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Firouzjaie F, Taghipour N, Akhavan AA, Seyyed Tabaei SJ, Rouhani S, Shirazian M, Koochaki A, Fatemi M, Mosaffa N, Moin Vaziri V. Neutrophil extracellular traps formation: effect of Leishmania major promastigotes and salivary gland homogenates of Phlebotomus papatasi in human neutrophil culture. BMC Microbiol 2024; 24:117. [PMID: 38575882 PMCID: PMC10993452 DOI: 10.1186/s12866-024-03270-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Leishmaniasis as a neglected tropical disease (NTD) is caused by the inoculation of Leishmania parasites via the bite of phlebotomine sand flies. After an infected bite, a series of innate and adaptive immune responses occurs, among which neutrophils can be mentioned as the initiators. Among the multiple functions of these fighting cells, neutrophil extracellular traps (NETs) were studied in the presence of Leishmania major promastigotes and salivary gland homogenates (SGH) of Phlebotomus papatasi alone, and in combination to mimic natural conditions of transmission. MATERIAL & METHODS The effect of L. major and SGH on NETs formation was studied in three different groups: neutrophils + SGH (NS), neutrophils + L. major (NL), neutrophils + L. major + SGH (NLS) along with negative and positive controls in 2, 4 and 6 h post-incubation. Different microscopic methods were used to visualize NETs comprising: fluorescence microscopy by Acridine Orange/ Ethidium Bromide staining, optical microscopy by Giemsa staining and scanning electron microscopy. In addition, the expression level of three different genes NE, MPO and MMP9 was evaluated by Real-Time PCR. RESULTS All three microscopical methods revealed similar results, as in NS group, chromatin extrusion as a sign of NETosis, was not very evident in each three time points; but, in NL and especially NLS group, more NETosis was observed and the interaction between neutrophils and promastigotes in NL and also with saliva in NLS group, gradually increased over times. Real-time reveals that, the expression of MPO, NE and MMP9 genes increased during 2 and 4 h after exposure, and then decreased at 6 h in most groups. CONCLUSION Hence, it was determined that the simultaneous presence of parasite and saliva in NLS group has a greater impact on the formation of NETs compared to NL and NS groups.
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Affiliation(s)
- Fahimeh Firouzjaie
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Niloofar Taghipour
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Ahmad Akhavan
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyyed Javad Seyyed Tabaei
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soheila Rouhani
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Shirazian
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ameneh Koochaki
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahboubeh Fatemi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nariman Mosaffa
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Vahideh Moin Vaziri
- Department of Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Karakavuk M, Can H, Çeltik A, Karakavuk T, Gül C, Erdem HA, Pullukçu H, Taşbakan M, Taşbakan MS, Gürüz AY, Döşkaya M, Değirmenci Döşkaya A. Genetic characterization of Toxoplasma gondii strains isolated from humans living in İzmir, Türkiye. Indian J Med Microbiol 2024; 49:100571. [PMID: 38554777 DOI: 10.1016/j.ijmmb.2024.100571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/22/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
PURPOSE Toxoplasma gondii is an obligate intracellular zoonotic parasite that can infect all warm-blooded animals, including humans. Currently, clinical findings of toxoplasmosis are being related to T. gondii strains such as Type I genotype may cause high pathogenicity and Type II genotype causes a milder clinical presentation. We have showed in our previous that Type II genotype is the most frequent strain detected in stray cats and wild birds living in natural life of İzmir. The aim of this study was to assess toxoplasmosis seroprevalence in immunocompromised patients, investigate the presence of T. gondii DNA in their blood samples, and genotype the PCR positive ones. METHODS The 42 buffy-coat and serum samples were collected from immunocompromised patients who were from various clinics. Thereafter, Real-Time PCR targeting RE gene of T. gondii was performed with DNA samples obtained from buffy-coat samples. Genotyping was performed by sequencing of GRA6 and GRA7 gene regions of positive DNA samples obtained from tissues of bioassay and PCR positive samples. RESULTS According to Real-Time PCR results, T. gondii DNA was detected in 23.8% (10/42) samples. Among these 10 samples, two samples were determined as T. gondii Type II genotype. Anti-Toxoplasma IgG antibodies were detected in 28.57% (12/42) samples. CONCLUSIONS Overall, the detection of Type II genotype in humans in İzmir province suggested that T. gondii infection in humans, stray cats, and wild animals may be associated to each other in terms of transmission.
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Affiliation(s)
- Muhammet Karakavuk
- Ege University, Odemis Vocational School, Ödemiş, İzmir, Türkiye; Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye
| | - Hüseyin Can
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, Bornova, İzmir, Türkiye
| | - Aygül Çeltik
- Ege University, Faculty of Medicine, Department of Internal Medicine, Division of Nephrology, Bornova, İzmir, Türkiye
| | - Tuğba Karakavuk
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye
| | - Ceren Gül
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye
| | - Hüseyin Aytaç Erdem
- Ege University, Faculty of Medicine, Department of Infectious Diseases, Bornova, İzmir, Türkiye
| | - Hüsnü Pullukçu
- Ege University, Faculty of Medicine, Department of Infectious Diseases, Bornova, İzmir, Türkiye
| | - Meltem Taşbakan
- Ege University, Faculty of Medicine, Department of Infectious Diseases, Bornova, İzmir, Türkiye
| | - Mehmet Sezai Taşbakan
- Ege University, Faculty of Medicine, Department of Chest Diseases, Bornova, İzmir, Türkiye
| | - Adnan Yüksel Gürüz
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Türkiye
| | - Mert Döşkaya
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Türkiye
| | - Aysu Değirmenci Döşkaya
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Türkiye.
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Kahya Demirbilek S, Yıldız M, Akkoç A, Mutlu AM, Ardıçlı Ö, Aner H. Comparison of bacteriological culture method and multiplex real-time PCR for detection of mastitis. Res Vet Sci 2024; 172:105237. [PMID: 38555775 DOI: 10.1016/j.rvsc.2024.105237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/29/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
This study includes the evaluation of multiplex real-time PCR (rPCR) kit, which was developed to provide rapid diagnosis of mastitis infections, by working with milk samples of 2 different sources of mastitis and comparing the results with the classical bacteriological culture method (BC). A total of 273 bacteria were isolated in 226 samples (47.88%) out of 472 samples by BC. These were 139 (50.91%) Staphylococcus spp., 61 (22.34%) Streptococcus spp., 15 (5.49%) E. coli, 8 (2.93%) Enterococcus spp., 50 (18.31%) other bacteria. When we look at the multiplex rPCR results; 1052 positive were obtained for the gene regions of 14 different bacteria, 1 yeast, and 1 β-lactamase gene examined in 472 samples. While no searched gene region was found by rPCR in 78 (16.5%) of the 472 samples studied, at least 1 gene was detected in 394 (83.5%) samples. These 1052 positive samples by rPCR were; 263 (28.43%) Staphylococcus spp., 51 (5.51%) S. aureus, 57 (6.16%) Enterococcus spp., 49 (5.29%) C. bovis, 16 (1.73%) S. dysgalactiae, 84 (9.08%) S. agalactiae, 71 (7.67%) S. uberis, 73 (7.89%) E. coli, 14 (1.51%) Prototheca spp., 39 (4.21%) T. pyogenes/P. indolicus, 5 (0.54%) S. marcescens, 15 (1.62%) K. oxytoca/pneumonia, 117 (12.64%) Mycoplasma spp., 31 (3.35%) M. bovis, 40 (4.32%) yeast, and 127 samples (26.90%) were β-lactamase positive. When the antibiotic resistance of the isolates was evaluated, 78 (31.96%) tetracycline, 72 (29.5%) penicillin, and 60 (24.59%) clindamycin resistance were observed predominantly in Gram-positive isolates, while 6 (23.07%) tigecycline, 6 (23.07%) netilmicin, 6 (23.07%) pipercillin resistance was found in gram-negative isolates. While a bacteria and/or yeast gene was found by rPCR in 187 of 246 (76.01%) samples with no bacterial growth, a bacterium was isolated with BC in only 20 (8.84%) samples whose gene region was not found by rPCR. As a result, the multiplex rPCR system used in the diagnosis of mastitis has been found to be quite reliable as it can detect a large number of bacteria in a very short time compared to classical methods. Therefore, we advise the use of rPCR and/or culture for confirmation of clinical signs in mastitis and at routine mastitis surveillance.
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Affiliation(s)
| | - Merve Yıldız
- Uludag University, Faculty of Veterinary Medicine, Department of Microbiology, Turkey.
| | - Ahmet Akkoç
- Uludag University, Faculty of Veterinary Medicine, Department of Pathology, 16.000 Görükle-Bursa, Turkey.
| | - Ayşe Meriç Mutlu
- Uludag University, Faculty of Veterinary Medicine, Department of Pathology, 16.000 Görükle-Bursa, Turkey
| | - Özge Ardıçlı
- Uludag University, Faculty of Veterinary Medicine, Department of Microbiology, Turkey.
| | - Havva Aner
- Uludag University, Faculty of Veterinary Medicine, Department of Microbiology, Turkey
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Chen J, Gao Y, Xiong S, Peng Z, Zhan P. Expression Profiles of Protease in Onychomycosis-Related Pathogenic Trichophyton rubrum and Tinea Capitis-Related Pathogenic Trichophyton violaceum. Mycopathologia 2024; 189:14. [PMID: 38265566 DOI: 10.1007/s11046-024-00828-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/01/2024] [Indexed: 01/25/2024]
Abstract
The two fungal species Trichophyton rubrum and Trichophyton violaceum are common pathogens on human, infecting keratinized tissue of the outer body parts. Both species are belonging to the "Trichophyton rubrum complex" and share very high similarity in the genome. Secreted proteinases, key factors for keratin degradation, are nearly identical. Contrary, the ecological niches are differing. Trichophyton rubrum preferably infects skin and nails, whereas T. violaceum preferably infects the scalp. We postulate, that differences in the protease expression contribute to differences in ecological preferences. We analyzed the expression profiles of all 22 endoprotease genes, 12 subtilisins (S8A), 5 deuterolysins (M35) and 5 fungalysins (M36), for both species. To compare the influence of the keratin source, we designed experiments with human nail keratin, sheep wool keratin and keratin free cultivation media. Samples were taken at 12 h, 24 h, 48 h and 96 h post incubation in keratin medium. The expression of the proteases is higher in wool-keratin medium compared to human nail medium, with the exception of MEP4 and SUB6. Expression in the keratin-free medium is lowest. The expression profiles of the two species are remarkable different. The expression of MEP1, MEP3, SUB5, SUB11 and SUB12 are higher in T. rubrum compared to T. violaceum. MEP2, NpIIc, NpIIe, SUB1, SUB3, SUB4, SUB7 and SUB8 are higher expressed in T. violaceum compared to T. rubrum. The differences of the protease expression in the two species may expalin the differences in the ecological niches. Further analysis are necessary to verify the hypothesis.Please check and conform the edit made in title.Here I thinke the species of strains shouldnt be capital, and the right expression should be, "Expression Profiles of Protease in Onychomycosis-Related Pathogenic Trichophyton rubrum and Tinea Capitis-Related Pathogenic Trichophyton violaceum"Author names: Please confirm if the author names are presented accurately and in the correct se-quence (given name, middle name/initial, family name). Author 1 Given name: [Jingjing] Last name [Chen], Author 2 Given name: [Yangmin] Last name [Gao], Author 3 Given name: [Shuzhen] Last name [Xiong], Author 4 Given name: [Ping] Last name [Zhan]. Also, kindly confirm the details in the metadata are correct.YesPlease check and confirm the inserted city and country are correctly identified for affiliation 3.Please change the affiliations, Affiliation 2: ²Jiangxi Provincial Clinical Research Center for Skin Diseases, Dermatology Hospital of Jiangxi Province,The Affiliated Dermatology Hospital of Nanchang University, Nanchang, 330200, Jiangxi; Affiliation 3: 3Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College,Nanchang 330001, Jiangxi. Thanks a lot!
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Affiliation(s)
| | - Yangmin Gao
- Jiangxi Provincial Clinical Research Center for Skin Diseases, Dermatology Hospital of Jiangxi Province, The Affiliated Dermatology Hospital of Nanchang University, Nanchang, 330200, Jiangxi, China
| | | | - Zimei Peng
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330001, Jiangxi, China
| | - Ping Zhan
- Nanchang University, Nanchang, 330006, China.
- Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, 330006, China.
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Shoushtari M, Zeinoddini M, Fathi J, Keshavarz Alikhani H, Shiekhi F. One-step and Rapid Identification of SARS-CoV-2 using Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). Avicenna J Med Biotechnol 2024; 16:3-8. [PMID: 38605744 PMCID: PMC11005395 DOI: 10.18502/ajmb.v16i1.14165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/29/2023] [Indexed: 04/13/2024] Open
Abstract
Background SARS-CoV-2 as the cause of novel coronavirus disease (COVID-19) is a member of the family Coronaviridea that has generated an emerging global health concern. Controlling and preventing the spread of the disease requires a simple, portable, and rapid diagnostic method. Today, a standard method for detecting SARS-CoV-2 is quantitative real-time reverse transcription PCR, which is time-consuming and needs an advanced device. The aim of this study was to evaluate a faster and more cost-effective field-based testing method at the point of risk. We utilized a one-step RT-LAMP assay and developed, for the first time, a simple and rapid screening detection assay targeting the Envelope (E) gene, using specific primers. Methods For this, the total RNA was extracted from respiratory samples of COVID-19 infected patients and applied to one-step a RT-LAMP reaction. The LAMP products were visualized using green fluorescence (SYBR Green I). Sensitivity testing was conducted using different concentrations of the designed recombinant plasmid (TA-E) as positive control constructs. Additionally, selectivity testing was performed using the influenza H1N1 genome. Finally, the results were compared using with conventional real time RT-PCR. Results It was shown that the RT-LAMP assay has a sensitivity of approximately 15 ng for the E gene of SARS-CoV-2 when using extracted total RNA. Additionally, a sensitivity of 112 pg was achieved when using an artificially prepared TA-E plasmid. Accordingly, for the detection of SARS-CoV-2 infection, the RT-LAMP had high sensitivity and specificity and also could be an alternative method for real-time RT-PCR. Conclusion Overall, this method can be used as a portable, rapid, and easy method for detecting SARS-CoV-2 in the field and clinical laboratories.
