EP1539782A2 - Hochauflösendes typisierungssystem für pathogene borrelien - Google Patents

Hochauflösendes typisierungssystem für pathogene borrelien

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Publication number
EP1539782A2
EP1539782A2 EP03763263A EP03763263A EP1539782A2 EP 1539782 A2 EP1539782 A2 EP 1539782A2 EP 03763263 A EP03763263 A EP 03763263A EP 03763263 A EP03763263 A EP 03763263A EP 1539782 A2 EP1539782 A2 EP 1539782A2
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EP
European Patent Office
Prior art keywords
seq
primer
vntr
borrelia
complementary sequence
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EP03763263A
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English (en)
French (fr)
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EP1539782A4 (de
Inventor
Paul S. Keim
Jason Farlow
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Arizona State University ASU
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Arizona State University ASU
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria

Definitions

  • the present invention is generally directed to sub-typing Borrelia spirochetes, the causative agent of Lyme Disease, and is more specifically directed to PCR amplification of variable number tandem repeat sequences (VNTR) with primer pairs designed to bind specifically to certain VNTR identified in Borrelia isolates. Results of the analysis may be compared to results from known Borrelia species to determine the sub-type of the species for epidemiological and diagnostic purposes.
  • VNTR variable number tandem repeat sequences
  • LB Human Lyme Borreliosis
  • Borreliae spirochetes are 5 to 25 ⁇ m long and 0.2 to 0.5 ⁇ m wide (24). These organisms are highly motile, microaerophilic, slow-growing, and fastidious (24). Lyme disease is an inflammatory disorder characterized by the skin lesion erythema migrans and the potential development of neurologic, cardiac, and joint abnormalities (24).
  • the three Borrelia species that frequently cause Lyme disease in humans are Borrelia burgdorferi sensu stricto, Borrelia garinii, and Borrelia afzelii (19, 6). Specific Borrelia species can cause distinct clinical manifestations of Lyme disease.
  • B. burgdorferi can cause arthritis (2, 28).
  • garinii is known to cause serious neurological manifestations (2, 28).
  • B. afzelii causes a distinctive skin condition known as aero dermatitis chronica atrophicans (ACA) (27).
  • ACA aero dermatitis chronica atrophicans
  • EM characteristic erythema migrans
  • B. burgdorferi sensu stricto is found primarily in North America and Europe (6, 15, 19, 33).
  • B. garinii, B. afzelii, B. valaisiana, and B. lusitaniae have been isolated throughout Eurasia (33).
  • B. japonica, B. tanukii, and B. turdi are found primarily in Japan (17, 20).
  • B. andersonii and B. bissettii are predominantly distributed in North America (22, 31).
  • Ixodes scapularis, Ixodespacificus, and Ixodes ricinus are the three primary tick reservoirs for B. burgdorferi sensu lato (5).
  • the tick reservoir hosts include numerous small mammal species and birds (1, 18, 26).
  • the molecular mechanisms responsible for this genetic exchange are presently unknown.
  • the Borrelia genome exhibits significant genetic redundancy and carries 161 to 175 paralogous gene families (7). Such families may serve as foci for inter-plasmid homologous recombination. At least one linear plasmid gene is found within each of 107 gene families creating a significant amount of redundancy and an unusually large number of pseudogenes (7). Approximately 90% of Borrelia 's plasmid genes show little similarity to genes of other bacteria (7). It is possible these linear plasmids may be in a phase of rapid evolution and may undergo antigenic variation from immune selection.
  • Borrelia species including 16S rRNA gene sequence analysis, SDS PAGE, Western blot analysis, pulsed-f ⁇ eld gel electrophoresis (PFGE), plasmid fingerprinting, randomly amplified polymorphic DNA (RAPD) analysis, restriction fragment length polymorphism (RFLP) analysis, fatty acid profile analysis, and serotyping (4, 8, 15, 33).
  • PFGE pulsed-f ⁇ eld gel electrophoresis
  • RAPD randomly amplified polymorphic DNA
  • RFLP restriction fragment length polymorphism
  • fatty acid profile analysis and serotyping (4, 8, 15, 33).
  • VNTRs have been shown to provide a high level of discriminatory power (21). This stems from the significant mutability of repeat copy number.
  • Multiple-locus VNTR analysis MLVA has previously shown great discriminatory capacity and accurate estimation of genetic-relationships within bacterial pathogens such as Francisella tularensis and Bacillus anthracis (14, 21).
  • the present invention discloses methods and means for detecting and sub- typing Borrelia species by multi-locus analysis of VNTR identified- within the genome of Borrelia burgdorferi.
  • isolated nucleic acids comprising at least 12, 15, 18 or total consecutive nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3; SEQ ID NO: 4; SEQ ID NO: 5; SEQ ID NO: 6; SEQ ID NO: 7; SEQ ID NO: 8; SEQ ID NO: 9; SEQ ID NO: 10.
  • SEQ ID NO: 11 SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14; SEQ ID NO: 15; SEQ ID NO: 16; SEQ ID NO: 17; SEQ ID NO: 18, SEQ ID NO: 19; and SEQ ID NO: 20 and sequences complementary thereto.
  • these nucleic acids are immobilized on a solid surface and are useful, for example, in the detection of a Borrelia species in an assay employing probes, including, but not limited to, a nano-detection device.
  • primer pairs comprising a forward and a reverse primer
  • Primer pairs suitable for PCR amplification of VNTR may be selected from the group consisting of SEQ ID NO 1 and 2, SEQ ID NO: 3 and 4, SEQ ID NO: 5 and 6, SEQ ID NO: 7 and 8 SEQ ID NO: 9 and 10, SEQ ID NO: 11 and 12, SEQ ID NO: 13 and 14, SEQ ID NO: 15 and 16, SEQ ID NO: 17 and 18, and SEQ ID NO: 19 and 20.
