A protocol for a systematic review of the diagnostic accuracy of Loop-mediated-isothermal AMPlification (LAMP) in diagnosis of invasive meningococcal disease in children

Invasive meningococcal disease in older adults in North America and Europe: is this the time for action? A review of the literature

BACKGROUND

Neisseria meningitidis is an encapsulated Gram-negative diplococcus that asymptomatically colonises the upper respiratory tract in up to 25% of the population (mainly adolescents and young adults). Invasive meningococcal disease (IMD) caused by Neisseria meningitidis imposes a substantial public health burden,. The case fatality rate (CFR) of IMD remains high. IMD epidemiology varies markedly by region and over time, and there appears to be a shift in the epidemiology towards older adults. The objective of our review was to assess the published data on the epidemiology of IMD in older adults (those aged ≥ 55 years)in North America and Europe. Such information would assist decision-makers at national and international levels in developing future public health programmes for managing IMD.

METHODS

A comprehensive literature review was undertaken on 11 August 2020 across three databases: EMBASE, Medline and BIOSIS. Papers were included if they met the following criteria: full paper written in the English language; included patients aged ≥ 56 years; were published between 1/1/2009 11/9/2020 and included patients with either suspected or confirmed IMD or infection with N. meningitidis in North America or Europe. Case studies/reports/series were eligible for inclusion if they included persons in the age range of interest. Animal studies and letters to editors were excluded. In addition, the websites of international and national organisations and societies were also checked for relevant information.

RESULTS

There were 5,364 citations identified in total, of which 76 publications were included in this review. We identified that older adults with IMD were mainly affected by serogroups W and Y, which are generally not the predominant strains in circulation in most countries. Older adults had the highest CFRs, probably linked to underlying comorbidities and more atypical presentations hindering appropriate timely management. In addition, there was some evidence of a shift in the incidence of IMD from younger to older adults.

CONCLUSIONS

The use of meningococcal vaccines that include coverage against serogroups W and Y in immunization programs for older adults needs to be evaluated to inform health authorities' decisions of the relative benefits of vaccination and the utility of expanding national immunization programmes to this age group.

Rapid diagnosis of seven high-risk human papillomavirus subtypes by a novel loop-mediated isothermal amplification method

Current human papillomavirus (HPV) detection methods require complex instruments, skilled staff and have a high cost. Therefore, novel testing approaches are needed which are easy to implement, highly sensitive, and low cost. Loop-mediated isothermal amplification (LAMP) is an isothermal amplification technique. In this study, according to the conditions in China, a novel LAMP method for detecting seven high-risk HPV subtypes (16, 18, 33, 39, 45, 52, and 58) was designed and evaluated. The DNA from plasmid and cervical specimens was extracted using Chelex 100 and measured by qPCR and LAMP assay. LAMP products were observed under ultraviolet light. HPV sequences were successfully amplified and a plateau time of 19-75 min was maintained. The concentration of positive reactions ranged between 20 copies/μL and 200000 copies/μL. Additionally, there was no cross-reactivity between HPV16, 18, 33, 39, 45, 52, 58, 31, 35, 45, 51, 56, 59, 66, or 68. For clinical samples, the LAMP assay had high sensitivity and specificity for HPV16, 18, 33, 39, 45, 52, and 58. However, 5% (72/1447) of the samples tested yielded false-positive results. In conclusion, the novel LAMP assay for HPV16, 18, 33, 39, 45, 52, and 58 has high sensitivity and specificity, a low cost, and is simple and rapid to perform. The LAMP assay can improve HPV detection in resource-limited settings, especially in primary care hospitals and rural areas.

Two target genes based multiple cross displacement amplification combined with a lateral flow biosensor for the detection of Mycobacterium tuberculosis complex

Background

Tuberculosis (TB) is a serious chronic infectious disease caused by Mycobacterium tuberculosis complex (MTBC). Hence, the development of a novel, simple, rapid and sensitive method to detect MTBC is of great significance for the prevention and treatment of TB.