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Affiliation(s)
| | - Mehdi Zeinoddini
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
| | - Javad Fathi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hani Keshavarz Alikhani
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Fatemeh Shiekhi
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
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Thomas S, Duraisamy SK, Ahmed R, Abraham A, Vishwabandhya A, Mathews V, Srivastava A, Samuel P, Kannangai R, Abraham OC, George B, Abraham AM. Early detection, reactivation of cytomegalovirus DNA & immediate early (IE)-mRNA expression in hematopoietic stem cell-transplant patients. Indian J Med Microbiol 2024; 47:100521. [PMID: 38072066 DOI: 10.1016/j.ijmmb.2023.100521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
BACKGROUND Human cytomegalovirus (HCMV) reactivation is a major cause of morbidity and mortality among stem cell transplant recipients post-transplantation. AIM HCMV immediate-early messenger RNA (IE-mRNA) was evaluated as marker of post-transplant HCMV reactivation in bone marrow transplant recipients. METHOD ology: An in-house real-time reverse transcriptase PCR targeting IE-mRNA was developed to estimate HCMV mRNA levels post-transplantation. Blood samples collected in K2-EDTA tubes from patients (n = 162) admitted with Department of Clinical Hematology were transported in cold condition for routine HCMV DNA screening. For HCMV IE-mRNA quantification, peripheral blood mononuclear cells (PBMCs) were separated from whole blood and stored in RNA later at -70 °C until testing. Samples were collected weekly once for first 3 weeks post-transplantation and thereafter from week 4-12, samples were collected twice weekly. A total of 2467 samples were collected from 162 study participants. RESULTS Thirty five patients (21.6 %) had post-transplant HCMV reactivation. Twenty five patients with complete follow-up were selected for monitoring HCMV DNA. HCMV IE-mRNA PCR was performed for 15 patients and 7(46.6 %) patients had detectable mRNA levels. HCMV IE-mRNA was detected in all patients with increasing HCMV DNA levels except for one patient in whom IE-mRNA appeared 3 days before HCMV DNA was detected. One patient had detectable HCMV IE-mRNA during declining HCMV DNA level. However the patient showed an increased HCMV DNA one week later, indicating the importance of HCMV mRNA in predicting HCMV replication. CONCLUSION Quantification of HCMV IE-mRNA may be a valuable tool to predict progression of HCMV infection post-transplantation, with further prospective studies needed for validation.
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Affiliation(s)
- Sangeeta Thomas
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | | | - Rayaz Ahmed
- Department of Clinical Hematology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Aby Abraham
- Department of Clinical Hematology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Auro Vishwabandhya
- Department of Clinical Hematology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Vikram Mathews
- Department of Clinical Hematology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Alok Srivastava
- Department of Clinical Hematology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Prasanna Samuel
- Department of Biostatistics, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - O C Abraham
- Department of Medicine, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Biju George
- Department of Clinical Hematology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Asha Mary Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
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Gatica-Arias A, Muñoz-Flores C, Bolívar-González A. A General Protocol for Gene Expression Analysis in Chemically Mutant Coffee Plants in Response to Rust (Hemileia vastatrix Berk & Broome) Infection. Methods Mol Biol 2024; 2787:209-223. [PMID: 38656492 DOI: 10.1007/978-1-0716-3778-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Coffea spp. is the source of one of the most widely consumed beverages in the world. However, the cultivation of this crop is threatened by Hemileia vastatrix Berk & Broome, a fungal disease, which reduces the productivity and can cause significant economic losses. In this protocol, coffee leaf segment derived from a chemical mutagenesis process are inoculated with uredospores of the pathogen. Subsequently, the gene expression changes are analyzed over the time (0, 5, 24, 48, and 120 h) using quantitative real-time polymerase chain reaction (RT-qPCR). The procedures and example data are presented for expression analysis in the CaWRKY1 gene. This procedure can be applied for quantitative analysis of other genes of interest to coffee breeders and scientists for elucidating the molecular mechanisms involved in the interaction between the plant and pathogen, potentially leading to the development of more efficient approaches for managing this disease.
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Affiliation(s)
- Andrés Gatica-Arias
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.
- Programa de Posgrado en Ciencias Agrícolas y Recursos Naturales con énfasis en Biotecnologia (PPCARN), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Alejandro Bolívar-González
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Programa de Posgrado en Ciencias Agrícolas y Recursos Naturales con énfasis en Biotecnologia (PPCARN), Universidad de Costa Rica, San José, Costa Rica
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Patel MG, Patel AC, Raval SH, Sharma KK, Patel SS, Chauhan HC, Parmar RS, Shrimali MD, Vamja HG, Bhatol J, Mohapatra SK. Ante-mortem and Post-mortem Diagnosis Modalities and Phylogenetic Analysis of Rabies Virus in Domestic and Wild Animals of Gujarat, India. Indian J Microbiol 2023; 63:645-657. [PMID: 38031621 PMCID: PMC10682330 DOI: 10.1007/s12088-023-01126-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
In the present study, total of 32 ante-mortem (AM) samples (saliva = 18 and corneal smears = 14) from six animal species (cattle = 5; camel = 1; goat = 1; horse = 1; buffalo = 4; dog = 6) and 28 post-mortem (PM) samples of domestic (cattle = 6; camel = 1; goat = 1; buffalo = 5; dog = 7) and wild animals (lion = 4, mongoose = 2; bear = 1; leopard = 1) were examined for rabies diagnosis in Gujarat, India. Direct fluorescent antibody test (dFAT) and reverse transcriptase polymerase chain reaction (RT-PCR) were applied on AM samples, whereas along with dFAT and RT-PCR, histopathological examination, immunohistochemistry (IHC) and real time PCR (qPCR) were used for PM diagnosis. Nucleotide sequencing of full nucleoprotein (N) and glycoprotein (G) genes were carried out upon representative amplicons. In AM examination, 7/18 saliva and 5/14 corneal impressions samples were found positive in dFAT and 8/18 saliva samples were found positive in RT-PCR. In PM examination, 14/28 samples showed positive results in dFAT and IHC with unusual large fluorescent foci in two samples. In histopathology, 11/28 samples showed appreciable lesion and Negri bodies were visible in 6 samples, only. Out of 23 brain samples examined. 12 samples were found positive in N gene RT-PCR and qPCR, and 10 samples in G gene RT-PCR. Phylogenetic analysis of N gene revealed that test isolates (except sample ID: lion-1; lion, Gir) form a close group with sequence ID, KM099393.1 (Mongoose, Hyderabad) and KF660246.1 (Water Buffalo, Hyderabad) which was far from some south Indian and Sri Lankan isolates but similar to Indian isolates from rest of India and neighboring countries. In G gene analysis, the test isolates form a close group with sequence ID, KP019943.1. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01126-0.
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Affiliation(s)
- Maulik G. Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Arun C. Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Samir H. Raval
- Department of Veterinary Pathology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Kishan K. Sharma
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Sandip S. Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Harshad C. Chauhan
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Rohit S. Parmar
- Department of Veterinary Pathology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Mehul D. Shrimali
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
| | - Hitesh G. Vamja
- Gir (East) Forest Division-Dhari, Gov. of Gujarat, Dhari, Gujarat India
| | - Jitendra Bhatol
- Forest Division- Banaskantha, Gov. of Gujarat, Banaskantha, Gujarat India
| | - Sushil K. Mohapatra
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Sardarkrushinagar Dantiwada Agricultural University (Now Under Kamdhenu University), Sardarkrushinagar, Banaskantha, Gujarat 385005 India
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9
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Safdar T, Tahir MHN, Ali Z, Ur Rahman MH. Exploring the role of HaTIPs genes in enhancing drought tolerance in sunflower. Mol Biol Rep 2023; 50:8349-8359. [PMID: 37606830 DOI: 10.1007/s11033-023-08679-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/14/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Activity of plant aquaporins (AQPs) is extremely sensitive to environmental variables such as temperature, drought, atmospheric vapor pressure deficit, cell water status and also appears to be closely associated with the expression of plant tolerance to various stresses. The spatial and temporal expression patterns of genes of Tonoplast Intrinsic Proteins (TIPs) in various crops indicate the complex and diverse regulation of these proteins and are important in understanding their key role in plant growth, development and stress responses. METHODS AND RESULTS Based on phylogenetic analysis, six distinct HaTIPs were selected for studying their spatial and temporal expression in sunflower (Helianthus annuus). In this study semi quantitative polymerase chain reaction (semi q-PCR) and real time polymerase chain reaction (q-PCR) analysis were used to study the spatial and temporal expression of HaTIPs in sunflower. The results indicated that all of HaTIPs showed differential expression specific to both the tissues and the accessions. Moreover, the expression of all HaTIPs was higher in cross compared to the parents. Results of semi q-PCR and real time PCR indicated an upregulation of expression of HaTIP-RB7 and HaTIP7 in drought tolerant entries at 12 h of 20% polyethylene glycol (PEG) treatment compared to 0 h. CONCLUSION Hence these genes can be utilized as potential target in improving water use efficiency and for further genetic manipulation for the development of drought tolerant sunflower. This study may further contribute to our better understanding regarding the precise role of HaTIPs through their spatial and temporal expression analysis and their application in sunflower drought stress responses.
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Affiliation(s)
- Tania Safdar
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan, Pakistan.
| | - Muhammad Hammad Nadeem Tahir
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef, University of Agriculture, Multan, Pakistan
| | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Habib Ur Rahman
- Department of Agronomy, Muhammad Nawaz Shareef, University of Agriculture, Multan, Pakistan
- Institute of crop science and resource conservation (INRES), University of Bonn, Bonn, Germany
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10
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Dirican E, Özcan H, Uzunçakmak SK, Takım U. Evaluation Expression of the Caspase-3 and Caspase-9 Apoptotic Genes in Schizophrenia Patients. Clin Psychopharmacol Neurosci 2023; 21:171-178. [PMID: 36700323 PMCID: PMC9889905 DOI: 10.9758/cpn.2023.21.1.171] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023]
Abstract
Objective Apoptosis is programmed cell death that occurs by several pathways. Caspase-3 is induced by active caspase-9 via the intrinsic pathway. The aim of this research was to explore the expression of caspase-3 and caspase-9 in schizophrenia patients and healthy samples. Methods RNA was isolated from the peripheral blood of 39 schizophrenia patients' and healthy samples. After cDNA synthesis, real time PCR (RT-PCR) was used to analyse caspase-3 and caspase-9 gene expression. The severity of psychopathological symptoms of schizophrenia was evaluated using the Positive and Negative Symptoms Scale for schizophrenia (PANSS) and Clinical Global Impressions (CGI). Results The expression of caspase-3 and caspase-9 genes was higher in schizophrenia patients than in healthy samples (p = 0.012, p = 0.002, respectively). The increase in caspase-3 gene expression was significant with being male, smoking and with a duration of less than 6 years (p = 0.047, p = 0.049, p = 0.034, respectively). On the other hand, the increase in caspase-9 gene expression was significant in patients who is smoke, have children, and are under 33 years old (p = 0.040, p = 0.043, p = 0.045, respectively). A significant positive correlation was detected between the caspase-3 and caspase-9 gene expression (r = 0.3218, p = 0.049). Conclusion Our findings indicate that caspase-3 and caspase-9 gene expression may activate cell death mechanisms by intrinsic apoptotic genes. Furthermore, caspase-3 and caspase-9 may play essential roles in different ways in schizophrenia. Hence there is a need to further study the apoptotic mechanism with expanded patient populations.
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Affiliation(s)
- Ebubekir Dirican
- Health Services Vocational School, Bayburt University, Bayburt, Turkey,Address for correspondence: Ebubekir Dirican Health Services Vocational School, Bayburt University, Dede Korkut Campus, Bayburt 69000, Turkey, E-mail: , ORCID: https://orcid.org/0000-0001-9260-5223
| | - Halil Özcan
- Department of Mental Health and Related Disorders, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | | | - Uğur Takım
- Department of Mental Health and Related Disorders, Faculty of Medicine, Atatürk University, Erzurum, Turkey
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11
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Srivastava P, Mishra S, Agarwal A, Pandey A, Husain N. Circulating microRNAs in gallbladder cancer: Is serum assay of diagnostic value? Pathol Res Pract 2023; 242:154320. [PMID: 36682281 DOI: 10.1016/j.prp.2023.154320] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
The microRNAs (miRNAs) in circulation could serve as biomarkers for cancer detection. Gallbladder carcinoma (GBC) is mostly asymptomatic; therefore, using microRNAs (miRNAs) as an early diagnostic biomarker could be a valuable tool. We aimed to identify the tumor-associated miR-1, miR130, miR-146, miR-182, and miR-21expression in serum as a biomarker for early detection of GBC and identify their possible diagnostic role. The study group comprised of paired serum and tissue samples from 34 GBC, 19 cholecystitis (CC), 21 normal controls (uninflamed gall bladder), and additional 29 serum-only samples of GBC. Total RNA was isolated using a commercially available RNA isolation kit (Applied Biosystem, USA) and reverse transcribed using Advanced Taqman MicroRNA reverse transcription kit. The relative expression of miRNAs was analyzed using Quantitative real-time polymerase chain reaction. The diagnostic potential of these miRNAs was assessed by ROC analysis. In paired samples, the trend towards up and down regulation for miR-182, miR-21, miR-1, miR-130, and miR-146 was similar in both tissue and sera of GBC. The expression pattern of serum miR-1, miR130, and miR-146 gradually decreased from normal control (NC) to CC to GBC, while miR-21 and miR-182 gradually increased from NC to CC to GBC. The miR-1, miR-121, miR-182, and miR-146 significantly differed between CC vs. early stage and early stage vs. NC. Among these miRNAs, the sensitivity of miR-1 (85.71 %) was the highest, and the specificity of miR-21 was the highest (92.73 %). The combined sensitivity for miRNAs ranged from 73.13 % (CI: 60.90-83.24 %) to 98.63 % (CI: 89.0-99.61 %); however, the specificity was lower. In stage I&II vs. III&IV discrimination, the diagnostic sensitivity of miR-1 was highest (89.36 %, CI: 76.90-96.45). The two miRNAs, in combination, increase the diagnostic sensitivity. Circulating serum miRNAs may provide a new approach for clinical application. Panels of specific circulating miRNA, which require further validation, could be potential non-invasive diagnostic biomarkers for GBC in combination with abnormal radio diagnostic scans.