  • Certain preferred primer pairs have, in addition, an observable group whereby amplified product may be detected.
  • Such groups may be, for example, a fluorescent group or a radioactive group.
  • the method comprises the steps of:
  • MLVA methods are presented for observing polymorphisms at VNTR loci in DNA from more than one Borrelia species to resolve unique genotypes between the species and to allow sub-typing of the species into distinct groups. These MLVA methods provide a convenient and rapid method for strain discrimination in Borrelia. MLVA may be applied for strain discrimination among globally diverse Borrelia isolates including B. burgdorferi, B. afzelii, and B. garinii.
  • kits for detecting and sub-typing Borrelia species.
  • the kits comprise one or more primer pairs suitable for amplifying VNTR in DNA in a sample of said species and may comprise, in addition, nucleic acids, enzymes, tag polymerase, for example, and buffers suitable for causing amplification by PCR, by MLVA or by multiplex, for example.
  • the primers comprise a label whereby amplified VNTR may be detected.
  • labeled nucleic acids are provided. Observable labels are preferably fluorescent molecules or radionucleotides.
  • a method of sub-typing a Borrelia strain comprising the steps of:
  • obtaining DNA from said strain i. amplifying said DNA with one or more primer pairs selected from the goup consisting of SEQ ID NOS : 1 -20; iii. detecting said amplified product; iv. determining the diversity number of said amplified product; and v. comparing said diversity number with the diversity number for a known strain of Borrelia.
  • Figure 1 illustrates genetic relationships among Borrelia isolates.
  • Unweighted Pair Group Method with Arithmetic Mean cluster analysis based upon allelic differences from ten VNTR markers across 41 5. burgdorferi, B. afzelii, and B, garinii isolates was used to construct this dendogram. Letters to the right of each branch correspond to the individual sample identification (Table 2) followed by Borrelia species designation. The horizontal axis indicates estimated VNTR allelic differences (Allelic differences are a measure of genetic evolutionary distance). Roman numerals indicate arbitrary groupings of species.
  • Figure 2 illustrates the correlation between repeat copy number and diversity measures.
  • Crosses (+) indicate the marker's total observed allele number versus repeat copy number at an individual marker locus.
  • Diamonds ( ⁇ ) indicate the marker's calculated diversity value versus the repeat copy number of an individual marker. Analysis was performed using only data from the eight Borrelia markers with non-complex repeat motifs.
  • the present invention discloses the successful application of MLVA for strain discrimination among globally diverse Borrelia isolates including B. burgdorferi, B. afzelii, and B. garinii.
  • Ten VNTR loci have been identified from genomic and plasmid sequences of Borrelia strains (Table 3, Marker locus number BR-Vl to BR-V10) Polymorphisms at these loci were may be used to resolve genotypes into distinct groups.
  • Figure 1 is a dendogram illustrating the resolution of 30 unique genotypes into five to seven distinct groups. This sub-typing scheme is useful for the epidemiological study of Borrelia and may be applied to the local detection of the pathological causative agent of Lyme Disease.
  • Polymerase chain reaction or "PCR” a technique in which cycles of denaturation, annealing with primer, and extension with DNA polymerase are used to amplify the number of copies of a target DNA sequence by approximately 106 times or more.
  • the polymerase chain reaction process for amplifying nucleic acid is disclosed in US Pat. Nos. 4,683,195 and 4,683,202, which are incorporated herein by reference.
  • Primer a single-stranded oligonucleotide or DNA fragment which hybridizes with a DNA strand of a locus in such a manner that the 3' terminus of the primer may act as a site of polymerization using a DNA polymerase enzyme.
  • Primer pair two primers including, primer 1 that hybridizes to a single strand at one end of the DNA sequence to be amplified and primer 2 that hybridizes with the other end on the complementary strand of the DNA sequence to be amplified.
  • Primer site the area of the target DNA to which a primer hybridizes.
  • Multiplexing is a capability to perform simultaneous, multiple determinations in a single assay process and a process to implement such a capability in a process is a “multiplexed assay.”
  • Systems containing several loci are called multiplex systems described, for example, in US Patent No. 6,479,235 to Schumm, et al., US Patent No. 6,270,973 to Lewis, et al. and 6,449,562 to Chandler, et al.
  • Isolated nucleic acid is a nucleic acid which may or may not be identical to that of a naturally occurring nucleic acid.
  • isolated nucleic acid is used to describe a primer, the nucleic acid is not identical to the structure of a naturally occurring nucleic acid spanning at least the length of a gene.
  • the primers herein have been designed to bind to sequences flanking VNTR loci in Borrelia species. It is to be understood that primer sequences containing insertions or deletions in these disclosed sequences that do not impair the binding of the primers to these flanking sequences are also intended to be incorporated into the present invention.
  • the present invention provides primer pairs for PCR amplification of
  • the primer pairs comprise a forward primer and a reverse primer.
  • Table 1 illustrates the Borrelia Primer Sequences of the present invention. Table 1. Borrelia Primer Sequence
