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Article ; Online: Clinical Evaluation of Commercial HARDSON COVID-19 Antigen Rapid Test Kit for Routine COVID-19 Diagnosis.

Kakhki, Reza Kamali / Neshani, Alireza / Kakhki, Mohammad Kamali / Zare, Hosna

Infectious diseases & clinical microbiology

2023 Volume 5, Issue 2, Page(s) 113–117

Abstract: Objective: This study aimed to evaluate the sensitivity, specificity, and accuracy of the commercial HARDSON COVID-19 Antigen Rapid Test Kit for diagnosing COVID-19 among the Iranian population by compared with the results of commercial RT-PCR.: ... ...

Abstract	Objective: This study aimed to evaluate the sensitivity, specificity, and accuracy of the commercial HARDSON COVID-19 Antigen Rapid Test Kit for diagnosing COVID-19 among the Iranian population by compared with the results of commercial RT-PCR. Materials and methods: Two nasopharyngeal swabs were collected from each patient. One swab was tested with HARDSON COVID-19 Antigen Rapid Test Kit, and the second swab was placed in 3 mL of a virus-transmitted inactivated media for RT-PCR testing. Then, the results of both tests were compared to investigate the diagnostic accuracy of the rapid antigen test. Results: A total of 275 suspected COVID-19 patients' samples were collected to investigate the diagnostic accuracy of HARDSON COVID-19 Antigen Rapid Test Kit. In this study, 162 positive and 113 negative samples were evaluated. As a result, the sensitivity, specificity, and accuracy of HARDSON COVID-19 Antigen Rapid Test Kit were 90%, 100%, and 94%, respectively. Conclusion: The diagnostic kit analyzed in this study indicated excellent specificity and a relatively good overall sensitivity for the diagnosis of COVID-19 when compared with the RT-PCR detection kit. Based on the result of this study, COVID-19 Antigen Rapid Test Kit indicated a good sensitivity (96%) in low cycle threshold (Ct) value, and it would be recommended to be integrated into routine diagnostic laboratories and used as an at-home rapid antigen test.
Language	English
Publishing date	2023-06-23
Publishing country	Turkey
Document type	Journal Article
ISSN	2667-646X
ISSN (online)	2667-646X
DOI	10.36519/idcm.2023.224
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: A New Specific DNA Target Sequence for Identification of

Khoshbakht, Reza / Zare, Hosna / Kamali Kakhki, Reza / Neshani, Alireza / Arfaatabar, Maryam

Avicenna journal of medical biotechnology

2022 Volume 14, Issue 3, Page(s) 216–222

Abstract: Background: Staphylococcus epidermidis (S. epidermidis): Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect : Results: The 400 : Conclusion: The Se400 sequence can be considered as a ... ...

Abstract	Background: Staphylococcus epidermidis (S. epidermidis) Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect Results: The 400 Conclusion: The Se400 sequence can be considered as a specific target for detecting
Language	English
Publishing date	2022-08-19
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2520683-7
ISSN	2008-4625 ; 2008-2835
ISSN (online)	2008-4625
ISSN	2008-2835
DOI	10.18502/ajmb.v14i3.9828
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Article: COVID-19 target: A specific target for novel coronavirus detection.

Kakhki, Reza Kamali / Kakhki, Mohammad Kamali / Neshani, Alireza

Gene reports

2020 Volume 20, Page(s) 100740

Abstract: 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 ... ...

Abstract	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.
Keywords	covid19
Language	English
Publishing date	2020-05-30
Publishing country	United States
Document type	Journal Article
ISSN	2452-0144
ISSN	2452-0144
DOI	10.1016/j.genrep.2020.100740
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Article ; Online: COVID-19 target

Kakhki, Reza Kamali / Kakhki, Mohammad Kamali / Neshani, Alireza

Gene Reports

A specific target for novel coronavirus detection

2020 Volume 20, Page(s) 100740

Keywords	covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ISSN	2452-0144
DOI	10.1016/j.genrep.2020.100740
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay.

Kamali Kakhki, Reza / Najafzadeh, Mohammad Javad / Kachuei, Reza / Ghazvini, Kiarash

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2020 Volume 39, Issue 8, Page(s) 1535–1542

Abstract: The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, ... ...