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12
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Khan MJR, Bhuiyan MA, Tabassum S, Munshi SU. Use of whole blood and dried blood spot for detection of HIV-1 nucleic acids using reverse transcription loop-mediated isothermal amplification. J Virol Methods 2023; 312:114642. [PMID: 36375538 DOI: 10.1016/j.jviromet.2022.114642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/15/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
For monitoring viral load (VL) or Early Infant Diagnosis (EID) of HIV-1, real-time Polymerase Chain Reaction (qPCR) is used to perform on plasma or Dried Blood Spot (DBS) sample. The qPCR method is expensive and requires sophisticated equipment. Therefore, there is a requirement for newer and cheaper technology for VL measurement or EID. In this analytical study, a Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) assay was optimized and applied for amplification of HIV nucleic acids (NA) extracted from plasma, heat-treated plasma, heat-treated whole blood and lysis buffer-treated dried blood spot (DBS). The amplified product of RT-LAMP assay was detected by color change of Hydroxy naphthol blue (HNB) dye, step ladder pattern band on agarose gel after electrophoresis and sigmoid-shaped curve in the real-time thermal cycler. Comparing the results from RT-LAMP testing of all conditions with the results obtained by RT-qPCR results, viewed as the gold standard; a relative analytical sensitivity and specificity of RT-LAMP was calculated as 100 % and 90 % respectively. The corresponding positive predictive value (PPV) and negative predictive value (NPV) were 93.75 % and 100 %, respectively. The percentage of agreement between the RT-LAMP and RT-qPCR was 88.46% and Cohen's kappa value was 0.75 shows a substantial agreement between the two tests. This study suggests that whole blood or DBS may be useful specimens for analysis by HIV-1 specific RT-LAMP, to provide a cost effective alternative to RT-qPCR for the detection of HIV-1 nucleic acid at the point of care, or in early infant diagnoses.
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13
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Sanaullah I, Khan HN, Sajjad A, Khan S, Sabri AN, Naseem S, Riaz S. Improved osteointegration response using high strength perovskite BaTiO 3 coatings prepared by chemical bath deposition. J Mech Behav Biomed Mater 2023; 138:105635. [PMID: 36603524 DOI: 10.1016/j.jmbbm.2022.105635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/15/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
A wide range of bioactive materials have been investigated for tissue engineering and regeneration. Barium titanate is a promising smart material to be used as scaffold for bone tissue engineering. Barium titanate coatings are prepared in the present study using chemical bath deposition technique. Coatings are prepared at room temperature with the variation in solution molarity from 0.1 to 1.2 M. Perovskite tetragonal phase is observed after annealing the samples at 300 °C using 1.0-1.2 M solutions. Normal-anomalous dielectric response is observed for annealed coatings. Maximum transmission of ∼55% and ∼82% is observed under as-prepared and annealed coatings, respectivly. Variation in direct band gap, i.e. 3.45-3.64 eV, is observed with varying molarity. High hardness of the coatings (∼1180 HV) is observed at 1.2M with fracture toughness of ∼22 MPam-1/2. Biodegradation studies show smaller values of weight loss even after immersion in simulated body fluid (SBF) after 26 weeks. Barium titanate coatings also show high antioxidant activity. BaTiO3's antibacterial reaction is evaluated against microorganisms such as Escherichia coli (E. coli) and Staphylococcus aureus. Antibacterial activity shows highest zone of inhibition (∼31 mm) against Staphylococcus aureus bacteria. Quantitative real-time PCR is used to assess the gene expression profile in cultivated cells. Thus, coatings produced without the use of hazardous solvents/reagents utilizing CBD technique are a potential material for biomedical applications.
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Affiliation(s)
- Ifra Sanaullah
- Centre of Excellence in Solid State Physics, University of the Punjab, Lahore, 54590, Pakistan
| | - Hera N Khan
- Centre of Excellence in Solid State Physics, University of the Punjab, Lahore, 54590, Pakistan; Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Amna Sajjad
- Department of Zoology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Sidra Khan
- Centre of Excellence in Solid State Physics, University of the Punjab, Lahore, 54590, Pakistan
| | - Anjum N Sabri
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Shahzad Naseem
- Centre of Excellence in Solid State Physics, University of the Punjab, Lahore, 54590, Pakistan
| | - Saira Riaz
- Centre of Excellence in Solid State Physics, University of the Punjab, Lahore, 54590, Pakistan.
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Nandi S, Mahajan S, Mishra R, Nautiyal S, Agrawal RK, Singh M, Biswas SK, Chander V, Singh KP, Sharma GK. LSDV126 gene based molecular assays for specific detection and characterization of emerging Lumpy Skin Disease virus. J Virol Methods 2023; 312:114665. [PMID: 36509247 DOI: 10.1016/j.jviromet.2022.114665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/10/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
Lumpy skin disease (LSD) is a highly infectious and economically important viral disease, which is currently emerging in the Indian subcontinent. LSD is caused by Lumpy Skin Disease Virus (LSDV) under the genus Capripoxvirus and the family Poxviridae. Since its first incursion in India in the year 2019, the virus is rapidly disseminating through different means like direct contact, fomites and mainly by blood-feeding insects. As the disease has never been reported from India or neighbouring countries, there is a lack of planning and preparatory measures in terms of diagnostics and vaccines to control the disease. In the absence of any homologous vaccine, a live attenuated heterologous goat pox vaccine (Uttarkashi strain) is now being widely used in the country for the prevention of LSDV infection. Use of live attenuated goat pox virus vaccine necessitates the availability of an assay which could specifically detect and differentiate LSDV from goat pox virus. In this study, nucleotide sequences of LSDV126 gene encoding extracellular enveloped virus protein of circulating LSDV and goat pox virus were determined and analyzed. Deletion of 27 nt tandem repeats was observed in LSDV in comparison to goat pox and LSDV vaccine viruses. The deletion region was targeted for designing primers specific to LSDV, but not goat pox virus. A novel isothermal polymerase spiral reaction (PSR) was optimized as pen side diagnostic for prompt and sensitive detection of genomic DNA of LSDV. The assay was found to be highly sensitive and specific when compared to the real-time PCR. The assay was found to be specifically detecting only LSDV but not the goat pox virus. The limit of detection was identified as 9 × 10-6 ng of positive DNA. The assay will provide a point of care tool that will be a boon for the successful control of LSD in India.
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Affiliation(s)
- Sukdeb Nandi
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Sonalika Mahajan
- Division of Veterinary Biotechnology ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Ragini Mishra
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Sushmita Nautiyal
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Ravi Kant Agrawal
- Division of Veterinary Biotechnology ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Mithilesh Singh
- Immunology Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Sanchay K Biswas
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Vishal Chander
- Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Uttrakhand, India
| | - Karam Pal Singh
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India
| | - Gaurav Kumar Sharma
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP 243122, India.
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Padmanabhan C, Nunziata S, Leon M. G, Rivera Y, Mavrodieva VA, Nakhla MK, Roy A. High-throughput sequencing application in the detection and discovery of viruses associated with the regulated citrus leprosis disease complex. Front Plant Sci 2023; 13:1058847. [PMID: 36762187 PMCID: PMC9907091 DOI: 10.3389/fpls.2022.1058847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/24/2022] [Indexed: 06/18/2023]
Abstract
Citrus leprosis (CiL) is one of the destructive emerging viral diseases of citrus in the Americas. Leprosis syndrome is associated with two taxonomically distinct groups of Brevipalpus-transmitted viruses (BTVs), that consist of positive-sense Cilevirus, Higrevirus, and negative-sense Dichorhavirus. The localized CiL symptoms observed in multiple citrus species and other alternate hosts indicates that these viruses might have originated from the mites and eventually adopted citrus as a secondary host. Genetic diversity in the genomes of viruses associated with the CiL disease complex have complicated current detection and diagnostic measures that prompted the application of High-Throughput Sequencing (HTS) protocols for improved detection and diagnosis. Two cileviruses are known to infect citrus, and among them only citrus leprosis virus C2 (CiLV-C2) hibiscus strain (CiLV-C2H) has been reported in hibiscus and passion fruit in the US. Based on our current CiL disease complex hypothesis, there is a high probability that CiL disease is associated with more viruses/strains that have not yet been identified but exist in nature. To protect the citrus industry, a Ribo-Zero HTS protocol was utilized for detection of cileviruses infecting three different hosts: Citrus spp., Swinglea glutinosa, and Hibiscus rosa-sinensis. Real-time RT-PCR assays were used to identify plants infected with CiLV-C2 or CiLV-C2H or both in mixed infection in all the above-mentioned plant genera. These results were further confirmed by bioinformatic analysis using HTS generated data. In this study, we utilized HTS assay in confirmatory diagnostics to screen BTVs infecting Dieffenbachia sp. (family: Araceae), Passiflora edulis (Passifloraceae), and Smilax auriculata (Smilacaceae). Through the implementation of HTS and downstream data analysis, we detected not only the known cileviruses in the studied hosts but also discovered a new strain of CiLV-C2 in hibiscus from Colombia. Phylogenetically, the new hibiscus strain is more closely related to CiLV-C2 than the known hibiscus strain, CiLV-C2H. We propose this strain to be named as CiLV-C2 hibiscus strain 2 (CiLV-C2H2). The findings from the study are critical for citrus growers, industry, regulators, and researchers. The possible movement of CiLV-C2H2 from hibiscus to citrus by the Brevipalpus spp. warrants further investigation.
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Affiliation(s)
- Chellappan Padmanabhan
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Schyler Nunziata
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | | | - Yazmín Rivera
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Vessela A. Mavrodieva
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Mark K. Nakhla
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
| | - Avijit Roy
- United States Department of Agriculture (USDA), Animal Plant Health Inspection Service, Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, MD, United States
- United States Department of Agriculture (USDA), Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, United States
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Zaretsky A. Qualitative Bioinformatics: Towards a Public Understanding of Neurodegenerative Disease Research through BioArt, Data-Art, Hands-on BioMedia Workshops, Immersive Environments, and Artists in Labs. Adv Exp Med Biol 2023; 1425:663-664. [PMID: 37581839 DOI: 10.1007/978-3-031-31986-0_64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Neurodegenerative disease (ND) research is producing new pharmaceutical compounds for chronic diseases utilizing bioinformatics. Algorithmic data mining of high-throughput omics systems is conjoined with the study of the in vitro dynamics of protein folding through visualization techniques, i.e., Bio-AFM. Novel models of disease pathway diagrams are being produced and the processes are in place to enhance the validation of these models. From bench work to BLAST to bedside, globally standardized research is led by collaborative clusters, working on cloud-based platforms, with crowd sourced human cohort collections, pairing pure, curiosity-based neurological research with deep learning data analysis techniques. ND research is leading the way towards clinical applications for preventing, curing, or ameliorating major diseases of neurological dysfunction, such as Alzheimer's disease (AD) and Parkinson's disease (PD).Most of this is too complex for the average citizen to comprehend. Can bioart and data-art contribute to the public understanding of genome sequencing and bioinformatics databases in the context of ND research? Informal studies towards demystifying bioinformatics through creative practices have been tested, revealing significant qualitative benefits for public well-being while introducing bioinformatics databases, for instance, previous projects: the VASTAL Bioinformatics and Literary Studies: (De)Mystified Genetic Code Lab, held at the Waag in Amsterdam, NL, 2009 and more recently the Creative Germline Constructs Bank (CGCB) of the transgenic human Genome Alternatives Project (thGAP), held at Hackteria ZET, Zurich, Switzerland, 2021.For the Hub of Art Laboratories (HAL), of the Department of Audio & Visual Arts (AVArts), Ionian University in Corfu, Greece, the animation node is challenged to create audiovisual, immersive, and interactive environments that highlight natural processes and phenomena of the microcosm and macrocosm through nature/data interface experimentation. It is the intention of the node's researchers to expand these notions to be inclusive of the processes of the biotechnological and bioinformatics interrogation of human disease as a part of local clades and global nature. In our productions, we would like to emphasize: cryogenic storage, genome analysis, bioinformatic database management, biomarkers for polygenic abnormalities, genotyping/phenotyping, gene expression patterns over time, AI reading of cloud-based research, experiencial DNA/RNA synthesis, the development of novel DNA, RNA and protein-based therapeutic agents for biomedical applications and CRISPR construct design for model organisms. It is the HAL animation node's goal to design and explore bioart-based, hands-on public workshops that mix bioinformatics and data-art with in-depth knowledge of the scientific community around ND research bodies.To develop these labs, dedicated artistic research is required to be undertaken through laboratory immersion, interactions with scientists, and hands-on experience in the lab. Artists must experience scientific processes through residencies in labs to learn both how to convey the techniques and the social implications of novel methodologies. Artists developing bioart workshops that can introduce non-specialists to a dizzying array of research methodologies need to know what they are talking about. It takes experience and dedication to convey simplified versions of real-time biosensor data, automated histology, clinical databases of medical case studies (anonymized clients), real-time PCR, novel diagnostic biomarker development, etc. As qualitative researchers, artists in labs ensure creative yet informed art and science (SciArt) outcomes able to stimulate public debate through unorthodox education and accurate playfulness. Obviously, the immersive experience of lab research provides an artist's projects with both nuance and knowledge. How can artists in labs also add to the scientific potentials of a laboratory's research goals?
