or identification of Chlamydia trachomatis in a biological sample, comprising:

• (a) contacting the sample with an antibody under conditions suitable for the formation of immune complexes;
• and
• (b) detecting the presence of immune complexes in the sample, in which the detection of immune complexes indicates the presence of Chlamydia trachomatis in the sample;
• said antibody immunospecifically reacting with a polypeptide, or fragment thereof, comprising:
• (i) a Chlamydia trachomatis transmembrane polypeptide, or a fragment thereof, having between 1 and 3 transmembrane domains;
• (ii) a Chlamydia trachomatis transmembrane polypeptide, or a fragment thereof, having between 4 and 6 transmembrane domains;
• (iii) a Chlamydia trachomatis transmembrane polypeptide, or a fragment thereof, having at least 7 transmembrane domains;
• (iv) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in intermediate metabolism of sugars and/or cofactors;
• (v) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in intermediate metabolism of nucleotides or nucleic acids;
• (vi) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in metabolism of amino acids or polypeptides;
• (vii) a Chlamydia trachomatis polypeptide, or a fragment thereof, having involved in metabolism of fatty acids;
• (viii) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in the synthesis of the cell wall;
• (ix) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in transcription, translation, and/or maturation process;
• (x) a Chlamydia trachomatis transport polypeptide, or a fragment thereof,
• (xi) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in the virulence process;
• (xii) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in the secretory system and/or which is secreted;
• (xiii) a Chlamydia trachomatis polypeptide, or a fragment thereof, of the cellular envelope or outer cellular envelope of Chlamydia trachomatis;
• (xiv) a Chlamydia trachomatis surface exposed polypeptide, or a fragment thereof;
• (xv) a Chlamydia trachomatis lipoprotein, or a fragment thereof;
• (xvi) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in lipopolysaccharide biosynthesis;
• (xvii) a Chlamydia trachomatis KDO-related polypeptide, or a fragment thereof;
• (xviii) a Chlamydia trachomatis phosphomannomutase-related polypeptide, or a fragment thereof;
• (xix) a Chlamydia trachomatis phosphoglucomutase-related polypeptide, or a fragment thereof;
• (xx) a Chlamydia trachomatis lipid A component-related polypeptide, or a fragment thereof;
• (xxi) a Chlamydia trachomatis polypeptide, or a fragment thereof, that contains an RGD sequence;
• (xxii) a Chlamydia trachomatis Type III secreted polypeptide, or a fragment thereof;
• (xxiii) a Chlamydia trachomatis cell wall anchored surface polypeptide, or a fragment thereof;
• (xxiv) a Chlamydia trachomatis polypeptide, or a fragment thereof, that is not found in Chlamydia trachomatis;
• (xxv) a polypeptide, or a fragment thereof, having at least 80% sequence homology to a polypeptide comprising any one of ORF 2 to ORF 1197;
• (xxvi) a fusion protein comprising any one of ORF 2 to ORF 1197, or a fragment thereof, ligated in frame to a polynucleotide encoding a heterologous polypeptide;
• or
• (xxvii) a polypeptide, or fragment thereof, comprising any one of ORF 2 to ORF 1197.

A method of immunizing against Chlamydia trachomatis, comprising:

