SAMPLE PREPARATION METHODS

Information

  • Patent Application
  • 20150031038
  • Publication Number
    20150031038
  • Date Filed
    September 06, 2012
    12 years ago
  • Date Published
    January 29, 2015
    9 years ago
Abstract
The present invention provides whole blood nucleic acid extraction methods, compositions, and kits, as well as nested isothermal amplification methods, compositions, and kits. In certain embodiments, these methods are applied to detecting Lyme disease, including in patients without classic erythema migrans skin lesions.
Description
FIELD OF THE INVENTION

The present invention provides whole blood nucleic acid extraction methods, compositions, and kits, as well as nested isothermal amplification methods, compositions, and kits. In certain embodiments, these methods are applied to detecting Lyme disease, including in patients without classic erythema migrans skin lesions.


BACKGROUND

The diagnosis of acute infectious diseases is problematic when the pathogens are not in abundance, not easily cultured or the antibody response to them is delayed. Lyme disease is such an example. Infection by the causative agent, Borrelia burgdorferi1,2, is often difficult to diagnose because of clinical variability, including variations of the erythema migrans (EM) skin lesion and the lack of high performing diagnostic tests. A strategy that results in early unambiguous diagnosis of the infection will favorably impact management of the patient.


There are currently clinical limitations to early diagnosis. The best clinical marker of acute infection, the skin lesion erythema migrans (EM), is absent in at least 30% of the cases.3 Even when present, the EM is often not the classic bull's-eye lesion but rather an uncharacteristic variant as reported in 25-30% of cases.4,5 This may require referral to a specialist or prompt further diagnostic testing, thereby delaying the start of antibiotic therapy at the time for the best chance of cure without sequelae.


These clinical hurdles to diagnosis are compounded by the limitations of current laboratory tests. The most commonly used assays are serologic. However, these assays have been hampered by the biologically delayed antibody response (often 3 weeks or more to reach detectable levels). They are further limited because a single positive test is an indirect measure of exposure and cannot distinguish active from past infection. A direct Borrelia molecular test such as PCR can have high specificity but typically the tests have lacked sensitivity when applied to blood. In the past, PCR assays for Lyme disease did not have the benefit of current advances in sample preparation.6 and enhancement methods.7,8 such as Borrelia-targeted DNA enrichment (akin to a “molecular culture”) that may allow detection of a low number of nucleic acid copies in the blood. In addition, the optimal blood volume and component of the sample, such as whole blood versus serum, may have contributed to prior limitations of PCR based diagnostics.


SUMMARY OF THE INVENTION

The present invention provides whole blood nucleic acid extraction methods, compositions, and kits, as well as nested isothermal amplification methods, compositions, and kits. In certain embodiments, these methods are applied to detecting Lyme disease, including in patients without classic erythema migrans skin lesions.


In some embodiments, the present description provides methods of nucleic acid extraction comprising: a) contacting a sample of whole blood (e.g., EDTA treated whole blood) with beads, a proteinase, and an anionic surfactant (e.g., SDS) to generate a treated sample; b) homogenizing the treated sample to generate a cell lysate; c) centrifuging the cell lysate comprising a supernatant; d) separating the supernatant from the cell lysate; e) adding magnetic particles and lysis buffer to the supernatant to generate a magnetic-particle sample, wherein the magnetic particles are configured to bind nucleic acid molecules; f) washing the magnetic-particle sample with a wash buffer; g) treating the magnetic-particle sample in order to generate a dried magnetic bead sample; and h) treating the dried magnetic bead sample with an elution buffer such that a purified nucleic acid sample is generated that comprises purified nucleic acid.


In certain embodiments, the methods further comprise subjecting the purified nucleic acid to PCR and/or isothermal nested PCR to generate amplified nucleic acid. In some embodiments, the methods further comprise subjecting the amplified nucleic acid to mass spectrometry bioagent analysis in order to identify the source of the purified nucleic acid. In other embodiments, the mass spectrometry bioagent analysis comprises electrospray ionization mass spectrometry and base composition analysis.


In some embodiments, the present disclosure provides methods comprising: a) contacting a sample comprising isolated nucleic acid with a buffer, dNTPs, and a plurality of nested PCR primer pairs configured to amplify at least part of at least one bioagent target sequence; b) incubating the sample with a DNA polymerase under isothermal conditions such that amplified nucleic acid is generated; c) inactivating the DNA polymerase; and d) subjecting the amplified nucleic acid to mass spectrometry bioagent analysis in order to identify the source of the isolated nucleic acid.


In other embodiments, the mass spectrometry bioagent analysis comprises electrospray ionization mass spectrometry and base composition analysis. In certain embodiments, the DNA polymerase comprises BstE DNA polymerase. In additional embodiments, the incubating is conducted at about 56 degrees Celsius. In further embodiments, inactivating the DNA polymerase comprises heating the sample to at least about 80 degrees Celsius. In other embodiments, the plurality of nested PCR primer pairs comprises at least 10 primer pairs (e.g., 10 . . . 15 . . . 19, etc). In particular embodiments, the plurality of nested PCR primer pairs comprises at least 20 primer pairs (e.g., 20 . . . 25 . . . 35 . . . 45 . . . etc.). In further embodiments, the at least one bioagent target sequence comprises at least five bioagent target sequences. In certain embodiments, the methods further comprise a step after c) but before d) of further amplifying the amplified nucleic acid without any purification of the amplified nucleic acid.





DESCRIPTION OF THE FIGURES


FIG. 1 shows an atypical EM lesion from a patient who was PCR positive and seronegative with a negative ELISA after eight days of illness. Repeat serology at the end of therapy 3 weeks later showed a positive ELISA, positive IgM western blot and negative IgG western blot.





DETAILED DESCRIPTION

The present invention provides whole blood nucleic acid extraction methods, compositions, and kits, as well as nested isothermal amplification methods, compositions, and kits. In certain embodiments, these methods are applied to detecting Lyme disease, including in patients without classic erythema migrans skin lesions.


The methods, kits, and compositions are useful with any target nucleic acid sequence and are not limited to any particular target sequence (e.g., not limited to nucleic acid sequences from B. burgdorferi). The discussion below is focused on detecting sequence from B. burgdorferi. Such target sequences are exemplary and are not intended to limit the scope of the present description. Other target sequences (e.g., from infections disease) are well known in the art. Also well know in the art are primers, including nested prior sets, that are useful in the present description.


Lyme disease is representative of an infectious disease where early diagnosis is imperative to avoid sequelae. However diagnosis is often difficult because the clinical manifestations, including the rash, are variable and the pathogens are often not in abundance, not easily cultured, and the antibody response to them is delayed. In the past PCR for B. burgdorferi in blood had low sensitivity. This may be related to low copy number, insufficient volume of blood or targeting the wrong component of blood


The present description overcomes some of these obstacles by combining a pre-PCR nucleic acid enrichment with sensitive PCR detection from nucleic acid extraction from 1.25 ml of whole blood from patients with skin lesions and early Lyme disease. With this strategy, PCR positivity was found in 14 of 29 (p=0·0001) endemic area subjects with typical erythema migrans (EM) or a variant, often before seroconversion was positive. The enrichment technique increased the yield from 2 to 14. None of 44 control subjects were positive. A serendipitous and unexpected finding of clinical importance was the observation that 8 of 14 (57%) of PCR positive subjects had an atypical EM.