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Affiliation(s)
- Adam Zaretsky
- Hub of Art Laboratories (HAL), of the Department of Audio & Visual Arts (AVArts), Ionian University in Corfu, Corfu, Greece
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Alejandro Mateo S, Azami-Conesa I, Martín-Maldonado B, Pastor-Tiburón N, Martín-Hernández R, González-González F, Gómez-Muñoz MT. Adaptation of the classical end-point ITS-PCR for the diagnosis of avian trichomonosis to a real-time PCR reveals Bonelli's eagle as a new host for Trichomonas gypaetinii. Parasitol Res 2022. [PMID: 36260254 DOI: 10.1007/s00436-022-07693-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/11/2022] [Indexed: 10/24/2022]
Abstract
Avian trichomonosis is a parasitic disease caused mainly by Trichomonas gallinae and other Trichomonas species. It can be asymptomatic, or it can produce a necrotic lesion in the upper digestive tract and spread to other organs, causing the death of the infected birds. In this study, we aimed to evaluate an adapted real-time PCR method for the diagnosis of different genotypes and species of avian oropharyngeal trichomonads. Fifty-six samples from the oropharynx of Bonelli's eagles (Aquila fasciata) obtained between 2018 and 2019 were analyzed using the real-time PCR and the end-point PCR, both targeting trichomonads ITS, and the results were compared by a coefficient of agreement. All positive samples were sequenced. The analysis showed a higher percentage of detection of real-time PCR ITS compared with end-point PCR ITS (64.3 vs 55.4%), and good agreement value (Kappa = 0.816). Melting temperature value for resulting amplicons of real-time PCR for avian trichomonads was 83.45 ± 0.72 °C. Genotypes A, D, and III were found among the sequences. Moreover, Trichomonas gypaetinii, a common species in scavenger birds, is reported for the first time in Bonelli's eagles.
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Najjari M, Sadjjadi SM, Khodadadi H, Farzaneh MR, Mattiucci S. Anisakis spp, DNA detection in paraffin-embedded tissue biopsies recovered from patients with gastritis using real-time PCR in Bushehr, Persian Gulf, Iran. Mol Biochem Parasitol 2022; 251:111494. [PMID: 35817309 DOI: 10.1016/j.molbiopara.2022.111494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
Anisakiasis is a zoonotic fish-born parasitic disease caused by anisakid nematodes. Paraffin-embedded blocks containing biopsy samples taken from patients suffering gastritis with unknown causes were investigated by real-time PCR, in the Bushehr region, Iran; where human anisakiasis has not been reported, so far. A total of 50 paraffin-embedded blocks were randomly selected from 250 archived blocks of the patients with gastritis. A SYBER green-based real-time PCR targeting the ITS1 region was developed for the identification of Anisakis genus. An 86 bp partial fragment of the Anisakis spp. ITS1 gene was amplified successfully. A total of 3 out of 50 samples (6 %) had positive amplification in the samples and their pathology reports showed a significant finding of moderate chronic gastritis with or without ulcers. In conclusion, the developed qPCR could be used for detecting Anisakis spp. larval DNA in human biopsy blocks. This study showed the hidden human cases of anisakiasis in the Bushehr for the first time.
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Affiliation(s)
- Mohsen Najjari
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mahmoud Sadjjadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Hossein Khodadadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Reza Farzaneh
- Department of Pathology, Faculty Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Simonetta Mattiucci
- Department of Public Health and Infectious Diseases, Section of Parasitology, Sapienza University, Rome, Italy.
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Yadav R, Saini R, Adhikary A, Kumar S. Unravelling cross priming induced heat stress, combinatorial heat and drought stress response in contrasting chickpea varieties. Plant Physiol Biochem 2022; 180:91-105. [PMID: 35398655 DOI: 10.1016/j.plaphy.2022.03.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/10/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Drought and high temperature stress affect chickpea growth and productivity. Often these stresses occur simultaneously in the field and lead to a wide range of molecular and metabolic adaptations. Two chickpea varieties; GPF2 (heat sensitive) and PDG4 variety (heat tolerant) were exposed to 35 °C for 24 h individually and along with drought stress. Five heat responsive signalling genes and 11 structural genes were analyzed using qPCR along with untargeted metabolites analysis using GC MS. Expression of antioxidant genes (CaSOD and CaGPX, CaAPX and CaCAT), transcription factors (CaHSFB2, CaHSFB2A, CaHSFB2B, CaHSP17.5 and CaHSP22.7) and signalling genes (CaCAM, CaGAD, and CaMAPK) were upregulated in GPF2 as compared to PDG4 variety. Principal component analysis (PCA), partial least-square discriminant analysis (PLS-DA), and heat map analysis were applied to the metabolomics data to identify the differential response of metabolites in two chickpea varieties. GC-MS analysis identified 107 and 83 metabolites in PDG4 and GPF2 varieties respectively. PDG4 variety accumulated more sugars, amino acids, sugar alcohols, TCA cycle intermediates which provided heat resistance. Additionally, the differential metabolic pathways involved in heat tolerance were alanine, aspartate, and glutamate metabolism, pantothenate CoA biosynthesis, fructose and mannose metabolism and pentose phosphate pathway in PDG4 variety. There was less accumulation of metabolites in the primed plants of both varieties as compared to the non-primed plants indicating less damage due to heat stress. The present study gives an overview of the molecular changes occurring in response to heat stress in sensitive and tolerant chickpea.
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Affiliation(s)
- Renu Yadav
- Centre for Biosciences, School of Basic and Applied Science, Central University of Punjab, Bathinda, 151401, India.
| | - Rashmi Saini
- Centre for Biosciences, School of Basic and Applied Science, Central University of Punjab, Bathinda, 151401, India.
| | - Arindam Adhikary
- Centre for Biosciences, School of Basic and Applied Science, Central University of Punjab, Bathinda, 151401, India.
| | - Sanjeev Kumar
- Centre for Biosciences, School of Basic and Applied Science, Central University of Punjab, Bathinda, 151401, India; Department of Botany, School of Basic Science, Central University of Punjab, Bathinda, 151401, India.
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20
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Freire MP, de Oliveira Garcia D, Lima SG, Pea CRD, Reusing Junior JO, Spadão F, Cury AP, Rossi F, Nahas WC, David-Neto E, Pierrotti LC. Performance of two methods of carbapenem-resistant Enterobacterales surveillance on a kidney transplant ward: selective culture of and real-time PCR directly from rectal swabs. Infection 2022; 50:1525-1533. [PMID: 35534755 DOI: 10.1007/s15010-022-01839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Infection with carbapenem-resistant Enterobacterales (CRE) is associated with a high mortality rate in kidney transplant recipients, and colonization with CRE is one of the major risk factors for CRE infection. There is, therefore, a need to improve the capacity to detect colonization with CRE among inpatients. METHODS In this prospective study, we compared the performance of real-time PCR for carbapenemase directly from rectal swabs with that of conventional CRE surveillance culture in all patients admitted to a kidney transplant ward between February 2019 and March 2020. Surveillance culture and real-time PCR were performed at admission and weekly until hospital discharge. Two perineum-rectal swabs were collected: one for culture and one for PCR. RESULTS We collected 905 paired samples for CRE surveillance from 399 patients, of whom 347 (87.0%) were kidney transplant recipients and 52 were waiting list patients. CRE was detected by culture and/or PCR in 75 patients (18.8%). Positivity for CRE was identified by PCR in 62 (15.5%) of the 399 patients and by culture in 55 (13.8%); 20 (5.0%) of the patients tested positive only on PCR, and 13 (3.3%) tested positive only on culture. The most common carbapenemase and species were, respectively, blaKPC (in 85.5%) and Klebsiella pneumoniae (in 80.0%). Infection with CRE occurred in 21.6% of the colonized patients, those cases occurred only among kidney transplant recipients. None of the patients who tested negative on culture developed CRE infection. CONCLUSION In conclusion, the two methods are complementary and could be useful in a scenario of high CRE prevalence.
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Affiliation(s)
- Maristela P Freire
- Working Committee for Hospital Epidemiology and Infection Control, School of Medicine, Hospital 18 das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Rua Dr Eneas de 19 Carvalho Aguiar, 255, São Paulo, SP, 05403-900, Brazil.
| | | | | | | | - Jose Otto Reusing Junior
- Department of Urology, Renal Transplantation Unit, University of São Paulo School of Medicine Hospital das Clínicas, São Paulo, Brazil
| | - Fernanda Spadão
- Working Committee for Hospital Epidemiology and Infection Control, School of Medicine, Hospital 18 das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Rua Dr Eneas de 19 Carvalho Aguiar, 255, São Paulo, SP, 05403-900, Brazil
| | - Ana Paula Cury
- Microbiology Laboratory, Central Laboratory, University of São Paulo School of Medicine Hospital das Clínicas, São Paulo, Brazil
| | - Flavia Rossi
- Microbiology Laboratory, Central Laboratory, University of São Paulo School of Medicine Hospital das Clínicas, São Paulo, Brazil
| | - William C Nahas
- Department of Urology, Renal Transplantation Unit, University of São Paulo School of Medicine Hospital das Clínicas, São Paulo, Brazil
| | - Elias David-Neto
- Department of Urology, Renal Transplantation Unit, University of São Paulo School of Medicine Hospital das Clínicas, São Paulo, Brazil
| | - Ligia C Pierrotti
- Department of Infectious Diseases, University of São Paulo School of Medicine Hospital das Clínicas, São Paulo, Brazil
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21
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Soejima M, Koda Y. Detection of five common variants of ABO gene by a triplex probe-based fluorescence-melting-curve-analysis. Anal Biochem 2022; 648:114668. [PMID: 35341729 DOI: 10.1016/j.ab.2022.114668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/01/2022]
Abstract
Current studies have suggested that the ABO blood group system is associated with several clinical conditions. For large-scale genotyping of ABO alleles, we developed a triplex fluorescence melting curve analysis (FMCA) to determine five single nucleotide variants (SNVs), c.261delG, c.796C>A, c.802G>A and c.803G>C and c.1061delC, responsible for common ABO phenotypes using dual-labeled self-quenched (TaqMan) probes in a single tube. We accurately determined c.796C>A, c.802G>A, and c.803G>C genotypes using a FAM-labeled probe, c.261delG using a CAL Fluor Orange 560- labeled probe, and c.1061delC using a Cy5-labeled probe. The present genotyping results of five SNVs in 214 subjects of the 1000 Genomes Project were in full agreement with those of the database sequence. The predicted ABO phenotypes using combinations of these five SNVs by this method in 288 Japanese subjects were in complete agreement with those by hemagglutination assay, although we did not find any A2 (alleles containing c.1061delC) or O.02 (alleles containing c.802G>A) alleles. The present triplex probe-based FMCA is a valid and credible method for a considerably accurate large-scale determination of ABO allele genotypes and estimation of phenotypes.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan.
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22
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Hindupur A, Menon T, Dhandapani P. Molecular investigation of human metapneumovirus in children with acute respiratory infections in Chennai, South India, from 2016-2018. Braz J Microbiol 2022; 53:655-661. [PMID: 35118597 PMCID: PMC9151977 DOI: 10.1007/s42770-022-00689-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Human metapneumovirus (hMPV) has emerged as a frequent cause of acute respiratory infections (ARI) among young children. The prevalence and genetic diversity of hMPV circulating in Chennai, Southern India, has not been studied yet. Hence, this study was aimed to investigate the prevalence, co-infection with other respiratory viruses like HRSV A and B, influenza A and B, hRV and HPIV 1-4 viruses, socio-demographic associations, and genotypes of hMPV among children in Chennai. A total of 350 nasal swab specimens were collected from children with ARI during April 2016 to August 2018 and tested for hMPV by real time PCR method. In this study, hMPV was detected in 4% (14/350) of the samples. One hMPV positive sample was found to be co-infected with influenza B virus. The mean and median ages of the children with hMPV infection were 61.5 months (5.1 years) and 83 months (6.9 years), respectively. Phylogenetic analysis of the partial F gene revealed the presence of A2c subcluster among the study strains as well as with B1 and B2 lineages. The prevalence data obtained in this study is important in evaluating the role of hMPV in childhood ARI and emphasizes the importance of routine viral diagnosis in hospitals. To the best of our knowledge, this is the first study to report the prevalence, seasonality, and genetic diversity of hMPV in Chennai as well as the first study to report A2c subcluster of hMPV among children in India.
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Affiliation(s)
- Anusha Hindupur
- grid.413015.20000 0004 0505 215XDepartment of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu India
| | - Thangam Menon
- Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu India
| | - Prabu Dhandapani
- grid.413015.20000 0004 0505 215XDepartment of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu India
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Barros FR, Leite DC, Guimarães LJ, Lopes JM, Vasconcelos MW, Ferreira LX, Gonçalves S, Pastre VG, Pereira G, Trentin AB, Gabiatti NC, Kuhn BC, Perseguini JM, Wendt SN, Ghisi NC. Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene Allplex TM 2019-nCoV protocol. J Virol Methods 2022; 300:114429. [PMID: 34919975 PMCID: PMC8668600 DOI: 10.1016/j.jviromet.2021.114429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen's Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.