Abstract	The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.
MeSH term(s)	Aspergillus/genetics ; Aspergillus/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Bronchopneumonia/diagnosis ; Cryptococcus/genetics ; Cryptococcus/isolation & purification ; Humans ; Multiplex Polymerase Chain Reaction ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/isolation & purification ; Nocardia/genetics ; Nocardia/isolation & purification ; Sensitivity and Specificity ; Streptomyces/genetics ; Streptomyces/isolation & purification ; Tuberculosis, Pulmonary/diagnosis
Language	English
Publishing date	2020-04-06
Publishing country	Germany
Document type	Evaluation Study ; Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-020-03879-8
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Article: COVID-19 target: A specific target for novel coronavirus detection

Kakhki, Reza Kamali / Kakhki, Mohammad Kamali / Neshani, Alireza

Gene Rep.

Abstract	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.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #436638
Database	COVID19

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Article: Development of a Cost-Effective Line Probe Assay for Rapid Detection and Differentiation of

Kamali Kakhki, Reza / Aryan, Ehsan / Meshkat, Zahra / Sankian, Mojtaba

Reports of biochemistry & molecular biology

2020 Volume 8, Issue 4, Page(s) 383–393

Abstract: Background: The line probe assay (LPA) is one of the most accurate diagnostic tools for detection of different : Methods: One pair of biotinylated primers and 15 designed DNA oligonucleotide probes were used based on multiple aligned internal ... ...

Abstract	Background: The line probe assay (LPA) is one of the most accurate diagnostic tools for detection of different Methods: One pair of biotinylated primers and 15 designed DNA oligonucleotide probes were used based on multiple aligned internal transcribed spacer (ITS) sequences. Specific binding of the PCR-amplified products to the probes immobilized on nitrocellulose membrane strips was evaluated by the hybridization method. Experiments were performed three times on separate days to evaluate the assay's repeatability. The PCR-LPA was evaluated directly on nine clinical samples and their cultivated isolates. Results: All 15 probes used in this study hybridized specifically to ITS sequences of the corresponding standard species. Results were reproducible for all the strains on different days. Mycobacterium species of the nine clinical specimens and their cultivated isolates were correctly identified by PCR-LPA and confirmed by sequencing. Conclusion: In this study, we describe a PCR-LPA that is readily applicable in the clinical laboratory. The assay is fast, cost-effective, highly specific, and requires no radioactive materials.
Language	English
Publishing date	2020-06-04
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2743890-9
ISSN	2322-3480
ISSN	2322-3480
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Article: Antibacterial Activity of

Roointan, Amir / Kamali-Kakhki, Reza / Fathalipour, Mohammad / Hashemi, Zohreh / Zarshenas, Mohammad Mehdi / Soleimani, Mohammad / Mirjani, Ruhola

Iranian journal of medical sciences

2020 Volume 45, Issue 6, Page(s) 444–450

Abstract: Background: Burn wound infection and sepsis are serious medical conditions requiring prompt intervention. Plants are a good natural source for the development of novel, safe, and cost-effective antibacterial agents. The objective of the present study ... ...

Abstract	Background: Burn wound infection and sepsis are serious medical conditions requiring prompt intervention. Plants are a good natural source for the development of novel, safe, and cost-effective antibacterial agents. The objective of the present study was to assess the antibacterial potential of aqueous, chloroform, and methanol extracts of the Methods: The present experimental study was conducted at Shiraz University of Medical Sciences (Shiraz, Iran) during 2018-2019. The antibacterial activity of the total plant extract was assayed using the broth microdilution method. Fractionation was performed using a separation funnel and solvents with different polarities. Broth microdilution and agar well diffusion assays were performed to determine the antibacterial potential of the obtained fractions. Quantitative and qualitative phytochemical analyses were performed to confirm the presence of secondary metabolites in both the total extract and the fractions. Results: Methanolic extract of Conclusion: For the first time, we demonstrated the antibacterial activity of the
Language	English
Publishing date	2020-12-03
Publishing country	Iran
Document type	Journal Article
ZDB-ID	603872-4
ISSN	1735-3688 ; 0253-0716
ISSN (online)	1735-3688
ISSN	0253-0716
DOI	10.30476/ijms.2019.82071
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Article ; Online: The short-chain dehydrogenases/reductases (SDR) gene: A new specific target for rapid detection of Mycobacterium tuberculosis complex by modified comparative genomic analysis.

