Patent Publication Number: US-2013252248-A1

Title: Detection of neisseria meningitidis by loop mediated isothermal amplification

Description:
The present invention relates to a test for meningitis. More specifically the invention relates to a near bedside assay for  Neisseria meningitidis.    
     The pathogenic bacterium  Neisseria meningitidis  (NMG) is a major worldwide cause of invasive bacterial meningitis and septicaemia, known as ‘meningococcal disease’ (MD). Although relatively rare in developed countries (1-3 cases per 100,000 population per year), MD has serious consequences for those who are affected, especially children. Vaccination has reduced the incidence of MD in recent years, although no effective vaccine is available for Group B NMG, which causes &gt;40% of UK cases. MD has a mortality rate of between 15% (meningococcal meningitis) and 50% (meningococcal septicaemia), despite the availability of effective antibiotic therapy. This is partly because of difficulty with diagnosis of early-stage MD, which can lead to delayed diagnosis. 
     Diagnosis of MD currently relies entirely on correct interpretation of clinical symptoms, which are frequently absent or equivocal. This makes clinical diagnosis challenging, especially in very young children, and there is no reliable diagnostic test available to assist physicians with making a diagnosis of early-stage MD. Existing laboratory tests for NMG infection involve either conventional isolation and culture—which takes too long to be useful as part of a clinical diagnosis, or ‘polymerase chain reaction’ (PCR) tests—which can also be time-consuming, and are often available only in reference laboratory settings. The most rapid current test to detect NMG (gene-specific PCR) is not available in most hospital bacteriology laboratories, due to lack of expertise/specialist equipment for molecular diagnostic testing. For this reason, the currently available tests are used only to confirm a clinical diagnosis of MD. 
     The consequences of delayed diagnosis for the patient can be catastrophic—leading to permanent disability (often in the form of serious neurological damage or multiple limb amputations) or death. There is a clear need for a rapid and reliable molecular diagnostic test, offering high positive predictive value (PPV) and negative predictive value (NPV) to assist with diagnosis of early-stage MD. Most importantly, a test which could be applied either at the point of care, or in a near-patient setting, and which gave a rapid result (1-2 hours) would provide physicians with timely information which is currently only useful to confirm a diagnosis 
       Neisseria meningitidis  is a major cause of bacterial meningitis and septicaemia worldwide. Early diagnosis of meningococcal disease (MD) is difficult because the initial presenting features are common to those of simple upper respiratory tract infection such as coryza and sore throat. Delayed diagnosis of MD can have catastrophic consequences for the patient, and contributes to the high levels of morbidity and mortality which can be associated with MD, especially in children. The classical features of MD, which include haemorrhagic rash, meningism and reduced level of consciousness, may come on rapidly but still relatively late (e.g. 12-24 hours) after the first symptoms of the illness start. A recent study (reference 1) has suggested that leg pains, cold extremities and abnormal skin colour are seen in the first 12 hours of MD. However, the positive and negative predictive value of these signs is not known, and these symptoms are likely to be present in children with other infections such as influenza. Similar difficulties also surround early clinical diagnosis of meningitis and septicaemia caused by other bacteria, especially  Streptococcus pneumoniae . Significantly, there is no reliable test to assist clinicians with diagnosis of early-stage MD; diagnosis can be made only on the basis of clinical symptoms, with inevitably serious consequences if these symptoms are absent or overlooked. 
     Laboratory-based molecular tests are currently not useful as diagnostic tools (except for confirming a diagnosis) because laboratory turn around times can be significant, even for the fastest tests. The transport time between specimen collection and laboratory testing also has a significant adverse effect on positivity rates for confirmatory MD molecular assays (reference 2), leading to false-negative test results. While laboratory culture of  N. meningitidis  has historically been the gold standard for confirming diagnosis of MD, pre-admission antibiotic therapy has greatly reduced the value of routine culture, and the time required (24-48 hours) generally limits its role to confirming antibiotic susceptibility in culture-positive specimens. Data from a previous study in our laboratory (reference 3) illustrates the very low success rate of culture in confirming diagnosis of MD. 
     In view of these problems, a rapid and reliable molecular diagnostic test, offering high positive predictive value (PPV) and negative predictive value (NPV), would be extremely useful. Most importantly, a test which could be applied either at the point of care, or in a near-patient setting, and which gave a rapid result (1-2 hours) could avoid the critical delays which are associated with submitting a specimen for laboratory testing. This would assist clinicians by providing information which is currently only available to confirm a diagnosis of MD. 