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Affiliation(s)
- Flavia R.O. Barros
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | - Deborah C.A. Leite
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nédia C. Ghisi
- Corresponding authors at: Universidade Tecnológica Federal do Paraná, Estrada para Boa Esperança, Km 4, Dois Vizinhos, PR, 85660-000, Brazil
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Karakavuk M, Can H, Karakavuk T, Gül A, Alak SE, Gül C, Ün C, Gürüz AY, Döşkaya M, Döşkaya AD. Rapid detection of Toxoplasma gondii DNA in cat feces using colorimetric loop-mediated isothermal amplification (LAMP) assays targeting RE and B1 genes. Comp Immunol Microbiol Infect Dis 2022; 81:101745. [PMID: 35030533 DOI: 10.1016/j.cimid.2022.101745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022]
Abstract
Toxoplasma gondii is an obligate protozoan parasite that can infect mammals and birds. Cats are the definitive host of T. gondii and have a very important role in transmission of toxoplasmosis due to the shedding of millions of unsporulated oocysts, that become infective in the environment. Since cats play a major key role in the epidemiology of toxoplasmosis, rapid and accurate diagnosis of infected cats has utmost importance. In this study, we developed a novel colorimetric loop mediated isothermal amplification (LAMP) assay detecting T. gondii RE gene and modified a previously developed colorimetric LAMP assay targeting B1 gene to detect T. gondii DNA in cat feces for the first time. The analytical sensitivity of colorimetric LAMP assays was determined using plasmid controls. The clinical sensitivities of both colorimetric LAMPs were determined using cat fecal DNA samples that were confirmed to be positive by two different real-time PCRs in our previous study. According to the results, analytical sensitivities of both assays were 1 copy plasmid/reaction. Using real-time PCR as a reference method, sensitivities of colorimetric LAMP assays targeting RE and B1 genes were 100% and 97.56% whereas specificities of both assays were 100%. Overall, the colorimetric LAMP RE assay developed in this study brings an advantage in the diagnosis of T. gondii in cat fecal samples since it has higher sensitivity, does not need for experienced personnel, and can be applied in basic laboratories or in the field.
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Abstract
The most commonly used molecular diagnostic technique is the polymerase chain reaction (PCR). PCR detects a short section of genetic code of interest, a cancer gene, human mRNA or a pathogen's genome. It is used by every specialty in medicine and surgery, with increasing frequency and importance. In this article, the history, steps of the cycle, uses, forms, advantages and disadvantages of PCR are discussed. With the SARS coronavirus-2 pandemic having such an enormous impact on the delivery of elective surgery, decisions to proceed or defer are made by surgeons on a daily basis, based on PCR results. An understanding of these results is provided, what they tell us, what they do not and what other information is required to make these decisions. It is imperative to also look beyond PCR results, seeing the patient within the context of their symptoms, other pathology and imaging results, with the assistance of a medical virologist or microbiologist, in complex cases.
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Affiliation(s)
- Adhyana Mahanama
- is a Senior Clinical Fellow in Medical Virology at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared.,is a Consultant Medical Virologist at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared
| | - Eleri Wilson-Davies
- is a Senior Clinical Fellow in Medical Virology at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared.,is a Consultant Medical Virologist at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared
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26
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Vasanth S, Mohanraj RS, Mandal J. In-vitro study of the effect of Centella asiatica on cholera toxin production and the gene expression level of ctxA gene in Vibrio cholerae isolates. J Ethnopharmacol 2021; 279:113930. [PMID: 33596471 DOI: 10.1016/j.jep.2021.113930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 12/09/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Centella asiatica (L.) Urb or Indian pennywort is a plant of ethnopharmacological relevance, commonly called as Brahmi in South India known for its antimicrobial property in gut and for the treatment of other gut ailments. Natural anti-virulence drugs that disarm pathogens by directly targeting virulence factors or the cell viability and are thus preferred over antibiotics as these drugs impose limited selection pressure for resistance development. In this regard, an in-vitro experimental study was conducted to know the effect of extract of Centella asiatica(L.) Urb. on cholera toxin, gene expression and its vibriocidal effect on five standard strains of Vibrio cholerae; IDH03097 (El Tor variant), N16961 (El Tor), O395 (Classical) as well as five clinical strains (Haitian variant). AIM OF THE STUDY To study the effect of extract of Centella asiatica on Vibrio cholerae. MATERIALS AND METHODS Crude extract was prepared from the leaves and stem part of the plant. The vibriocidal concentration was tested at different concentrations of the extract. The amount of cholera toxin released from the strains before and after exposure to the extract of Centella asiatica to Vibrio cholerae was measured using Bead ELISA. ctxA gene expression in the strains before and after exposure to extract of Centella asiatica was measured using quantitative real time PCR. All the above assays were performed with commercially obtained asiaticoside as well. RESULTS The vibriocidal activity was tested at the different concentration of the extract, where 1g/mL of crude extract and 12.5mg/mL of asiaticoside was found to be vibriocidal. The amount of cholera toxin released before and after the exposure to extract of C. asiatica was measured using Bead ELISA, showing a reduction of 70%, 89% and 93% toxin produced by classical, El Tor and variant respectively. ctxA gene expression before and after exposure to extract of Centella asiatica as well as asiaticoside was measured using qRT-PCR. We found a decrease in expression of ctxA gene transcription by 6.19 fold in classical strain, 4.29 fold in El Tor, 1.133 fold in variant strains and about 10.13-10.20 fold for the clinical strains of V. cholerae using the extract of C.asiatica while, the reduction with the exposure to the asiaticoside were 2.762 fold in classical strain, 4.809 in El Tor, 24.1 in variant strain and 34.77 - 34.8 for the clinical strains. CONCLUSION Centella asiatica extract inhibited the CT production in Vibrio cholerae as well as decreased the transcription of ctxA gene expression.
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Affiliation(s)
| | | | - Jharna Mandal
- Department of Microbiology, JIPMER, Pondicherry, India.
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27
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Naeem M, Iqbal M, Ul-Allah S, Chaudhary HJ, Nazeer W, Ashraf J, Baloch FS. Expression studies of stress responsive genes in cotton Gossypium hirsutum L. Mol Biol Rep 2021; 48:7077-7085. [PMID: 34535835 DOI: 10.1007/s11033-021-06696-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Cotton is the world's richest source of natural fiber. Meanwhile cotton plant is top ranked stress sensitive plant thereby affecting its yield and fiber quality. But, in climate change scenario, fiber yield and quality are being affected due to environmental stresses, especially heat, drought and salinity. Present study is aimed to identify cotton genotype harboring prominently expressed stress responsive genes. METHODS Four cotton genotypes (IUB-13, IUB-222, IUB-09 and MM-58) were evaluated under drought and salinity stress for yield traits and expression of different stress responsive genes (GhWRKY3, GhDREB2 and GhRDR6). RESULTS Pronounced expression of GhWRKY3, GhDREB2and GhRDR6 was observed in cotton variety IUB-13 in stress condition (drought and salinity) as compared to control followed by IUB-222 which revealed that these genotypes might possess substantial potential to cope with environmental hazards encountered in growing season CONCLUSION: Utilization of cotton genotypes i.e., IUB-13 and IUB-222 in cotton breeding program can be very much fruitful for developing cotton genotypes adoptable to climate change.
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Affiliation(s)
- Muhammad Naeem
- Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Muhammad Iqbal
- Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sami Ul-Allah
- College of Agriculture, Bahadur Sub Campus Layyah, Bahauddin Zakariya University, Multan, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wajad Nazeer
- Department of Plant Breeding and Genetics, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Javeria Ashraf
- Department of Plant Breeding and Genetics, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Faheem Shahzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey.
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Hagag MM, Ghazy MM, Elhelbawy NG. Tumor necrosis factor-α gene promoter -308 and -238 polymorphisms and its serum level in psoriasis. Biochem Biophys Rep 2021; 27:101050. [PMID: 34169157 PMCID: PMC8209664 DOI: 10.1016/j.bbrep.2021.101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Psoriasis is a chronic, immune-mediated, inflammatory skin disease affecting genetically predisposed individuals and requiring long-term treatment. The etiology of psoriasis is not fully understood. This article aimed to determine association between genetic polymorphisms in tumor necrosis factor-α (TNF -α) promoter -308 (rs1800629) and -238 (rs 361,525) and its serum level in psoriasis patients. METHODS The study was conducted on 70 patients with psoriasis and 70 age and sex-matched, healthy individuals. All patients were subjected to history taking and complete medical examination. The polymorphisms of TNF -α promoter gene -308 (rs1800629) and -238 (rs 361,525) were detected by real time PCR and Serum levels of TNF -α were measured by ELISA technique. RESULTS AG polymorphism and A allele of TNF-α -238 G/A (rs 361,525) were significantly more in patients than controls, whereas AG polymorphism and A allele of TNF-α -308 G/A (rs1800629) were significantly more in controls than patients. There were significant high levels of TNF-α in serum of patients in comparison to controls. CONCLUSIONS The AG polymorphism and A allele of TNF-α -238G/A (rs 361,525) may act as a risk factor for occurrence of psoriasis, whereas AG polymorphism and A allele of TNF-α -308G/A (rs1800629) may have protective role. There is pivotal role of TNF-α as a pro-inflammatory mediator in pathogenesis of psoriasis.
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Affiliation(s)
- Magda M. Hagag
- Dermatology, Andrology and Sexually Transmitted Diseases (STDs) Department, Faculty of Medicine, Menoufia University, Egypt
| | - Mai M. Ghazy
- Dermatology, Andrology and Sexually Transmitted Diseases (STDs) Department, Ministry of Health, Kafrelsheikh, Egypt
| | - Nesreen G. Elhelbawy
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Egypt
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Fouda E, Elrazek Midan DA, Ellaban R, El-kousy S, Arafat E. The diagnostic and prognostic role of MiRNA 15b and MiRNA 378a in neonatal sepsis. Biochem Biophys Rep 2021; 26:100988. [PMID: 33817353 PMCID: PMC8010206 DOI: 10.1016/j.bbrep.2021.100988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Sepsis is one of the major factors for both term and preterm babies with morbidity and mortality. On the basis of recent clinical trials, altered circulating micro-RNAs (miRNAs) may serve as possible biomarkers in sepsis for diagnosis and prognosis. The aim of this research is to assess the diagnostic and prognostic biomarkers of miRNA 15b and miRNA 378a for neonatal sepsis. SUBJECTS & METHODS This study was carried out 25 neonates with sepsis admitted to neonatal ICU of Menoufia University Hospital and 25 healthy controls from February 2019 to May 2020. The relative quantification (RQ) of miRNA-15b and miRNA-378a expression was assessed using real time PCR technique. Results: Our results demonstrated that patients with sepsis had significantly higher level of MiRNA-15b than the healthy volunteers. On the other hand, patients with sepsis had significantly lower level of MiRNA-378a than the healthy volunteers. The ROC curve showed that the serum MiRNA-15b was a significant discriminator of sepsis with a combined sensitivity and specificity of 76% and 88% with cutoff point of 3.24. In addition, serum MiRNA-378a was a significant discriminator of sepsis with a combined sensitivity and specificity of 60% and 88% with cutoff point of 0.361. The miRNA-15b expression significantly correlated positive with respiratory rate (r =0.415,p =0.039), WBCs (r = 0.408, p =0.043), and CRP (r =0.407, p=0.043). Likewise, miRNA-378a expression significantly correlated negative with respiratory rate (r =-0.415p =0.024), WBCs (r =- 0.442, p =0.027), and CRP (r =- 0.459, p=0.021). CONCLUSION Both MiRNA 15b and 378a are promising biomarker for neonatal sepsis.
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Affiliation(s)
- Eman Fouda
- Faculty of Science, Menoufia University, Egypt
| | | | - Rania Ellaban
- Diploma of Biochemistry, Faculty of Science, Menoufia University, Egypt
| | | | - Eman Arafat
- Faculty of Medicine, Menoufia University, Egypt
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Yuan F, Fu J, Liu X, Bai J, Peddireddi L. Development of a quantitative real time RT-PCR assay for sensitive and rapid detection of emerging Atypical Porcine Pestivirus associated with congenital tremor in pigs. J Virol Methods 2021; 296:114220. [PMID: 34182037 DOI: 10.1016/j.jviromet.2021.114220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022]
Abstract
Atypical Porcine Pestivirus (APPV) is reported as the etiologic agent for type AII congenital tremors in newborn piglets. Initial PCR-based diagnostic tests to detect APPV were designed based on the limited sequence information and are not capable of detecting the majority of APPV strains. A sensitive and reliable PCR-based diagnostic test is critical for accurate detection of APPV. In this study, a quantitative reverse transcription PCR (RT-qPCR) assay was developed for reliable detection of all currently known APPV strains. The assay design also included swine 18S rRNA gene as an internal control to monitor RNA extraction efficiency. Two APPV gene fragments, one each from NS5b and NS3, were cloned and used to determine the dynamic range of detection, linearity and analytical sensitivity/limit of detection (LOD). Both individual and multiplex assays (duplex and triplex) had correlation coefficients of >0.99 and PCR amplification efficiencies of >90 %. Comparison of detection limit and analytical sensitivity between individual, and multiplex assays indicated no inhibition of PCR sensitivity upon multiplexing. The detection limit for APPV target, based on analytical sensitivity, is 7.75 copies (NS5b) and 5.2 copies (NS3) per reaction. Assay specificity was verified by testing nucleic acids of other closely related pestiviruses and clinical samples that are positive for other common swine pathogens. Assay sensitivity was also assessed on synthesized gene fragments of the most divergent China strains. Testing 339 known APPV-positive and 202 negative clinical samples demonstrated a good diagnostic sensitivity and specificity. Data from six independent runs, including 5 replicates of three clinical samples with three Ct ranges, were utilized to assess inter-assay repeatability and intra-assay reproducibility. This analysis demonstrated intra-assay/inter-assay coefficients of variation of 0.71 % and 0.01 %, respectively, with a PCR efficiency of 92.71 % for the triplex assay. Testing of 1785 clinical samples revealed ∼19 % prevalence of APPV in the US swine herds and oral fluids demonstrates to be a reliable specimen for viral detection. This multiplex RT-qPCR assay offers a rapid and reliable detection of APPV in swine herds and serves as useful tool in APPV surveillance and epidemiological investigations.