The description provides improved early diagnosis of Lyme disease by combination of a pre-PCR Borrelia DNA enhancement, sensitive PCR, and targeting sufficient volumes of whole blood. The surprise finding of non-classic EM lesions in the majority of microbiologically proven Lyme disease cases serves as alert to clinicians evaluating patients with endemic area exposure.


In certain embodiments, the PCR generated amplicons are detected by mass spectrometetry methods using bioagent identifying amplicons. In some embodiments, primers are selected to hybridize to conserved sequence regions of nucleic acids derived from a bioagent and which flank variable sequence regions to yield a bioagent identifying amplicon which can be amplified and which is amenable to base composition analysis. In some embodiments, the corresponding base composition of one or more different amplicons is queried against a database of base compositions indexed to bioagents and to the primer pair used to generate the amplicon. A match of the measured base composition to a database entry base composition associates the sample bioagent to an indexed bioagent in the database. Thus, the identity of the unknown bioagent is determined. No prior knowledge of the unknown bioagent is necessary to make an identification. In some instances, the measured base composition associates with more than one database entry base composition. Thus, a second/subsequent primer pair is generally used to generate an amplicon, and its measured base composition is similarly compared to the database to determine its identity in triangulation identification. Furthermore, the methods and other aspects of the invention can be applied to rapid parallel multiplex analyses, the results of which can be employed in a triangulation identification strategy. Thus, in some embodiments, the present invention provides rapid throughput and does not require nucleic acid sequencing or knowledge of the linear sequences of nucleobases of the amplified target sequence for bioagent detection and identification.


Methods of employing base compositions, databases containing base composition entries, and triangulation using primers, are described in the following patents, patent applications and scientific publications, all of which are herein incorporated by reference as if fully set forth herein: U.S. Pat. Nos. 7,108,974; 7,217,510; 7,226,739; 7,255,992; 7,312,036; 7,339,051; US patent publication numbers 2003/0027135; 2003/0167133; 2003/0167134; 2003/0175695; 2003/0175696; 2003/0175697; 2003/0187588; 2003/0187593; 2003/0190605; 2003/0225529; 2003/0228571; 2004/0110169; 2004/0117129; 2004/0121309; 2004/0121310; 2004/0121311; 2004/0121312; 2004/0121313; 2004/0121314; 2004/0121315; 2004/0121329; 2004/0121335; 2004/0121340; 2004/0122598; 2004/0122857; 2004/0161770; 2004/0185438; 2004/0202997; 2004/0209260; 2004/0219517; 2004/0253583; 2004/0253619; 2005/0027459; 2005/0123952; 2005/0130196 2005/0142581; 2005/0164215; 2005/0266397; 2005/0270191; 2006/0014154; 2006/0121520; 2006/0205040; 2006/0240412; 2006/0259249; 2006/0275749; 2006/0275788; 2007/0087336; 2007/0087337; 2007/0087338 2007/0087339; 2007/0087340; 2007/0087341; 2007/0184434; 2007/0218467; 2007/0218467; 2007/0218489; 2007/0224614; 2007/0238116; 2007/0243544; 2007/0248969; WO2002/070664; WO2003/001976; WO2003/100035; WO2004/009849; WO2004/052175; WO2004/053076; WO2004/053141; WO2004/053164; WO2004/060278; WO2004/093644; WO 2004/101809; WO2004/111187; WO2005/023083; WO2005/023986; WO2005/024046; WO2005/033271; WO2005/036369; WO2005/086634; WO2005/089128; WO2005/091971; WO2005/092059; WO2005/094421; WO2005/098047; WO2005/116263; WO2005/117270; WO2006/019784; WO2006/034294; WO2006/071241; WO2006/094238; WO2006/116127; WO2006/135400; WO2007/014045; WO2007/047778; WO2007/086904; WO2007/100397; and WO2007/118222, all of which are herein incorporated by reference.


Exemplary base-count related methods and other aspects of use in the methods, systems, and other aspects of the invention are also described in, for example, Ecker et al., Ibis T5000: a universal biosensor approach for microbiology. Nat Rev Microbiol. 2008 Jun. 3.; Ecker et al., The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents.; Ecker et al., The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing.; Ecker et al., The Microbial Rosetta Stone Database: A common structure for microbial biosecurity threat agents.; Ecker et al., Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry. J Clin Microbiol. 2006 August; 44(8):2921-32.; Ecker et al., Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proc Natl Acad Sci USA. 2005 May 31; 102(22):8012-7. Epub 2005 May 23.; Wortmann et al., Genotypic evolution of Acinetobacter baumannii Strains in an outbreak associated with war trauma, Infect Control Hosp Epidemiol. 2008 June; 29(6):553-555.; Hannis et al., High-resolution genotyping of Campylobacter species by use of PCR and high-throughput mass spectrometry. J Clin Microbiol. 2008 April; 46(4): 1220-5.; Blyn et al., Rapid detection and molecular serotyping of adenovirus by use of PCR followed by electrospray ionization mass spectrometry. J Clin Microbiol. 2008 February; 46(2):644-51.; Eshoo et al., Direct broad-range detection of alphaviruses in mosquito extracts, Virology. 2007 Nov. 25; 368(2):286-95.; Sampath et al., Global surveillance of emerging Influenza virus genotypes by mass spectrometry. PLoS ONE. 2007 May 30; 2(5):e489.; Sampath et al., Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann N Y Acad Sci. 2007 April; 1102: 109-20.; Hujer et al., Analysis of antibiotic resistance genes in multidrug-resistant Acinetobacter sp. isolates from military and civilian patients treated at the Walter Reed Army Medical Center. Antimicrob Agents Chemother. 2006 December; 50(12):4114-23.; Hall et al., Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans. Anal Biochem. 2005 Sep. 1; 344(1):53-69.; Sampath et al., Rapid identification of emerging pathogens: coronavirus. Emerg Infect Dis. 2005 March; 11(3):373-9.; Jiang Y, Hofstadler S A. A highly efficient and automated method of purifying and desalting PCR products for analysis by electrospray ionization mass spectrometry; Jiang et al., Mitochondrial DNA mutation detection by electrospray mass spectrometry; Russell et al., Transmission dynamics and prospective environmental sampling of adenovirus in a military recruit setting; Hofstadler et al., Detection of microbial agents using broad-range PCR with detection by mass spectrometry: The TIGER concept. Chapter in; Hofstadler et al., Selective ion filtering by digital thresholding: A method to unwind complex ESI-mass spectra and eliminate signals from low molecular weight chemical noise.; Hofstadler et al., TIGER: The Universal Biosensor.; Van Ert et al., Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis.; Sampath et al., Forum on Microbial Threats: Learning from SARS: Preparing for the Next Disease Outbreak—Workshop Summary (ed. Knobler S E, Mahmoud A, Lemon S.) The National Academies Press, Washington, D.C. 2004. 181-185.


EXAMPLES
Examples 1
Early Lyme Patient Specimens.

The current Example is part of a larger, ongoing longitudinal cohort study of early Lyme disease being conducted in a suburban community of a medium-sized, Northeast city since the summer of 2008. Adult patients with early, untreated Lyme disease are referred to a primary care physician with infectious disease training (JA) and provide written consent to participate.