Results

In this study, multiple cross displacement amplification (MCDA) combined with a nanoparticle-based lateral flow biosensor (LFB) was developed to simultaneously detect two target genes (IS6110 and mpb64) of MTBC (MCDA-LFB). One suite of specific MCDA primers designed for the IS6110 and mpb64 genes was validated using genomic DNA extracted from the reference strain H37Rv. The MCDA amplicons were analyzed using a real-time turbidimeter, colorimetric indicator (malachite green, MG) and LFBs. The optimal amplification temperature and time were confirmed, and the MCDA-LFB method established in the current report was evaluated by detecting various pathogens (i.e., reference strains, isolates and clinical sputum samples). The results showed that the two sets of MCDA primers targeting the IS6110 and mpb64 genes could effectively detect MTBC strains. The optimal reaction conditions for the MCDA assay were determined to be 67 °C for 35 min. The MCDA assay limit of detection (LoD) was 100 fg per reaction for pure genomic DNA. The specificity of the MCDA-LFB assay was 100%, and there were no cross-reactions for non-MTBC strains. For sputum samples and MTBC strain detection, the positive rate of MCDA-LFB for the detection of MTBC strains was consistent with seminested automatic real-time PCR (Xpert MTB/RIF) and higher than acid-fast staining (AFS) and culture assays when used for sputum samples. The MCDA-LFB assay was a rapid tool, and the whole procedure for MCDA-LFB, including DNA template preparation, MCDA reaction and amplification product analysis, was completed within 70 min.

Conclusion

The MCDA-LFB assay targeting the IS6110 and mpb64 genes is a simple, rapid, sensitive and reliable detection method, and it has potential significance for the prevention and treatment of TB.

The rapid and visual detection of methicillin-susceptible and methicillin-resistant Staphylococcus aureus using multiplex loop-mediated isothermal amplification linked to a nanoparticle-based lateral flow biosensor

Background

Staphylococcus aureus (S. aureus), including methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA), is an eminent human pathogen that can colonize the human host and cause severe life-threatening infections. The development of a reliable, simple and rapid assay for detecting S. aureus and identifying MRSA is important for diagnosis and follow-up treatment.

Methods

A novel molecular diagnosis technique, named multiplex loop-mediated isothermal amplification linked to a nanoparticle-based lateral flow biosensor (m-LAMP-LFB), was applied to detect all S. aureus species and identify MRSA. Two sets of primers were designed based on the femA gene (S. aureus-specific gene) and the mecA gene (encoding penicillin-binding protein 2a), and the multiple-LAMP products were analyzed using LFB. The m-LAMP-LFB amplification conditions, including the target DNA concentration, reaction temperature and time, were optimized. The sensitivity and specificity of the m-LAMP-LFB method were tested in the current study, and the multiple-LAMP-LFB technology was applied to detect the MSSA and MRSA strains from clinical samples.

Results

The S. aureus- and MRSA-specific primers based on the femA and mecA genes allowed the multiple-LAMP technology to detect S. aureus and MRSA, respectively. The multiple-LAMP conditions were optimized at 63 °C for 40 min. The full process, including genomic DNA template preparation, LAMP, and product identification, could be achieved in 80 min. The limit of detection (LoD) of the multiple-LAMP assay for femA and mecA detection was 100 fg of genomic DNA template per reaction. The specificity of m-LAMP-LFB detection was 100 %, and no cross-reactions to non-S. aureus strains were observed.

Conclusion

The multiple-LAMP-LFB technique developed in the current study is a reliable, simple, rapid, specific and sensitive method to identify MSSA and MRSA infections for appropriate antibiotic therapy.

Rapid identification and detection of Vibrio parahaemolyticus via different types of modus operandi with LAMP method in vivo

Purpose

Vibrio parahaemolyticus, an easy-ignored food-borne pathogen, can cause bacterial outbreaks and human disease during early-stage infection. In this study, we aimed to evaluate the detection efficiency of loop-mediated isothermal amplification (LAMP) as an emerging technique to directly detect V. parahaemolyticus infection in mammalian hosts and assess its potential in clinical applications.

Methods

A LAMP assay was used for rapid identification of V. parahaemolyticus in a variety of mouse models in which animals were infected via the digestive tract, wounds, or through general infection, and the results were compared with routine analytical methods.

Results

Our results confirmed that the LAMP assay was capable of detecting V. parahaemolyticus in different mouse organs independent of the source of bacteria, although its sensitivity depended on the route of infection and the organ affected. Foodborne-derived V. parahaemolyticus was the most sensitive route, with the small intestine being the most sensitive organ. The LAMP assay indicated that V. parahaemolyticus that spread through the blood stream had the most serious consequences during early-stage infection. Positive LAMP results were identified in all blood samples from i.v. injected mice. Furthermore, the LAMP method could directly detect trace quantities of V. parahaemolyticus in fresh peripheral blood while conventional methods failed to do so, thereby shortening the time-to-result from days to minutes.