     A number of molecular tests for laboratory detection of  N. meningitidis  have been described in the literature. These tests generally rely on the Polymerase Chain Reaction (PCR) to amplify and detect virulence genes, and focus on identification of cultured  N. meningitidis  isolates (references 4 &amp; 5) or detection using invasive specimens such as blood or cerebrospinal fluid (references 6 &amp; 7). In the course of a recent research project investigators demonstrated an effective combined PCR laboratory assay which detects two important virulence genes from  N. meningitidis  in nose and throat swab specimens (Dr. K. Dunlop, MD Thesis; reference 3). This assay proved to be very effective for confirming diagnosis of MD in a case-control clinical trial (n=104 suspected cases, n=104 case controls), which showed that the test has high sensitivity (81%), specificity (100%), PPV (100%) and NPV (92%). The study clearly showed that these gene targets are useful diagnostic biomarkers of MD, and they can be easily detected in non-invasive clinical specimens. Current recommendations from the Chief Medical Officer include taking blood samples for PCR analysis and nose/throat swabs for culture only. Published PHLS guidelines (reference 8) note that molecular testing of throat swab specimens is effective, although they do not consider this to be ‘definitively diagnostic’ for confirmatory testing by reference laboratories at present. Nevertheless, recent data strongly suggest that the use of combined molecular testing directly on nasal and pharyngeal swab specimens has considerable potential for improving the diagnosis of MD in this hospital and elsewhere. 
     While PCR assays are clearly a valuable laboratory diagnostic method, it would not be practical to apply these tests in a near-patient setting, as they require both laboratory skills and specialised instruments (a thermal cycler and gel electrophoresis equipment, or a ‘real-time’ PCR instrument). 
     It is an aim of the present invention to develop a test which detects the same gene targets as the current PCR assay, but using an alternative ‘isothermal’ DNA amplification technique, in a format which would be practical for near-patient testing by staff without specialised laboratory skills. 
     It is an aim of the present invention to provide a rapid qualitative molecular test to detect  Neisseria meningitidis  DNA in patient specimens, allowing rapid confirmation of meningococcal infection. 
     There is currently no rapid diagnostic test which can be used to assist with clinical diagnosis of early-stage meningococcal disease, and significant turnaround times are required even for the fastest laboratory tests. In contrast, the proposed new test would be available for near-patient testing by staff without laboratory skills and without highly specialized or costly equipment (i.e. it could be used in hospital A&amp;E/E.R. departments, large primary care units or pharmacies). 
     According to the present invention there is provided a diagnostic test for meningococcal disease, the test comprising nucleic acid primer sets capable of detecting  Neisseria meningitides  in a LAMP based molecular test, the primer set being chosen from the primer sets listed in Table 1 as LAMP SETS 1 to 12 comprising a set of SEQUENCE IDs selected from ID: 1 to ID: 69. 
     A LAMP primer set consists of one pair of forward (FIP) and reverse (BIP) inner primers, forward (F3) and reverse (B3) outer primers. FIP, BIP, F3 &amp; B3 primers are essential for amplification to proceed. The addition of loop forward (LF) and/or loop back (LB) primers significantly accelerates amplification reducing overall detection times by 50% 
     The invention also provides any of the primers as set out in Table 1 as Sequence ID: 1 through Sequence ID: 69, individually or in combination with any of the other listed primers for use in an assay for  Neisseria meningitides.    
     Preferably the assay is a LAMP assay. 
     Preferred primer sets are chosen from the group consisting of LAMP SETS 1, 3, 5, 6, 7 and 12. 
     Particularly preferred primers sets are 3, 5, 1, 7, 12 and 6. 
     In a preferred embodiment of the invention the primer set is chosen from LAMP primer sets 3 or 5 as shown in Table 1. 
     The nomenclature used herein to describe the primer sequences for preferred LAMP sets is as follows. L3L3 refers to LAMP set 3 (FIP, BIP, F3 &amp; B3) and loop set 3 i.e. —Seq IDs 11 to 14 and 16 and 17. L3L1 refers to LAMP set 3 (FIP, BIP, F3 &amp; B3) and loop set 1 i.e. —Seq IDs 11 to 14 and 15 and 16. In each case the first 4 sequences are essential and the additional two loop primers accelerate the reaction. 
     Preferably the LAMP primer set comprises SET 3 (L3L3) consisting of Seq IDs 11 to 14 and IDs 16 and 17. 
     An alternative preferred primer set comprises SET 3 (L3L1) consisting of Seq IDs 11 to 16. 
     Another preferred primer set comprises SETS (L5L1) consisting of Seq IDs 24 to 29. 
     The preferred primer sets are listed in Table 2 
     The invention therefore provides the use of the listed primers in a diagnostic test for  Neisseria meningitides.    
    