Eligible patients are required to be treatment naïve, to have a documented rash diagnosed as EM at time of enrollment, and to have evidence of systemic infection; typically manifest as dissemination of the primary EM lesion or concurrent onset of new flu-like or other symptoms. Patients with a prior history of Lyme disease or symptom duration of their current illness of longer than 3 months are excluded.20. Forty four negative control specimens were obtained from Biomed Supply Inc. (Carlsbad, Calif.). Specimens were collected at a donation site in Pennsylvania from healthy donors screened by Biomed Supply Inc. A paired 7 mL tube of EDTA treated whole blood and 5-12 mL of serum was provided for each control patient.


Serological and Other Analyses.

At the initial, pre-treatment study visit, self-report demographics, medical history information, complete blood counts (CBC), complete metabolic panels (CMP) and 2-tier antibody testing for B. burgdorferi were performed as part of the patient clinical evaluation. All serologic testing for both the patient specimens and the negative controls was performed through the same commercial laboratory, and results were interpreted according to CDC criteria11. Based on these criteria, approximate illness duration was documented and included in determining serostatus; patients with less than 4 weeks illness duration were positive based on either IgM or IgG positivity on western blot analysis, whereas patients with greater than 4 weeks illness duration were required to be IgG positive. Photos of EM rashes were reviewed by a panel of experienced clinicians without knowledge of serologic or PCR status. Skin lesions with classic bull's eye appearance with central clearing and peripheral erythema were classified as classic EM lesions. EM with uniform red or red-blue appearance which lacked central clearing were classified as non-classic EM lesions.


DNA Extraction from Blood Specimens:


A combination of bead-beating and magnetic bead isolation was used to extract nucleic acids from 1.25 mL of whole EDTA blood. The blood was mixed in 2.0 mL screw-cap tubes (Sarstedt, Newton N.C.) filled with 1.35 g of 0.1-mm yttria-stabilized zirconium oxide beads (Glen Mills, Clifton, N.J.), 25 μL proteinase K solution (Qiagen, Valencia, Calif.), 142 μL of 20% SDS solution (Ambion, Austin, Tex.) and 1 uL of DNA extraction control (Abbott Molecular, Des Plains, Ill.). The mixture was then homogenized in a Precellys 24 tissue homogenizer (Bioamerica Inc., Miami, Fla.) at 6,200 rpm for 3 sets of 90 sec with 5 sec between sets. The homogenized lysates were then incubated at 56° C. for 15 min and then centrifuged for 3 min at 16,000 g in a bench top microcentrifuge. To isolate nucleic acids 1 mL of the supernatant was transferred to a 24-well deep-well Kingfisher plate (Thermo Scientific, Waltham, Mass.) along with 1.1 mL of Abbott lysis buffer (Abbott Molecular), and 160 μL of magnetic particles (Abbott Molecular). The specimens were incubated for 16.5 minutes in the lysis buffer at 56° C. Specimens were then washed once in Wash buffer I (Abbott Molecular), and three times in Wash buffer II (Abbott Molecular), with 1 min incubation for each wash step. The magnetic beads were then dried for 3 min at 65° C., and nucleic acids were eluted into 250 μL of elution buffer (Abbott Molecular), by incubating the magnetic particles at 65° C. for 3 min.


Nested Isothermal Amplification of B. burgdorferi Target DNA.


To increase sensitivity of B. burgdorferi detection by PCR/ESI-MS the seven target regions (eight primer pairs) of the previously described Borrelia genotyping assay21 were enriched by a nested isothermal amplification. For each of the seven target regions were amplified using 50 oligonucleotide primers: 25 upstream and 25 downstream to the DNA region of interest (Table 1).












