1
|
Singh R, Singh KP, Singh R, Singh V, Kumar P, Varshney R, Yadav A, Mote A, Gangwar M, Prasath NB. Preliminary investigation reveals novel pathological consequences of bluetongue virus-1 infection in the endocrine glands of pregnant Indian sheep. Anim Biotechnol 2024; 35:2269428. [PMID: 37850824 DOI: 10.1080/10495398.2023.2269428] [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: 10/19/2023]
Abstract
Bluetongue virus (BTV), a major peril to the sheep industry, infects a wide range of the cells in the infected animals including mononuclear, dendritic and epithelial cells. However, little is known about its tropism for the secretory epithelial cells of endocrine glands and the pathogenesis it induces. The aim of the study was to assess the BTV load, antigen distribution in the tissue of the pituitary, thyroid as well as adrenal glands and associated histopathological consequences. BTV antigens were localized using immunohistochemistry in the thyroid's epithelial cells, zona fasciculata and zona reticularis cells and the anterior pituitary epithelial cells. The real-time PCR portrayed the high viral load in adrenals at 7th days postinoculation (DPI) and in thyroid and pituitary glands at 15th DPI. Serum examination revealed variation in the T-3 and T-4 of infected animals in comparison to the control group. Caspase-3 immunolocalization revealed BTV-1 induces apoptosis in the affected cells of endocrine gland of infected animals. Further, this study signifies the tropism of BTV in the novel sites (endocrine glands) of the host that might be one of the reasons for the poor performance of infected animals.
Collapse
Affiliation(s)
- Rohit Singh
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | | | - Rajendra Singh
- SOA Institute of Veterinary Science and Animal Husbandry, Bhubaneswar, India
| | - Vidya Singh
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Pawan Kumar
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Rajat Varshney
- Department of Veterinary Microbiology, Faculty of Veterinary and Animal Sciences, I.Ag.Scs, RGSC, Banaras Hindu University, Mirzapur, India
| | - Akanksha Yadav
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Akash Mote
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Mukesh Gangwar
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - N Babu Prasath
- ICAR-Indian Veterinary Research Institute, Bareilly, India
| |
Collapse
|
2
|
Mostafa HH, Wall G, Su SC, Hysa G, Gong L, Dadjeu UC, Cheung H, Pekosz A, De Smet D, Sklenovská N, Laenen L, Viñuela L, de Salazar A, Fuentes A, Padalko E, Garcia F. Multi-center evaluation of the Research Use Only NeuMoDx monkeypox virus (MPXV) fully automated real-time PCR assay. J Clin Microbiol 2024:e0002824. [PMID: 38639489 DOI: 10.1128/jcm.00028-24] [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: 01/09/2024] [Accepted: 03/29/2024] [Indexed: 04/20/2024] Open
Abstract
The mpox outbreak, caused by monkeypox virus (MPXV), accelerated the development of molecular diagnostics. In this study, we detail the evaluation of the Research Use Only (RUO) NeuMoDx MPXV assay by multiple European and US sites. The assay was designed and developed by Qiagen for the NeuMoDx Molecular Systems. Primers and probes were tested for specificity and inclusivity in silico. The analytical sensitivity of the assay was determined by testing dilutions of synthetic and genomic MPXV DNA. A total of 296 clinical samples were tested by three sites; the Johns Hopkins University (US), UZ Gent (Belgium, Europe), and Hospital Universitario San Cecilio (Spain, Europe). The analytical sensitivity of the assay was 50 copies/mL for both clades I and II. The assay showed 100% in silico identity for 80 clade I and 99.98% in silico identity for 5,162 clade II genomes. Clade II primers and probes showed 100% in silico specificity; however, identity of at least one of the two sets of clade I primers and probes with variola, cowpox, camelpox, and vaccinia viruses was noticed. The clinical validation showed sensitivity of 99.21% [95% confidence interval (CI): 95.66-99.98%] and specificity of 96.64% (95% CI: 91.62-99.08%) for lesion swab samples. The NeuMoDx MPXV Test shows acceptable analytical and clinical performance. The assay improves the laboratory's workflow as it consolidates nucleic acid extraction, PCR, data analysis, and interpretation and can be interfaced. The Test Strip can differentiate clades I and II, which has important laboratory safety implications. IMPORTANCE In this manuscript, we provide detailed in silico analysis and clinical evaluation of the assay using a large cohort of clinical samples across three academic centers in Europe and the United States. Because the assay differentiates MPXV clades I and II, this manuscript is timely due to the current need to rule out the regulated clade I by diagnostic clinical laboratories. In December 2023, and due to first report of cases of sexually transmitted clade I infections in the Democratic Republic of the Congo, when generic assays that do not differentiate the clades are used, samples are considered regulated. The assay meets the need of full automation and has a marked positive impact on the laboratory workflow.
Collapse
Affiliation(s)
- Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | - Szu-Chi Su
- NeuMoDx Molecular Inc, a QIAGEN company, Ann Arbor, Michigan, USA
| | - Gerta Hysa
- NeuMoDx Molecular Inc, a QIAGEN company, Ann Arbor, Michigan, USA
| | - Lijie Gong
- NeuMoDx Molecular Inc, a QIAGEN company, Ann Arbor, Michigan, USA
| | - Urbain Charly Dadjeu
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Helen Cheung
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Nikola Sklenovská
- Laboratory of Clinical and Epidemiological, Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Laura Viñuela
- Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, Madrid, Spain
| | - Adolfo de Salazar
- Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, Madrid, Spain
| | - Ana Fuentes
- Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, Madrid, Spain
| | | | - Federico Garcia
- Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Granada, Spain
- Ciber de Enfermedades Infecciosas, CIBERINFEC, Madrid, Spain
| |
Collapse
|
3
|
Wang C, Wang F, Chang J, Jiang Z, Han Y, Wang M, Jing B, Zhao A, Yin X. Development and application of one-step multiplex Real-Time PCR for detection of three main pathogens associated with bovine neonatal diarrhea. Front Cell Infect Microbiol 2024; 14:1367385. [PMID: 38628550 PMCID: PMC11018945 DOI: 10.3389/fcimb.2024.1367385] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction Neonatal calf diarrhea (NCD) is one of the most common diseases in calves, causing huge economic and productivity losses to the bovine industry worldwide. The main pathogens include bovine rotavirus (BRV), bovine coronavirus (BCoV), and Enterotoxigenic Escherichia coli (ETEC) K99. Since multiple infectious agents can be involved in calf diarrhea, detecting each causative agent by traditional methods is laborious and expensive. Methods In this study, we developed a one-step multiplex Real-Time PCR assay to simultaneously detect BRV, BCoV, and E. coli K99+. The assay performance on field samples was evaluated on 1100 rectal swabs of diseased cattle with diarrhea symptoms and compared with the conventional gel-based RT-PCR assay detect BRV, BCoV, and E. coli K99+. Results The established assay could specifically detect the target pathogens without cross-reactivity with other pathogens. A single real-time PCR can detect ~1 copy/µL for each pathogen, and multiplex real-time PCR has a detection limit of 10 copies/µL. Reproducibility as measured by standard deviation and coefficient of variation were desirable. The triple real-time PCR method established in this study was compared with gel-based PT-PCR. Both methods are reasonably consistent, while the real-time PCR assay was more sensitive and could rapidly distinguish these three pathogens in one tube. Analysis of surveillance data showed that BRV and BCoV are major enteric viral pathogens accounting for calves' diarrhea in China. Discussion The established assay has excellent specificity and sensitivity and was suitable for clinical application. The robustness and high-throughput performance of the developed assay make it a powerful tool in diagnostic applications and calf diarrhea research. .
Collapse
Affiliation(s)
- Chaonan Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Fang Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jitao Chang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji, China
| | - Zhigang Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuxin Han
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Meixi Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bo Jing
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Aiyun Zhao
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Xin Yin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
4
|
Datta P, Rattan D, Sharma D, Sharma N, Kalra N, Duseja A, Angrup A, Sehgal R. Novel diagnostic approach for amoebic liver abscess using cell free (cf) DNA: a prospective study. Infect Dis (Lond) 2024; 56:259-267. [PMID: 38112684 DOI: 10.1080/23744235.2023.2294119] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Amoebic liver abscess (ALA) is commonly seen in tropical countries and diagnosis of ALA relies mainly on non-specific serological and imaging techniques as well as PCR from pus. OBJECTIVE This study evaluated the potential of using cell free DNA (cfDNA) from serum and urine for diagnosing ALA. METHODS We prospectively evaluated quantitative PCR (qPCR) for detection of cf DNA in serum and urine sample in all liver abscess patients. The samples were collected from patients reporting to emergency ward of Postgraduate Institute of Medical Education and Research, Chandigarh, India with symptoms suggestive of liver abscess. Real time PCR was done to detect cf DNA in serum and urine by targeting 99-bp unit of small subunit rRNA of Entamoeba histolytica and conventional PCR for pus. RESULTS A total 113 samples (serum and urine) and 100 pus samples were analysed. A total of 62 ALA patients were confirmed; with maximum 57 patients detected by qPCR for cfDNA in the serum, 55 patients by PCR on pus aspirate and 50 ALA patients by qPCR for cfDNA in urine sample. Therefore, the sensitivity of qPCR for detection of cf DNA in serum was 91.94% and for urine was 80.65%. CONCLUSION A total of 11.2% of ALA patients were diagnosed only through detection of E. histolytica cf DNA in their serum and urine. Detection of cfDNA from serum, urine of ALA has a potential role in future especially for developing countries as it is a rapid, sensitive and patient friendly diagnostic approach.