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Ramezani A. CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm. J Microbiol Methods 2021; 187:106267. [PMID: 34116107 DOI: 10.1016/j.mimet.2021.106267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/05/2021] [Accepted: 06/06/2021] [Indexed: 11/25/2022]
Abstract
In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for converting the data obtained from different runs containing identical standard samples into one run with the same amplification efficiency and threshold value. For this purpose, two formulas were designed; one to convert the amplification efficiency of the each run to 100%, and the other one for converting data from different runs into one run. Utilizing these two formulas, an algorithm was developed and named CtNorm. The online version of CtNorm algorithm is available at http://ctnorm.sums.ac.ir/. We used qRT-PCR technique to validate the accuracy of the designed algorithm for the normalization of four different human internal control genes. Normalizing the Ct values obtained from separate runs with the CtNorm algorithm has eliminated the differences and the average of the Ct values has become similar to the condition in which all the samples were amplified in a single run. The CtNorm algorithm could be utilized for equalizing the Ct values of several qRT-PCR runs with the same standard samples. The algorithm has also the ability to convert the amplification efficiency to 100% which is useful in absolute and relative quantification.
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Affiliation(s)
- Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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Daprà V, Alliaudi C, Galliano I, Dini M, Curcio GL, Calvi C, Archetti M, Gavatorta M, Bergallo M. TaqMan real time PCR for the Detection of the Gilbert's Syndrome Markers UGT1A1*28; UGT1A1*36 and UGT1A1*37. Mol Biol Rep 2021; 48:4953-9. [PMID: 34089128 DOI: 10.1007/s11033-021-06454-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Gilbert's syndrome is characterized by mild unconjugated hyperbilirubinemia. The key of this disease is a diminished activity of UDP-glucuronosyltransferase 1A1 (UGT1A1). TA insertion into the TATA box promoter region of the UGT1A1 gene on chromosome 2 is the genetic basis of Gilbert's syndrome (UGT1A1*28). An extra TA insert leads to eight (TA)8 repeats (UGT1A1*37) resulting in a further reduction of glucuronidation activity. A variant lacking one TA repeat (TA)5 (UGT1A1*36) has been identified. (TA)8 repeats (UGT1A1*37) and (TA)5 (UGT1A1*36) have been detected in Africans (frequency up to 0.07 and 0.08 respectively). We present a real time PCR method for genotyping the UGT1A1 (TA)n polymorphism (UGT1A1*28, UGT1A1*36, UGT1A1*37) using Taqman PCR on 7500 and cfx96 Real-Time PCR System. We present a real time PCR method for genotyping the UGT1A1 (TA)n polymorphism (UGT1A1*28, UGT1A1*36, UGT1A1*37) using Taqman PCR. About clinical validation, all 53 samples collected from patients referred for suspected Gilbert's syndrome were analyzed. We found 21 on the 53 patients (39.6%) were homozygotes (UGT1A1-TATA (TA)6) and referred as wild-type, 13 on the 53 patients (24.5%) were homozygotes (UGT1A1-TATA (TA)7) and referred as mutated, 1 on the 53 patients (1.9%) were homozygotes (UGT1A1-TATA (TA)8) and referred as mutated, 1 on the 53 patients (1.9%) were heterozygotes (UGT1A1-TATA (TA)7/8) and referred as mutated, 1 on the 53 patients (1.9%) were heterozygotes (UGT1A1-TATA (TA)5/6) and referred as mutated, and 16 on the 53 patients (30.2%) were heterozygotes (UGT1A1-TATA (TA)6/7). None were homozygotes UGT1A1-TATA (TA)5, homozygotes UGT1A1-TATA (TA)8, or heterozygotes with (TA)5 or (TA)8 alleles. The newly described technique represents a valid alternative method to sequencing, mainly due to its rapidity, easiness, and minor costs.
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Dharmaratnam A, Sudhagar A, Nithianantham SR, Das S, Swaminathan TR. Evaluation of candidate reference genes for quantitative RTqPCR analysis in goldfish (Carassius auratus L.) in healthy and CyHV-2 infected fish. Vet Immunol Immunopathol 2021; 237:110270. [PMID: 34015681 DOI: 10.1016/j.vetimm.2021.110270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022]
Abstract
The accuracy of quantitative real time PCR (RTqPCR) can be attained only when a suitable reference gene is used. The gene expression for a particular gene may vary within different cells at different conditions. Hence, the suitability and stability of various potential reference genes have to be determined for expression studies. In this study, we have examined the potential of four different reference genes including β-Actin (ACTB), 18S ribosomal RNA (18S), glyceraldehyde-3P-dehydrogenase (GAPDH), and elongation factor 1 alpha (EF1AA) in seven different tissues including gill, liver, kidney, spleen, heart, muscle and intestine of goldfish (Carassius auratus). The housekeeping genes were analyzed from healthy fish and in CyHV-2 challenged fish. Based upon the real time PCR results the gene expression varied among the genes and in tissues. The expression levels of the housekeeping genes were then compared and evaluated with the RefFinder web tool which analyses results using four different algorithms - BestKeeper, delta Ct, geNorm and NormFinder. EF1AA was ranked to be the best gene in healthy fish by BestKeeper and geNorm analysis. The delta Ct and NormFinder algorithm have found 18S to be a stable gene in healthy fish but 18S was given to be least expressed in challenged fish. ACTB was also given as a stable gene by geNorm analysis in both healthy and challenged fish. Also, in CyHV-2 challenged fish, EF1AA was identified as the best gene by all the three analysis except by BestKeeper analysis, where it has ranked GADPH as the best housekeeping gene. Expression of the four candidate reference genes differed across all tissue types tested, inferring that a thorough study of the reference genes is necessary for cross tissue comparison. These results can be further used in the immune gene response study of goldfish infected with any viral pathogen to develop better health strategies in the disease management of goldfish aquaculture.
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Affiliation(s)
- Arathi Dharmaratnam
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, ICAR CMFRI Campus, Kochi - 682 018, Kerala, India.
| | - Arun Sudhagar
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, ICAR CMFRI Campus, Kochi - 682 018, Kerala, India
| | - Sundar Raj Nithianantham
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, ICAR CMFRI Campus, Kochi - 682 018, Kerala, India
| | - Sweta Das
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, ICAR CMFRI Campus, Kochi - 682 018, Kerala, India
| | - Thangaraj Raja Swaminathan
- Peninsular and Marine Fish Genetic Resources Centre, ICAR- National Bureau of Fish Genetic Resources, ICAR CMFRI Campus, Kochi - 682 018, Kerala, India.
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Salehi-Vaziri M, Arashkia A, Mostafavi E, Jalali T, Hassan Pouriayevali M, Fazlalipour M, Shoja Z, Rohani M, Esmaeili S, Fotouhi-Chahooki F, Baesi K, Maleki A, Dawood Mousavi Nasab S, Ahmadi Z, Mohammadi T, Azad-nManjiri S, Sadegh Shams Nosrati M, Tavakoli M, Fereydouni Z, Khakifirouz S, Mirab Samiee S, Biglari A, Azadmanesh K. How Iran responded to expanding need for laboratory services for COVID-19? Health Policy Technol 2021; 10:100506. [PMID: 33880324 DOI: 10.1016/j.hlpt.2021.100506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
After the emergence of SARS-CoV-2 in early 2020 in Iran, the rapid response team of Pasteur Institute of Iran was the first lab starting detection and report of suspected human samples. This article is a short summery of all actions from the preparedness for detecting the first cases of COVID-19, expanding the nationwide laboratory service, choosing the suitable laboratory tests and other challenges in laboratory detection during SARS-CoV-2 pandemic in Iran.
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Key Words
- AUMS, Arak University of Medical Sciences
- CLN, COVID-19 laboratory network
- COVID-19
- EVAg, European Virus Archive – GLOBAL
- HKU, Hong Kong University
- Iran
- PII, Pasteur Institute of Iran
- QUMS, Qom University of Medical Sciences
- RdRp, RNA dependent RNA polymerase
- Real time PCR
- SARS-CoV-2
- SBUMS, Shahid Beheshti University of Medical Sciences
- TIB, TIB MOLBIOL Company
- TUMS, Tehran University of Medical Sciences
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Agarwal R, Gupta E, Dubey S, Padhi A, Khodare A, Kumar G, Sarin SK. Pooled nasopharyngeal swab collection in a single vial for the diagnosis of SARS CoV-2 infection: An effective cost saving method. Indian J Med Microbiol 2021; 39:231-234. [PMID: 33515633 PMCID: PMC7839627 DOI: 10.1016/j.ijmmb.2020.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Pool testing is one of the strategy to expedite testing capacities while simultaneously conserving various diagnostic kits, reagents and consumables and time. In the present study, we investigated potential role of combined specimen collection technique for the diagnosis of SARS-CoV-2 virus infection where five nasopharyngeal swabs were collected from different individuals and pooled together in a single viral transport medium (VTM). MATERIAL AND METHODS This pilot study was conducted on different cohorts of Delhi state. Two nasopharyngeal swabs were collected from each enrolled individual. One swab was put into VTM vial to be further used for individual swab testing (ID). The other swab was put into a fresh VTM for pool swab collection. Each pool comprised five swabs collected from five different patients in one VTM vial. Both IDs and pools were tested in parallel for the detection of SARS-CoV-2 using real time PCR. RESULTS A total of 46 pools were collected from 230 enrolled individuals.Among 230 ID tested, 60 were found to be positive for both E and RdRp gene. Among 46 pools, 25 pools included all negatives samples and remaining 21 pools included one or more positives. Comparing ID with pool results, overall concordance was seen in 42 pools (91.3%). Four pools showed false positive results as all included samples on ID testing were found to be negative. Considering ID results as reference, swab pool showed 100% sensitivity, 84% specificity, 84% positive predictive value and 100% negative predictive value. CONCLUSION The pooling of swab strategy could be beneficial only among asymptomatic in low prevalence areas.
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Affiliation(s)
- Reshu Agarwal
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India.
| | - Shantanu Dubey
- Department of Hospital Operations, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Abhishek Padhi
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Arvind Khodare
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Guresh Kumar
- Department of Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
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Ricci I, Cersini A, Manna G, Marcario GA, Conti R, Brocherel G, Grifoni G, Eleni C, Scicluna MT. A Canine Distemper Virus Retrospective Study Conducted from 2011 to 2019 in Central Italy (Latium and Tuscany Regions). Viruses 2021; 13:272. [PMID: 33578722 DOI: 10.3390/v13020272] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 12/03/2022] Open
Abstract
Canine distemper virus (CDV) is a highly lethal contagious viral pathogen mainly found in domestic and wild canids and mustelids. Although, in Italy, circulating strains of Europe 1, Europe wildlife and Arctic type are reported, data relating to Latium and Tuscany regions are limited. In view of this, through passive surveillance, we investigated the presence of CDV and which strains were circulating in these Regions. From March 2017 to October 2019, a group of 122 subjects were tested for CDV using a PCR protocol described in the literature, with 12 detected positive; analyses were carried out on a set of target samples (brain and lung, conjunctival, nasal and rectal swabs, urine or swab from bladder and intracardiac clot) that was defined for the detection of CDV in both live and dead animals. The rectal swab, easily collected also from live animals, represented the most suitable sample for CDV diagnosis, with 9 positive of the 11 (81.82%) tested. In addition, brain and lung of 15 subjects out of 181 susceptible animals collected between 2011 and 2018, during post mortem investigations in routine diagnostic activity, were CDV positive. Molecular analyses of all positive samples, using a 287 bp fragment located within the conserved N terminus of the morbillivirus nucleoprotein gene, detected the circulation of strain CDV599/2016 (KX545421.1) belonging to the “Europe wildlife” lineage, and of strain CDV12254/2015 (KX024709.1), belonging to the Arctic-lineage, thus confirming the co-circulation of the two lineages, as already noted in previous studies.
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Cui Y, Guo F, Cai X, Cao X, Guo J, Wang H, Yang B, Zhou H, Su X, Blackall PJ, Xu F. Ct value-based real time PCR serotyping of Glaesserella parasuis. Vet Microbiol 2021; 254:109011. [PMID: 33610013 DOI: 10.1016/j.vetmic.2021.109011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/03/2021] [Indexed: 11/24/2022]
Abstract
Glaesserella parasuis is the causative agent of Glässer's disease in swine. Serotyping plays an essential role in prevalence investigations and in the development of vaccination strategies for the prevention of this disease. Molecular serotyping based on variation within the capsule loci of the 15 serovars is more accurate and efficient than traditional serological serotyping. To reduce the running time and facilitate ease of data interpretation, we developed a simple and rapid cycle threshold (Ct) value-based real time PCR (qPCR) method for the identification and serotyping of G. parasuis. The qPCR method distinguished between all 15 serovar reference strains of G. parasuis with efficiency values ranging between 85.5 % and 110.4 % and, R2 values > 0.98. The qPCR serotyping was evaluated using 83 clinical isolates with 43 of the isolates having been previously assigned to a serovar by the gel immuno-diffusion (GID) assay and 40 non-typeable isolates. The qPCR results of 41/43 (95.3 %) isolates were concordant with the GID assay except two isolates of serovar 12 were assigned to serovar 5. In addition, the qPCR serotyping assigned a serovar to each of the 40 non-typeable isolates. Of the 83 isolates tested to assign a serovar, a concordance rate of 98.8 % (82/83) was determined between the qPCR and the previously reported multiplex PCR of Howell et al. (2015) (including those that were either serovars 5 or 12). Despite the inability to differentiate between serovars 5 and 12, the Ct value-based qPCR serotyping represents an attractive alternative to current molecular serotyping method for G. parasuis and could be used for both epidemiological monitoring and the guidance of vaccination programs.