• administering to a host an immunizing amount of an immunogenic composition comprising a polypeptide, or a fragment thereof, or a polynucleotide or a fragment thereof,
• said polypeptide comprising:
• (i) a Chlamydia trachomatis transmembrane polypeptide, or a fragment thereof, having between 1 and 3 transmembrane domains;
• (ii) a Chlamydia trachomatis transmembrane polypeptide, or a fragment thereof, having between 4 and 6 transmembrane domains;
• (iii) a Chlamydia trachomatis transmembrane polypeptide, or a fragment thereof, having at least 7 transmembrane domains;
• (iv) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in intermediate metabolism of sugars and/or cofactors;
• (v) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in intermediate metabolism of nucleotides or nucleic acids;
• (vi) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in metabolism of amino acids or polypeptides;
• (vii) a Chlamydia trachomatis polypeptide, or a fragment thereof, having involved in metabolism of fatty acids;
• (viii) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in the synthesis of the cell wall;
• (ix) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in transcription, translation, and/or maturation process;
• (x) a Chlamydia trachomatis transport polypeptide, or a fragment thereof;
• (xi) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in the virulence process;
• (xii) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in the secretory system and/or which is secreted;
• (xiii) a Chlamydia trachomatis polypeptide, or a fragment thereof, of the cellular envelope or outer cellular envelope of Chlamydia trachomatis;
• (xiv) a Chlamydia trachomatis surface exposed polypeptide, or a fragment thereof;
• (xv) a Chlamydia trachomatis lipoprotein, or a fragment thereof;
• (xvi) a Chlamydia trachomatis polypeptide, or a fragment thereof, involved in lipopolysaccharide biosynthesis;
• (xvii) a Chlamydia trachomatis KDO-related polypeptide, or a fragment thereof;
• (xviii) a Chlamydia trachomatis phosphomannomutase-related polypeptide, or a fragment thereof;
• (xix) a Chlamydia trachomatis phosphoglucomutase-related polypeptide, or a fragment thereof;
• (xx) a Chlamydia trachomatis lipid A component-related polypeptide, or a fragment thereof;
• (xxi) a Chlamydia trachomatis polypeptide, or a fragment thereof, that contains an RGD sequence;
• (xxii) a Chlamydia trachomatis Type III secreted polypeptide, or a fragment thereof;
• (xxiii) a Chlamydia trachomatis cell wall anchored surface polypeptide, or a fragment thereof;
• (xxiv) a Chlamydia trachomatis polypeptide, or a fragment thereof, that is not found in Chlamydia trachomatis;
• (xxv) a polypeptide, or a fragment thereof, having at least 80% sequence homology to a polypeptide comprising any one of ORF 2 to ORF 1197;
• (xxvi) a fusion protein comprising any one of ORF 2 to ORF 1197, or a fragment, thereof ligated in frame to a polynucleotide encoding a heterologous polypeptide;
• or
• (xxvii) a fusion protein comprising a polypeptide as set forth herein ligated in frame to a polynucleotide encoding a heterologous polypeptide;
• or
• (xxvii) a polypeptide, or fragment thereof, comprising any one of ORF 2 to ORF 1197;
• and said polynucleotide comprising:
• (1) the nucleotide sequence, or a fragment thereof, of SEQ ID NO:
• 1;
• (2) the nucleotide sequence, or a fragment thereof, contained within the Chlamydia trachomatis genomic DNA in ECACC Deposit No. 98112618;
• (3) the nucleotide sequence, or a fragment thereof, contained in a clone insert in ECACC Deposit No. 98112617;
• (4) a nucleotide sequence, or a fragment thereof, exhibiting at least 99.9% identity with the sequence, or a fragment thereof, of SEQ ID NO:
• 1;
• (5) a nucleotide sequence, or a fragment thereof, exhibiting at least 80% homology to SEQ ID NO:
• 1;
• (6) a polynucleotide, or a fragment thereof, which hybridizes to SEQ ID NO:
• 1 or to the Chlamydia trachomatis genomic DNA contained in ECACC Deposit No. 98112618 or to a clone insert in ECACC Deposit No. 98112617 under conditions of high stringency;
• (7) a polynucleotide, or a fragment thereof, which hybridizes to SEQ ID NO:
• 1 or to the Chlamydia trachomatis genomic DNA contained in ECACC Deposit No. 98112618 under conditions of intermediate stringency;
• (8) a polynucleotide, or a fragment thereof, having a nucleotide sequence, of an open reading frame (ORF) of a Chlamydia trachomatis genome, comprising:
• (i) a nucleotide sequence, or a fragment thereof, chosen from one of ORF 2 to ORF 1197;
• (ii) a nucleotide sequence, or a fragment thereof, exhibiting at least 99.9% identity with one of ORF 2 to ORF 1197;
• or
• (iii) a nucleotide sequence, or a fragment thereof, exhibiting at least 80% homology to one of ORF 2 to ORF 1197;
• (9) a polynucleotide, or a fragment thereof, which hybridizes to any one of ORF 2 to ORF 1197, or a fragment thereof, under conditions of high stringency;
• (10) a polynucleotide, or a fragment thereof, which hybridizes to any one of ORF 2 to ORF 1197, or a fragment thereof, under conditions of intermediate stringency;
• (11) a polynucleotide, or a fragment thereof, which encodes the following polypeptides or fragments thereof:
• (i) a Chlamydia trachomatis transmembrane polypeptide having between 1 and 3 transmembrane domains;
• (ii) a Chlamydia trachomatis transmembrane polypeptide having between 4 and 6 transmembrane domains;
• (iii) a Chlamydia trachomatis transmembrane polypeptide having at least 7 transmembrane domains;
• (iv) a Chlamydia trachomatis polypeptide involved in intermediate metabolism of sugars and/or cofactors;
• (v) a Chlamydia trachomatis polypeptide involved in intermediate metabolism of nucleotides or nucleic acids;
• (vi) a Chlamydia trachomatis polypeptide involved in metabolism of amino acids or polypeptides;
• (vii) a Chlamydia trachomatis polypeptide having involved in metabolism of fatty acids;
• (viii) a Chlamydia trachomatis polypeptide involved in the synthesis of the cell wall;
• (ix) a Chlamydia trachomatis polypeptide involved in transcription, translation, and/or maturation process;
• (x) a Chlamydia trachomatis transport polypeptide;
• (xi) a Chlamydia trachomatis polypeptide involved in the virulence process;
• (xii) a Chlamydia trachomatis polypeptide involved in the secretory system and/or which is secreted;
• (xiii) a Chlamydia trachomatis polypeptide of the cellular envelope or outer cellular envelope of Chlamydia trachomatis;
• (xiv) a Chlamydia trachomatis surface exposed polypeptide;
• (xv) a Chlamydia trachomatis lipoprotein;
• (xvi) a Chlamydia trachomatis polypeptide involved in lipopolysaccharide biosynthesis;
• (xvii) a Chlamydia trachomatis KDO-related polypeptide;
• (xviii) a Chlamydia trachomatis phosphomannomutase-related polypeptide;
• (xix) a Chlamydia trachomatis phosphoglucomutase-related polypeptide;
• (xx) a Chlamydia trachomatis lipid A component-related polypeptide;
• (xxi) a Chlamydia trachomatis polypeptide that contains an RGD sequence;
• (xxii) a Chlamydia trachomatis Type III secreted polypeptide;
• (xxiii) a Chlamydia trachomatis cell wall anchored surface polypeptide;
• (xxiv) a Chlamydia trachomatis polypeptide that is not found in Chlamydia trachomatis;
• (xxv) a polypeptide having at least 80% sequence homology to a polypeptide comprising any one of ORF 2 to ORF 1197;
• (xxvi) a fusion protein comprising any one of ORF 2 to ORF 1197, or a fragment thereof, ligated in frame to a polynucleotide encoding a heterologous polypeptide;
• (xxvii) a polypeptide comprising any one of ORF 2 to ORF 1197.