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A pangenome approach-based loop-mediated isothermal amplification assay for the specific and early detection of
Eduardo Juscamayta-López1,2, Faviola Valdivia3, María Pía Soto3
1Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú. jjuscamamayta@ins.gob.pe.
Insights
A new colorimetric assay accurately detects Bordetella pertussis, the bacteria causing whooping cough. This rapid, inexpensive test is ideal for early diagnosis and preventing pertussis spread, especially in resource-limited settings.
Area of Science:
- Microbiology
- Molecular Diagnostics
- Public Health
Background:
- Bordetella pertussis causes widespread pertussis (whooping cough), posing significant risks to infants.
- Timely and accessible diagnostic methods are crucial for managing pertussis and preventing transmission.
- Current diagnostic tools can be complex and costly, limiting their use in primary care.
Purpose of the Study:
- To develop and validate a novel colorimetric loop-mediated isothermal amplification (LAMP) assay for detecting B. pertussis.
- To utilize a new target, uvrD_2, informed by pangenome analysis for enhanced specificity.
- To assess the assay's diagnostic performance against a gold-standard multitarget quantitative polymerase chain reaction (qPCR).
Main Methods:
- Development of a colorimetric LAMP assay targeting the uvrD_2 gene of B. pertussis.
- Validation using a large cohort of 600 clinical nasopharyngeal swab specimens.
- Comparative analysis against a multitarget qPCR assay.
Main Results:
- The uvrD_2 LAMP assay demonstrated high diagnostic sensitivity (100.0%) and specificity (98.6%).
- Excellent agreement (99.7%) was observed between the LAMP assay and multitarget qPCR.
- The assay proved to be faster, simpler, and more cost-effective than traditional qPCR.
Conclusions:
- The novel colorimetric uvrD_2 LAMP assay offers a highly sensitive and specific method for B. pertussis detection.
- This assay provides comparable diagnostic accuracy to complex qPCR methods.
- Its ease of use and affordability make it suitable for timely pertussis diagnosis in primary healthcare and resource-limited settings, aiding disease control efforts.
Abstract:
Despite widespread vaccination, Bordetella pertussis continues to cause pertussis infections worldwide, leaving infants at the highest risk of severe illness and death, while people around them are likely the main sources of infection and rapidly spread the disease. Rapid and less complex molecular testing for the specific and timely diagnosis of pertussis remains a challenge that could help to prevent the disease from worsening and prevent its transmission. We aimed to develop and validate a colorimetric loop-mediated isothermal amplification (LAMP) assay using a new target uvrD_2 informed by the pangenome for the specific and early detection of B. pertussis. Compared to that of multitarget quantitative polymerase chain reaction (multitarget qPCR) using a large clinical DNA specimen (n = 600), the diagnostic sensitivity and specificity of the uvrD_2 LAMP assay were 100.0% and 98.6%, respectively, with a 99.7% degree of agreement between the two assays. The novel colorimetric uvrD_2 LAMP assay is highly sensitive and specific for detecting B. pertussis DNA in nasopharyngeal swabs and showed similar diagnostic accuracy to complex and high-cost multitarget qPCR, but it is faster, simpler, and inexpensive, which makes it very helpful for the reliable and timely diagnosis of pertussis in primary health care and resource-limited settings.
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