Collapse
Affiliation(s)
- Priya Datta
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| | - Divya Rattan
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| | - Devyani Sharma
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| | - Navneet Sharma
- Department of Internal Medicine, PGIMER, Chandigarh, India
| | - Naveen Kalra
- Department of Radiodiagnosis & Imaging, PGIMER, Chandigarh, India
| | - Ajay Duseja
- Department of Hepatology, PGIMER, Chandigarh, India
| | - Archana Angrup
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| |
Collapse
|
5
|
Knight NL, Adhikari KC, Dodhia KN, Mair WJ, Lopez-Ruiz FJ. Workflows for detecting fungicide resistance in net form and spot form net blotch pathogens. Pest Manag Sci 2024; 80:2131-2140. [PMID: 38145910 DOI: 10.1002/ps.7951] [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] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Fungicide resistance in Pyrenophora teres f. maculata and P. teres f. teres has become an important disease management issue. Control of the associated barley foliar diseases, spot form and net form net blotch, respectively, relies on three major groups of fungicides, demethylation inhibitors (DMIs), succinate dehydrogenase inhibitors (SDHIs) and quinone outside inhibitors (QoIs). However, resistance has been reported for the DMI and SDHI fungicides in Australia. To enhance detection of different resistance levels, phenotyping and genotyping workflows were designed. RESULTS The phenotyping workflow generated cultures directly from lesions and compared growth on discriminatory doses of tebuconazole (DMI) and fluxapyroxad (SDHI). Genotyping real-time polymerase chain reaction (PCR) assays were based on alleles associated with sensitivity or resistance to the DMI and SDHI fungicides. These workflows were applied to spot form and net form net blotch collections from 2019 consisting predominantly of P. teres f. teres from South Australia and P. teres f. maculata from Western Australia. For South Australia the Cyp51A L489-3 and SdhC-R134 alleles, associated with resistance to tebuconazole and fluxapyroxad, respectively, were the most prevalent. These alleles were frequently found in single isolates with dual resistance. This study also reports the first detection of a 134 base pair insertion located at position-66 (PtTi-6) in the Cyp51A promoter of P. teres f. maculata from South Australia. For Western Australia, the PtTi-1 insertion was the most common allele associated with resistance to tebuconazole. CONCLUSION The workflow and PCR assays designed in this study have been demonstrated to efficiently screen P. teres collections for both phenotypic and genetic resistance to DMI and SDHI fungicides. The distribution of reduced sensitivity and resistance to DMI and SDHI fungicides varied between regions in south-western Australia, suggesting the emergence of resistance was impacted by both local pathogen populations and disease management programmes. The knowledge of fungicide resistance in regional P. teres collections will be important for informing appropriate management strategies. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Kul C Adhikari
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Kejal N Dodhia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Wesley J Mair
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| |
Collapse
|
6
|
Madamet M, Fonta I, Mosnier J, Benoit N, Amalvict R, Briolant S, French National Reference Centre for Imported Malaria Study Group, Pradines B. Comparison of SD Bioline Malaria Ag Pf/Pan and Acro Malaria P.f./P.v./Pan with Microscopy and Real Time PCR for the Diagnosis of Human Plasmodium Species. Diagnostics (Basel) 2024; 14:721. [PMID: 38611637 PMCID: PMC11011331 DOI: 10.3390/diagnostics14070721] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The early diagnosis of malaria is crucial to controlling morbidity and mortality. The World Health Organization (WHO) recommends diagnosing malaria either using light microscopy or a malaria rapid diagnostic test (RDT). Most RDTs use antibodies to detect two P. falciparum histidine-rich proteins named PfHRP2 and PfHRP3. However, false-negative results are known to occur due to the poor performance of RDTs depending on the species and the deletion of the Pfhrp2 and Pfhrp3 genes. This study evaluated new malaria RDTs for the detection of the human Plasmodium species. The Acro Malaria P.f./P.v./Pan Rapid Test Cassette allows the qualitative detection of parasite antigens, such as PfHRP2 specific to Plasmodium falciparum, PvLDH specific to Plasmodium vivax, and/or panLDH Plasmodium genus lactate dehydrogenase, in the blood of infected individuals. This RDT was assessed against 229 samples collected from imported malaria cases, mainly from Africa. The samples were previously diagnosed using light microscopy and RDT (SD Malaria Ag P.f./Pan, SD Bioline Alere Abbott), then confirmed using real time PCR. The two RDTs were evaluated using a comparison with real time PCR as the reference method, and their performances were compared with each other. Compared to SD RDT, the Acro RDT showed a better sensitivity to P. falciparum (96.8% vs. 89.8%), P. vivax (78.6% vs. 64.3%), P. ovale (73.7% vs. 5.3%), and P. malariae (20.0% vs. 0%). The respective specificities of the Acro RDT and SD RDT are 90.7% vs. 95.3% to P. falciparum, 100% to P. vivax, and 100% vs. 100% to Plasmodium genus. Therefore, Acro RDT showed better performance in the identification of P. ovale and low parasitaemia of P. falciparum. In addition, Acro RDT has the advantage of detecting PvLDH-specific antigens. The Acro Malaria RDT presents the benefits of detecting a P. falciparum antigen (PfHRP2) and a P. vivax antigen (PvLDH) with high sensitivity (96.8% and 73.7%, respectively) and specificity (90.7% and 100%, respectively). Acro Malaria P.f./P.v./Pan rapid diagnostic tests could be effectively used in endemic areas, especially when microscopic examination cannot be performed.
Collapse
Affiliation(s)
- Marylin Madamet
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Nicolas Benoit
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Rémy Amalvict
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Sébastien Briolant
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | | | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.); (I.F.); (J.M.); (N.B.); (R.A.); (S.B.)
- Aix Marseille Univ, SSA, AP-HM, RITMES, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| |
Collapse
|
7
|
Fattouh R, Boissinot K, Jeong E, Mendlowitz AB, Sjaarda CP, Wong H, Kozak R, Sheth PM, Matukas LM. Evaluation of 5 Polymerase Chain Reaction Assays for the Detection of Mpox Virus. J Infect Dis 2024; 229:S156-S162. [PMID: 38531075 DOI: 10.1093/infdis/jiad464] [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] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND In 2022, the global dissemination of mpox virus (MPXV) outside endemic regions prompted the expansion of diagnostic testing worldwide. This study assesses the performance characteristics of 5 real-time polymerase chain reaction (PCR) assays in detecting MPXV during the 2022 outbreak. METHODS Clinical specimens collected from patients across Ontario, Canada, were tested on the following assays: RealStar Orthopoxyvirus PCR and FlexStar Monkeypox virus PCR (Altona Diagnostics), Novaplex MPXV (Seegene), VIASURE Monkeypox virus Real Time PCR Reagents (CerTest Biotec), and a laboratory-developed test. Positive percent agreement (PPA), negative percent agreement (NPA), relative limit of detection (LOD), and precision were evaluated and MPXV lineages were determined using an amplicon-based whole-genome sequencing (WGS) assay. RESULTS Swabs were collected from various anatomic sites (65 positive and 30 negative). All assays demonstrated 100% NPA (95% confidence interval, 88.4%/88.1%-100.0%), with PPA ranging from 92.2% (82.7%-97.4%) to 96.9% (89.3%-99.6%). LOD and precision were comparable across assays, with coefficient of variations <3%. WGS analysis identified 6 lineages, all belonging to subclade IIb. CONCLUSIONS The assays exhibited excellent PPA, NPA, LOD, and precision. Ongoing performance monitoring is essential to detect assay escape mutants and ensure universal detection of evolving MPXV strains.
Collapse
Affiliation(s)
- Ramzi Fattouh
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Canada
| | - Karel Boissinot
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Esther Jeong
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Andrew B Mendlowitz
- Toronto Centre for Liver Disease/Viral Hepatitis Care Network (VIRCAN), University Health Network, Toronto, Canada
| | - Calvin P Sjaarda
- Division of Microbiology, Kingston Health Sciences Centre, Kingston, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Henry Wong
- Division of Microbiology, Kingston Health Sciences Centre, Kingston, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Robert Kozak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Prameet M Sheth
- Division of Microbiology, Kingston Health Sciences Centre, Kingston, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Larissa M Matukas
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| |
Collapse
|
8
|
Aydoğan A. Comparison of different screening methods for the selection of Ascochyta blight disease on chickpea ( Cicer arietinum L.) genotypes. Front Plant Sci 2024; 15:1347884. [PMID: 38595758 PMCID: PMC11002132 DOI: 10.3389/fpls.2024.1347884] [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: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Chickpea (Cicer arietinum L.) is the second most important edible food grain legume, widely grown all over the world. However, the cultivation and production of chickpea are mainly affected by the Ascochyta blight (AB) disease, which causes losses of up to 100% in areas with high humidity and warm temperature conditions. Various screening methods are used in the selection of chickpea genotypes for resistance to AB disease. These methods are natural field condition (NFC), artificial epidemic field condition (AEC), marker-assisted selection (MAS), and real-time PCR (RT-PCR). The study was conducted with 88 chickpea test genotypes between the 2014 and 2016 growing seasons. The results of the screening were used to sort the genotypes into three categories: susceptible (S), moderately resistant (MR), and resistant (R). Using MAS screening, 13, 21, and 54 chickpea genotypes were identified as S, MR, and R, respectively. For RT-PCR screening, 39 genotypes were S, 31 genotypes were MR, and 18 genotypes were R. In the AEC method for NFC screening, 7, 17, and 64 genotypes were S, MR, and R, while 74 and 6 genotypes were S and MR, and 8 genotypes were R-AB disease. As a result of screening chickpea genotypes for AB disease, it was determined that the most effective method was artificial inoculation (AEC) under field conditions. In the study, Azkan, ICC3996, Tüb-19, and Tüb-82 were determined as resistant within all methods for Pathotype 1.
Collapse
Affiliation(s)
- Abdulkadir Aydoğan
- Head of Food Legumes Breeding, Central Research Institute for Field Crops, Yenimahalle, Türkiye
| |
Collapse
|
9
|
Park K, Yoo SJ. Clinical application of a real-time polymerase chain reaction test for CYP2C19 genotyping based on genotype distribution in a healthy Korean population. Lab Med 2024; 55:234-237. [PMID: 37543868 DOI: 10.1093/labmed/lmad070] [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: 08/07/2023] Open
Abstract
OBJECTIVE With the recent reports of additional alleles of the CYP2C19 gene with decreased or no function, the clinical utility of real-time polymerase chain reaction (PCR)-based testing that detects only a small number of variant targets needs to be evaluated. METHOD We retrospectively reviewed 7-year data for real-time PCR test records from a single hospital and analyzed CYP2C19 genotypes from publicly available whole-genome or whole-exome data from a healthy Korean population. RESULTS Of the 2327 test results in this hospital, the *1 allele was most common (60.5%), followed by *2 (28.0%), *3 (10.1%), and *17 (1.4%). Among 5305 healthy Korean individuals, the frequencies of the *2, *3, and *17 alleles were 28.6%, 9.9%, and 1.0%, respectively, which were not statistically different from those of the hospital data (P = .4439, P = .6025, and P = .1142, respectively). Interestingly, the total frequency of additional nonfunctional alleles (*4, *6, *22, and *24) that could not be detected using real-time PCR was only 0.1%, with a total allele count of 8. CONCLUSION Our study shows that the clinical utility of real-time PCR for CYP2C19 genotyping remains satisfactory. However, caution should be exercised because the test can miss patients with decreased CYP2C19 function.