TABLE 1





Primer Pair
Gene 




Target
Target
Primer
Sequence 3′-5′







BCT3514
rpoC
3514E3-F1
CCGAAAAAGATGGGCTTTT




3514E3-F2
AGGTTAAAAAGTCCGAAACTATT




3514E3-F3
TCTCCCGATCAAATTAGAAATTG




3514E3-F4
AAAGAGATAAAAGATTTTGAAAGAATAAA




3514E3-F5
AAAGCTAGGTTTTTGGAGTTTT




3514E3-F6
ACAGAAAAAGAAGAAGAATTGATTAA




3514E3-F7
ATGATGCTGGGAATCAGGTTC




3514E3-F8
GGGCTTGGACTTGATTTG




3514E3-F9
GTCTTTTAATGTGCTAATGCAAGA




3514E3-F10
GGTTCCTACTAATGTATCAGGG




3514E3-F11
GGCAGAGTTAAAATATATGAAAATATAG




3514E3-F12
CACCCTTCAAGAACTTTTAACAG




3514E3-F13
GGCTCTTGAAGCTTATGG




3514E3-F14
AGACTTGGAGAAATGGAGG




3514E3-F15
GAGGAAAGGCTCAATTTGG




3514E3-F16
TCTTGTTTCTCAGCAACCT




3514E3-F17
CGCAAGATCAACAGGC




3514E3-P18
ACTACACCATCTTGTTGATGATA




3514E3-F19
GTAATGGTTGGGGTGATTTAC




3514E3-F20
GGAGAGCCGTTCGAAA




3514E3-F21
CCAACTTCTAAAGAAATTTTATATGATGG




3514E3-F22
AGGAAAAATTAAAAACTGCTGGA




3514E3-F23
TGTTTTTGAATCTGCTACAAATGA




3514E3-F24
CTGGTAAATATCTTGGTGAATCTTATAA




3514E3-F25
GGACAGTTAATGGAATCTCAAT




3514E3-R1
ATACCAAATATGAGCAACTGGGGC




3514E3-R2
AAGCCCAATCCTAGAGGGTA




3514E3-R3
TAGAATTCAAACTAGATGCTGTAAT




3514E3-R4
GCCTTCAATTACTACATATTTTTCATA




3514E3-R5
GGCCGGTTCAATTACTACA




3514E3-R6
TCTTCATTTAAAAGCTGCATTTTT




3514E3-R7
GCTCTCTAGCTTCTATGTACTCA




3514E3-R8
AAGCATTAAAAGACATACCATATCGC




3514E3-R9
GAAGAGTTTTAATAGCCTCAGCCC




3514E3-R10
GACGAAAGCTCATCAAGATCA




3514E3-R11
CAGTTTTATCATCTTTATCTATCATTTGAA




3514E3-R12
AAATTCTCAATAATTTCAAGACGTCTT




3514E3-R13
ATCCACTCTGGCTTATTGCCA




3514E3-R14
GGGGAATAACAGGAAGAAC




3514E3-R15
GCTGAACCATTGGCC




3514E3-R16
ATGTTGCAAAGCGCC




3514E3-R17
CGATTATTTCTATTTATGACTCTTCTATAAAGATC




3514E3-R18
GCATTAAGAAGAAGCAACTTTCT




3514E3-R19
ATTCTTTTTTCGTTTCTCACAATAATC




3514E3-R20
GTCAAAAAGAGAGTCTACTGATTC




3514E3-R21
GAACCTTTGACAACCTTTCTTTTA




3514E3-R22
CGACTTGAGAGGCCT




3514E3-R23
CCTGCTTACCTTTTAATGCAT




3514E3-R24
TTTTACCAAGAAGATTTTGCCTAA




3514E3-R25
CAATAACAGAACGACCAGAATAA





BCT3515
rplB
3515E3-F1
GTGTTGCTATGAATCCTGTTG




3515E3-F2
GGTAGAAGACCCAAGGT




3515E3-F3
GGAAAGCTGGTAAAAGTAGG 




3515E3-F4
TGGAAATGAAGATTATGCCAATATTT




3515E3-F5
TTTTAAAAAATGTATTGCAACAATTGG




3515E3-F6
TTATCATCTGGCGAGATGAG




3515E3-F7
GACGGGAATTATGTCACTG




3515E3-F8
GGTGGATATGCTATGATACTTG




3515E3-F9
GGGTGGACAGCTTATAAGA




3515E3-F10
CGTTCACAATATTGAGCTTAATGT




3515E3-F11
CTTACCTCTTGAAAATATTCCTATTGG




3515E3-F12
CTAATGCTCCAATTAAAATTGGC




3515E3-F13
GGTTGGAGATGTTTTGGAAAG




3515E3-F14
AAAGGTATATTATTTCTCCTAAAGGC




3515E3-F15
GCTAATATAGCTTTGCTTGTTTATAAAG




3515E3-F16
GTTGCTTCTATTGAATATGATCCTAA




3515E3-F17
CGAAGAGATAAATTTAGCATTCCTG




3515E3-F18
GCATAAGAGAAAGTATAGGTTGATTG




3515E3-F19
CTGGTAGGATTAGTATTAGAAGAAGAG




3515E3-F20
AAAAGGTAAAAAATTTAAATCGGGC




3515E3-F21
CAAAGGTAATGATCCTTTGAAATC




3515E3-F22
GCTATAAGACGACTTTATCTTTTGAT




3515E3-F23
AGACTTATAAGCCAAAAACTTCTTC




3515E3-F24
GGTTTTGGAGAAAAATAAATATGGG




3515E3-F25
CAAAAAGGAAGATAAAATAGATATTTTTTAGTC




3515E3-R1
TTTCTTGCGAGTCTTATAACCT




3515E3-R2
TTTATTTCTTCTTTTAATAATAAATTTATCTGAATATC




3515E3-R3
TTTTTTAATAGATCTTGCCACTATACTC




3515E3-R4
ACTTTTTGATAAAGACTCTTTTCTATAAAAG




3515E3-R5
CTTCTCACTTCCAAAAGACG




3515E3-R6
AAGATCTGGAGTAGGTTTTAATAAC 




3515E3-R7
GGCTTACCATTTCAGGAATTAT




3515E3-R8
AAGTTTTGCCATTGTAAACAGATAT




3515E3-R9
CAAGATCCTCGGTAATATAAATAGGT




3515E3-R10
CTCGCCAAGCTTATGTC




3515E3-R11
CCTCTAAAAATCCTTGTAGGTG




3515E3-R12
CCTCTAAAAATCCTTGTAGGTG




3515E3-R13
CTTCCCTTTTTATCTGACTTAGC




3515E3-R14
ATCTTCTATTTACCAACATAACTACTTAC




3515E3-R15
AGGGTAAATTTTTGCCCTTTG




3515E3-R16
CTATTGGCCTAACTTTTTTTGG




3515E3-R17
AGACTCTCCCCGGATATT




3515E3-R18
AAAGCACTGCAATAGCC




3515E3-R19
TAAAAGCTTAGCTCCTTTATTAGG




3515E3-R20
TGATGCTGCTGACTTAACAA




3515E3-R21
CTCGGAAAGATTTTTATTGTGATACA 




3515E3-R22
CATCAACCATAACTGTTTTAACAAATATC




3515E3-R23
GCCAAATCTTTTTACGACGAC




3515E3-R24
TATCAGCTCTACCCCTAGC




3515E3-R25
CTTCAACAAAAATATGACAATTTCTATTAAC





BCT3516
leuS
3516E3-F1
CCTATCCTTCTGCCAACG




3516E3-F2
GGAAAAAAGATTGTATATACTTGACATG




3516E3-F3
CAAAGTAGAAGAAGATCCAAGTATTC




3516E3-F4
GGCAAGAATTTTGGGATAATAACA




3516E3-F5
TGTCTAAATACGAATTCATAAAAATTGAAA




3516E3-F6
GAATAAGTTGTTATGAGTTAATTTTCAAGA




3516E3-F7
TAAATAAAATTAACAAAAATGCAATCTAAAAGAA




3516E3-F8
CACAGCATCAAAATTGTTAGC




3516E3-F9
CCGTGCTGGTTCAAG




3516E3-F10
GAGGGGCTAGTGGG




3516E3-F11
GGAAGTGGTAGACACGC




3516E3-F12
AAAAAATATAATGGTTAATAGTGCTGTG




3516E3-F13
GTAATTAAAAAAAATAAAAAAGTTGACAAAAATT




3516E3-F14
CGCTGTAATAGCAACAACAATAATA




3516E3-F15
AATAATATTTTCAAAAATAAAAATAATTATATTTGCAA




3516E3-F16
CTCTAAGCTTCAAACTAGGTCA




3516E3-F17
AACTTTGCTCTCAATAGTTGTTT




3516E3-F18
TATGAAATCTAATCTATTTATTGTTTCTGACT




3516E3-F19
GCAATATTTATGTCAGCAGGAA




3516E3-F20
GAAGGTTTATACCCTTTGGAG