Kakhki, Reza Kamali / Neshani, Alireza / Sankian, Mojtaba / Ghazvini, Kiarash / Hooshyar, Amin / Sayadi, Mahsa

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2019 Volume 70, Page(s) 158–164

Abstract: Background: Early detection of tuberculosis is one of the crucial steps for TB control. Although, the sensitivity of conventional methods like Lowenstein Jensen (LJ) culture and direct staining is quite low, molecular techniques like polymerase chain ... ...

Abstract	Background: Early detection of tuberculosis is one of the crucial steps for TB control. Although, the sensitivity of conventional methods like Lowenstein Jensen (LJ) culture and direct staining is quite low, molecular techniques like polymerase chain reaction (PCR) are more sensitive and be considered as useful tools for rapid detection of tuberculosis. Various genes like IS6110 and mpb64 have been used as target for detection of M. tuberculosis, but more research is needed to find the most specific targets. The short-chain dehydrogenases/reductases family (SDR) is one of a very large family of NAD- or NADP-dependent oxidoreductase enzymes which is present in all M. tuberculosis strains. The large part of SDR sequences in tuberculosis is completely conserved and different from non-tuberculosis mycobacterium. The aim of the study was to develop an in-house PCR assay using the SDR target for rapid detection of M. tuberculosis from clinical specimens. Method: M. tuberculosis-specific sequences were found using modified genome comparison method and the primers were designed by the Primer Premier 5.0 software. A PCR assay was developed targeting the nucleotide sequences within the SDR gene. A total of 50 cultivated specimens and 120 clinical specimens were evaluated by PCR. Results: The clinical evaluation of SDR PCR assay showed high specificity (100%) and high sensitivity (88.5%). The analytical sensitivity was 10 fg of template DNA which is theoretically equivalent to 2 copy of genomic DNA per microliter. The SDR is a new specific target of M. tuberculosis and no cross-reactivity was observed to non-tuberculosis mycobacterium and other pathogenic bacteria. Conclusions: Based on our results, the SDR gene can be considered as a useful target for detection of M. tuberculosis complex from clinical specimens.
MeSH term(s)	Bacterial Proteins/genetics ; Genomics/methods ; Humans ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/isolation & purification ; Polymerase Chain Reaction ; Short Chain Dehydrogenase-Reductases/genetics ; Tuberculosis/microbiology ; Tuberculosis/prevention & control
Chemical Substances	Bacterial Proteins ; Short Chain Dehydrogenase-Reductases (EC 1.1.1.-)
Language	English
Publishing date	2019-01-12
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2019.01.012
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Article ; Online: Antibacterial Activity of Prunus Scoparia Root Methanol Extract against Most Common Burn Wound Pathogens

Amir Roointan / Reza Kamali-Kakhki / Mohammad Fathalipour / Zohreh Hashemi / Mohammad Mehdi Zarshenas / Mohammad Soleimani / Ruhola Mirjani

Iranian Journal of Medical Sciences, Vol 45, Iss 6, Pp 444-

2020 Volume 450

Abstract	Background: Burn wound infection and sepsis are serious medical conditions requiring prompt intervention. Plants are a good natural source for the development of novel, safe, and cost-effective antibacterial agents. The objective of the present study was to assess the antibacterial potential of aqueous, chloroform, and methanol extracts of the Prunus scoparia (P. scoparia) root against the most common burn wound pathogens. Methods: The present experimental study was conducted at Shiraz University of Medical Sciences (Shiraz, Iran) during 2018-2019. The antibacterial activity of the total plant extract was assayed using the broth microdilution method. Fractionation was performed using a separation funnel and solvents with different polarities. Broth microdilution and agar well diffusion assays were performed to determine the antibacterial potential of the obtained fractions. Quantitative and qualitative phytochemical analyses were performed to confirm the presence of secondary metabolites in both the total extract and the fractions. Results: Methanolic extract of P. scoparia root exhibited antibacterial activity against all tested bacterial strains, especially against Methicillin-resistant Staphylococcus aureus (MRSA) isolates. This extract, compared to the aqueous and chloroformic extracts, exhibited the presence of active antibacterial compounds. The quantitative and qualitative results of phytochemical screening showed that phenols and flavonoids were the main antibacterial compounds in the methanolic extract of the plant. Conclusion: For the first time, we demonstrated the antibacterial activity of the P. scoparia root against MRSA isolates and other common burn wound pathogens.
Keywords	herbal medicine ; anti-bacterial agents ; wounds and injuries ; phenols ; flavonoids ; Medicine (General) ; R5-920
Subject code	580
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Shiraz University of Medical Sciences
Document type	Article ; Online
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