Collapse
Affiliation(s)
- Kuenyoul Park
- Department of Laboratory Medicine, Sanggye Paik Hospital, School of Medicine, Inje University, Seoul, Republic of Korea
| | - Soo Jin Yoo
- Department of Laboratory Medicine, Sanggye Paik Hospital, School of Medicine, Inje University, Seoul, Republic of Korea
| |
Collapse
|
10
|
Liao C, Chen Y, Yan Z, Song Y, Zhou Q, Zhu P, He X, Li W, Chen F. Development of a rapid quantitative method to differentiate MS1 vaccine strain from wild-type Mycoplasma synoviae. Front Vet Sci 2024; 11:1354548. [PMID: 38496312 PMCID: PMC10940412 DOI: 10.3389/fvets.2024.1354548] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/19/2024] [Indexed: 03/19/2024] Open
Abstract
Mycoplasma synoviae (MS) is an economically important pathogen in the poultry industry. Vaccination is an effective method to prevent and control MS infections. Currently two live attenuated MS vaccines are commercially available, the temperature-sensitive MS-H vaccine strain and the NAD-independent MS1 vaccine strain. Differentiation of vaccine strains from wild-type (WT) strains is crucial for monitoring MS infection, especially after vaccination. In this study, we developed a Taqman duplex real-time polymerase chain reaction (PCR) method to identify MS1 vaccine strains from WT strains. The method was specific and did not cross-react with other avian pathogens. The sensitivity assay indicated that no inhibition occurred between probes or between mixed and pure templates in duplex real-time PCR. Compared with the melt-based mismatch amplification mutation assay (MAMA), our method was more sensitive and rapid. In conclusion, the Taqman duplex real-time PCR method is a useful method for the diagnosis and differentiation of WT-MS and MS1 vaccine strains in a single reaction.
Collapse
Affiliation(s)
- Changtao Liao
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China
| | - Yiquan Chen
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhuanqiang Yan
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China
| | - Yiwei Song
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China
| | - Qi Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China
| | - Puduo Zhu
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China
| | - Xudong He
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Yunfu Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China
| | - Wenyang Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Feng Chen
- College of Animal Science, South China Agricultural University, Guangzhou, China
| |
Collapse
|
11
|
Giménez E, Gozalbo-Rovira R, Albert E, Piñana JL, Solano C, Navarro D. Letermovir use may impact on the Cytomegalovirus DNA fragmentation profile in plasma from allogeneic hematopoietic stem cell transplant recipients. J Med Virol 2024; 96:e29564. [PMID: 38506145 DOI: 10.1002/jmv.29564] [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: 02/05/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/21/2024]
Abstract
Cytomegalovirus (CMV) DNA in plasma is mainly unprotected and highly fragmented. The size of the amplicon largely explains the variation in CMV DNA loads quantified across PCR platforms. In this proof-of-concept study, we assessed whether the CMV DNA fragmentation profile may vary across allogeneic hematopoietic stem cell transplant recipients (allo-SCT), within the same patient over time, or is affected by letermovir (LMV) use. A total of 52 plasma specimens from 14 nonconsecutive allo-SCT recipients were included. The RealTime CMV PCR (Abbott Molecular), was used to monitor CMV DNA load in plasma, and fragmentation was assessed with a laboratory-designed PCR generating overlapping amplicons (around 90-110 bp) within the CMV UL34, UL80.5, and UL54 genes. Intrapatient, inter-patient, and LMV-associated qualitative and quantitative variations in seven amplicons were observed. These variations were seemingly unrelated to the CMV DNA loads measured by the Abbott PCR assay. CMV DNA loads quantified by UL34_4, UL54.5, and UL80.5_1 PCR assays discriminate between LMV and non-LMV patients. Our observations may have relevant implications in the management of active CMV infection in allo-SCT recipients, either treated or not with LMV, although the data need further validation.
Collapse
Affiliation(s)
- Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | | | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - José Luis Piñana
- Hematology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Microbiology School of Medicine, University of Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
12
|
Alex CE, Kvapil P, Busch MDM, Jensen T, Conley K, Jackson K, Stubbs EL, Gjeltema J, Garner MM, Kubiski SV, Pesavento PA. Amdoparvovirus-associated disease in red pandas ( Ailurus fulgens). Vet Pathol 2024; 61:269-278. [PMID: 37681307 DOI: 10.1177/03009858231196860] [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: 09/09/2023]
Abstract
The roster of amdoparvoviruses (APVs) in small carnivores is growing rapidly, but in most cases, the consequences of infection are poorly understood. Red panda amdoparvovirus (RPAV) is highly prevalent in zoo-housed red pandas and has been detected in both healthy and sick animals. Clarifying the clinical impact of RPAV in this endangered species is critical, and zoological collections offer a unique opportunity to examine viral disease association in carefully managed populations. We evaluated the potential impact of RPAV in captive red pandas with a combination of prospective and retrospective analyses. First, we collected feces from 2 healthy animals from one collection over a 6-year period and detected virus in 72/75 total samples, suggesting that RPAV can be a long-term subclinical infection. We next investigated the infections using a retrospective study of infection status and tissue distribution in a cohort of necropsied animals. We performed polymerase chain reaction and in situ hybridization on 43 necropsy cases from 4 zoo collections (3 from the United States, 1 from Europe, 1997-2022). RPAV was present in these populations for at least 2 decades before its discovery and is detectable in common and significant lesions of zoo-housed red pandas, including myocarditis (3/3 cases), nephritis (9/10), and interstitial pneumonia (2/4). RPAV is also detectable in sporadic lesions, including multisystemic pyogranulomatous inflammation, oral/pharyngeal mucosal inflammation, and dermatitis. The colocalization of virus with lesions supports a role in causation, suggesting that despite the apparently persistent and subclinical carriage of most infections, RPAV may have a significant impact in zoo collections.
Collapse
Affiliation(s)
- Charles E Alex
- University of California, Davis, CA
- Wildlife Conservation Society, Bronx, NY
| | | | | | - Trine Jensen
- Aalborg Zoo/Aalborg University, Aalborg, Denmark
| | - Kenneth Conley
- Wildlife Conservation Society, Bronx, NY
- Disney's Animals, Science and Environment, Lake Buena Vista, FL
| | | | | | | | | | | | | |
Collapse
|
13
|
Ferrari S, Zanoni M, Mangeli A, Pigoli C, D'Incau M, Alborali GL, Pacciarini ML, Boniotti MB. Bacteriological culture and direct PCR for detecting the Mycobacterium tuberculosis complex in the Italian eradication campaign: a decade of experience at the National Reference Laboratory. J Appl Microbiol 2024; 135:lxae064. [PMID: 38520154 DOI: 10.1093/jambio/lxae064] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
AIMS Our study evaluates the capacity of direct real-time PCR for detecting Mycobacterium tuberculosis complex (MTBC), with a focus on diagnostic performances and the feasibility of implementing this protocol in an eradication campaign. Specifically, we compare the effectiveness of the direct PCR method to various culture systems used by the Italian National Reference Laboratory over the last decade to detect MTBC. METHODS AND RESULTS Bovine tissue samples were routinely tested and analyzed for bovine tuberculosis (bTB) confirmation using microbiological culture (solid and liquid media), histopathological analysis, and a direct PCR assay targeting IS6110, an insertion sequence specific to the MTBC that is widely used for tuberculosis diagnosis. The direct real-time PCR demonstrated a high concordance (K = 0.871) with microbiological culture, as well as good sensitivity (91.84%) and specificity (95.24%). In contrast, histopathology demonstrated lower concordance (K = 0.746) and performance levels (sensitivity 91.41%, specificity 82.88%). Liquid media promoted faster and more efficient growth of MTBC than solid media. M. bovis and M. caprae had the comparable ability to respond to the direct real-time PCR test and grow on the microbiological medium. CONCLUSIONS This study confirms that direct real-time PCR can detect MTBC with high diagnostic accuracy within a few days. This study found no significant differences in performance between culture media and direct PCR for M. bovis and M. caprae.
Collapse
Affiliation(s)
- Stefania Ferrari
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| | - Mariagrazia Zanoni
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| | - Anna Mangeli
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| | - Claudio Pigoli
- Sede Territoriale di Milano, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milano, Italy
| | - Mario D'Incau
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| | - Giovanni Loris Alborali
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| | - Maria Lodovica Pacciarini
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| | - Maria Beatrice Boniotti
- Centro Nazionale di Referenza per la Tubercolosi Bovina (CNR-bTB), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), via Bianchi 9, 25124 Brescia, Italy
| |
Collapse
|
14
|
Demircioglu A, Coskun AG, Kanar TS, Eyigor A, Temelli S. High Salmonella load with serovar virchow dominance pose major public safety risk in postchill broiler carcasses. Poult Sci 2024; 103:103584. [PMID: 38471227 DOI: 10.1016/j.psj.2024.103584] [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: 01/16/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
The objective of this study was to determine Salmonella contamination levels, presence and serovar distribution in broiler carcasses before and after chilling, as well as to evaluate the effectiveness of chilling process. A total of 96 pooled neck skin samples (PNSS) of 48 prechill (PreC) and 48 postchill (PosC) carcasses, representing 480 broilers collected in 6 mo' period were analyzed using ISO 6579-2:2012 Miniaturized Most Probable Number (ISO-mMPN) technique. Species confirmation and serovar identification was performed by Salmonella-specific real-time PCR (Salm-PCR) and conventional serotyping, respectively. Mean Salmonella count was 1.84 log10 MPN/g in PreC, and 1.48 log10 MPN/g in PosC samples, indicating a statistically significant reduction of 0.36 log10 MPN/g (p < 0.05) in the counts by plant's air chill system. Salmonella positivity reduced from 97.9% (47/48) in PreC to 85.42% (41/48) in PosC samples, confirmed by Salm-PCR with identified serovars as S. Virchow (89.77 %) followed by S. Schwarzengrund (9.09%) and S. Bredeney (1.14%). Persistence of high load and prevalence of Salmonella with serovar Virchow dominance (other than the ones mandated in current guidelines) in the final product contributes significant and up to date data to relevant literature, and provides unbiased epidemiological reference to legal authorities for future relevant revisions.