3516E3-F21
TGGTCAATATGGGGTATTAACTTTAT




3516E3-F22
CAATAACCTGCTTGACAAAATAAATTA




3516E3-F23
GGAAATTAATGGGAAATAAATTATTTAAAAACA




3516E3-F24
AGACATAATATCTTTTTACATTGGGAAA




3516E3-F25
TTTAGGAATTTTTTGGGGAGC




3516E3-R1
TGAGGGTGAGTTCCTGT




3516E3-R2
TTGTTTTTTAAACTTATTAATATTTTCTTCTGTAC




3516E3-R3
GGCAAACCCCAAAGC




3516E3-R4
GTGTTCTAATTTCTCGATCCC




3516E3-R5
ACTGTGTCCATTTATAGTAATTCTC




3516E3-R6
CTAGCCCTTTTTTATATAATTGCAGG




3516E3-R7
GTACCATACAGGCATTTCTTTTA




3516E3-R8
CTAGTACCGTTCCAAGCT




3516E3-R9
GTCCATCTGAAGTTTGAATAATCTC




3516E3-R10
ACGCTGTAAGATCCTCTC




3516E3-R11
GTAATTTTTAAAACCCACTGTCTTAAATA




3516E3-R12
CGTCTAGCAATCTTTCAGC




3516E3-R13
AGATTCAGGCCATTCTAATTCT




3516E3-R14
TCCAATTTCGCTGCATTTC




3516E3-R15
AATTCAATTTCAACTCCTGTTGAT




3516E3-R16
TTTTATCGCTGTGGCCTT




3516E3-R17
CTTTACAACAAGGCCAGAC




3516E3-R18
CGATCACTAAATATGTGATGCC




3516E3-R19
GTTGTTCTTTGTTATTTTTTCTATTAGTTTATT




3516E3-R20
CTTCGTGCTTTACATATTTTAAAACATT




3516E3-R21
GAGAAGTCCTATTAAGATCGCT




3516E3-R22
CTGTGAAAACTCCCGATTTATC




3516E3-R23
CATTTGTTATTGGATGAAATGCG




3516E3-R24
GCTTCCAACCCAAATTG




3516E3-R25
CGGTTCCGTAAGTTCCT





BCT3517
flaB
3517E3-F1
TCTGCTTCTCAAAATGTAAGAACA




3517E3-F2
TAACCAAATGCACATGTTATCAAA




3517E3-F3
TTGCTGATCAAGCTCAATAT




3517E3-F4
GCAACTTACAGACGAAATTAAT




3517E3-F5
AGACAGAGGTTCTATACAAATTGA




3517E3-F6
AGGTAACGGCACATATTCAGA




3517E3-F7
TAAGAATGAAGGAATTGGCAGTT




3517E3-F8
AATTTAAATGAAGTAGAAAAAGTCTTAGT




3517E3-F9
GGCTATTAATTTTATTCAGACAACAGA




3517E3-F10
TTGTCACAAGCTTCTAGAAATA




3517E3-F11
TTTCTGGTAAGATTAATGCTCAAAT




3517E3-F12
GAGCTTCTGATGATGCTGCT




3517E3-F13
GAAAAGCTTTCTAGTGGGTAC




3517E3-F14
CATTAACGCTGCTAATCTTAGTAA




3517E3-F15
CATCAGCTATTAATGCTTCAAGA




3517E3-F16
CATGGAGGAATGATATATGATTATCATG




3517E3-F17
TTTTTTTTTAATTTTTGTGCTATTCTTTTTAAC




3517E3-F18
TAATAATAATTATTTTTAATGCTATTGCTATTTGC




3517E3-F19
ATTAAAGGCTTTTGATTTTAATCAAAGA




3517E3-F20
TTAAGCGCATGAAAGATCAAG




3517E3-F21
GTGGAAGGTGAACTTAATACC




3517E3-F22
GATTATAAAAAGAAGTACGAAGATAGAGAG




3517E3-F23
TTATTTTTTTGATTAAAAATTTTCAAGTCGTAA




3517E3-F24
GCTTCCGGAGGAGTTATTTAT




3517E3-F25
TAGGAGATTGTCTGTCGC




3517E3-R1
GCAACATTAGCTGCATAAATAT




3517E3-R2
TCCCTCACCAGAGAAAG




3517E3-R3
ACACCCTCTTGAACCGGTG




3517E3-R4
TGAGAAGGTGCTGTAGCAGG




3517E3-R5
TTGTAACATTAACAGGAGAATTAACTC




3517E3-R6
TTAGCAAGTGATGTATTAGCATCA




3517E3-R7
TGATCACTTATCATTCTAATAGCATTT




3517E3-R8
CTATTTTGGAAAGCACCTAAAT




3517E3-R9
GCATACTCAGTACTATTCTTTATAGAT




3517E3-R10
TGAGCATAAGATGCTTTTAGATTT




3517E3-R11
TCTGTCATTGTAGCATCTTTTA




3517E3-R12
TTAAAATACTATTAGTTGTTGCTGCTAC




3517E3-R13
ATTAGCCTGCGCAATCAT




3517E3-R14
GCAATGACAAAACATATTGGG




3517E3-R15
TTAATACAATTTATACCAATTAAACTAGAATTTT




3517E3-R16
ATAAAAAAACAAAAGATCCTTTAAAGGATC




3517E3-R17
ATAAATTATACTAAAATTATTAAATTTTTGCCGAT




3517E3-R18
GCCTGCATTATGCTTTATAACA




3517E3-R19
CCTACTCAAAGCAAACTCC




3517E3-R20
CGAAAATACTTTATAACAATCTTTAATTTTAACA




3517E3-R21
TCGACTTATCTGCTTTTTGTTAAC




3517E3-R22
CTATCTTTGCCATCTTCATAGTC




3517E3-R23
GCAATAAAAATAGAAGATTCTTTGTAGAT




3517E3-R24
TAAAATTTCATTTTCATAAACATCAAGATTAATA




3517E3-R25
GCCCGACATACCCA





BCT3518
ospC
3518E3-F1
TTAATGAAAAAGAATACATTAAGTGCAATAT




3518E3-F2
CTAATAATTCATAAATAAAAAGGAGGCAC




3518E3-F3
TTTTCAAATAAAAAATTGAAAAACAAAATTGT




3518E3-F4
AATATTTATTCAAGATATTGAAGAATTTGAAAAA




3518E3-F5
TTTAAAATCAAATTAAGACAATATTTTTCAAATTC




3518E3-F6
AGCATATTTGGCTTTGCTTATG




3518E3-F7
AAATTAAAACTTTTTTTATTAAAGTATACTTCATTTAA 




3518E3-F8
GCCTGAGTATTCATTATATAAGTCC




3518E3-F9
TATATTGGGATCCAAAATCTAATACAAG




3518E3-F10
CAATTTCTCTAATTCTTCTTGCAATTAG




3518E3-F11
GGAGTATAGTAAGGTATTACTTTTGTATAAA




3518E3-F12
TTCCTGAGATATTCATATTTTTAATTTCTTTT




3518E3-F13
GCAGGACTTCCACTTAGTA




3518E3-F14
GGTAGGAGCTTCTTTTGAATAAAC




3518E3-F15
CAAAATAGGTATTTTCAAATTAAAAATTTCCATA




3518E3-F16
AATTTAACAATTATTTGCATTCCATAACATA




3518E3-F17
GCTTAGAGTCTTTAGATACTAGGC




3518E3-F18
AAAGATTTCAGAGCTCCCATAT




3518E3-F19
TTCTGAAAATAAAAGAGATTTTTCATCTC




3518E3-F20
TGACTCATGATAATTTGAAATTTGTTTG




3518E3-F21
AAATTATCAGGCCTTTTTTCAATACTGTC




3518E3-F22
GCAATACAATTTTTTGTAAAAGCTAATTG




3518E3-F23
CCGTAAATTTTTTGAGTTTCATTTGAT




3518E3-F24
AGTTACTTCTGGATGGAATTGT




3518E3-F25
AATTTTTAATTATTTGATCACCAAATTCAG




3518E3-R1
ACCGCATTAGAATCCGTAAT




3518E3-R2
ACCTCTTTCACAGCAAGTT




3518E3-R3
CATCTATAGATGACAGCAACG




3518E3-R4
TTACCAATAGCTTTAGCAGCA




3518E3-R5
GTATCCAAACCATTATTTTGGTGTA




3518E3-R6
GCTAACAATGATCCATTGTGATTAT




3518E3-R7
TATTAGGGTTGATATTGCATAAGC




3518E3-R8
CTTCATTTTTCAATCCATCTAATTTTTG




3518E3-R9
TTAGCCGCATCAATTTTTTCC




3518E3-R10
TCTTTTAATTTATTAGTAAATGTTTCAGAACA




3518E3-R11
CTTCTTTACCAAGATCTGTGTG




3518E3-R12
CTTTTGCATCAGCATCAGT




3518E3-R13
TTTAGTTTTAGTACCATTTGTTTTTAAAATG