    
     
       The invention will be further described with reference to the following experimental details and with reference to the accompanying FIGURE wherein 
         FIG. 1  illustrates Real Time ctrA LAMP plot total fluorescence against time in mins. for  Neisseria meningitidis  serogroups A NCTC10025, serogroup B NCTC10026, serogroup Y NCTC10791 , Neisseria flavescens  NCTC 3191 , Neisseria polysaccharea  NCTC1858 , Neisseria lactamica  NCTC 10616 , Neisseria cinerea  NCTC 10294 total nucleic acid extracts &amp; No Template Control (Nuclease Free Water) 
     
    
    
     The exemplification of the utility of the invention involves consecutive phases:
         Phase 1—Assay development and laboratory optimisation   Phase 2—Transfer of the assay to a ‘near patient’ clinical setting   Phase 3—Clinical validation of the near-patient assay   Phase 4—Data analysis and reporting       

     Phase 1—Assay Development and Laboratory Optimisation 
     Target Selection and Assay Design: 
     The proposed test detects the same gene targets as the existing PCR assay. These are: ctrA, encoding a capsule polysaccharide export outer membrane protein; and porA, encoding a separate outer membrane protein. The products of these genes are important virulence determinants in  N. meningitidis , and the inventor&#39;s data demonstrates that the conserved regions within these genes are useful biomarkers of MD. 
     It would not be practical to apply existing PCR tests in a near-patient setting so the inventors have developed a test which detects the same targets, but uses an alternative ‘isothermal’ DNA amplification technique. Unlike PCR, isothermal methods do not require expensive or complicated thermal cycling instruments, which makes them very attractive for point-of-care or near-patient testing. An isothermal technique called ‘Loop-mediated isothermal Amplification’ (LAMP), used both in laboratory and near-patient settings has distinct advantages over the current PCR laboratory test. 
     The LAMP method (references 9, 10 &amp; 11) is a type of ‘strand displacement’ amplification, which utilises a specially designed set of oligonucleotide primers, and a specific thermophilic DNA polymerase derived from  Bacillus stearothermophilus . The primers are designed to promote the formation of ‘hairpin-loop’ structures during the initial stages of the reaction, allowing high levels of self-primed DNA synthesis to occur from these structures as the reaction continues. In brief, the reaction is initiated by annealing and extension of a pair of ‘loop-forming’ primers, followed by annealing and extension of a pair of flanking primers. Extension of these primers results in strand-displacement of the loop-forming elements, which fold up to form terminal hairpin-loop structures. Once these key structures have appeared, the amplification process becomes self-sustaining, and proceeds at 60-65 degrees C. in a continuous and exponential manner (rather than a cyclic manner, like PCR) until all of the nucleotides (dATP, dTTP, dCTP &amp; dGTP) in the reaction mixture have been incorporated into the amplified DNA. LAMP allows amplification of target DNA sequences with higher sensitivity and specificity than PCR, often with reaction times of below 30 minutes, which is equivalent to the fastest real-time PCR tests. The target sequence which is amplified is typically 200-300 base-pairs (bp) in length, and the reaction relies upon recognition of between 120 bp and 160 bp of this sequence by several primers simultaneously during the amplification process. This high level of stringency makes the amplification highly specific, such that the appearance of amplified DNA in a reaction occurs only if the entire target sequence was initially present. While characterisation of the amplified DNA (on the basis of its restriction pattern or DNA sequence) is possible, this is generally not necessary as the reaction is so specific; the presence of amplified DNA indicates that the target sequence was present. Significantly, the yield of amplified target DNA in positive reactions is so high, it can be easily and directly detected in the reaction tube (references 12 &amp; 13) allowing rapid discrimination between positive and negative specimens. 
     A number of diagnostic LAMP assays have been described in the literature, including tests to detect causes of viral meningitis such as mumps virus (using RT-LAMP; reference 14) and human herpes virus 7 (HHV-7; reference 15). The published HHV-7 LAMP assay was clinically validated, and used to detect primary HHV-7 infection in serum samples in a 60 minute assay. Although there is growing interest in the use of LAMP to develop rapid diagnostic tests, no studies using LAMP to detect  N. meningitidis  have been published to date. 
     The very high sensitivity of LAMP may allow the initial DNA extraction step during the assay to be avoided, allowing a diluted specimen lysate to be used instead of purified DNA. This has the potential to further reduce the total time required to complete the test, as the extraction stage forms an increasingly large proportion of the total assay time as faster amplification and detection methods are employed. A published allele-specific LAMP assay for human cytochrome P450 ‘single nucleotide polymorphism’ genotyping (reference 17) has been used to selectively amplify target sequences from whole-blood lysates, which suggests that this approach is viable. The P450 study also demonstrated that LAMP can be used to discriminate between closely related genotypes, which is relevant for the  N. meningitidis  genotyping test (using the siaD gene) proposed here. 
     The inventors have now developed a prototype LAMP assay which can detect the  N. meningitidis  etrA gene target in extracted clinical specimens in 60 minutes using LAMP primers as set out in Table 1. 
     This initial part of the project involved detailed gene sequence analysis, followed by the design and testing of a range of LAMP primer sets. The laboratory performance of each set has been examined, and the most effective and practical primers selected for transfer to a clinical setting (Phase 2) and clinical validation (Phase 3). 
     The designed primer sets are set out in Table 1 and identified as LAMP SETS 1 to 12 consisting of primers being sequence ID: 1 through to sequence ID: 69, together with an indication of their effectiveness with different strains. 
     Assay Optimisation and Laboratory Validation: 
     The principal objective of this part of the study is an optimised and robust test which will be useable by a member of staff with minimal technical training. This work will compare LAMP with the existing nested PCR test method, and will focus on the ctrA and porA targets, with the siaD and lytA targets as secondary objectives. Laboratory validation work will include:
         Optimisation of the LAMP reaction conditions (by varying the reagent composition, incubation temperature, reaction time etc.).   Preparation of control and reference material (i.e. cloned reference targets).   Determination of the analytical sensitivity of the test (using reference materials).   Determination of clinical sensitivity (using ‘spiked’ and real clinical samples).   Specificity testing, using typed  N. meningitidis  strains, other clinically relevant bacteria, and human genomic DNA. The specificity panel will include NCMBI reference strains from 9 serogroups known to cause invasive disease (A, B, C1+, C1−, X, Y, W-135, Z &amp; L) and clinical isolates from this hospital. Identification of clinical isolates will be confirmed by 16S sequencing.   Comparison of test performance using fresh vs. stored specimens.       

     A major objective is to understand possible sources of false-positive and false-negative results, in order to maximize the PPV and NPV of the test. A positive control LAMP assay will also be developed, allowing control reactions to be included with every batch of unknowns. Phage Lambda DNA will be used as a control target, as this is readily available, easily standardized, and will not interfere or cross-react with detection of any of the intended target genes. 
     As an additional benefit of this project, it should be noted that the optimised and laboratory-validated tests will be immediately useful for rapid identification of  N. meningitidis  and  S. pneumoniae  isolates as part of the routine clinical microbiology service in this hospital, and elsewhere. 
     Real-Time Detection Methods: 
     Real-time detection of amplified DNA during LAMP reactions is possible, using three different methods: by turbidometry (detection of insoluble magnesium pyrophosphate accumulation in reactions), by ethidium bromide fluorescence, or by SYBR Green I fluorescence (which both detect accumulation of double-stranded DNA in reactions). Real-time monitoring increases the complexity of the test/instrument format required, as some form of optical or fluorescence measurement must be used. However, this is offset by the fact that provisional positive results may be obtained much more quickly (i.e. as soon as an amplified product is detected in a reaction). Detectable amounts of DNA may be synthesised in a little as 15 minutes in LAMP reactions (reference 18) and in some cases the positive reaction can even be visualized by eye. 
     Following the assay optimisation stage, the proposed project will also assess the available real-time monitoring methods, to see whether they could usefully be incorporated into a near-patient test. 
     Extraction Methods: 
     An important part of the study will be the development of a rapid DNA extraction method which can be used for near-patient testing. Current laboratory protocols for DNA extraction are too cumbersome for use in near-patient settings, so a simpler method involving specimen lysis and dilution will also be developed, using both PCR and the optimised LAMP test to assess performance. The inventors are investigating whether the use of crude specimen lysates for molecular assays is feasible, in order to simplify the process further, and to minimise the specimen processing time required. 
     Sequencing: 
     Some DNA sequencing work is being conducted for two reasons:
         i) to confirm the taxonomic position of  N. meningitidis  isolates obtained during the study, and previously isolated reference strains (by 16S rDNA sequencing). This will rule out misidentification of the putative pathogen in cases where near-patient and/or laboratory molecular tests to detect  N. meningitidis  prove to be negative.   ii) to increase the number of ctrA, porA and siaD sequences in the database. This will allow more detailed sequence analysis to be undertaken, and the design of primer sets to be refined further, especially for genotyping purposes.       