Collapse
Affiliation(s)
- A Demircioglu
- Bursa Uludag University, Institute of Health Sciences, Department of Food Hygiene & Technology, Bursa, Turkiye
| | - A G Coskun
- Bursa Uludag University, Institute of Health Sciences, Department of Food Hygiene & Technology, Bursa, Turkiye
| | - T S Kanar
- Bursa Uludag University, Institute of Health Sciences, Department of Microbiology, Bursa, Turkiye
| | - A Eyigor
- Bursa Uludag University, Faculty of Veterinary Medicine, Department of Food Hygiene & Technology, Bursa, Turkiye.
| | - S Temelli
- Bursa Uludag University, Faculty of Veterinary Medicine, Department of Food Hygiene & Technology, Bursa, Turkiye
| |
Collapse
|
15
|
Beyer B, Obrist D, Czarda P, Pühringer K, Vymyslicky F, Siegmund B, D'Amico S, Cichna-Markl M. Influence of Roasting Temperature on the Detectability of Potentially Allergenic Lupin by SDS-PAGE, ELISAs, LC-MS/MS, and Real-Time PCR. Foods 2024; 13:673. [PMID: 38472786 DOI: 10.3390/foods13050673] [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: 11/13/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Seeds of "sweet lupins" have been playing an increasing role in the food industry. Lupin proteins may be used for producing a variety of foods, including pasta, bread, cookies, dairy products, and coffee substitutes. In a small percentage of the population, lupin consumption may elicit allergic reactions, either due to primary sensitization to lupin or due to cross-allergy with other legumes. Thus, lupin has to be declared on commercial food products according to EU food regulations. In this study, we investigated the influence of roasting seeds of the L. angustifolius cultivar "Boregine" on the detectability of lupin by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), ELISAs, LC-MS/MS, and real-time PCR. Seeds were roasted by fluidized bed roasting, and samples were drawn at seed surface temperatures ranging from 98 °C to 242 °C. With increasing roasting temperature, the extractability of proteins and DNA decreased. In addition, roasting resulted in lower detectability of lupin proteins by ELISAs and LC-MS/MS and lower detectability of DNA by real-time PCR. Our results suggest reduced allergenicity of roasted lupin seeds used for the production of "lupin coffee"; however, this has to be confirmed in in vivo studies.
Collapse
Affiliation(s)
- Bruno Beyer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Dominik Obrist
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Philipp Czarda
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Katharina Pühringer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
- Doctoral School in Chemistry, University of Vienna, Währinger Str. 38-40, 1090 Vienna, Austria
| | - Filip Vymyslicky
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8/2030, 12843 Prague 2, Czech Republic
| | - Barbara Siegmund
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, 8010 Graz, Austria
| | - Stefano D'Amico
- AGES-Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| |
Collapse
|
16
|
Di Maro O, Proroga YT, Castellano S, Balestrieri A, Capuano F, Arletti E, Vietina M, Bizzarri M, Murru N, Peruzy MF, Cristiano D. Detection of pathogenic Vibrio spp. in foods: polymerase chain reaction-based screening strategy to rapidly detect pathogenic Vibrio parahaemolyticus, Vibrio cholerae, and Vibrio vulnificus in bivalve mollusks and preliminary results. Ital J Food Saf 2024; 13:11635. [PMID: 38623280 PMCID: PMC11017957 DOI: 10.4081/ijfs.2024.11635] [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] [Received: 08/03/2023] [Accepted: 01/09/2023] [Indexed: 04/17/2024] Open
Abstract
The majority of human diseases attributed to seafood are caused by Vibrio spp., and the most commonly reported species are Vibrio parahaemolyticus, Vibrio vulnificus, and Vibrio cholerae. The conventional methods for the detection of Vibrio species involve the use of selective media, which are inexpensive and simple but time-consuming. The present work aimed to develop a rapid method based on the use of multiplex real-time polymerase chain reaction (PCR) to detect V. parahaemolyticus, V. vulnificus, and V. cholerae in bivalve mollusks. 30 aliquots of bivalve mollusks (Mytilus galloprovincialis) were experimentally inoculated with two levels of V. parahaemolyticus, V. vulnificus, and V. cholerae. ISO 21872-1:2017 was used in parallel for qualitative analysis. The limit of detection of 50% was 7.67 CFU/g for V. cholerae, 0.024 CFU/g for V. vulnificus, and 1.36 CFU/g for V. parahaemolyticus. For V. vulnificus and V. cholerae, the real-time PCR protocol was demonstrated to amplify the pathogens in samples seeded with the lowest and highest levels. The molecular method evaluated showed a concordance rate of 100% with the reference microbiological method. V. parahaemolyticus was never detected in samples contaminated with the lowest level, and it was detected in 14 samples (93.33%) seeded with the highest concentration. In conclusion, the developed multiplex real-time PCR proved to be reliable for V. vulnificus and V. cholerae. Results for V. parahaemolyticus are promising, but further analysis is needed. The proposed method could represent a quick monitoring tool and, if used, would allow the implementation of food safety.
Collapse
Affiliation(s)
- Orlandina Di Maro
- Department of Food Inspection, Experimental Zooprophylactic Institute of Southern Italy, Portici
| | - Yolande T.R. Proroga
- Department of Food Inspection, Experimental Zooprophylactic Institute of Southern Italy, Portici
| | - Silvia Castellano
- Department of Food Inspection, Experimental Zooprophylactic Institute of Southern Italy, Portici
| | - Anna Balestrieri
- Department of Food Inspection, Experimental Zooprophylactic Institute of Southern Italy, Portici
| | - Federico Capuano
- Department of Food Inspection, Experimental Zooprophylactic Institute of Southern Italy, Portici
| | | | | | | | - Nicoletta Murru
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Italy
| | - Maria Francesca Peruzy
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Italy
| | - Daniela Cristiano
- Department of Food Inspection, Experimental Zooprophylactic Institute of Southern Italy, Portici
| |
Collapse
|
17
|
Wilkin T, Hamilton NA, Cawley AT, Bhat S, Baoutina A. PCR-Based Equine Gene Doping Test for the Australian Horseracing Industry. Int J Mol Sci 2024; 25:2570. [PMID: 38473816 DOI: 10.3390/ijms25052570] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
The term 'gene doping' is used to describe the use of any unauthorized gene therapy techniques. We developed a test for five likely candidate genes for equine gene doping: EPO, FST, GH1, IGF1, and ILRN1. The test is based on real-time polymerase chain reaction (PCR) and includes separate screening and confirmation assays that detect different unique targets in each transgene. For doping material, we used nonviral (plasmid) and viral (recombinant adeno-associated virus) vectors carrying complementary DNA for the targeted genes; the vectors were accurately quantified by digital PCR. To reduce non-specific amplification from genomic DNA observed in some assays, a restriction digest step was introduced in the PCR protocol prior to cycling to cut the amplifiable targets within the endogenous genes. We made the screening stage of the test simpler and faster by multiplexing PCR assays for four transgenes (EPO, FST, IGF1, and ILRN1), while the GH1 assay is performed in simplex. Both stages of the test reliably detect at least 20 copies of each transgene in a background of genomic DNA equivalent to what is extracted from two milliliters of equine blood. The test protocol was documented and tested with equine blood samples provided by an official doping control authority. The developed tests will form the basis for screening official horseracing samples in Australia.
Collapse
Affiliation(s)
- Tessa Wilkin
- National Measurement Institute, Lindfield, NSW 2070, Australia
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW 2006, Australia
| | - Natasha A Hamilton
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW 2006, Australia
- Equine Genetics Research Centre, Racing Australia, Sydney, NSW 2000, Australia
| | - Adam T Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW 2000, Australia
- Racing Analytical Services Limited, Flemington, VIC 3031, Australia
| | - Somanath Bhat
- National Measurement Institute, Lindfield, NSW 2070, Australia
| | - Anna Baoutina
- National Measurement Institute, Lindfield, NSW 2070, Australia
| |
Collapse
|
18
|
Tramuta C, Decastelli L, Ingravalle F, Barcucci E, Fragassi S, Bianchi DM. Performance Evaluation of a Commercial Real-Time PCR Method for the Detection of Lupin Traces in Food. Foods 2024; 13:609. [PMID: 38397586 PMCID: PMC10888417 DOI: 10.3390/foods13040609] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
In accordance with U.S. FDA Foods Program Regulatory Science Steering Committee guidelines, with this study, we optimized and validated a commercial real-time PCR method for the detection of low amounts of lupin in four classes of food matrices: chocolate cookies, ragù, Olivier salad, and barley and rice flour. DNA extracted from blank (true negative) samples artificially contaminated with lupin (Lupinus albus) flour at 1000 ppm underwent dilutions with the DNA extracted from the true negative samples up to 0.5 ppm. The limit of detection for real-time PCR was 0.5 ppm in the complex matrices (range, Ct 26-34), making this a specific, robust, and rapid method for lupin allergen detection and labeling. Our validation data support the suitability of this commercially available real-time PCR method for this purpose.
Collapse
Affiliation(s)
- Clara Tramuta
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Valle d’Aosta, Italian National Reference Center for the Detection of Food Allergens and Substances Causing Food Intolerance (CReNaRiA), 10154 Turin, Italy; (L.D.); (E.B.); (S.F.); (D.M.B.)
| | - Lucia Decastelli
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Valle d’Aosta, Italian National Reference Center for the Detection of Food Allergens and Substances Causing Food Intolerance (CReNaRiA), 10154 Turin, Italy; (L.D.); (E.B.); (S.F.); (D.M.B.)
| | - Francesco Ingravalle
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Valle d’Aosta, Department Biostatistics, Epidemiology and Risk Analysis (BEAR), 10154 Turin, Italy;
| | - Elisa Barcucci
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Valle d’Aosta, Italian National Reference Center for the Detection of Food Allergens and Substances Causing Food Intolerance (CReNaRiA), 10154 Turin, Italy; (L.D.); (E.B.); (S.F.); (D.M.B.)
| | - Sandra Fragassi
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Valle d’Aosta, Italian National Reference Center for the Detection of Food Allergens and Substances Causing Food Intolerance (CReNaRiA), 10154 Turin, Italy; (L.D.); (E.B.); (S.F.); (D.M.B.)
| | - Daniela Manila Bianchi
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Valle d’Aosta, Italian National Reference Center for the Detection of Food Allergens and Substances Causing Food Intolerance (CReNaRiA), 10154 Turin, Italy; (L.D.); (E.B.); (S.F.); (D.M.B.)
| |
Collapse
|
19
|
Alič Š, Bačnik K, Dreo T. Retrospective survey of Dickeya fangzhongdai using a novel validated real-time PCR assay. Front Microbiol 2024; 14:1249955. [PMID: 38414710 PMCID: PMC10896844 DOI: 10.3389/fmicb.2023.1249955] [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: 06/29/2023] [Accepted: 12/27/2023] [Indexed: 02/29/2024] Open
Abstract
Dickeya fangzhongdai, an aggressive plant pathogen, causes symptoms on a variety of crops and ornamental plants including bleeding canker of Asian pear trees. Historical findings stress the need for a specific detection tool for D. fangzhongdai to prevent overlooking the pathogen or assigning it to general Dickeya spp. Therefore, a qualitative real-time PCR for specific detection of D. fangzhongdai has been developed and validated. The developed assay shows selectivity of 100%, diagnostic sensitivity of 76% and limit of detection with 95% confidence interval in plant matrices ranging from 311 to 2,275 cells/mL of plant extracts. The assay was successfully used in a retrospective survey of selected host plants of relevance to Europe and environmental niches relevant to D. fangzhongdai. Samples of potato tubers and plants, plants from the Malinae subtribe (apple, pear, quince, and Asian pear tree) and fresh surface water from Slovenia were analyzed. D. fangzhongdai was not detected in any plant samples, however, 12% of surface water samples were found to be positive.