3518E3-R14
GATTCAAATAATTTTCCAAGTTCTTCAG




3518E3-R15
CTGCTTTTGACAAGACCTC




3518E3-R16
TTTAACTGAATTAGCAAGCATCTC




3518E3-R17
CCACAACAGGGCTTG




3518E3-R18
GATCTTAATTAAGGTTTTTTTGGACTT




3518E3-R19
CCAGTTACTTTTTTAAAACAAATTAATCTTATA




3518E3-R20
AGAAATCTTTCTTGACTTATATTGACTTT




3518E3-R21
GAATTTTAAGAAATTTTTTGAGAAAATAAAAAAATAAAA




3518E3-R22
TATTCTTTAAGAGAAGAGCTTAAAGTT




3518E3-R23
AAATTCAATTTATTAACGGCTTTTGTAATA




3518E3-R24
TCTAGCACCCAATTTTGTTTATATTTA




3518E3-R25
GTTTAAGCCTACTTAAAGTCTTTAAAATC





BCT3519
hbb
3519-20E3-F1
CCCACACTCTCTCTTTCAAA


and

3519-20E3-F2
GATATTAACCGGCATTTAACCTT


BCT3520

3519-20E3-F3
TCTAGCTTACAATCCCATTTATAAGA




3519-20E3-F4
CCTTCAAATTTTAATTTTCCTCTAAAAGTTA




3519-20E3-F5
CCTTCAAAAGAAGAATCAAGATACAA




3519-20E3-F6
CACACCCCCTTTTGAAGATA




3519-20E3-F7
GTAATAACCTTACTATTCTTGCCAATA




3519-20E3-F8
TTCTACTATTAATGTATCACAAATTACCAC




3519-20E3-F9
GCATTTACATTGCCCTTCAA




3519-20E3-F10
CAACCGCTGTTTAAATAAACCTT




3519-20E3-F11
AATATTTTTTTTGTTTTTACATCCCCATAT




3519-20E3-F12
CACACTTACCATCAAAAATTATATTATCAT




3519-20E3-F13
AAGAAAATAAATCTACAATTTCATTAGACTTTA 




3519-20E3-F14
CAAAGTATCTTTTATTTGTGAAACGG




3519-20E3-F15
TCTACTTATTATTAATTAATAAAAAACACTGACC




3519-20E3-F16
CTCTACGAATTAAATTTTTAAGAAAGGATTTTA




3519-20E3-F17
ATCAAATCCACCATTTTTTTTATCCA




3519-20E3-F18
CCAACCGCCTTATTTCAC




3519-20E3-F19
TTTTCAAATTATCTTCAATCTTAAACTCTTTAG




3519-20E3-F20
TTTTAGCAACAACTTTAACCACTTT




3519-20E3-F21
TGTCACGCTAGATGCAG




3519-20E3-F22
CTTTACGCCACTTAAATCTGC




3519-20E3-F23
AATCAGAAAATATTACCCCGTTTG




3519-20E3-F24
ATATTATTTTCTAAACCTGAAGAAGGAATAT




3519-20E3-F25
CATTAAAAAATTTGATGATATTACTTTGCTC




3519-20E3-R1
GTTTTGCTGTTAAAGTAAGGAAATTAG




3519-20E3-R2
GCTGCTAGAAAAAAATCTCGTT




3519-20E3-R3
CTGCTAGAAAGCGAATAATTCATAA




3519-20E3-R4
GAATTTTTTAAATTTGTTGCAAAAAAACTAG




3519-20E3-R5
GCGGGTAAGAAAGACGAA




3519-20E3-R6
GAAAAACGCTGTATCAACATGA




3519-20E3-R7
ATTAGAAATGTAAGTGTAAAAAGTGAATTAAAA




3519-20E3-R8
CGCTCTCGTCAAAATTTAAAAAG




3519-20E3-R9
CTTGAGAAAAAATGCATCTGC




3519-20E3-R10
GATATATTAAAGCTATTGTTTAATAATATTATTAAGGA




3519-20E3-R11
ATTAACTTAAATCTTTGATTGACTATATTTGAAT




3519-20E3-R12
AGGTTTTTGAATATATTAATCAAAACTATTGT




3519-20E3-R13
ATTTTGAATAAAAAAATTTCTTATTCCATGC




3519-20E3-R14
CAAAGAAAATCATCAGACAAAAAAGG




3519-20E3-R15
GAATTTGAATTTAACAATAAAAATTATTTATGCTT




3519-20E3-R16
GAATTTTTTGAAAAAATTTTTATTGCCAG




3519-20E3-R17
CTGTGAAAGAAAAATTTTTAAAAGTGAAAT




3519-20E3-R18
CAATATAGTGTTATTTTATGAGTTTAGGAAAG




3519-20E3-R19
TTTTGTTGGGGGATTTTTCAG




3519-20E3-R20
TTTTGTTGGGGGATTTTTCAG




3519-20E3-R21
GCAATATATTTATTTTTTTATTTATTTGTTTTATTGATATTA




3519-20E3-R22
GTATTATGATTGCTTTATTTGTTTATTACATTTC




3519-20E3-R23
GATATTATTTATCTTGTACTTATCTTTTTATGTTTT




3519-20E3-R24
GTCCCAAAATTGGAAAATTTTCC




3519-20E3-R25
TATTTAAAGAGCTTAAAATTAAGAGAAAAGATC





BCT3511
gyrB
3511E3-F1
CGTGAAGCTGCAAGAAAA




3511E3-F2
TGGAAAAGCAATAAAAGCTGCTG




3511E3-F3
TGTTGTATATGAACATTTATTGGAAAT




3511E3-F4
GCTTGGTAATTCTGAGATAAGAAA




3511E3-F5
CCTCAATTTGAAGGTCAAACAAA




3511E3-F6
ATTTTAAAGAGGGGCTTACAGCT




3511E3-F7
GCCATGAATGAAGCTTTTAAA




3511E3-F8
CTCATGTTATGGGATTTAGAAGTGG




3511E3-F9
CTGACAACATTCTTCTTTTGTTAA




3511E3-F10
TGTTAATGTGGGGCTTAAATG




3511E3-F11
GCTTTTCAATCAGAACCTTATT




3511E3-F12
GAGGGTGGGATAAAATCTTTTT




3511E3-F13
TGGTAAAGAAAAATCTTCAAAATTTTAT




3511E3-F14
CGATAAAATATACATTTCAATTGAAGATAA




3511E3-F15
GGCTTAAAGAGCTTGCTTTT




3511E3-F16
AGATTATAATTTCGATGTTCTTGAAAAA




3511E3-F17
CGGATTCTGAAATTTTTGAAACTTT




3511E3-F18
GGGGACTAAGGTTACTTTTTT




3511E3-F19
AGAAGTTGTGGGGGAATCTTCTGTT




3511E3-F20
CTTTTTCAAAAGGTATTCCGACTT




3511E3-F21
GGTTTATGTTAATAGAGATGGAAAAAT




3511E3-F22
GGTTGTAAATGCTCTATCTTCGTT




3511E3-F23
TGGTAAGTTTAATAAAGGCACGTAT




3511E3-F24
CCTTGAACTTGTTTTAACAAAATTAC




3511E3-F25
ACCGATATTCATGAAGAGGAG




3511E3-R1
TACCCATTTTAGCACTTCCTCCA




3511E3-R2
TGGCAAAATGGCCTGAAAAA




3511E3-R3
TTGTTTTCTCAACATTAAGCATTTT




3511E3-R4
ATCATTGGTGATAACCTTATCTTCT




3511E3-R5
ACTCCTGCACCAAGAGAT




3511E3-R6
ATCTTGTGATAACGAAGTTTTGTA




3511E3-R7
TCCATCAACATCGGCATCTG




3511E3-R8
AAAAGCTAAAAGCAAAGTTCTAAT




3511E3-R9
ATATATCCATTTTCAATTAAATCTCTCAT




3511E3-R10
TATAAAGAGGAGGCATGGCT




3511E3-R11
TAAAAATAATAAATACGATTGTCATACTTT




3511E3-R12
TATTGCGATTTTTAGTTTCAATAGAA




3511E3-R13
CCCAAGCCCTTTATATCTCTGAA




3511E3-R14
AGCTGCGTTGGATTCATC




3511E3-R15
CTAGCAGGATCCATAGTTGTTT




3511E3-R16
ATCATCTATATTCATCAATCTCATTTTT




3511E3-R17
GAGTAACAAAAATTTTTTCAGCTTCA




3511E3-R18
TTTCTGGGCTCAACTAAATCT




3511E3-R19
GATTAATTACATTAAGTGCATTCTGTTC




3511E3-R20
CCATTAACGCTCCAATTACAC




3511E3-R21
TCCTAACATTTAATATTTGTTCTTTATTTTC




3511E3-R22
GCATAATTTAAATAAGAAGTTTTTATTTCATCT




3511E3-R23
GAAGAGCTCTAGAAACAATAACTGA




3511E3-R24
TGGTTTAAGACCATCTCTTACGT




3511E3-R25