     Only the optimised  N. meningitidis  ctrA and porA LAMP assays will be used for subsequent near-patient testing. 
     Phase 2—Transfer of (ctrA and porA) Tests to Near-Patient Setting 
     Protocol Development: 
     Some additional method development is expected, both to deliver a usable near-patient testing protocol, and for the comparative laboratory testing protocols. In particular, the issues surrounding specimen collection and processing will be addressed at this stage, and detailed ‘standard operating procedures’ will be written. All specimens will be subjected to culture through the routine bacteriology service, and specimens will be processed in parallel using the previously developed PCR assay and the optimised near-patient method in a laboratory setting, for comparison. 
     Training: 
     As a central objective of the proposed work is to develop a test which can be used by non-laboratory staff, appropriate training, supervision and mentoring will be provided for the non-technical staff (research nurses) who will conduct the test in a near-patient setting. The high sensitivity of molecular tests makes them susceptible to contamination by amplified test products, which can lead to false-positive results. An important part of the training will be to ensure that the staff involved understand the issues surrounding contamination, and can avoid contamination of the near-patient testing area. The final assay will incorporate negative control reactions at all stages so that contamination problems can be quickly identified and addressed. 
     Pre-Clinical Validation: 
     Pre-clinical validation of the optimised test will be essential to assess the performance of assay in a near-patient setting. This phase will therefore conclude with blinded and randomized processing of a number of spiked and control specimens, to confirm that the new protocols can be used as anticipated. 
     Phase 3—Clinical validation 
     Study Design: Modified Case-Control. 
     Patient Groups 
     Group 1: All children with suspected meningococcal disease (MD) are entered into a ‘clinical care pathway’ and have a standardised set of investigations (to make diagnosis, assessment of severity and initial treatment) performed. In the recently completed one year study in the inventors&#39; unit, 104 suspected MD children were recruited in 12 months and over 33% had proven MD (clinical picture PLUS blood culture +ve or +ve meningococcal PCR at Manchester Reference Laboratory). The inventors will perform a case control study over at least a 2½ year period. The new test (measured from a combined nasal and throat swab, and blood) would be applied to all children with suspected MD entering the MD care pathway (estimated N=250 children) over this period (giving about 80 definite cases). This group of children is already ‘filtered as possible cases of MD’. The inventors want to be sure that the newly developed test has a high sensitivity. If the true sensitivity were 90% then a study of 80 affected children would give an estimate of the sensitivity with 95% exact confidence intervals of width no wider than 81% to 95%. Children entered into this group would include those in whom the A&amp;E doctor considered might possibly have MD (fever, petechial rash or signs of meningism and those with signs of possible septicaemia—eg. features of circulatory failure). These children routinely have a ‘meningococcal pack’ performed (blood cultures, serology, PCR for reference laboratory, blood count and ESR, CRP) and a nasal and pharyngeal swab taken for PCR and culture. In this study an additional combined nasal and throat swab will be taken from every child entered into this MD care pathway. 
     Group 2: The inventors want their newly developed test (assessed on a combined nasal and throat swab, and blood where possible) to have a very high specificity/NPV. If the true specificity was 98% then a study of 750 unaffected children would give an estimate of the specificity with 95% exact confidence intervals of width no wider than 97% to 99%. They plan to study  750  children attending the A&amp;E department with non-specific febrile or upper respiratory tract illnesses who are not being entered into the meningococcal care pathway. 
     Included in this group will be children with; 
     i] simple febrile illnesses with features of a head cold (excluding children with classical respiratory infections eg ‘croup’)
 
ii] non-specific fevers including those with leg pains, cold hands and feet but who are not considered to be ‘ill’ to enter into the MD care pathway which could include those with early features of sepsis. Such patients were described recently as risk factors for early MD (Reference 1) but the frequency of these symptoms in the non-meningitis population is not known. A combined throat and nasal swab for the new MD test will be taken from these children by the researchers, along with a blood sample, where this is possible. As most of these children will likely be sent home from A&amp;E a follow-up telephone call will be made 24, 48 and 72 hours after recruitment to determine the natural resolution (or not) of the illness.
 
     In conclusion design and testing of new LAMP primer sets has been developed and the results are shown in detail in Table 1. LAMP reactions will be optimized together with development of rapid extraction protocols for clinical specimens (nasal and pharyngeal swabs). 
     Comparison of LAMP and PCR assays with respect to specificity, analytical/clinical sensitivity, time-to-result, and practicality for near-patient use, using both standard and rapid extraction protocols will be undertaken to demonstrate rapid and robust laboratory validated assays which can detect the target genes with high specificity and known analytical sensitivity. 
     This invention will provide rapid laboratory assays for  N. meningitidis  detection and genotyping, and rapid diagnostic tests for detection of  N. meningitidis  in non-invasive specimens, validated in both laboratory and clinical settings, which will be effective enough to be widely adopted in near-patient settings. 
     A LAMP assay to detect the lytA gene (encoding the protein autolysin) from  Streptococcus pneumoniae , has been described previously (reference 16). This laboratory assay was shown to detect  S. pneumoniae  DNA with high specificity, and a sensitivity 10 3  times higher than conventional single-round PCR. As a secondary objective, the inventors propose to validate this published assay in the laboratory alongside the new test during this study, for testing of ctrA and porA negative specimens. This will also enable them to collect preliminary data on whether molecular detection of  S. pneumoniae  in nasal or throat swab specimens might correlate with diagnosis of pneumococcal meningitis or septicaemia in the study group. 
     Results 
     LAMP Primer Design 
     Oligonucleotide primers specific for  N. meningitidis  ctrA gene were designed corresponding to recognised conserved genomic regions (Positions in ctrA gene AF520902.1) using online LAMP primer design software Primer Explorer version 3.0 available at http://loopamp.eiken.co.jp/e/lamp/primer.html (NB. LAMP &amp; LOOP primer set ID: 1 was designed by one of the inventors without aid of software). A LAMP primer set consisted of one pair of forward (FIP) and reverse (BIP) inner primers, forward (F3) and reverse (B3) outer primers. FIP, BIP, F3 &amp; B3 primers are essential for amplification to proceed. The addition of loop forward (LF) and/or loop back (LB) primers significantly accelerates amplification reducing overall detection times by 50% (Nagamine, et al, 2002) and this was confirmed by data generated in the inventors&#39; laboratory. With certain LAMP primer sets it was possible to design only Loop back (LB) primers (eg. LAMP6, LAMP4) and for others no forward or back Loop primers could be designed. See Table 1 for list of primer sets. 
     The primers are designed to promote the formation of ‘hairpin-loop’ structures during the initial stages of the reaction, allowing high levels of self-primed DNA synthesis to occur from these structures as the self sustaining reaction proceeds (Notomi, et al, 2000). A by-product of LAMP reactions is magnesium pyrophosphate which can be measured by turbidity/fluorescence endpoint or in Real Time (Tomita, et al, 2008). Animation of the reaction (minus loop primers) can be seen at http://loopamp.eiken.co.jp/e/lamp/anim.html and the loop principle is outlined by Nagamine, et al, 2002 and at http://loopamp.eiken.co.jp/e/lamp/loop.html. 
       Neisseria Meningococcus  ctrA LAMP Primer Sets 
     All primer sets designed using LAMP software July 2007, except ID: 1 designed March 2006). Core sequences shown in bold. 
     Primers: FIP=forward inner; BIP=backward inner; F3=forward outer; B3=backward outer; LF=loop forward; LB=loop backward.
 