Collapse
Affiliation(s)
| | | | - Tanja Dreo
- National Institute of Biology, Ljubljana, Slovenia
| |
Collapse
|
20
|
Dong X, Chen Y, Lou H, Wang G, Zhou C, Wang L, Li X, Luo J, Huang J. Development of a Melting Curve-Based Triple Eva Green Real-Time PCR Assay for Simultaneous Detection of Three Shrimp Pathogens. Animals (Basel) 2024; 14:592. [PMID: 38396559 PMCID: PMC10886148 DOI: 10.3390/ani14040592] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Infections with Enterocytozoon hepatopenaei (EHP), infectious hypodermal and hematopoietic necrosis virus (IHHNV), and Decapod iridescent virus 1 (DIV1) pose significant challenges to the shrimp industry. Here, a melting curve-based triple real-time PCR assay based on the fluorescent dye Eva Green was established for the simultaneous detection of EHP, IHHNV, and DIV1. The assay showed high specificity, sensitivity, and reproducibility. A total of 190 clinical samples from Shandong, Jiangsu, Sichuan, Guangdong, and Hainan provinces in China were evaluated by the triple Eva Green real-time PCR assay. The positive rates of EHP, IHHNV, and DIV1 were 10.5%, 18.9%, and 44.2%, respectively. The samples were also evaluated by TaqMan qPCR assays for EHP, DIV1, and IHHNV, and the concordance rate was 100%. This illustrated that the newly developed triple Eva Green real-time PCR assay can provide an accurate method for the simultaneous detection of three shrimp pathogens.
Collapse
Affiliation(s)
- Xuan Dong
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
- Jiangsu Shufeng Aquatic Seed Industry Co., Ltd., Gaoyou 255654, China
| | - Yujin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
- School of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Haoyu Lou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
| | - Guohao Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
| | - Chengyan Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
| | - Liying Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
| | - Xuan Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
| | - Jingfei Luo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
| | - Jie Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao 266071, China; (Y.C.); (C.Z.); (X.L.); (J.L.); (J.H.)
- Jiangsu Shufeng Aquatic Seed Industry Co., Ltd., Gaoyou 255654, China
- Network of Aquaculture Centres in Asia-Pacific, Bangkok 10090, Thailand
| |
Collapse
|
21
|
Li X, Zhang T, Jiang L, Fan G. Evaluation of Suitable Reference Genes for Quantitative Real-Time PCR in Various Tissues of Apocynum venetum. Genes (Basel) 2024; 15:231. [PMID: 38397220 PMCID: PMC10888412 DOI: 10.3390/genes15020231] [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: 12/28/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Apocynum venetum L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of A. venetum using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (TUA), β-tubulin (TUB), actin (ACT), cyclophilin (CYP), elongation factor-1α (EF-1α), the B family of regulatory subunits of protein phosphatase (PPP2R2, PPP2R3, and PPP2R5), and phosphoglycerate kinase (PGK), to determine the most appropriate reference genes in the leaf, stem, and root tissues of A. venetum. A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were CYP and TUA in leaves, PGK and PPP2R3 in stems, and TUA and EF-1α in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in A. venetum. They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species.
Collapse
Affiliation(s)
- Xiaoshuang Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Tingting Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Guizhi Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| |
Collapse
|
22
|
Durmanova V, Tedla M, Rada D, Bandzuchova H, Kuba D, Suchankova M, Ocenasova A, Bucova M. Analysis of HLA-G 14 bp Insertion/Deletion Polymorphism and HLA-G, ILT2 and ILT4 Expression in Head and Neck Squamous Cell Carcinoma Patients. Diseases 2024; 12:34. [PMID: 38391781 PMCID: PMC10888050 DOI: 10.3390/diseases12020034] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
HLA-G is the checkpoint molecule involved in the suppression of the immune response. Increased expression of HLA-G and its ILTs receptors have been correlated with tumor progression in various cancer types. In head and neck squamous cell carcinoma (HNSCC) tumors, the effect of HLA-G, ILT2 and ILT4 expression on cancer development has to be explained. The 34 HNSCC patients and 98 controls were genotyped for the HLA-G 14 bp ins/del polymorphism. In HNSCC lesions, HLA-G, ILT2 and ILT4 mRNA expression was analysed using real-time PCR. The association between HLA-G, ILT2 and ILT4 mRNA expression and clinical variables (age at onset, TNM staging system and p16 positivity) was also evaluated. No genetic association between the HLA-G 14 bp ins/del and HNSCC risk was detected (p > 0.05). However, in the non-metastatic HNSCC group, a significantly higher HLA-G mRNA expression was noted in tumors in the T4 stage compared to those in the T1 and T2 stages (p = 0.0289). ILT2 mRNA expression was significantly increased in non-metastatic vs. metastatic tumors (p = 0.0269). Furthermore, a significantly higher ILT4 mRNA expression was noted in tumors in the T1+T2 stage compared to those in the T3 stage (p = 0.0495). Our results suggest that the HLA-G molecule creates an immunological microenvironment involved in HNSCC development.
Collapse
Affiliation(s)
- Vladimira Durmanova
- Institute of Immunology, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Miroslav Tedla
- Department of Ears, Nose and Throat and Head and Neck Surgery, Faculty of Medicine, University Hospital Bratislava, Comenius University in Bratislava, 851 07 Bratislava, Slovakia
| | - Dusan Rada
- Department of Ears, Nose and Throat and Head and Neck Surgery, Faculty of Medicine, University Hospital Bratislava, Comenius University in Bratislava, 851 07 Bratislava, Slovakia
| | | | - Daniel Kuba
- National Transplant Organisation, 831 01 Bratislava, Slovakia
| | - Magda Suchankova
- Institute of Immunology, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Agata Ocenasova
- Institute of Immunology, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| | - Maria Bucova
- Institute of Immunology, Faculty of Medicine, Comenius University in Bratislava, 811 08 Bratislava, Slovakia
| |
Collapse
|
23
|
Na B, Lee J, Chang HE, Park E, Park S, Lee J, Oh S, Shin DW, Hong YJ, Park KU. Verification of a method using magnetic bead enrichment and nucleic acid extraction to improve the molecular detection of bacterial contamination in blood components. Microbiol Spectr 2024; 12:e0276023. [PMID: 38319091 PMCID: PMC10913752 DOI: 10.1128/spectrum.02760-23] [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: 07/04/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
Bacterial contamination of blood products poses a significant risk in transfusion medicine. Platelets are particularly vulnerable to bacterial growth because they must be stored at room temperature with constant agitation for >5 days. The limitations of bacterial detection using conventional methods, such as blood cultures and lateral flow assays, include the long detection times, low sensitivity, and the requirement for substantial volumes of blood components. To address these limitations, we assessed the performance of a bacterial enrichment technique using antibiotic-conjugated magnetic nanobeads (AcMNBs) and real-time PCR for the detection of bacterial contamination in plasma. AcMNBs successfully captured >80% of four bacterial strains, including Staphylococcus aureus, Bacillus cereus, Escherichia coli, and Klebsiella pneumoniae, in both plasma and phosphate-buffered saline. After 24-h incubation with bacterial enrichment, S. aureus and B. cereus were each detected at 101 CFU/mL in all trials (5/5), E. coli at 101 CFU/mL in 1/5 trials, and K. pneumoniae at 10² CFU/mL in 4/5 trials. Additionally, without incubation, the improvement was also achieved in samples with bacterial enrichment, S. aureus at 10² CFU/mL and B. cereus at 101 CFU/mL in 1/5 trials each, E. coli at 10³ CFU/mL in 3/5 trials, and K. pneumoniae at 10¹ CFU/mL in 2/5 trials. Overall, the findings from this study strongly support the superiority of bacterial enrichment in detecting low-level bacterial contamination in plasma when employing AcMNBs and PCR.IMPORTANCEThe study presents a breakthrough approach to detect bacterial contamination in plasma, a critical concern in transfusion medicine. Traditional methods, such as blood cultures and lateral flow assays, are hampered by slow detection times, low sensitivity, and the need for large blood sample volumes. Our research introduces a novel technique using antibiotic-conjugated magnetic nanobeads combined with real-time PCR, enhancing the detection of bacteria in blood products, especially platelets. This method has shown exceptional efficiency in identifying even low levels of four different species of bacteria in plasma. The ability to detect bacterial contamination rapidly and accurately is vital for ensuring the safety of blood transfusions and can significantly reduce the risk of infections transmitted through blood products. This advancement is a pivotal step in improving patient outcomes and elevating the standards of care in transfusion medicine.