CTCATACATAGAATAAAGTATTCTCCTG









Since two of the target regions are close a single set of flanking oligos was designed to cover both targets. All primers were brought up to an initial concentration of 1 mM in 10 mM Tris pH 8.0 and 50 uM EDTA (pH 8.0). The primers were mixed in equal proportions to create a 1 mM oligo mix. Primers were designed using B. burgdorferi B31 genome sequence (gi|15594346) and have a GC content of 25 to 50%, spaced 6-10 nucleotides apart and have a target TM of 52° C. To ensure removal of any contaminating salts the pooled primers were dialyzed twice for 4 hours at 4° C. against a 4 L solution containing 10 mM Tris pH 8.0 and 50 uM EDTA pH 8.0 using a 5 mL Float-A-Lyzer G2 (Spectrum Laboratories, Rancho Dominguez, Calif.) with a molecular weight cutoff of 0.5-1 kDa.


The nested isothermal amplification was performed in a 225 ul reaction in a 0.6 mL PCR tube (Axygen Inc., Union City, Calif.) containing 200 uL of nucleic acid extract, 22.5 ul Ibis 10× PCR Buffer II21 (Ibis Biosciences, Carlsbad, Calif.), 0.2 uM dNTPs (Bioline, Tauton, Mass.), and 10 uM oligo mix. The reactions were incubated at 95° C. for 10 min followed by a cooling to 56° C. in a MJ Thermocycler (Bio-Rad Laboratories, Hercules, Calif.). The reactions were then removed to a heat block at 56° C. and 11.25 U of BstE DNA polymerase (Lucigen, Middleton, Wis.) enzyme added and the reactions incubated at 56° C. for 2 hours followed by an 80° C. heat inactivation for 20 min. The resulting reaction was used directly in the subsequent PCR without purification.


Detection of B. burgdorferi from Whole Blood from Patients with Clinically Diagnosed Early Lyme Disease.



Borrelia was detected by processing 2 ul of Borrelia enriched nucleic acid extracts per PCR reaction on a previously described broad-range PCR/ESI-MS assay designed to detect and characterize Borrelia burgdorferi as previously described.21. Electrospray ionization mass spectrometry was performed on the PLEX-ID biosensor (Abbott Molecular). Briefly, after PCR amplification, 30 μL aliquots of each PCR reaction were desalted and analyzed by mass spectrometry as previously described21-23 (herein incorporated by reference as if fully set forth herein). Analysis of amplicons from any one of the eight primer pairs in the assay can be used to positively identify Borrelia DNA in a specimen.


Results

The data are supportive that this new strategy can positively impact current clinical and laboratory impediments to early diagnosis of Lyme disease. A serendipitous finding of clinical importance was that the majority (˜60%), of rashes were not the classic EM in PCR positive cases.


Detection of Lyme disease in 29 patients with classic and non-classic EM Examination of nucleic acid extract from 1.25 ml of whole blood from the independent set of 29 endemic patients with clinically diagnosed Lyme disease with classic or non-classic EM and 44 healthy controls showed that 14 of the 29 Lyme patients, and 0 of 45 controls, (48%, p=0.0001) had detectable B. burgdorferi. The pre-PCR enrichment step enabled increased detection of Borrelia from 2 to 14 cases (7×) when assessed by the PCR/ESI-MS assay. Two-tiered serology was positive in 14 of the 29 specimens, not all of which overlapped with the 14 specimens positive by NIA/PCR/ESI-MS from Table 2. Nine of the clinically defined early Lyme disease specimens tested negative by both PCR and serology assays. However, we did not have skin isolates to determine if the Borrelia was actually present as a skin-restricted strain which did not disseminate to blood.23,24 Table 2 is presented to show PCR detection is possible even when serology is negative or not yet positive. The data support the concept that unambiguous diagnosis can be made early, before seroconversion.









TABLE 2







EM, B. burgdorferi PCR and serological analysis of 14 Early Lyme


disease specimens positive by NIA/PCR/ESI-MS from whole blood.











PCR
Early 2-tier
Follow-up two-tier


















EM
PCR


# IgM
# IgG


# IgM
# IgG


ID
EM1
Result
Result2
ELISA
bands
bands
Result2
ELISA
bands
bands




















26
NC
Pos
Neg
≦0.90


Pos
 4.35
3
1


33
C
Pos
Pos
>5.00
3
4
ND





37
C
Pos
Neg
1
1
3
Pos
>5.00
3
5


40
NC
Pos
Pos
>5.00
3
4
ND





44
NC
Pos
Neg
≦0.90


Pos
>5.00
3
6


45
NC
Pos
Neg
1.36
1
1
Pos
>5.00
2
2


46
NC
Pos
Pos
>5.00
3
1
ND





47
C
Pos
Pos
>5.00
3
4
ND





48
NC
Pos
Neg
≦0.90


Neg
 1.46
1
2


49
NC
Pos
Pos
2.49
2
0
ND





51
C
Pos
Neg
4.49
1
3
Neg
>5.00
2
4


52
NC
Pos
Pos
3.54
2
3
ND





53
NC
Pos
Pos
4.73
3
2
ND





54
NC
Pos
Pos
2.86
2
2
ND









1C = classic erythema migrans; NC= non-classic erythema migrans




2Positivity based upon CDC two tiered serologic criteria



Results illustrated for 14/29 patients who were PCR+.