Positions in ctrA gene AF520902.1
 
                     TABLE 1                   ctrA LAMP primer sets and Sequence ID numbers.                         ctrA   PRIMER   SEQUENCE 5′-3′       LAMP SET   SEQ ID               SET 1   ID1 FIP   CGTCTATGGGTGCGGTGGGGAGACGATCTTGCAAACCGCCCATAC           ID2 BIP   GTAACCACATCACCGCGACGCAGCATGTGCAGCTGACACGTGGCAATG           ID3 F3   CCACGCGCATCAGAACGG           ID4 B3   CGGCAAATGTGCAGGATACGA           ID5 LF1   GCTTATCGCTTTCTGAAGC           ID6 LB1   GCAACTAAATCTTCCAAGGC               SET 2   ID7 FIP   ATCACCGCGACGCAGCAAAATAAGTACGAACTGTTGCCTTGG           ID8 BIP   ACCTTTACGTCTATGGGTGCGGAAGCCTCTYGCTGAAAAACC           ID9 F3   GCTGACACGTGGCAATGT           ID10 B3   CCAATGGCTTCAGAAAGCGA               SET 3   ID11 FIP   CAAACACACCACGCGCATCAGATCTGAAGCCATTGGCCGTA           ID12 BIP   TGTTCCGCTATACGCCATTGGTACTGCCATAACCTTGAGCAA           ID13 F3   AGCYAGAGGCTTATCGCTT           ID14 B3   ATACCGTTGGAATCTCTGCC           ID15 LF1   CGATCTTGCAAACCGCCCA           ID16 LB1 &amp; LB3   GCAGAACGTCAGGATAAATGGA           ID17 LF3   CGATCTTGCAAACCGCCC               SET 4   ID18 FIP   CAAACCGCCCATACGGCCAAATCGGTTTTTCAGCYAGAGG           ID19 BIP   AAGATCGCCGTTCTGATGCGCCGTTCTGCCGGCAATTCC           ID20 F3   CGGTGGGGAGAACACAAG           ID21 B3   ACTGCCATAACCTTGAGCAA           ID22 LB1   GTGGTGTGTTTGTGTTCCGCTAT           ID23 LB2   GTGGTGTGTTTGTGTTCCGCTATA               SET 5   ID24 FIP   CACCACGCGCATCAGAACGGCAGCYAGAGGCTTATCGC           ID25 BIP   TGTTCCGCTATACGCCATTGGTTGCCTCACTGCCATAACCT           ID26 F3   CGGTGGGGAGAACACAAG           ID27 B3   GCGCATCAGCCATATTCACA           ID28 LF1 &amp; LF3   CGGCCAATGGCTTCAGAAA           ID29 LB1   GGAATTGCCGGCAGAACGTC           ID30 LB3   GAATTGCCGGCAGAACGTC               SET 6   ID31 FIP   TCCCCACCGCACCCATAGACCGGTGATGTGGTTACCATGA           ID32 BIP   ATCGGTTTTTCAGCYAGAGGCTTTGCAAACCGCCCATACG           ID33 F3   AGTTGCAAATCCGCGACAA           ID34 B3   CGCATCAGAACGGCGATC           ID35 LB1   ATCGCTTTCTGAAGCCATTGG           ID36 LB2   TCGCTTTCTGAAGCCATTGG               SET 7   ID37 FIP   GCGAATGCGCATCAGCCATATTTGCTCAAGGTTATGGCAGTG           ID38 BIP   TTGTATGTGTCGAATGCGCCGTCGGCGAGAACACAAACGA           ID39 F3   GAATTGCCGGCAGAACGT           ID40 B3   ATACTGTTCGCGCCACTG           ID41 LF1 &amp; LF2   CACGATATACCGTTGGAATCTCTG           ID42 LB1   TGGCTGAAGTGCAGAAATTCTT           ID43 LF6   ACACGATATACCGTTGGAATCTCT           ID44 LB2 &amp; LB6   TGGCTGAAGTGCAGAAATTCTTG               SET 8   ID45 FIP   CCATCACTTGTGGCTGATTGGCGGTCGGTAAAACGCCTGG           ID46 BIP   GGCGAATGTGTCGGTGATTCGTGCATCCAACACACGCTCA           ID47 F3   TGCCGTTTGTTGGCGATA           ID48 B3   CACATTTGCCGTTGAACCAC               SET 9   ID49 FIP   GGCGTTTTACCGACCACCGAGGCACGTGGTACGGTTTC           ID50 BIP   AGGCCGCCTGAAAAAAATGGCCGACACATTCGCCGCATTA           ID51 F3   AGTTGCCAGAGCAGTTGG           ID52 B3   CGCACACTATTCCCAGCAC               SET 10   ID53 FIP   CACCACGCGCATCAGAACGGCAGCYAGAGGCTTATCGC           ID54 BIP   TGTTCCGCTATACGCCATTGGTTGCCTCACTGCCATAACCT           ID55 F3   CGGTGGGGAGAACACAAG           ID56 B3   GCGCATCAGCCATATTCACA           ID57 LF1   CGGCCAATGGCTTCAGAAA           ID58 LB1   GGAATTGCCGGCAGAACGTC               SET 11   ID59 FIP   GGCCATTTTTTTCAGGCGGCCTTGGCGATATTTCGGTGGTC           ID60 BIP   CAAGTGATGGTGCGTTTGGTGCAGCGGCATACGCACACTA           ID61 F3   ACGTGGTACGGTTTCTGTG           ID62 B3   CCACCGCATCCAACACAC               SET 12   ID63 FIP   CAACACACGCTCACCGGCTGGGCGAATGTGTCGGTGATT           ID64 BIP   GCGGTAGGTGGTTCAACGGCACTACATTGCCACGTGTCAG           ID65 F3   GGTGCGTTTGGTGCAGAA           ID66 B3   TTCCAAGGCAACAGTTCGT           ID67 LF1   CGTGCTGGGAATAGTGTGCGT           ID68 LB1 &amp; LB2   ATGTGCAGGATACGAATGTGC           ID69 LF2   GGSAATAGTGTGCGTATGCCG               Degenerate bases key(Y = C/T) (S = G/C)            
ctrA LAMP Optimisation
 
