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Evaluation of nested PCR and loop mediated isothermal amplification assay (LAMP) targeting 47 ​kDa gene of Orientia tsutsugamushi for diagnosis of scrub typhus.
Indian J Med Microbiol. 2021 Oct-Dec; 39(4):475-478.IJ

Abstract

PURPOSE

Diagnostic testing, in particular early detection, is critical for scrub typhus, as most infected individuals have nonspecific symptoms that are easily confused with dengue and malaria. PCR and LAMP offer an alternative DNA amplification method for detection of Orientia tsutsugamushi. Detection of Orientia tsutsugamushi DNA by targeting the 47-kDa gene using nested PCR and LAMP for diagnosis of scrub typhus.

METHODS

A cross-sectional study in a tertiary care hospital in central India. The present study was done on a total of 274 patients with fever of five days or more and negative for other causes of fever viz. malaria, dengue and enteric fever. From each patient 5 ​ml of blood samples was collected in EDTA vial for molecular tests (PCR and LAMP) and in plain vial for serological tests (IgM IFA). The data was entered in Excel sheet and 2 ​× ​2 tables were created to find sensitivity, specificity, positive and negative likelihood ratios, disease prevalence, positive and negative predictive values and accuracy.

RESULTS

PCR showed a sensitivity of 29.73% while the sensitivity of LAMP was 16.22%. The specificity of nested PCR and LAMP was very high, 99.58% and 99.16% respectively. The diagnostic accuracy of nested PCR (90.15%) was found to be marginally better than LAMP (87.96%).

CONCLUSIONS

For the treatment of scrub typhus, a gene-based diagnostic test would enable earlier and more accurate detection of the causative agents of the disease than serology in admission samples of patients with acute febrile illness in endemic areas.

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Authors+Show Affiliations

Roy S
Dept. of Microbiology, Mahatma Gandhi Institute of Medical Science, Sewagram, Wardha, Maharashtra, 442102, India. Electronic address: dr.subhasish78@gmail.com.
Yadav S
Dept. of Microbiology, Mahatma Gandhi Institute of Medical Science, Sewagram, Wardha, Maharashtra, 442102, India. Electronic address: sneha.0211s@gmail.com.
Garg S
Dept. of Microbiology, Mahatma Gandhi Institute of Medical Science, Sewagram, Wardha, Maharashtra, 442102, India. Electronic address: shreyakgarg98@gmail.com.
Deshmukh PR
Department of Community Medicine, All India Institute of Medical Science (AIIMS), Nagpur, 441108, India. Electronic address: prdeshmukh@aiimsnagpur.edu.in.
Narang R
Dean, AIIMS Bibinagar, Hyderabad. Electronic address: rahuldevnarang@gmail.com.

MeSH

Cross-Sectional StudiesFeverHumansIndiaMolecular Diagnostic TechniquesNucleic Acid Amplification TechniquesOrientia tsutsugamushiPolymerase Chain ReactionScrub TyphusSensitivity and SpecificityTertiary Care Centers

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34215476

Citation

Roy, Subhasish, et al. "Evaluation of Nested PCR and Loop Mediated Isothermal Amplification Assay (LAMP) Targeting 47 ​kDa Gene of Orientia Tsutsugamushi for Diagnosis of Scrub Typhus." Indian Journal of Medical Microbiology, vol. 39, no. 4, 2021, pp. 475-478.
Roy S, Yadav S, Garg S, et al. Evaluation of nested PCR and loop mediated isothermal amplification assay (LAMP) targeting 47 ​kDa gene of Orientia tsutsugamushi for diagnosis of scrub typhus. Indian J Med Microbiol. 2021;39(4):475-478.
Roy, S., Yadav, S., Garg, S., Deshmukh, P. R., & Narang, R. (2021). Evaluation of nested PCR and loop mediated isothermal amplification assay (LAMP) targeting 47 ​kDa gene of Orientia tsutsugamushi for diagnosis of scrub typhus. Indian Journal of Medical Microbiology, 39(4), 475-478. https://doi.org/10.1016/j.ijmmb.2021.06.011
Roy S, et al. Evaluation of Nested PCR and Loop Mediated Isothermal Amplification Assay (LAMP) Targeting 47 ​kDa Gene of Orientia Tsutsugamushi for Diagnosis of Scrub Typhus. Indian J Med Microbiol. 2021 Oct-Dec;39(4):475-478. PubMed PMID: 34215476.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evaluation of nested PCR and loop mediated isothermal amplification assay (LAMP) targeting 47 ​kDa gene of Orientia tsutsugamushi for diagnosis of scrub typhus. AU - Roy,Subhasish, AU - Yadav,Sneha, AU - Garg,Shreyak, AU - Deshmukh,Pradeep R, AU - Narang,Rahul, Y1 - 2021/06/30/ PY - 2021/02/27/received PY - 2021/06/12/revised PY - 2021/06/18/accepted PY - 2021/7/4/pubmed PY - 2021/12/29/medline PY - 2021/7/3/entrez KW - Nested PCR KW - Orientia tsutsugamushi, LAMP KW - Scrub typhus SP - 475 EP - 478 JF - Indian journal of medical microbiology JO - Indian J Med Microbiol VL - 39 IS - 4 N2 - PURPOSE: Diagnostic testing, in particular early detection, is critical for scrub typhus, as most infected individuals have nonspecific symptoms that are easily confused with dengue and malaria. PCR and LAMP offer an alternative DNA amplification method for detection of Orientia tsutsugamushi. Detection of Orientia tsutsugamushi DNA by targeting the 47-kDa gene using nested PCR and LAMP for diagnosis of scrub typhus. METHODS: A cross-sectional study in a tertiary care hospital in central India. The present study was done on a total of 274 patients with fever of five days or more and negative for other causes of fever viz. malaria, dengue and enteric fever. From each patient 5 ​ml of blood samples was collected in EDTA vial for molecular tests (PCR and LAMP) and in plain vial for serological tests (IgM IFA). The data was entered in Excel sheet and 2 ​× ​2 tables were created to find sensitivity, specificity, positive and negative likelihood ratios, disease prevalence, positive and negative predictive values and accuracy. RESULTS: PCR showed a sensitivity of 29.73% while the sensitivity of LAMP was 16.22%. The specificity of nested PCR and LAMP was very high, 99.58% and 99.16% respectively. The diagnostic accuracy of nested PCR (90.15%) was found to be marginally better than LAMP (87.96%). CONCLUSIONS: For the treatment of scrub typhus, a gene-based diagnostic test would enable earlier and more accurate detection of the causative agents of the disease than serology in admission samples of patients with acute febrile illness in endemic areas. SN - 1998-3646 UR - https://www.unboundmedicine.com/medline/citation/34215476/Evaluation_of_nested_PCR_and_loop_mediated_isothermal_amplification_assay__LAMP__targeting_47_​kDa_gene_of_Orientia_tsutsugamushi_for_diagnosis_of_scrub_typhus_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0255-0857(21)04135-9 DB - PRIME DP - Unbound Medicine ER -