Pos = positive, Neg = negative, ND = not done







Of the 14 early Lyme specimens that tested positive by the NIA/PCR/ESI-MS assay, 6 were negative by the 2-tiered test at the time of presentation before the initiation of antibiotics (Table 2). Of these 6 specimens, 4 seroconverted by the follow-up serological testing 3 weeks later indicating that these were likely recent infections. Two of the NIA/PCR/ESI-MS positive specimens (#48 and #51) did not seroconvert sufficiently to meet the CDC surveillance criteria25 but both specimens showed an increase in ELISA titers and increased IgG/IgM blot reactivity, indicating that these patients were most likely represent weak or slow responders possibly due to antibiotic therapy26 or for unknown reasons. Of the 44 control patient sera, a single sample was seropositive by ELISA and IgG western blot, but was PCR negative. This low rate in our sample set from the eastern United States is consistent with the known background seroreactivity from remote exposure in an endemic region.


These results demonstrate that B. burgdorferi infection can be diagnosed early, and even prior to seroconversion, from whole blood in a high percentage of patients with suspected Lyme using a pre-PCR Borrelia-DNA enhancing method coupled with PCR/ESI-MS assay. Other isothermal amplification methods to generate genetic material has been described but not for Borrelia.7,8 In this case, a novel nested isothermal amplification (NIA) was coupled with a PCR/ESI-MS assay and results were contrasted with the two-tier serology. However, in a clinical situation, finding Borrelia DNA circulating in blood in an ill person with endemic area exposure will have such a strong possibility of a current infection that it would support a clinical decision to treat regardless of whether there is a classical EM, an atypical skin lesion, or extracutaneous systemic symptoms and signs suggestive of Lyme disease. The could allow for early diagnosis of the 20-30% of patients with early Lyme disease that present with “viral-like” symptoms indistinguishable for other community acquired infectious diseases. In contrast, a single serologic test, even if positive, may be difficult to interpret in a person living in an endemic area because this single result could represent past exposure. The present strategy has the potential to remove this ambiguity.


Work conducted during development of embodiments of the present invention led to the conclusion that hold blood may be preferable to serum or plasma for detection of Borrelia. While not limited to any mechanism, this may be due to the pathogen adhering to particular blood cells. In contrast to many diagnostics based on analysis of small (ul) of samples, the present disclosure is configured to handle larger volumes (mls), but within clinical practice volumes, to increase the detection of pathogens that may be present only in low copy numbers. A recent paper27 showed that B. burgdorferi may be present in a high percentage of patients with Lyme disease but may require “teasing” it out with combinations of cultures and PCR. Although this method is not as easily performed within a clinically useful time period, as that which is described herein, it does suggest that there is an attainable target should it be present.


A serendipitous observation in this Example and an important clinical finding was the high percentage (57%) of PCR positive patients whose skin rash was not the classical EM but an atypical lesion (see FIG. 1) that could be easily misdiagnosed. Photographs of lesions (all greater than 5 cm) were presented to four physicians experienced with Lyme disease, including two dermatologists. Without knowledge of the laboratory data they were asked to categorize the lesions into 1) those that they would expect any reasonably trained physician to recognize as EM and 2) into those that they would not fault such a physician from referring the patient or desiring supportive laboratory tests or more time for observation.28,29 Based on previous reports, including a vaccine trial, of atypical rashes in 25-30% of microbiologically confirmed B. burgdorferi infected subjects4,5 it was expected a similar percentage, but were surprised by almost 60%. This high percentage serves as an alert for physicians to consider Lyme disease in the differential diagnosis of patients with endemic area exposure and a rash that is not the classic EM. These atypical lesions serve as a reminder of the need for diagnostics for the endemic area patient who only has a flu-like illness during the high season for Lyme disease. Such a patient may benefit from the testing strategy described in this Example or, at the very least, closer monitoring.


It is believed that these results demonstrate a useful strategy to the diagnosis of infections when there is a paucity of pathogens or the immune response cannot provide an unambiguous result. It is likely that many of these difficult to diagnose infections will require a battery of diagnostic platforms each with advantages depending on when the patient presents.


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All publications and patents mentioned in the present application are herein incorporated by reference. Various modification and variation of the described methods and compositions of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in the relevant fields are intended to be within the scope of the following claims.

Claims
  • 1. A method of nucleic acid extraction comprising: a) contacting a sample whole blood with beads, a proteinase, and an anionic surfactant to generate a treated sample;b) homogenizing said treated sample to generate a cell lysate;c) centrifuging said cell lysate comprising a supernatant;d) separating said supernatant from said cell lysate;e) adding magnetic particles and lysis buffer to said supernatant to generate a magnetic-particle sample, wherein said magnetic particles are configured to bind nucleic acid molecules;f) washing said magnetic-particle sample with a wash buffer;g) treating said magnetic-particle sample in order to generate a dried magnetic bead sample; andh) treating said dried magnetic bead sample with an elution buffer such that a purified nucleic acid sample is generated that comprises purified nucleic acid.
  • 2. The method of claim 1, further comprising subjecting said purified nucleic acid to PCR and/or isothermal nested PCR to generate amplified nucleic acid.
  • 3. The method of claim 2, further subjecting said amplified nucleic acid to mass spectrometry bioagent analysis in order to identify the source of said purified nucleic acid.
  • 4. The method of claim 3, wherein said mass spectrometry bioagent analysis comprises electrospray ionization mass spectrometry and base composition analysis.
  • 5. A method comprising: a) contacting a sample comprising isolated nucleic acid with a buffer, dNTPs, and a plurality of nested PCR primer pairs configured to amplify at least part of at least one bioagent target sequence;b) incubating said sample with a DNA polymerase under isothermal conditions such that amplified nucleic acid is generated;c) inactivating said DNA polymerase; andd) subjecting said amplified nucleic acid to mass spectrometry bioagent analysis in order to identify the source of said isolated nucleic acid.
  • 6. The method of claim 5, wherein said mass spectrometry bioagent analysis comprises electrospray ionization mass spectrometry and base composition analysis.
  • 7. The method of claim 5, wherein said DNA polymerase comprises BstE DNA polymerase.
  • 8. The method of claim 5, wherein said incubating is conducted at about 56 degrees Celsius.
  • 9. The method of claim 5, wherein said inactivating said DNA polymerase comprises heating said sample to at least about 80 degrees Celsius.
  • 10. The method of claim 5, wherein said plurality of nested PCR primer pairs comprises at least 10 primer pairs.
  • 11. The method of claim 5, wherein said plurality of nested PCR primer pairs comprises at least 20 primer pairs.
  • 12. The method of claim 5, wherein said at least one bioagent target sequence comprises at least five bioagent target sequences.
  • 13. The method of claim 5, further comprising a step after c) but before d) of further amplifying said amplified nucleic acid without any purification of said amplified nucleic acid.
CROSS-REFERENCE TO RELATED APPLICATIONS

The present Application claims priority to U.S. Provisional Application Ser. No. 61/531,471 filed Sep. 6, 2011, the entirety of which is incorporated by reference herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under 1R43AI077156-01 awarded by the National Institutes of Health. The government has certain rights in the invention.

PCT Information
Filing Document Filing Date Country Kind 371c Date
PCT/US12/53909 9/6/2012 WO 00 9/15/2014
Provisional Applications (1)
Number Date Country
61531471 Sep 2011 US