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Affiliation(s)
- Yifang Cui
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Fangfang Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuwang Cai
- State Key Laboratory of Agricultural Microbiology, Division of Animal Infectious Disease, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaoya Cao
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jie Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongjun Wang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bing Yang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Hongzhuan Zhou
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xia Su
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fuzhou Xu
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Vanshika S, Preeti A, Sumaira Q, Vijay K, Shikha T, Shivanjali R, Shankar SU, Mati GM. Incidence OF HPV and EBV in oral cancer and their clinico-pathological correlation- a pilot study of 108 cases. J Oral Biol Craniofac Res 2021; 11:180-184. [PMID: 33598395 DOI: 10.1016/j.jobcr.2021.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/05/2021] [Indexed: 12/07/2022] Open
Abstract
Introduction Out of all non-communicable diseases, cancer is the leading cause of death in the 21st century. Oral cancer ranks in top ten cancers in the world and oncogenic viruses contribute to its development and are a major preventable risk factor for it. Material and methods In the present study we intend to find the incidence of HPV and EBV by PCR in 108 sporadic oral cancer patients and study the clinico-pathological variables in agreement to their presence or absence. Results We found that the incidence of EBV in oral cancer is much higher (30/108; 27.8%) than HPV 16 (14/108; 13%) and, a complete absence of HPV 18 (0/108) was reported by real time PCR. Co-infection by EBV and HPV was reported in 5.6% cases (6/108). However, on comparing this data with the corresponding clinico-pathological cofactors (age, gender, grade of tumour, tumour size, nodal status, metastasis, DOI, TIL, ENE) it was found that there was no statistical significance between the two. Conclusion Hence, we conclude that these oncogenic viruses are independent cofactors to oral cancer development and none of the clinico-morphologic variable is associated with the viral etiology.
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Affiliation(s)
- Shahi Vanshika
- Department of Pathology, King George's Medical University, Lucknow, UP, India
| | - Agarwal Preeti
- Department of Pathology, King George's Medical University, Lucknow, UP, India
| | - Qayoom Sumaira
- Department of Pathology, King George's Medical University, Lucknow, UP, India
| | - Kumar Vijay
- Department of Surgical Oncology, King George's Medical University, Lucknow, UP, India
| | - Tewari Shikha
- Department of Laboratory Medicine and Pathology, Medanta Hospital, Lucknow, UP, India
| | | | - Singh Uma Shankar
- Department of Pathology, King George's Medical University, Lucknow, UP, India
| | - Goel Madhu Mati
- Department of Laboratory Medicine and Pathology, Medanta Hospital, Lucknow, UP, India
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Gupta E, Khodare A, Rani N, Singh G, Aggarwal K, Sharma M. Performance evaluation of Xpert HBV viral load (VL) assay: Point-of-care molecular test to strengthen and decentralize management of chronic hepatitis B (CHB) infection. J Virol Methods 2021; 290:114063. [PMID: 33453301 DOI: 10.1016/j.jviromet.2021.114063] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/05/2021] [Accepted: 01/10/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Estimation of hepatitis B (HBV) viral load (VL) is critical in hepatitis-B cascade-of-care and at present there is no point of care (POC) molecular assay available for the same. This study evaluated the performance of a new near point of care molecular assay Xpert HBV- VL assay against the approved assays. MATERIALS & METHODS In this study 172 archived previously tested samples, were simultaneously re-tested for HBV DNA on 3 real-time PCR assays: Abbott Real-Time HBV, Roche TaqMan® HBV and Xpert HBV assay. RESULTS Out of 172 samples, 119 were previously positive for HBV DNA with a median VL 4.46 (IQR: 1-8.76)log10IU/mL and 53 were HBV DNA negative. Genotyping could be done in 95 (79.8 %) samples and genotype D (83; 87.3 %) was the commonest type. The Xpert assay demonstrated a good correlation with Abbott (R2 = 0.94) and Roche (R2 = 0.96). On comparison, the mean difference with 95 % Confidence Interval of Xpert assay was -0.018 and -0.043 log10 IU/mL with Abbott and Roche assay, respectively. The overall sensitivity, specificity, negative predictive value, and positive predictive value of the Xpert assay was found 97.5 %, 100 %, 94.65 & 100 % respectively. CONCLUSION Xpert HBV-VL assay which has a potential for near point of care molecular testing has shown excellent performance and found to be a reliable method for HBV DNA quantification.
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Affiliation(s)
- Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India.
| | - Arvind Khodare
- Department of Clinical Virology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India
| | - Nitiksha Rani
- Department of Clinical Virology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India
| | - Gaurav Singh
- Department of Clinical Virology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India
| | - Kavita Aggarwal
- Department of Clinical Virology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India
| | - Manoj Sharma
- Department of Hepatology, Institute of Liver and Biliary Sciences (ILBS), New Delhi, India
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Morabito S, Minelli F, Tozzoli R. Integrated Approach for the Diagnosis of Shiga Toxin-Producing Escherichia coli Infections in Humans. Methods Mol Biol 2021; 2291:1-17. [PMID: 33704747 DOI: 10.1007/978-1-0716-1339-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are human pathogens causing severe diseases, such as hemorrhagic colitis and the hemolytic uremic syndrome. The prompt diagnosis of STEC infection is of primary importance to drive the most appropriate patient's management procedures. The methods to diagnose STEC infections include both direct isolation of the STEC from stool samples and the identification of indirect evidences based on molecular, phenotypic, and serological applications. Here, the procedures in use at the Italian Reference Laboratory for E. coli infections are described.
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Singh T, Dar SA, Singh S, Shekhar C, Wani S, Akhter N, Bashir N, Haque S, Ahmad A, Das S. Integron mediated antimicrobial resistance in diarrheagenic Escherichia coli in children: in vitro and in silico analysis. Microb Pathog 2020; 150:104680. [PMID: 33301859 DOI: 10.1016/j.micpath.2020.104680] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 11/05/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023]
Abstract
The exchange of genes between bacterial chromosome and plasmid(s) and their integration into integrons are mainly responsible for acquisition and dissemination of antibiotic resistance. We investigated the role of integrons and their underlying molecular mechanisms leading to development of adaptability in E. coli and eventual resistance to antimicrobials. Escherichia coli isolates (n = 120); including 40 diarrheagenic isolates, an even number of isolates from cases other than diarrhea, and equal number of isolates from healthy children recovered from fresh stool samples were used for identification of integron genes and gene cassettes. The association of integrons with antibiotic resistance was assayed before phylogenetic analysis. DNA sequence analysis revealed class 1 and 2 integrons in 55.83% and 21.66% isolates, respectively. The integron presence was found significantly associated with the probability of antibiotic resistance in E. coli; the association being highest with class 1 integron. Modelling and molecular docking along with molecular dynamics simulation analyses found ceftriaxone and amoxicillin as potential inhibitors of dihydrofolate reductase (DHFR). The class 1 integrons of these pathogenic isolates can serve as prospective therapeutic targets using specific silencing strategies and combinational antimicrobial therapy. The findings may be useful for the development of a potent and versatile drug for DHFR inhibition.
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Affiliation(s)
- Taru Singh
- Epidemiology and Environmental Biology, Indian Council of Medical Research (ICMR)-ICMR-National Institute of Malaria Research, New Delhi, India.
| | - Sajad A Dar
- Department of Microbiology, University College of Medical Sciences & GTB Hospital (University of Delhi), Delhi, India; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saurabh Singh
- Department of Mechanical Engineering, Delhi Technological University, Delhi, India
| | - Chandra Shekhar
- Department of Microbiology, University College of Medical Sciences & GTB Hospital (University of Delhi), Delhi, India
| | - Sayim Wani
- Department of Minimal Access and Bariatric Surgery, Fortis Flt. Rajan Dhall Hospital, Delhi, India
| | - Naseem Akhter
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Nasreena Bashir
- College of Applied Medicine, King Khalid University, Abha, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Shukla Das
- Department of Microbiology, University College of Medical Sciences & GTB Hospital (University of Delhi), Delhi, India.
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Wang Z, Yue T, Yuan Y, Zhang Y, Gao Z, Cai R. Targeting the vanillic acid decarboxylase gene for Alicyclobacillus acidoterrestris quantification and guaiacol assessment in apple juices using real time PCR. Int J Food Microbiol 2020; 338:109006. [PMID: 33302194 DOI: 10.1016/j.ijfoodmicro.2020.109006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/31/2020] [Accepted: 11/27/2020] [Indexed: 11/19/2022]
Abstract
Alicyclobacillus spp. has recently received much attention due to its implication in the spoilage of pasteurized fruit juices, which is characterized by the formation of guaiacol. Previous researches indicate that not all Alicyclobacillus spp. are able to produce guaiacol. The aim of this study was to identify possible differences in the vanillic acid decarboxylase gene involved in guaiacol biosynthesis and then develop specific detection methods for guaiacol producing Alicyclobacillus. Agarose gel electrophoresis results showed that the partial vdcC gene was present in all the guaiacol producing Alicyclobacillus, but absent in non-guaicaol producing strains apart from A. fastidiosus DSM 17978. On the basis of the vdcC gene sequence, a primer pair specific to A. acidoterrestris was designed; then a SYBR Green I real time PCR was established for the direct quantification of A. acidoterrestris in apple juice, and the detection limit was 2.6 × 101 CFU/mL. The developed real time PCR system was used to detect A. acidoterrestris in 36 artificially contaminated apple juice samples and guaiacol production in the sample was also analyzed by GC-MS. The Gompertz model was employed to describe the relationship between A. acidoterrestris cell concentration and guaiacol content, and the value of R2 was 0.854. This work provides an alternative to conventional methods of guaiacol quantification and A. acidoterrestris detection and could be very useful for the early recognition of A. acidoterrestris contamination in fruit juices.
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Affiliation(s)
- Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China; National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China; National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi 712100, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China; National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi 712100, China
| | - Yanchen Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China; National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi 712100, China
| | - Zhenpeng Gao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China; National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi 712100, China
| | - Rui Cai
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; Laboratory of Quality & Safety Risk Assessment for Agro-products (YangLing), Ministry of Agriculture, Yangling, Shaanxi 712100, China; National Engineering Research Center of Agriculture Integration Test (Yangling), Yangling, Shaanxi 712100, China.
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Zekri ARN, Easa Amer K, Hafez MM, Hassan ZK, Ahmed OS, Soliman HK, Bahnasy AA, Abdel Hamid W, Gad A, Ali M, Ali Hassan W, Samir Madboly M, Abdel Raouf A, Khattab AA, Salah El Din Hamdy M, Sherif Soliman M, Hamdi El Sissy M, Mohamed El Khateeb S, Hosny Ezzelarab M, Fathalla LA, Abouelhoda M. Genomic characterization of SARS-CoV-2 in Egypt. J Adv Res 2020; 30:123-132. [PMID: 33262895 PMCID: PMC7688418 DOI: 10.1016/j.jare.2020.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Introduction The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.
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Affiliation(s)
- Abdel-Rahman N Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Khaled Easa Amer
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Mohammed M Hafez
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Zeinab K Hassan
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Ola S Ahmed
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Hany K Soliman
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, 11796, Egypt
| | - Abeer A Bahnasy
- Surgical Pathology Department National Cancer Institute, Cairo University, 11796, Egypt
| | | | - Ahmad Gad
- Military Central Laboratories, Egypt
| | - Mahmoud Ali
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | - Wael Ali Hassan
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | | | - Ayman A Khattab
- Egypt Center for Research and Regenerative Medicine ECRRM, Egypt
| | | | - May Sherif Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | - Maha Hamdi El Sissy
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Egypt
| | | | | | - Lamiaa A Fathalla
- Clinical Pathology Department, National Cancer Institute, Cairo University 11796, Egypt
| | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
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Morais RCSD, Melo MGND, Goes TCD, Pessoa E Silva R, Morais RFD, Guerra JADO, Brito MEFD, Brandão-Filho SP, Paiva Cavalcanti MD. Duplex qPCR for Leishmania species identification using lesion imprint on filter paper. Exp Parasitol 2020; 219:108019. [PMID: 33053400 DOI: 10.1016/j.exppara.2020.108019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND American cutaneous leishmaniasis (ACL) is caused by different Leishmania parasites, which stimulate and direct the immune response against the infection. OBJECTIVE To evaluate the TaqMan probe technology applicability to diagnose and identifying of Leishmania spp. related to the ACL etiology. METHODOLOGY Through the MEGA 6.0 software, performed an in silico analysis using multiple alignments of Leishmania spp. which were available on GenBank for different genomic targets. The efficiency (e), specificity and detection limit (DL) were calculated for each system, these were associated to compose a duplex-qPCR (DqPCR). The samples of blood, lesion biopsy and lesion imprint on filter paper from patients residing in states of Amazonas (AM) and Pernambuco (PE)-Brazil, (cases and controls) were used to perform the DqPCR technique. The capacity to identify the Leishmania species was determined by comparison with isoenzymes method and sequencing analysis. RESULTS Internal Transcribed Spacer 1 (rDNA) was the target selected. Two sets of primers and probes were designed and combined: SVS for subgenus Viannia and LaS for L. (L.) amazonensis. The results were: SVSe = 93.24%, SVS DL = 50 fg/μL; LaSe = 89.3%, LaSLD = 5 fg/μL presented 100% of specificity. In total, 236 individuals participated of the present study, wherein were 101 blood samples, 33 biopsies and 147 lesion imprints. The imprint was the most sensitive sample, showing 83.06% of sensitivity, 86.96% of specificity and substantial agreement between the techniques analysis (k = 0.531; p < 0,001). Regarding the species identification, DqPCR and sequencing/isoenzymes have agreed at 100%, since the infection is caused by a single Leishmania species. CONCLUSION The DqPCR technique was applicable in diagnosis and identification of Leishmania spp. (subgenus Viannia and L. amazonensis). Furthermore, the lesion imprint is less invasive, allowing a fewer discomfort and greater acceptance by the patients, in addition of being low cost and easy handling.