     The optimal operating temperature for each designed ctrA LAMP &amp; LOOP set (60 to 65° C. inclusive) was determined by testing against  N. meningitidis  serogroup A strain NCTC10025 (NmA NCTC 10025) &amp;  N. meningitidis  serogroup B clinical isolate 57/07 (NmB 57/07) QIAGEN total DNA extract ten fold dilutions (NB. LAMP sets 2, 8, 9 &amp;  11  excluded due to inability to design corresponding Loop primers additionally LAMP  4  was not assessed). See Table 2 for ranking. 
     LAMP&amp;LOOP primer sets were ranked based upon the following criteria; 
     i] Visual Sensitivity—presence of visible colour change and turbidity indicating positive reaction ie. The lowest Cut off point for NmB 57/07 &amp; NmA NCTC 10025 detectable by eye.
 
ii]. Speed of LAMP detection by Real Time analysis carried out on Applied Biosystems Real Time PCR instrument ABI7000 (ie Quickest ctrA LAMP for initial detection and time to reach fluorescent plateau/maximum—occurs—10 mins after first fluorescent signal is generated see  FIG. 1 )
 
iii]. ABI7000 Sensitivity (ie lowest cut off point as determined by Real Time LAMP)
 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                   N. meningitidis  ctrA LAMP &amp; LOOP primer set ranking (best performing No. 1 etc) with optimal 
               
               
                 operating temperature, cut off point (ctrA copies detected per reaction) &amp; time taken in minutes 
               
               
                 to reach maximum fluorescence/Turbidity for NmA NCTC10025 &amp; NmB 57/07 dilutions. Final Reaction 
               
               
                 volume = 25 μl (Specimen addition = 2.5 μl/LAMP Mastermix Vol. = 22.5 μl) 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 ctrA COPY NO. CUT OFF PER 
                 TIME (MINS) TO REACH 
               
               
                   
                 LAMP &amp; 
                   
                 25 μl REACTION 
                 MAX. FLUORO. 
               
            
           
           
               
               
               
               
               
               
               
            
               
                 RANK 
                 LOOP SET 
                 OPTIMAL TEMP. 
                 NmA 
                 NmB 
                 NmA 
                 NmB 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 1 
                 L3L1 
                 63° C. 
                 96.6 
                 118 
                 50 mins 
                 40 mins 
               
               
                 2 
                 L3L3 
                 61° C. 
                 96.6 
                 118 
                 50 mins 
                 49 mins 
               
               
                 3 
                 L5L1 
                 60° C.-61° C. 
                 96.6 
                 118 
                 53 mins 
                 60 mins 
               
               
                 4 
                 L13L1 
                 61° C. 
                 1.1 × 10 3   
                 1.1 × 10 3   
                 47 mins 
                 41 mins 
               
               
                 5 
                 L5L3 
                 62° C. 
                 96.6 
                 1.1 × 10 3   
                 40 mins 
                 49 mins 
               
               
                 6 
                 L12L2 
                 64° C. 
                 1.3 × 10 3   
                 1.1 × 10 3   
                 60 mins 
                 60 mins 
               
               
                 7 
                 L1L1 
                 63° C. 
                 1.6 × 10 4   
                 1.1 × 10 3   
                 55 mins 
                 57 mins 
               
               
                 8 
                 L12L1 
                 62° C. 
                 1.6 × 10 4   
                 1.6 × 10 4   
                 51 mins 
                 51 mins 
               
               
                 9 
                 L7L6 
                 60° C. 
                 1.6 × 10 4   
                 1.6 × 10 4   
                 52 mins 
                 50 mins 
               
               
                 10 
                 L7L1 
                 61° C. 
                 1.6 × 10 4   
                 1.6 × 10 4   
                 60 mins 
                 57 mins 
               
               
                 11 
                 L7L2 
                 60° C. 
                 1.3 × 10 3   
                 1.6 × 10 4   
                 60 mins 
                 55 mins 
               
               
                 12 
                 L6 (no loop) 
                 65° C. 
                 2.1 × 10 5   
                 1.7 × 10 5   
                 60 mins 
                 60 mins 
               
               
                   
               
            
           
         
       
     
     Based upon sensitivity ctrA LAMP3LOOP1 (L3L1), LAMP3LOOP3 (L3L1) &amp; LAMP5LOOP1 (L5L1) had same cut off points. Repeat investigations with L3L1, L3L3 &amp; L5L1 confirmed findings above. 
     The three best performing ctrA sets L3L1, L3L3 &amp; L5L1 were chosen for further evaluation using  N. meningitidis  57/07 spiked blood specimens. Investigations were carried out to determine if increasing overall specimen addition volume from 2.5 μl to 5 μl, 10 μl and 12 μl and incorporation of a prior preheat denaturation stage of 95° C. for 5 mins for specimens followed by immediate cooling on ice would improve overall sensitivity (protocol for prior heat denaturation published by Kamachi, et al, 2006 with impressive results). Results indicated that L3L1 preheat 95° C./5 mins in combination with a 5 μl specimen addition provided greatest sensitivity and reaction speed capable of detecting 28 ctrA gene copies per reaction in less than 40 minutes. See Table 3. L3L1 with prior specimen heat denaturation plus 5 μl specimen addition was chosen for clinical validation. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Effect of varying specimen addition volume and heat denaturation 95° C./5 mins of NmB 57/07 spiked blood 
               
               
                 specimens on analytical sensitivity of L3L1, L3L3 &amp; L5L1 and time in minutes required to reach maximum fluorescence. 
               