  • the polynucleotides of the present invention may be prepared by two general methods: (1) they may be synthesized from appropriate nucleotide triphosphates, or (2) they may be isolated from biological sources. Both methods utilize protocols well known in the art.
  • the availability of nucleotide sequence information enables preparation of an isolated nucleic acid molecule of the invention by oligonucleotide synthesis.
  • Synthetic oligonucleotides may be prepared by the phosphoramidite method employed in the Applied Biosystems 38A DNA Synthesizer or similar devices.
  • the resultant construct may be purified according to methods known in the art, such as high performance liquid chromatography (HPLC).
  • Complementary segments thus produced may be annealed such that each segment possesses appropriate cohesive termini for attachment of an adjacent segment.
  • Adjacent segments may be ligated by annealing cohesive termini in the presence of DNA ligase to construct an entire long double- stranded molecule.
  • a synthetic DNA molecule so constructed may then be cloned and amplified in an appropriate vecto
  • Kits are herein provided for use with commercially available PCR instruments to detect and sub-type strains of Borrelia.
  • the kits contain one or more primer pairs disclosed hereinabove having SEQ ID NOS 1-20 for amplifying the VNTR in DNA isolated from a Borrelia sample. If the sample is to be multiplexed, the kits may contain a suitable "cocktail" of primer pairs.
  • kits may also contain nucleic acids needed in the amplification process.
  • the nucleic acids may be tagged by a suitable marker, a fluorescent probe or a radioactive molecule. Any tag for marking the nucleic acid after amplification and size separation as by electrophoresis or other separation means is suitable.
  • the primer pairs themselves comprise a suitable marker.
  • kits may also comprise enzymes, taq polymerase, for example and salts and buffers suitable for causing amplification of DNA by PCR.
  • This kits may also comprise suitable containers and bottles for housing these reagents and or convenient use.
  • Kits for sub-typing strains of Borrelia comprise, in addition, DNA isolated from known Borrelia strains. This isolated DNA containing VNTR loci may be used as standards in the sub-typing of the species.
  • VNTR loci using the DNA Star program PrimerSelect.
  • Reagents used in the PCR reactions were obtained from Life Technologies. Primers were designed with annealing temperatures from 65°C to 61°C- Individual primer pair annealing temperatures were designed within 2°C of each other. .
  • Bacterial thermolysates Bacterial thermolysates. Borrelia strains were grown in BSK medium (Sigma) until they reached 10 7 bacteria/ml. One ml was harvested by centrifugation, washed in PBS and re-suspended in lOO ⁇ l of water before heating at 100°C for 20 minutes.
  • VNTR marker identification and diversity Analysis of the genomic sequence of B. burgdorferi type strain B31 revealed 225 genomic sequence motifs that potentially represent VNTR loci. An additional 167 potential VNTR loci were identified among the plasmid sequences of B. burgdorferi (type strain B31 46 repeated sequence motifs were chosen from these for MLVA analysis. MLVA revealed that 36 were monomorphic and only ten proved to be polymorphic loci (Table 3) among 41 globally diverse B. burgdorferi, B. afzelii, and B. garinii strains (Table 2). However, all loci did not support PCR amplification. A total of 19 isolates failed to yield PCR products across markers BR-V4, 6, 8, and 10 (Table 4). Sixteen of these 19 failures occurred within plasmid-based loci (Table 4).
  • VNTR loci lies in their diversity.
  • the present invention discloses the use of marker diversity using both allele number and frequency to sub-type Borrelia species.
  • the allele number observed ranged from two (BR-V7) to nine alleles (BR-V8) (Table 3).
  • marker BR-V8 has a repeat copy number of 8.3, in the B31 type strain, and exhibits 9 alleles (Table 3).
  • marker BR-V9 with a copy number of only three exhibits only three alleles in our study (Table 3).
  • a CH indicates chromosome locus
  • LP linear plasmid locus
  • D 1 - sum(allele frequency)2
  • CX indicates the complex nature of the repeat motif and consequently makes accurate array size calculation difficult.
  • VEERY 750 178 144 * 1 19 89 206 321 204 520
  • reaction mixtures were incubated at 94°C for 5 minutes in the PCR instrument (a commercially available thermocycler) and then cycled at 94°C for 30 seconds, 61°C or 56°C for 30 seconds, 72°C for 30 seconds and 94°C for 30 seconds for 35 cycles, with a final incubation of 72°C for 5 minutes.
  • This example illustrates the amplicon produced during the amplification of VNTR locus BR-Vl with primer pairs SEQ ID NO: 1 and SEQ ID NO: 2.
  • VNTR locus BR-V2 with primer pairs SEQ ID NO: 3 and SEQ ID NO: 4.
  • VNTR locus BR-V3 with primer pairs SEQ ID NO: 5 and SEQ ID NO: 6.
  • VNTR locus BR-V4 with primer pairs SEQ ID NO: 7 and SEQ ID NO: 8.
  • VNTR locus BR-V5 with primer pairs SEQ ID NO: 9 and SEQ ID NO: 10.
  • VNTR locus BR-V6 with primer pairs SEQ ID NO: 11 and SEQ ID NO: 12.
  • VNTR locus BR-V7 with primer pairs SEQ ID NO: 13 and SEQ ID NO: 14.
  • This example illustrates the amplicon produced during the amplification of VNTR locus BR-V8 with primer pairs SEQ ID NO 15 and SEQ ID NO 16.
  • EXAMPLE 10 This example illustrates the amplicon produced during the amplification of VNTR locus BR-V9 with primer pairs SEQ ID NO 17 and SEQ ID NO 18.
  • VNTR locus BR-V10 with primer pairs SEQ ID NO 19 and SEQ ID NO 20.
  • insertion elements, restriction fragment length polymorphism patterns, and discontinuous ' 23 S rRNA in Lyme disease spirochetes phylogenetic analyses of rRNA genes and their intergenic spacers in Borrelia japonica sp. nov. and genomic group 21038 (Borrelia andersonii sp. nov.) isolates. J. Clin. Microbiol. 33:2427-2414.