Collapse
Affiliation(s)
- Byungjoon Na
- KingoBio Inc. Research Center, Seoul, South Korea
| | - Jinyeop Lee
- KingoBio Inc. Research Center, Seoul, South Korea
| | | | - Eunseon Park
- KingoBio Inc. Research Center, Seoul, South Korea
| | - Sojin Park
- KingoBio Inc. Research Center, Seoul, South Korea
| | | | - Sujin Oh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Dong Woo Shin
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Yun Ji Hong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| |
Collapse
|
24
|
Xu G, Siegel E, Fernandez N, Bechtold E, Daly T, Dupuis AP, Ciota A, Rich SM. Active Surveillance of Powassan Virus in Massachusetts Ixodes scapularis Ticks, Comparing Detection Using a New Triplex Real-Time PCR Assay with a Luminex Vector-Borne Panel. Viruses 2024; 16:250. [PMID: 38400026 PMCID: PMC10892230 DOI: 10.3390/v16020250] [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: 01/15/2024] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Powassan virus is an emerging tick-borne pathogen capable of causing severe neuroinvasive disease. As the incidence of human Powassan virus grows both in magnitude and geographical range, the development of sensitive detection methods for diagnostics and surveillance is critical. In this study, a Taqman-based triplex real-time PCR assay was developed for the simultaneous and quantitative detection of Powassan virus and Powassan virus lineage II (deer tick virus) in Ixodes scapularis ticks. An exon-exon junction internal control was built-in to allow for accurate detection of RNA quality and the failure of RNA extraction. The newly developed assay was also applied to survey deer tick virus in tick populations at 13 sites on Cape Cod and Martha's Vineyard Island in Massachusetts. The assay's performance was compared with the Luminex xMAP MultiFLEX Vector-borne Panel 2. The results suggested that the real-time PCR method was more sensitive. Powassan virus infection rates among ticks collected from these highly endemic tick areas ranged from 0.0 to 10.4%, highlighting the fine-scale geographic variations in deer tick virus presence in this region. Looking forward, our PCR assay could be adopted in other Powassan virus surveillance systems.
Collapse
Affiliation(s)
- Guang Xu
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (G.X.); (N.F.); (E.B.); (T.D.)
| | - Eric Siegel
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (G.X.); (N.F.); (E.B.); (T.D.)
| | - Nolan Fernandez
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (G.X.); (N.F.); (E.B.); (T.D.)
| | - Emily Bechtold
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (G.X.); (N.F.); (E.B.); (T.D.)
| | - Timothy Daly
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (G.X.); (N.F.); (E.B.); (T.D.)
| | - Alan P. Dupuis
- New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA; (A.P.D.II); (A.C.)
| | - Alexander Ciota
- New York State Department of Health, Wadsworth Center, Slingerlands, NY 12159, USA; (A.P.D.II); (A.C.)
| | - Stephen M. Rich
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA; (G.X.); (N.F.); (E.B.); (T.D.)
| |
Collapse
|
25
|
Khunger S, Mewara A, Kaur U, Duseja A, Ray P, Kalra N, Sharma N, Sehgal R. Real-time loop-mediated isothermal amplification (real-time LAMP) assay for rapid diagnosis of amoebic liver abscess. Trop Med Int Health 2024; 29:104-112. [PMID: 38093589 DOI: 10.1111/tmi.13954] [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] [Indexed: 02/07/2024]
Abstract
Among the parasitic diseases, amoebic liver abscess (ALA) ranks second to malaria in terms of mortality. Due to the poor sensitivity of conventional diagnostic methods, there is a need for the development of effective and rapid diagnostic methods for ALA. Thus, the purpose of this work was to develop a real-time loop-mediated isothermal amplification (RT-LAMP) assay specific to Entamoeba histolytica. Further, we compared the performance of real-time LAMP with conventional and real-time PCR (RT-PCR) targeting 18S small subunit ribosomal RNA (18S SSU rRNA) gene of E. histolytica in patients with ALA. A total of 126 liver samples were obtained for the study. Of these, 96 aspirated pus samples were obtained from patients suffering from an ALA (serology confirmed, anti-amoebic immunoglobulin IgG positive), 19 aspirated pus samples from patients with pyogenic liver abscess (PLA, 16S RNA gene positive) and 11 autopsy liver tissues. The results showed that the DNA of E. histolytica was detected in 81 samples by conventional PCR, 93 by RT-PCR and 95 by RT-LAMP. The analytical sensitivity of the RT-LAMP assay was much higher than the other two techniques. RT-LAMP assay was able to amplify up to one copy of the targeted gene of E. histolytica while conventional PCR and RT-PCR could amplify up to 103 and 102 copies of the targeted gene of E. histolytica, respectively. In conclusion, RT-LAMP proved to be a sensitive, specific and rapid test which can be utilised as an effective tool for the diagnosis of ALA.
Collapse
Affiliation(s)
- Sandhya Khunger
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
- Department of Microbiology(FAHS), Shree Guru Gobind Singh Tricentanary University, Gurugram, India
| | - Abhishek Mewara
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Upninder Kaur
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Duseja
- Department of Hepatology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Naveen Kalra
- Department of Radiodiagnosis and Imaging, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Navneet Sharma
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Sehgal
- Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation-DU, Pondicherry, India
| |
Collapse
|
26
|
Duan R, Huang J, Zhang D, Tian E. Identification of lethal species in amanita section Phalloideae based on nucleotide signature and specific TaqMan-MGB probe and primer. Front Microbiol 2024; 15:1301085. [PMID: 38362500 PMCID: PMC10867329 DOI: 10.3389/fmicb.2024.1301085] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024] Open
Abstract
Amanita section Phalloideae consists of lethal toxic mushroom species, causing many fatal poisoning incidents worldwide. Molecular techniques of nucleotide signatures and single nucleotide polymorphism (SNP) detection could be used to develop a specific method for identifying lethal section (sect.) Phalloideae species. A comparison of 38 sequenced and 228 validated sequences from sect. Phalloideae species showed a 17-base pair nucleotide signature and an SNP site between the lethal and non-lethal species. A specific minor groove binder probe was designed based on them. The results indicated that this method exhibited excellent specificity for the lethal subgroup, good detection in samples subjected to simulated gastric digestion (60 min boiling and 120 min digestion), and a 10 pg./μL detection limit. This method enables accurate detection of target species in samples under complex conditions and can provide evidence for poisoning incidents caused by lethal sect. Phalloideae species to assist in targeted treatment strategies.
Collapse
Affiliation(s)
| | | | | | - Enjing Tian
- Country Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| |
Collapse
|
27
|
Mala R, Malhotra S, Singh N, Gupta S, Upadhyay DA, Kapil A, Sood S. Deciphering Intermediate Nugent scores: Utility of Real-time PCR for Bacterial Vaginosis diagnosis. Diagn Microbiol Infect Dis 2024; 108:116152. [PMID: 38061216 DOI: 10.1016/j.diagmicrobio.2023.116152] [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: 04/23/2023] [Revised: 11/16/2023] [Accepted: 11/26/2023] [Indexed: 01/22/2024]
Abstract
PURPOSE To optimize real-time PCR assays for diagnosis of Bacterial Vaginosis (BV) and determine cut-off loads by ROC analysis for Gardnerella vaginalis, Atopobium vaginae and Lactobacillus spp. as compared to Nugent scoring (Gold standard) in clinical samples. RESULTS Out of 125 women, 34 were positive, 26 intermediate and 65 negative for BV by Nugent scoring. All three real-time PCR assays were found to be highly sensitive & specific and AUC suggested excellent diagnostic accuracy. An optimal cut-off was >9.45 × 103 copies/ ml, >3.34 × 103 copies/ ml & ≤ 18.63 × 103 copies/ ml for G. vaginalis, A. vaginae and Lactobacillus spp. respectively, in BV positives. Gram staining and qPCR were discordant only in patients with intermediate scores (n = 26) where qPCR identified 15 (57.69%) as positive and 11 (42.3%) as negative. CONCLUSION PCR-based molecular BV diagnosis is more accurate and can be used for deciphering intermediate Nugent scores.
Collapse
Affiliation(s)
- R Mala
- Department of Microbiology, AIIMS, New Delhi, India
| | - S Malhotra
- Department of Microbiology, AIIMS, New Delhi, India
| | - N Singh
- Department of Obstetrics & Gynaecology, AIIMS, New Delhi, India
| | - S Gupta
- Department of Dermatology & Venereology, AIIMS, New Delhi, India
| | - D A Upadhyay
- Department of Biostatistics, AIIMS, New Delhi, India
| | - A Kapil
- Department of Microbiology, AIIMS, New Delhi, India
| | - S Sood
- Department of Microbiology, AIIMS, New Delhi, India.
| |
Collapse
|
28
|
Dashti A, Alonso H, Escolar-Miñana C, Köster PC, Bailo B, Carmena D, González-Barrio D. Evaluation of the Use of Singleplex and Duplex CerTest VIASURE Real-Time PCR Assays to Detect Common Intestinal Protist Parasites. Diagnostics (Basel) 2024; 14:319. [PMID: 38337835 PMCID: PMC10855428 DOI: 10.3390/diagnostics14030319] [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: 12/18/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Cryptosporidium spp., Giardia duodenalis and Entamoeba histolytica are species of protozoa- causing diarrhoea that are common worldwide, while Entamoeba dispar, Dientamoeba fragilis and Blastocystis sp. appear to be commensal parasites whose role in pathogenicity remains controversial. We conducted the clinical evaluation of five singleplex and one duplex CerTest VIASURE Real-Time PCR Assays against a large panel of positive DNA samples (n = 358), and specifically to Cryptosporidium spp. (n = 96), G. duodenalis (n = 115), E. histolytica (n = 25) E. dispar (n = 11), Blastocystis sp. (n = 42), D. fragilis (n = 37), and related parasitic phylum species such as Apicomplexa, Euglenozoa, Microsporidia and Nematoda. DNA samples were obtained from clinical stool specimens or cultured isolates in a national reference centre. Estimated diagnostic sensitivity and specificity values were 0.94-1 for Cryptosporidium spp., 0.96-0.99 for G. duodenalis, 0.96-1 for E. histolytica, 1-1 for E. dispar, and 1-0.99 for D. fragilis in the evaluated singleplex assays. In the duplex assay for the simultaneous detection of Blastocystis sp. and D. fragilis these values were 1-0.98 and 1-0.99, respectively. Measures of diagnostic precision for repeatability and reproducibility were found to be under acceptable ranges. The assays identified six Cryptosporidium species (C. hominis, C. parvum, C. canis, C. felis, C. scrofarum, and C. ryanae), four G. duodenalis assemblages (A, B, C, and F), and six Blastocystis subtypes (ST1-ST5, and ST8). The evaluated singleplex and duplex VIASURE Real-Time PCR assays provide sensitive, practical, and cost-effective choices to the molecular diagnosis of the main diarrhoea-causing intestinal protists in clinical microbiology and research laboratories.