            
           
           
               
               
            
               
                   
                 Specimen Addition Volume 
               
            
           
           
               
               
               
               
               
            
               
                   
                 2.5 μl 
                 5 μl 
                 10 μl 
                 12 μl 
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                 Preheat 
                   
                 Preheat 
                   
                 Preheat 
                   
                 Preheat 
                   
               
               
                   
                 95° C./5 mins 
                 No Heat 
                 95° C./5 mins 
                 No Heat 
                 95° C./5 mins 
                 No Heat 
                 95° C./5 mins 
                 No Heat 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                 L3L1 
                 175 
                 1.7 × 10 3   
                 28 
                 350 
                 700 
                 6.8 × 10 3   
                 8.2 × 10 3   
                 8.2 × 10 3   
               
               
                   
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
               
               
                   
                 (32 mins) 
                 (38 mins) 
                 (38 mins) 
                 (47 mins) 
                 (50 mins) 
                 (44 mins) 
                 (30 mins) 
                 (41 mins) 
               
               
                 L3L3 
                 175 
                 175 
                 28 
                 3.4 × 10 3   
                  56 
                 700 
                 67 
                 67 
               
               
                   
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
               
               
                   
                 (35 mins) 
                 (36 mins) 
                 (45 mins) 
                 (52 mins) 
                 (34 mins) 
                 (52 mins) 
                 (34 mins) 
                 (49 mins) 
               
               
                 L5L1 
                 175 
                 1.7 × 10 3   
                 350  
                 3.4 × 10 3   
                 700 
                 5.2 × 10 4   
                 8.2 × 10 3   
                 8.2 × 10 3   
               
               
                   
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
                 ctrA copies 
               
               
                   
                 (35 mins) 
                 (45 mins) 
                 (38 mins) 
                 (47 mins) 
                 (51 mins) 
                 (34 mins) 
                 (35 mins) 
                 (41 mins) 
               
               
                   
               
            
           
         
       
     
     Specificity 
     Total nucleic acid extractions from a total of 70 bacterial clinical and reference strains from 39 different bacterial species and 1 fungal reference strain were used in the present study to determine LAMP assay specificity. All designed ctrA LAMP &amp; LOOP primers specifically amplified DNA from all  N. meningitidis  NCTC type strains and from 10 clinical isolates of  N. meningitidis  serogroup B. There was no cross reactivity with other Neisseria species (n=6) tested or with 54 different bacterial &amp; fungal targets outlined in Table 4. ctrA LAMP &amp; LOOP primers were 100% specific for capsular  N. meningitidis  strains tested. See  FIG. 1  for example of specificity. 
     LAMP SETS 1, 2, 4, 7, 10 exhibited specificity for all NMG serotypes tested (A, B, C, Y, W135). SETS 8, 9, 11 will not detect NmA being specific for B, C, Y, W135 only. SETs 3, 5, 6, 10 detect all serotypes tested with wobble. SET 3 is non-A specific with C in wobble position or A specific with T in wobble position. Set 5 is non-A specific with C in wobble position, A specific and 29E with T in wobble position. Set 12 exhibits specificity for types B, C, Y, W135 with either loop primer set but detects A only using LB1/LF2 loop primers. 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 List of bacterial and fungal species tested to determine  
               
               
                 specificity of LAMP &amp; LOOP primer sets. 
               
            
           
           
               
               
               
            
               
                 SPECIES 
                 STRAIN 
                 SEROGROUP 
               
               
                   
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 10025 
                 A 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 10791 
                 Y 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 11203 
                 W135 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 8554 
                 C 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 10792 
                 Z 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 10790 
                 X 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 11202 
                 29E 
               
               
                 
                   Neisseria meningitidis 
                 
                 NCTC 10026,  
                 B 
               
               
                   
                 531/07, 44/06, 
                   
               
               
                   
                 217/06, 1386/06,  
                   
               
               
                   
                 839/06, 368/05,  
                   
               
               
                   
                 338/05, 57/07,  
                   
               
               
                   
                 1069/07, 304/06 
                   
               
               
                 
                   Neisseria gonorrhoeae 
                 
                 ATCC 49226 
                   
               
               
                 
                   Neisseria sicca 
                 
                 920/06 
                   
               
               
                 
                   Neisseria. flavescens 
                 
                 NCTC 3191 
                   
               
               
                 
                   Neisseria lactamica 
                 
                 NCTC 10616 
                   
               
               
                 
                   Neisseria cinerea 
                 
                 NCTC 10294 
                   
               
               
                 
                   Neisseria polysaccharea 
                 
                 NCTC 1858 
                   
               
               
                 
                   Haemophilus influenzae 
                 
                 NCTC 4560, 016/07 
                 B 
               
               
                 
                   Klebsiella pneumoniae 
                 
                 NCTC 10896, 45/07 
                   
               
               
                 
                   Enterococcus faecalis 
                 
                 009/07 
                   
               
               
                 
                   Enterobacter aerogenes 
                 
                 NCTC 10006,  
                   
               
               
                   
                 001/07 
                   
               
               
                 
                   Enterobacter cloacae 
                 
                 NCTC 9394 
                   
               
               
                 
                   Staphylococcus aureus 
                 
                 ATCC 25923,  
                   
               
               
                   
                 ATCC 29213,  
                   
               
               
                   
                 NCTC 10442,  
                   
               
               
                   
                 09/07, M04/0071, 
                   
               
               
                   
                 HT2000/0132 
                   
               
               
                 
                   Staphylococcus lugdunensis 
                 
                 RVH Isolate 
                   
               
               
                 
                   Staphylococcus capitis 
                 
                 RVH Isolate 
                   
               
               
                 
                   Staphylococcus sciuri 
                 
                 ATCC 29061 
                   
               
               
                 
                   Streptococcus pneumoniae 
                 
                 NCTC 7465,  
                   
               
               