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Affiliation(s)
| | | | - Tayná Correia de Goes
- Aggeu Magalhães Institute, FIOCRUZ-PE. Rego Avenue, University City, Recife, Pernambuco, ZIP 50670-420, Brazil.
| | - Rômulo Pessoa E Silva
- Aggeu Magalhães Institute, FIOCRUZ-PE. Rego Avenue, University City, Recife, Pernambuco, ZIP 50670-420, Brazil.
| | - Rômulo Freire de Morais
- Medicine Tropical Foundation, Dr. Heitor Vieira Dourado, Pedro Teixeira Avenue, Dom Pedro, Manaus, Amazonas, ZIP 69040-000, Brazil.
| | - Jorge Augusto de Oliveira Guerra
- Medicine Tropical Foundation, Dr. Heitor Vieira Dourado, Pedro Teixeira Avenue, Dom Pedro, Manaus, Amazonas, ZIP 69040-000, Brazil.
| | | | - Sinval Pinto Brandão-Filho
- Aggeu Magalhães Institute, FIOCRUZ-PE. Rego Avenue, University City, Recife, Pernambuco, ZIP 50670-420, Brazil.
| | - Milena de Paiva Cavalcanti
- Aggeu Magalhães Institute, FIOCRUZ-PE. Rego Avenue, University City, Recife, Pernambuco, ZIP 50670-420, Brazil.
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Arsand JB, Hoff RB, Jank L, Bussamara R, Dallegrave A, Bento FM, Kmetzsch L, Falção DA, do Carmo Ruaro Peralba M, de Araujo Gomes A, Pizzolato TM. Presence of antibiotic resistance genes and its association with antibiotic occurrence in Dilúvio River in southern Brazil. Sci Total Environ 2020; 738:139781. [PMID: 32526421 DOI: 10.1016/j.scitotenv.2020.139781] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 05/06/2023]
Abstract
It is known that antibiotics are widely used in human and veterinary medicine. In some countries the use is controlled, however few restrictions to their use are enforced in many countries. Antibiotics and their metabolites can reach the water bodies through sewage systems, especially in those countries with partial or absent wastewater treatment systems. The overuse and misuse of antibiotics has been linked with the increase of antibiotic resistant bacteria. The relation between the occurrence of antibiotics and resistance genes in surface waters has been widely studied worldwide evincing the great importance of this subject. In this work, a methodology for quantification of 40 antibiotics of 5 different classes, in river water, by SPE-LC-MS/MS was validated. Samples were taken during a two-year period from Dilúvio River, a stream that crosses the city of Porto Alegre (RS - Brazil) and receives in nature domestic effluent. The methodology met the requirements of validation, with Limit of Quantification varying from 20 ng L-1 to 100 ng L-1. A total of 48 samples was analyzed for the presence of antibiotics for two years. From the 40 antibiotics analyzed, 8 of them (Azithromycin, Cephalexin, ciprofloxacin, clindamycin, norfloxacin, sulfadiazine, sulfamethoxazole and trimethoprim) were present in all sampling points in the range of <LOQ to 344 ng L-1. The occurrence of antibiotics resistance genes in the sampling points was determined using qPCR. Specific primers were utilized to detected resistance genes to the β-lactam cephalexin (blaTEM gene), to the quilonones ciprofloxacin and norfloxacin (qnrS gene), to the macrolides azithromycin and clindamycin (ermB gene), and to the sulfonamides sulfadiazine and sulfamethoxazole (sulI gene), which were quantified the selected water samples. Quantitative PCR analysis revealed the presence of ARGs in all samples, with the highest concentration found for blaTEM.
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Affiliation(s)
- Juliana Bazzan Arsand
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Rodrigo Barcellos Hoff
- Laboratório Nacional Agropecuário - LANAGRO/RS, Ministério da Agricultura, Pecuária e Abastecimento do Brasil, Estrada da Ponta Grossa 3036, 91780-580 Porto Alegre, RS, Brazil
| | - Louise Jank
- Laboratório Nacional Agropecuário - LANAGRO/RS, Ministério da Agricultura, Pecuária e Abastecimento do Brasil, Estrada da Ponta Grossa 3036, 91780-580 Porto Alegre, RS, Brazil
| | - Roberta Bussamara
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Alexsandro Dallegrave
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Fatima Menezes Bento
- Departamento de Microbiologia, Imunologia e Parasitologia, ICBS/UFRGS, Rua Sarmento Leite 500, 90035-190 Porto Alegre, RS, Brazil
| | - Livia Kmetzsch
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil; Centro de Biotecnologia. Av. Bento Gonçalves 9500, prédio 43421
| | - Daiane Acosta Falção
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil; Centro de Biotecnologia. Av. Bento Gonçalves 9500, prédio 43421
| | - Maria do Carmo Ruaro Peralba
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Adriano de Araujo Gomes
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil
| | - Tânia Mara Pizzolato
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul - UFRGS, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS, Brazil.
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Young JF, Rasmussen MK. Differentially expressed marker genes and glycogen levels in pectoralis major of Ross308 broilers with wooden breast syndrome indicates stress, inflammation and hypoxic conditions. Food Chem (Oxf) 2020; 1:100001. [PMID: 35415620 PMCID: PMC8991981 DOI: 10.1016/j.fochms.2020.100001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 06/14/2023]
Abstract
The occurrence of wooden breast (WB) in broiler production is increasing, but onset of its development is only described in part. In this study, we determined the regulation of marker genes related to oxidative stress in Ross308 broilers categorized as no-, mild- or severe-WB, on days 21 and 30 of production. The biochemical parameters, lactate dehydrogenase and pro- and macro-glycogen, were also determined. On day 21, breast meat from birds affected severely by WB had increased mRNA abundances of heat-shock protein 70, heme-oxygenase 1, cyclooxygenase 2, tumor necrosis factor 1, and hypoxia inducible factors as well as higher pH and lower dry matter contents. On day 30, breast meat from both mild and severely affected birds had increased mRNA for heme oxygenase 1, lactate dehydrogenase, and hypoxia inducible factor. Moreover, pro- and micro-glycogen, as well as the total pool of glycogen, were decreased compared with the non-WB birds. In conclusion, this study indicates oxidative stress, inflammation and hypoxic conditions in WB.
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Affiliation(s)
- Jette Feveile Young
- Corresponding author at: Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Arhus N, Denmark.
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Belleggia L, Milanović V, Cardinali F, Garofalo C, Clementi F, Aquilanti L, Osimani A. Prevalence of Histidine Decarboxylase Genes of Gram-Positive Bacteria in Surströmming as Revealed by qPCR. Indian J Microbiol 2021; 61:96-9. [PMID: 33505099 DOI: 10.1007/s12088-020-00907-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022] Open
Abstract
Histamine is a degradation product of the bacterial decarboxylation of the amino acid histidine; such activity is determined by histidine decarboxylase encoded by a gene cluster, carried by some Gram-positive bacteria, that includes the hdcA gene. In this study, the presence of the hdcA gene in ready-to-eat surströmming samples collected from three producers based in Sweden was directly assessed via qPCR analysis for the very first time. Samples from producer A showed hdcA average gene abundance of 6.67 ± 0.13 Log cells/gene copies g-1; in samples from producer B the average value attested at 5.56 ± 0.06 Log cells/gene copies g-1, whereas for samples of producer C hdcA average gene abundance attested at 5.30 ± 0.08 Log cells/gene copies g-1. ANOVA showed a significantly higher average hdcA gene copy number in samples from producer A, whereas no significant differences were seen between average values of hdcA gene copy numbers detected in samples from producer B and C. The hdcA gene copies detected in the present study could give an estimation of the load of potential histamine-producing bacteria in surströmming.
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Chaudhari KV, Toi PC, Joseph NM. Evaluation of real time polymerase chain reaction targeting mpb64 gene for diagnosis of extrapulmonary tuberculosis. Indian J Tuberc 2020; 68:242-248. [PMID: 33845959 DOI: 10.1016/j.ijtb.2020.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Paucibacillary nature of extrapulmonary tuberculosis (EPTB) has paved way for molecular methods increasingly being used for diagnosis. We undertook a study for evaluation of sensitivity and specificity of real-time polymerase chain reaction (RT-PCR) targeting mpb64 gene for diagnosis of EPTB. METHODS A total of 152 clinical samples from suspected cases of EPTB were included in this study. All samples were extracted using spin column based commercial DNA extraction kit and were subjected to RT-PCR targeting mpb64 and IS6110. Smear and culture was also done for samples whenever quantity was sufficient. Cytology report was noted from hospital information system. Receiver operating characteristic (ROC) curve analysis was done for determining cut-off Ct value for mpb64 RT-PCR. Melt curve analysis was done for samples whose cycle threshold (Ct) value was more than 37. The sensitivity and specificity of the mpb64 RT-PCR was calculated using a composite gold standard i.e., positive for one or more of the following: microscopy (including fine needle aspiration cytology (FNAC), acid-fast bacilli positivity), culture and IS6110 RT-PCR. RESULTS Out of the 152 samples, 72 (47.4%) were positive for tuberculosis by composite gold standard. Samples consisted of ascitic fluid (12), CSF (35), pus (23), lymph node aspirate (35), pleural fluid (37), synovial fluid (4), urine (1), pericardial fluid (1) and tissue bits (4). Microscopy (AFB smear including lymph node aspirate) was done for 124 samples of which 43 (34.7%) were positive. Culture results were available for 79 samples, 25 (31.6%) of which were positive and 42 (27.6%) of the 152 samples were positive by IS6110 PCR. Based on ROC and melt curve analysis, mpb64 RT-PCR was able to detect 38 (52.8%) of the 72 positive samples. In comparison to IS6110 RT PCR, 4 additional cases were detected by mpb64 RT-PCR. Compared to composite gold standard mpb64 showed overall sensitivity of 52.8%. CONCLUSION The mpb64 RT-PCR is highly specific or MTB and can be used as a supplemental test for diagnosis of EPTB along with other diagnostic tests. However the overall sensitivity of mpb64 RT-PCR is too low to be used as an independent test for diagnosis of EPTB. Combining the results of IS6110 RT PCR and mpb64 RT PCR improved the overall sensitivity and hence mpb64 can be used as an additional target for diagnosis of EPTB.
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Affiliation(s)
| | - Pampa Ch Toi
- Department of Pathology, JIPMER, Puducherry, India
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Seyed Majidi A, Bazzazi H, Zamani S, Ghaemi EA. Comparison of hspX gene sequence in the Beijing and non-Beijing Mycobacterium tuberculosis. J Clin Tuberc Other Mycobact Dis 2020; 21:100187. [PMID: 32995569 PMCID: PMC7509209 DOI: 10.1016/j.jctube.2020.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Purpose The pathogenicity of various lineages of Mycobacterium tuberculosis (MTB) is different. This could be due to the difference in survival ability within the host macrophage. The alpha crystalline secretion protein, a product of the hspx gene, is one of the bacterial protection factors in these stressful situations. The Beijing family, part of the East Asian lineage, was reported to be more virulent. Regarding the importance of this protein in pathogenicity, this study was conducted to investigate the polymorphism of the hspx gene in Beijing family compared to non- Beijing strains. Method DNA of 50 MTB isolates were extracted by boiling method. The existence of hspx gene was determined using PCR-specific primer and finally PCR product was sequenced to examine the polymorphism in both direct and reverse directions. Sequencing results were aligned by chromas software. Results The hspx gene was detected in all of the Beijing and non-Beijing isolates. The polymorphism in the sequences of this gene were not observed in all of the MTB isolates. Discussion This study indicated that hspx gene is protected. Also it has showed that lineage type was not related to the sequence of hspX gene, but the expression of this protein may be different, which requires further studies.
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Affiliation(s)
- Ashkan Seyed Majidi
- Department of Microbiology, Islamic Azad University, Gorgan Branch, Gorgan, Iran
| | - Hadi Bazzazi
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Samin Zamani
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ezzat Allah Ghaemi
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran.,Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Boutin CA, Grandjean-Lapierre S, Gagnon S, Labbé AC, Charest H, Roger M, Coutlée F. Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument. J Clin Virol 2020; 132:104615. [PMID: 32927356 PMCID: PMC7472968 DOI: 10.1016/j.jcv.2020.104615] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/26/2020] [Indexed: 01/25/2023]
Abstract
OBJECTIVE Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown. METHODS The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. RESULTS The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3-99.9) and 77.1 % (95 % CI, 67.7-84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7-95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75-0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3-33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2-37.1; p = 0.0009). An excellent correlation (r2 = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r2 = 0.82). CONCLUSION Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform.
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Affiliation(s)
- Catherine-Audrey Boutin
- Service de Biologie Moléculaire, Département Clinique de Médecine de Laboratoire, Grappe Optilab Montréal-CHUM, Montréal, Québec, Canada
| | - Simon Grandjean-Lapierre
- Service de Biologie Moléculaire, Département Clinique de Médecine de Laboratoire, Grappe Optilab Montréal-CHUM, Montréal, Québec, Canada; Service d'Infectiologie du Département de Médecine et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Simon Gagnon
- Service de Biologie Moléculaire, Département Clinique de Médecine de Laboratoire, Grappe Optilab Montréal-CHUM, Montréal, Québec, Canada
| | - Annie-Claude Labbé
- Service de Biologie Moléculaire, Département Clinique de Médecine de Laboratoire, Grappe Optilab Montréal-CHUM, Montréal, Québec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada; Service d'Infectiologie, Département de Médecine, Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Hugues Charest
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada; Laboratoire de Santé Publique du Québec, Montréal, Québec, Canada
| | - Michel Roger
- Service d'Infectiologie du Département de Médecine et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada; Laboratoire de Santé Publique du Québec, Montréal, Québec, Canada
| | - François Coutlée
- Service de Biologie Moléculaire, Département Clinique de Médecine de Laboratoire, Grappe Optilab Montréal-CHUM, Montréal, Québec, Canada; Service d'Infectiologie du Département de Médecine et Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada; Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.
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