Conclusions

In this study, we demonstrated that the LAMP assay was effective in speeding up the detection of V. parahaemolyticus. Instead of being a secondary method to assist in the clinic, the LAMP assay has potential for use as the primary technique for rapid detection of V. parahaemolyticus in the future.

<p>Establishment and Evaluation of a Novel Method Based on Loop-Mediated Isothermal Amplification for the Rapid Diagnosis of Thalassemia Genes</p>

Purpose

Currently, thalassemia is commonly detected using gap-polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) reverse dot blot, which have high requirements of space, instruments, and personnel. Therefore, it is necessary to develop a new method for thalassemia detection with high sensitivity, low cost, and simple and fast operation. In this study, we aimed to design and evaluate a new method for detecting three α-thalassemia genes including –Southeast Asian (SEA), -α3.7, and -α4.2 and five β-thalassemia genes including 654M, 41/42M, −28M, 17M, and 27/28M based on loop-mediated isothermal amplification (LAMP).

Methods

Primer sequences were designed using Primer Explorer V4 software. Blood samples (5 mL) were collected from all participants in EDTA. DNA was extracted using Chelex 100 and was subjected to LAMP. LAMP products were detected by fluorescence development in ultraviolet light.

Results

We found that LAMP assays for positive samples of thalassemia reached a plateau before 60 minutes, whereas the negative control samples entered the plateau after 70 minutes or showed no amplification. The concentration range of positive reactions was between 20–60 pg/μL and 20–60 ng/μL. Additionally, there were no cross-reactivities among 8 thalassemia subtypes. For clinical samples, the positive sample tube showed strong green fluorescence, whereas the negative tube showed light green fluorescence. According to these results, the LAMP method has high sensitivity for detecting thalassemia (252/254). However, 43 false-positive results were obtained in the LAMP test. The LAMP assay was also of low cost and with simple and fast operation.

Conclusion

The novel LAMP assay can be completed within 60 min using a heating block or a water bath, and the result can be read visually based on color change to detect thalassemia. The LAMP assay fulfills the requirements of field application and resource-limited areas, especially those with primary hospitals and rural areas.

A systematic review of the diagnostic accuracy of Loop-mediated-isothermal AMPlification (LAMP) in the diagnosis of invasive meningococcal disease in children

BACKGROUND

The early recognition of meningococcal disease in children is vital. During the prodrome however, meningococcal infection presents similarly to many self-limiting viral infections. This mandates a cautious approach with many children receiving unnecessary broad-spectrum parenteral antibiotics. Advances in nucleic acid amplification techniques mean that it is now possible to test for Neisseria meningitidis DNA using Loop-mediated-isothermal AMPlification (LAMP). This technique is quicker than traditional PCR techniques and can be performed using simple equipment.

METHODS

Prior to performing this systematic review, a protocol was developed adhering to PRISMA P standards and underwent full external peer review. This systematic review was registered with PROSPERO (CRD42017078026). The index test assessed was LAMP for Neisseria meningitidis and the reference standard was culture or qPCR of a sterile site detecting Neisseria meningitidis.

RESULTS

We identified 95 records in total: 94 records from the electronic databases and 1 additional study from the grey literature. After removal of duplicates, 36 studies were screened, and 31 studies excluded based on the title/abstract. Five full text studies underwent full text review and three studies, including 2243 tests on 1989 patients aged between 7 days and 18 years were included in the final systematic review. In all studies the LAMP assay and qPCR primers were directed against the ctrA region of the Neisseria meningitidis bacteria. The diagnostic accuracy of LAMP testing for invasive meningococcal disease was reported as high (sensitivity 0.84-1.0 and specificity 0.94-1.0) in all studies irrespective of the sample tested (CSF, Blood, Swab).

CONCLUSIONS

We included three studies with 2243 tests on 1989 patients using CSF, blood samples or naso/oropharyngeal swabs. The studies were all of a high quality and deemed at low risk of bias. Results show that LAMP testing on blood and CSF was highly accurate when compared to qPCR/culture. LAMP testing for Neisseria meningitidis is fast and highly accurate and therefore has the potential to be used to rapidly rule in/out meningococcal disease in children. Given the life-threatening nature of meningococcal infection further research is required to demonstrate the safety and efficacy of using LAMP testing for Neisseria meningitidis as a rule in/out test.

TRIAL REGISTRATION

This systematic review was registered prospectively with PROSPERO on the 29/11/2017 (CRD42017078026).