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EP03763263A 2002-07-02 2003-07-02 Hochauflösendes typisierungssystem für pathogene borrelien Withdrawn EP1539782A4 (de)

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US39349702P 2002-07-02 2002-07-02
US393497P 2002-07-02
PCT/US2003/021153 WO2004005479A2 (en) 2002-07-02 2003-07-02 A high resolution typing system for pathogenic borrelia

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EP1539782A2 true EP1539782A2 (de) 2005-06-15
EP1539782A4 EP1539782A4 (de) 2005-11-16

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EP3248011A4 (de) * 2015-01-21 2018-11-14 T2 Biosystems, Inc. Nmr-verfahren und system zur schnellen detektion von durch zecken übertragenen pathogenen

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WO1998059071A1 (en) * 1997-06-20 1998-12-30 Human Genome Sciences, Inc. Lyme disease vaccines

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
FRASER ET AL: NATURE, MACMILLAN JOURNALS LTD. LONDON, GB, vol. 390, 11 December 1997 (1997-12-11), pages 580-586, XP002096130 ISSN: 0028-0836 *
SCHWEIGER M ET AL.: "Routine diagnosis of borrelia burgdorferi (sensu lato) infections using a real time PCR assay" CLIN MICROBIOL INFECT, vol. 7, no. 9, September 2001 (2001-09), - September 2001 (2001-09) pages 461-469, XP002346036 *
See also references of WO2004005479A2 *

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EP1539782A4 (de) 2005-11-16
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AU2003253805A1 (en) 2004-01-23
WO2004005479A3 (en) 2004-12-23

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