Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

Neshani, Alireza; Kakhki, Reza Kamali; Sankian, Mojtaba; Zare, Hosna; Chichaklu, Amin Hooshyar; Sayyadi, Mahsa; Ghazvini, Kiarash

doi:10.1186/s12879-018-3417-x

Cited by 16 publications

(9 citation statements)

References 35 publications

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“…In this case, acid-fast bacilli were found neither in the spinal bone biopsy nor in the BAL, but a bronchial biopsy revealed caseating granulomas, which is usually required to make a rapid diagnosis. Molecular techniques, such as PCR, have provided a new approach to the rapid diagnosis of TB (11). As it was reported in our patient who had psoas drainage abscess, PCR is positive for TB.…”

Section: Discussionsupporting

confidence: 71%

Disseminated Mycobacterium tuberculosis following renal transplant: A case report

Sadeghi–Haddad–Zavareh

Roushan

Afshar

et al. 2020

Pneumologia

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Miliary tuberculosis (TB) presents a major challenge following a renal transplant in humans. In the current report, we described a patient with disseminated TB following renal transplantation. The article presents the case of a 38-year-old man who presented an 8-month history of fever, chills, sweating, low-back pain and significant weight loss. Chest radiography and computed tomography (CT) scan showed miliary nodules distributed in the two lungs. The transbronchial lung biopsy revealed a granulomatous reaction with caseous necrosis. Magnetic resonance imaging (MRI) of the brain found multiple tuberculomas. Also, MRI of the lumbosacral was indicative of a psoas abscess. Therefore, miliary pulmonary, cerebral and spinal TB was confirmed. The patient was started on an anti-TB regimen and paravertebral aspiration was also done. The patient’s condition improved considerably. In conclusion, this case report can remind us of the importance of maintaining a high clinical suspicion and performing a thorough workup to establish a timely diagnosis and treatment of miliary TB.

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Section: Discussionsupporting

confidence: 71%

Disseminated Mycobacterium tuberculosis following renal transplant: A case report

Sadeghi–Haddad–Zavareh

Roushan

Afshar

et al. 2020

Pneumologia

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“…In this study, COVID-19 novel target was detected using the modified comparative genomic analysis (Kakhki et al, 2020;Kakhki et al, 2019;Neshani et al, 2018). The genome of Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1 (NC_045512) was considered as reference strain and compared with the other types of coronavirus isolates.…”

Section: Methodsmentioning

confidence: 99%

COVID-19 target: A specific target for novel coronavirus detection

Kakhki

Kakhki²,

Neshani

2020

Gene Reports

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An ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. To this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. The modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. We, for the first time, detected ORF8 gene as a potential target for the detection of the novel coronavirus. Unlike previous reported genes (RdRP, E and N genes), ORF8 is entirely specific to the novel coronavirus (COVID-19) and has no cross-reactivity with other kinds of coronavirus. Accordingly, ORF8 gene can be used as an additional confirmatory assay.

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“…One of the critical points for designing a NAAT is a completely specific DNA sequence for the desired micro-organism. The specific sequence should be present in all strains of such micro-organism but not found in any other micro-organism or has very low similarity 16 . In recent years, various PCR tests have been designed to detect S. epidermidis based on genes such as serp0107, gseA, Staphostatin A, and sesC [17][18][19][20] .…”

Section: Introductionmentioning

confidence: 99%

A New Specific DNA Target Sequence for Identification of Staphylococcus epidermidis using Modified Comparative Genomic Analysis

Khoshbakht¹,

Zare²,

Kakhki³

et al. 2022

AJMB

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Background: Staphylococcus epidermidis (S. epidermidis) is the most frequently isolated pathogen from prostheses infections in the body. Therefore, improving its diagnostic methods, including rapid Nucleic Acid Amplification Tests (NAAT), seems necessary. Since the first step in designing a NAAT is to find a specific sequence and all DNA targets that have been introduced so far are not completely specific, we introduced a new 100% specific DNA target sequence to identify S. epidermidis in this study. Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect S. epidermidis. A PCR method was designed for the evaluation of this target. To determine the detection limit and analytical specificity, pure genomic DNA of 18 bacteria include 12 standard strains (one S. epidermidis and 11 non-S. epidermidis) and six clinical isolates (five S. epidermidis and one non-S. epidermidis) were used. Results: The 400 bp sequence of S. epidermidis ATCC 14990 was identified as the most specific sequence (Se400), having a 100% sequence similarity to S. epidermidis genomes but not with other bacteria. The detection limit of Se400-PCR was 10 fg, equal to about 4 copies of S. epidermidis genomic DNA/μl. All pure DNA templates from S. epidermidis generated a detectable amplicon by 264 bp length, but the PCR test was negative for the non-S. epidermidis group. Conclusion: The Se400 sequence can be considered as a specific target for detecting S. epidermidis, based on our findings.

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Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

Cited by 16 publications

References 35 publications

Disseminated Mycobacterium tuberculosis following renal transplant: A case report

Disseminated Mycobacterium tuberculosis following renal transplant: A case report

COVID-19 target: A specific target for novel coronavirus detection

A New Specific DNA Target Sequence for Identification of Staphylococcus epidermidis using Modified Comparative Genomic Analysis

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