Collapse
Affiliation(s)
- Alejandro Dashti
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
| | - Henar Alonso
- Department of Microbiology, Paediatrics, Radiology, and Public Health, Faculty of Medicine, University of Zaragoza, 50009 Saragossa, Spain
| | - Cristina Escolar-Miñana
- Department of Animal Production and Food Science, Faculty of Veterinary, University of Zaragoza, 50013 Saragossa, Spain
| | - Pamela C. Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
- Faculty of Health Sciences, Alfonso X El Sabio University (UAX), 28691 Villanueva de la Cañada, Spain
- Faculty of Medicine, Alfonso X El Sabio University (UAX), 28691 Villanueva de la Cañada, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
- CIBER Infectious Diseases (CIBERINFEC), Health Institute Carlos III, 28008 Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28220 Majadahonda, Spain; (A.D.); (P.C.K.); (B.B.); (D.G.-B.)
| |
Collapse
|
29
|
Guo XM, Xing JY, Li A, Qiu L, Zhang QL, Huang J. Establishment of a real-time PCR for the detection of decapod iridescent virus 1 (DIV1). J Fish Dis 2024:e13926. [PMID: 38300509 DOI: 10.1111/jfd.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 02/02/2024]
Affiliation(s)
- Xiao-Meng Guo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jing-Yi Xing
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Aquaculture, Tianjin Agricultural University, Tianjin, China
| | - Anqi Li
- College of Aquaculture, Tianjin Agricultural University, Tianjin, China
| | - Liang Qiu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Qing-Li Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- College of Aquaculture, Tianjin Agricultural University, Tianjin, China
| | - Jie Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Network of Aquaculture Centres in Asia-Pacific, Bangkok, Thailand
| |
Collapse
|
30
|
Račka K, Bártová E, Hamidović A, Plault N, Kočišová A, Camacho G, Mercier A, Halajian A. First detection of Toxoplasma gondii Africa 4 lineage in a population of carnivores from South Africa. Front Cell Infect Microbiol 2024; 14:1274577. [PMID: 38352059 PMCID: PMC10861644 DOI: 10.3389/fcimb.2024.1274577] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction There have only been a few molecular studies conducted on the detection of T. gondii in tissues of carnivores in South Africa, with no data on the genetic diversity of this parasite. That is why the aim of this study was to detect and genotype T. gondii DNA in tissues of selected wild and domestic carnivores in South Africa. Methods Samples were collected from 80 animals of 20 species (mainly road-killed) in the four provinces of Limpopo (n=57), Mpumalanga (n=21), Gauteng (n=1) and Free State (n=1) during the period 2014-2018. Samples of brain (n=31), heart (n=4), liver (n=40), spleen (n=2) and lung (n=3) were used to detect T. gondii by real-time PCR targeting a 529 bp repeating fragment of T. gondii DNA. Samples that were positive in real-time PCR were genotyped using 15 microsatellite markers. Results T. gondii DNA was detected in 4 (5 %) samples: in the brain from a Black-backed Jackal (Canis mesomelas), in the liver from a African Wildcat (Felis silvestris lybica) and in the liver and heart of two Rusty-spotted Genets (Genetta maculata) respectively. The DNA sample from Black-backed Jackal was genotyped and characterized as belonging to the type Africa 4 lineage (equivalent to RFLP genotype ToxoDB#20), that is a widespread lineage in Africa. Discussion This is the first genetic characterization of T. gondii isolated from a wild carnivore on the African continent and the first report of T. gondii in Black-backed Jackal. The Africa 4 lineage was also confirmed in the region of Southern Africa for the first time.
Collapse
Affiliation(s)
- Karol Račka
- Department of Epizootology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Eva Bártová
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Azra Hamidović
- Inserm U1094, IRD U270, CHU Limoges, EpiMaCT - Epidémiologie des Maladies Chroniques en zone Tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, OmegaHealth, University of Limoges, Limoges, France
| | - Nicolas Plault
- Inserm U1094, IRD U270, CHU Limoges, EpiMaCT - Epidémiologie des Maladies Chroniques en zone Tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, OmegaHealth, University of Limoges, Limoges, France
| | - Alica Kočišová
- Department of Epizootology, Parasitology and Protection of One Health, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Gerrie Camacho
- Department of Scientific Services, Mpumalanga Tourism & Parks Agency (MTPA), Nelspruit, South Africa
| | - Aurelién Mercier
- Inserm U1094, IRD U270, CHU Limoges, EpiMaCT - Epidémiologie des Maladies Chroniques en zone Tropicale, Institut d’Epidémiologie et de Neurologie Tropicale, OmegaHealth, University of Limoges, Limoges, France
| | - Ali Halajian
- Research Administration and Development, University of Limpopo, Sovenga, South Africa
| |
Collapse
|
31
|
Kiselev A, Maretina M, Shtykalova S, Al-Hilal H, Maslyanyuk N, Plokhih M, Serebryakova E, Frolova M, Shved N, Krylova N, Il’ina A, Freund S, Osinovskaya N, Sultanov I, Egorova A, Lobenskaya A, Koroteev A, Sosnina I, Gorelik Y, Bespalova O, Baranov V, Kogan I, Glotov A. Establishment of a Pilot Newborn Screening Program for Spinal Muscular Atrophy in Saint Petersburg. Int J Neonatal Screen 2024; 10:9. [PMID: 38390973 PMCID: PMC10885106 DOI: 10.3390/ijns10010009] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Spinal muscular atrophy 5q (SMA) is one of the most common neuromuscular inherited diseases and is the most common genetic cause of infant mortality. SMA is associated with homozygous deletion of exon 7 in the SMN1 gene. Recently developed drugs can improve the motor functions of infants with SMA when they are treated in the pre-symptomatic stage. With aim of providing an early diagnosis, newborn screening (NBS) for SMA using a real-time PCR assay with dried blood spots (DBS) was performed from January 2022 through November 2022 in Saint Petersburg, which is a representative Russian megapolis. Here, 36,140 newborns were screened by the GenomeX real-time PCR-based screening test, and three genotypes were identified: homozygous deletion carriers (4 newborns), heterozygous carriers (772 newborns), and wild-type individuals (35,364 newborns). The disease status of all four newborns that screened positive for the homozygous SMN1 deletion was confirmed by alternate methods. Two of the newborns had two copies of SMN2, and two of the newborns had three copies. We determined the incidence of spinal muscular atrophy in Saint Petersburg to be 1 in 9035 and the SMA carrier frequency to be 1 in 47. In conclusion, providing timely information regarding SMN1, confirmation of disease status, and SMN2 copy number as part of the SMA newborn-screening algorithm can significantly improve clinical follow-up, testing of family members, and treatment of patients with SMA.
Collapse
Affiliation(s)
- Anton Kiselev
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Marianna Maretina
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Sofia Shtykalova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Haya Al-Hilal
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Natalia Maslyanyuk
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Mariya Plokhih
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Elena Serebryakova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Marina Frolova
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Natalia Shved
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Nadezhda Krylova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Arina Il’ina
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Svetlana Freund
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Natalia Osinovskaya
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Iskender Sultanov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Anna Egorova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Anastasia Lobenskaya
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Alexander Koroteev
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Irina Sosnina
- Saint Petersburg State Budgetary Healthcare Institution “Consulting and Diagnostic Center for Children”, Aleksa Dundić Street 36/2, 192289 Saint Petersburg, Russia;
| | - Yulia Gorelik
- Children’s City Multidisciplinary Clinical Specialized Center of High Medical Technologies, Avangardnaya Street 14, 198205 Saint Petersburg, Russia;
| | - Olesya Bespalova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Vladislav Baranov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Igor Kogan
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Andrey Glotov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| |
Collapse
|
32
|
Liempi D, Zulantay I, Varela NM, Canals M, Guevara A, Poulsen N, Apt W. Parasite Burden of Trypanosoma cruzi in Whole Blood and Buffy Coat Determined by Real-Time PCR in Individuals with Chronic Chagas Disease. Microorganisms 2024; 12:249. [PMID: 38399653 PMCID: PMC10893161 DOI: 10.3390/microorganisms12020249] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 02/25/2024] Open
Abstract
The objective of this study was to compare, by qPCR, the circulating blood parasite load of Trypanosoma cruzi in the buffy coat, and in whole blood mixed with boiled and unboiled guanidine hydrochloride-EDTA buffer, of individuals with chronic ChD. The concentration and purity of DNA were evaluated in a Nanodrop Denovix DS-11FX Series Spectrophotometer (DeNovix Inc., Wilmington, NC, USA). The parasite load was determined with the Taqman® qPCR system using a Stratagene Mx3000P thermocycler (Agilent Technologies, Santa Clara, CA, USA) with Cruzi 1 and Cruzi 2 satellite primers. Student's t-test with Bonferroni correction, Chi-squared (χ2) tests and Spearman's correlation coefficient were applied. The concentration and purity of DNA were higher in the buffy coat. Parasite DNA was detected and quantifiable in the three types of samples in seven patients, without statistically significant differences in the parasite load obtained. Higher correlations were found between the total DNA concentrations and the parasite loads obtained in the samples of the buffy coat.