                   
                 NCTC 7978,  
                   
               
               
                   
                 RVHType 2,  
                   
               
               
                   
                 59/07 
                   
               
               
                 
                   Streptococcus parasanquis 
                 
                 74/07 
                   
               
               
                 
                   Streptococcus intermedius 
                 
                 305/07 
                   
               
               
                 
                   Micrococcus luteus 
                 
                 290/07 
                   
               
               
                 
                   Serratia marcescens 
                 
                 NCTC 10211,  
                   
               
               
                   
                 287/07 
                   
               
               
                 
                   Acinetobacter baumanii 
                 
                 36/07 
                   
               
               
                 
                   Moraxella catarrhalis 
                 
                 RVH01, RVH09 
                   
               
               
                 
                   Escheria coli 
                 
                 NCTC 9001,  
                   
               
               
                   
                 ATCC 25922 
                   
               
               
                 
                   Pseudomonas aeroginosa 
                 
                 46/07 
                   
               
               
                 
                   Stenotrophomonas maltophilia 
                 
                 ATCC 17666 
                   
               
               
                 
                   Peptostreptococcus spp. 
                 
                 6004-4 
                   
               
               
                 
                   Bacteriodes fragilis 
                 
                 CAH 6046-4 
                   
               
               
                 
                   Clostridium difficile 
                 
                 CAH 72 
                   
               
               
                 
                   Sphingobacterium spiritivorum 
                 
                 ATCC 33861 
                   
               
               
                 
                   Sphingobacterium thalpophilum 
                 
                 1192/07 
                   
               
               
                 
                   Acinetobacter zwoffii 
                 
                 98/07 
                   
               
               
                 
                   Klebsiella oxytoca ESBL+ 
                 
                 135/07 
                   
               
               
                 
                   Burkholderia multivorans 
                 
                 BCH Isolate 
                   
               
               
                 
                   Proteus vulgaris 
                 
                 564/07 
                   
               
               
                 
                   Bordetella parapertussis 
                 
                 BCH Isolate 
                   
               
               
                 
                   Coxiella. burnetii 
                 
                 9 Mile Strain 
                   
               
               
                 
                   Citrobacter freundii 
                 
                 NCTC 9750 
                   
               
               
                 
                   Aeromonas hydrophilia 
                 
                 659 
                   
               
               
                 
                   Candida albicans 
                 
                 ATCC 10028 
               
               
                   
               
            
           
         
       
     
     Clinical Validation 
     A breakdown of L3L1 Clinical Validation results to date are outlined in Tables 5 &amp; 6 below. All specimens underwent total nucleic acid extraction using commercially available manual Qiagen QIAamp® kit. 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Using ctrA Real Time Taqman PCR Assay (Corless et al, 2001)  
               
               
                 as Gold Standard for all Specimen Types Tested 
               
            
           
           
               
               
               
            
               
                   
                   
                 GOLD STANDARD 
               
            
           
           
               
               
               
               
            
               
                   
                   
                 POSITIVE 
                 NEGATIVE 
               
               
                   
               
               
                 TEST 
                 POSITIVE 
                 TP = 24 
                 FP = 3 
               
               
                   
                 NEGATIVE 
                 FN = 0 
                 TN = 233 
               
               
                   
               
            
           
         
       
     
     Lamp Sensitivity Versus Taqman 
       Sensitivity= tp /( tp+fn )24/(24+3)×100=88.9%
 
     In reality 2 LAMP False Positives are true positives. These were not identified by Gold Standard Taqman PCR but had been found to be positive by Manchester Reference Lab. PCR (MPCR). Considering this sensitivity=96%. One specimen was Taqman negative but repeatably LAMP positive. It is possible that this individual was harboring a capsular meningococcus (ie. Carrier state) or had low grade infection. 
     Lamp Specificity 
       Specificity= tn /( fp+tn )233/(3+233)×100=98.7%
 
     (Again two False positives are in reality true positives taking this into consideration Specificity=100%) 
                     TABLE 6                  Specimen Type Breakdown % LAMP Positive                             NO.    NO. LAMP        SPECIMEN TYPE   TESTED   POSITIVES (%)                                     WHOLE BLOOD (B)   73   7    (9.6%)       THROAT SWAB (TS)   76   8    (10.5%)       EDTA BLOOD (EDTA)   53   3    (5.7%)       SWABS (SW)   13   2    (15.4%)       CEREBROSPINAL FLUID (CSF)   9   0    (0%)       SERA (S)   19   4    (21.1%)       FAECES SOLID (FS)   2   1    (50%)       FAECES (F)   1   0    (0%)       FAECES SEMI SOLID (FSS)   1   0    (0%)       NASAL SECRETIONS (NASE)   6   0    (0%)       SECRETIONS (SEC)   3   1    (33.3%)       TRACHEA SECRETIONS (TRSE)   1   1    (100%)       VIRAL SWAB (VIS)   1   0    (0%)       SPUTUM   1   0    (0%)       TOTALS   259   27    (10.4%)                    
Mean time (mins) to reach maximum Fluorescent intensity=28.6 mins
 
Range of detection=6.6×10 6 -4×10 3  ctrA copies per ml (3.3×10 4 -20 ctrA copies per reaction)
 
     Improved Accuracy of Diagnosis by LAMP on Upper Airway Secretions 
     Using a Likelihood Ratio analysis, based on the prevalence of true meningococcal disease in children admitted to the meningococcal care pathway in the Children&#39;s Hospital Belfast, combined with a LAMP sensitivity of 92% and specificity of 97% (allowing for a carriage rate of 2% in this age range) the Odds Ratio changes from 1:3 by clinical diagnosis to 10:1 by a LAMP diagnosis. This increased utility underlies the value of undertaking a LAMP test on upper respiratory secretions i.e. throat and nasal swabs. 
     Accordingly the present invention provides a series of near bedside real time LAMP assays for  Neisseria meningitidis  with varying specificities based on the LAMP sets and Sequence IDs set out in Table 1 and detailed in the following Sequence Listing prepared according to Patentin 3.5. 
     The assays of the invention can be used for early detection of N meningitides in samples which as easy to obtain and allow treatment of the individual to be tailored accordingly. 
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