Collapse
Affiliation(s)
- Daniela Liempi
- Institute of Parasitology, Faculty of Medicine, Austral University of Chile, Valdivia 5090000, Chile
- Master’s Program in Parasitology, Graduate School, Faculty of Medicine, University of Chile, Santiago 8380453, Chile
| | - Inés Zulantay
- Basic-Clinical Parasitology Laboratory, Cellular and Molecular Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago 8380453, Chile;
| | - Nelson M. Varela
- Basic-Clinical Oncology Department, Faculty of Medicine, University of Chile, Santiago 8500000, Chile;
| | - Mauricio Canals
- Department of Eastern Medicine and Environmental Health Program, School of Public Health, Faculty of Medicine, University of Chile, Santiago 8380453, Chile;
| | - Andrés Guevara
- School of Medical Technology, Faculty of Medicine, University of Chile, Santiago 8380000, Chile; (A.G.); (N.P.)
| | - Nicolás Poulsen
- School of Medical Technology, Faculty of Medicine, University of Chile, Santiago 8380000, Chile; (A.G.); (N.P.)
| | - Werner Apt
- Basic-Clinical Parasitology Laboratory, Cellular and Molecular Biology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago 8380453, Chile;
| |
Collapse
|
33
|
Kochan E, Sienkiewicz M, Szmajda-Krygier D, Balcerczak E, Szymańska G. Carvacrol as a Stimulant of the Expression of Key Genes of the Ginsenoside Biosynthesis Pathway and Its Effect on the Production of Ginseng Saponins in Panax quinquefolium Hairy Root Cultures. Int J Mol Sci 2024; 25:909. [PMID: 38255986 PMCID: PMC10815547 DOI: 10.3390/ijms25020909] [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: 12/15/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The accumulation of ginsenosides (triterpenic saponins) was determined in Panax quinquefolium hairy root cultures subjected to an elicitation process using carvacrol at 5, 10, 25, 50, 100, 250, and 500 μM concentrations during 24 and 72 h exposure. This study was the first one in which carvacrol was applied as an elicitor. The content of eight ginsenosides, Rb1, Rb2, Rb3, Rc, Rd, Rg1, Rg2, and Re, was determined using HPLC analysis. Moreover, the quantitative RT-PCR method was applied to assess the relative expression level of farnesyl diphosphate synthase, squalene synthase, and dammarenediol synthase genes in the studied cultures. The addition of carvacrol (100 μM) was an effective approach to increase the production of ginsenosides. The highest content and productivity of all detected saponins were, respectively, 20.01 mg∙g-1 d.w. and 5.74 mg∙L-1∙day-1 after 72 h elicitation. The production profile of individual metabolites in P. quinquefolium cultures changed under the influence of carvacrol. The biosynthesis of most examined protopanaxadiol derivatives was reduced under carvacrol treatment. In contrast, the levels of ginsenosides belonging to the Rg group increased. The strongest effect of carvacrol was noticed for Re metabolites, achieving a 7.72-fold increase in comparison to the control. Saponin Rg2, not detected in untreated samples, was accumulated after carvacrol stimulation, reaching its maximum concentration after 72 h exposure to 10 μM elicitor.
Collapse
Affiliation(s)
- Ewa Kochan
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
| | - Monika Sienkiewicz
- Department of Pharmaceutical Microbiology and Microbiological Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland;
| | - Dagmara Szmajda-Krygier
- Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (D.S.-K.); (E.B.)
| | - Ewa Balcerczak
- Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (D.S.-K.); (E.B.)
| | - Grażyna Szymańska
- Department of Pharmaceutical Biotechnology, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
| |
Collapse
|
34
|
Timofeeva AV, Fedorov IS, Suhova YV, Tarasova AM, Ezhova LS, Zabelina TM, Vasilchenko ON, Ivanets TY, Sukhikh GT. Diagnostic Role of Cell-Free miRNAs in Identifying Placenta Accreta Spectrum during First-Trimester Screening. Int J Mol Sci 2024; 25:871. [PMID: 38255950 PMCID: PMC10815502 DOI: 10.3390/ijms25020871] [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: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Placenta accreta spectrum (PAS) is a severe complication of pregnancy associated with excessive invasion of cytotrophoblast cells at the sites of the endometrial-myometrial interface and the myometrium itself in cases of adherent (creta) and invasive (increta and percreta) forms, respectively. This leads to a high risk of massive blood loss, maternal hysterectomy, and preterm birth. Despite advancements in ultrasound protocols and found associations of alpha-fetoprotein, PAPP-A, hCG, PLGF, sFlt-1, IL-8, and IL-33 peripheral blood levels with PAS, there is a high need for an additional non-invasive test to improve the diagnostic accuracy and to select the real PAS from the suspected ones in the first-trimester screening. miRNA signatures of placental tissue, myometrium, and blood plasma from women with PAS in the third trimester of pregnancy, as well as miRNA profiles in exosomes from the blood serum of women in the first trimester with physiologically progressing pregnancy, complicated by PAS or pre-eclampsia, were obtained using deep sequencing. Two logistic regression models were constructed, both featuring statistically significant parameters related to the levels of miR-26a-5p, miR-17-5p, and miR-101-3p, quantified by real-time PCR in native blood serum. These models demonstrated 100% sensitivity in detecting PAS during the first pregnancy screening. These miRNAs were identified as specific markers for PAS, showing significant differences in their blood serum levels during the first trimester in the PAS group compared to those in physiological pregnancies, early- or late-onset pre-eclampsia groups. Furthermore, these miRNAs exhibited differential expression in the PAS placenta and/or myometrium in the third trimester and, according to data from the literature, control angiogenesis. Significant correlations were found between extracellular hsa-miR-101-3p and nuchal translucency thickness, hsa-miR-17-5p and uterine artery pulsatility index, and hsa-miR-26a-5p and hsa-miR-17-5p with PLGF. The developed test system for early non-invasive PAS diagnosis based on the blood serum level of extracellular miR-26a-5p, miR-17-5p, and miR-101-3p can serve as an auxiliary method for first-trimester screening of pregnant women, subject to validation with independent test samples.
Collapse
Affiliation(s)
- Angelika V. Timofeeva
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology, Ministry of Health of Russia, Ac. Oparina 4, 117997 Moscow, Russia; (I.S.F.); (Y.V.S.); (A.M.T.); (L.S.E.); (T.M.Z.); (O.N.V.); (T.Y.I.); (G.T.S.)
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Bors A, Kozma A, Tomán Á, Őrfi Z, Kondor N, Tasnády S, Vályi-Nagy I, Reményi P, Mikala G, Andrikovics H. IGH::NSD2 Fusion Gene Transcript as Measurable Residual Disease Marker in Multiple Myeloma. Cancers (Basel) 2024; 16:283. [PMID: 38254774 PMCID: PMC10813871 DOI: 10.3390/cancers16020283] [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: 11/30/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy. Approximately 15% of MM patients are affected by the t(4;14) translocation resulting in the IGH::NSD2 fusion transcript. Breakage occurs in three major breakpoint regions within the NSD2 gene (MB4-1, MB4-2, and MB4-3), where MB4-1 leads to the production of full-length protein, while truncated proteins are expressed in the other two cases. Measurable residual disease (MRD) has been conclusively established as a crucial prognostic factor in MM. The IGH::NSD2 fusion transcript can serve as a sensitive MRD marker. Using bone marrow (BM) and peripheral blood (PB) samples from 111 patients, we developed a highly sensitive quantitative real-time PCR (qPCR) and digital PCR (dPCR) system capable of detecting fusion mRNAs with a sensitivity of up to 1:100,000. PB samples exhibited sensitivity three orders of magnitude lower compared to BM samples. Patients with an MB4-2 breakpoint demonstrated significantly reduced overall survival (p = 0.003). Our novel method offers a simple and sensitive means for detecting MRD in a substantial proportion of MM patients. Monitoring may be carried out even from PB samples. The literature lacks consensus regarding survival outcomes among patients with different NSD2 breakpoints. Our data align with previous findings indicating that patients with the MB4-2 breakpoint type tend to exhibit unfavorable overall survival.
Collapse
Affiliation(s)
- András Bors
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (A.K.); (Á.T.); (Z.Ő.); (H.A.)
| | - András Kozma
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (A.K.); (Á.T.); (Z.Ő.); (H.A.)
| | - Ágnes Tomán
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (A.K.); (Á.T.); (Z.Ő.); (H.A.)
| | - Zoltán Őrfi
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (A.K.); (Á.T.); (Z.Ő.); (H.A.)
| | - Nóra Kondor
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (A.K.); (Á.T.); (Z.Ő.); (H.A.)
| | - Szabolcs Tasnády
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (S.T.); (I.V.-N.); (P.R.); (G.M.)
| | - István Vályi-Nagy
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (S.T.); (I.V.-N.); (P.R.); (G.M.)
| | - Péter Reményi
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (S.T.); (I.V.-N.); (P.R.); (G.M.)
| | - Gábor Mikala
- Department of Hematology and Stem Cell Transplantation, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (S.T.); (I.V.-N.); (P.R.); (G.M.)
| | - Hajnalka Andrikovics
- Laboratory of Molecular Genetics, Central Hospital of Southern Pest-National Institute of Hematology and Infectious Disease, H-1097 Budapest, Hungary; (A.K.); (Á.T.); (Z.Ő.); (H.A.)
| |
Collapse
|
36
|
Gong C, Zhu P, Ye J, Lou J, Zhang L, Liu X, Kong W. Application and development of a TaqMan-based real-time PCR assay for rapid detection of snakehead vesiculovirus. FEMS Microbiol Lett 2024; 371:fnae018. [PMID: 38460951 DOI: 10.1093/femsle/fnae018] [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: 10/17/2023] [Revised: 01/26/2024] [Accepted: 03/08/2024] [Indexed: 03/11/2024] Open
Abstract
Snakehead vesiculovirus (SHVV) is one of the primary pathogens responsible for viral diseases in the snakehead fish. A TaqMan-based real-time PCR assay was established for the rapid detection and quantification of SHVV in this study. Specific primers and fluorescent probes were designed for phosphoprotein (P) gene, and after optimizing the reaction conditions, the results indicated that the detection limit of this method could reach 37.1 copies, representing a 100-fold increase in detection sensitivity compared to RT-PCR. The specificity testing results revealed that this method exhibited no cross-reactivity with ISKNV, LMBV, RSIV, RGNNV, GCRV, and CyHV-2. Repetition experiments demonstrated that both intra-batch and inter-batch coefficients of variation were not higher than 1.66%. Through in vitro infection experiments monitoring the quantitative changes of SHVV in different tissues, the results indicated that the liver and spleen exhibited the highest viral load at 3 poi. The TaqMan-based real-time PCR method established in this study exhibits high sensitivity, excellent specificity, and strong reproducibility. It can be employed for rapid detection and viral load monitoring of SHVV, thus providing a robust tool for the clinical diagnosis and pathogen research of SHVV.
Collapse
Affiliation(s)
- Cuiping Gong
- Huzhou Academy of Agricultural Sciences, Huzhou Municipal Bureau of Agriculture and Rural Affairs, Huzhou 313000, China
| | - Panpan Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiaxin Ye
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianfeng Lou
- Huzhou Academy of Agricultural Sciences, Huzhou Municipal Bureau of Agriculture and Rural Affairs, Huzhou 313000, China
| | - Liwen Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaodan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
| | - Weiguang Kong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
37
|
Rizzo D, Zubieta CG, Sacchetti P, Marrucci A, Miele F, Ascolese R, Nugnes F, Bernardo U. Diagnostic Tool for the Identification of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) Using Real-Time PCR. Insects 2024; 15:44. [PMID: 38249050 PMCID: PMC10815988 DOI: 10.3390/insects15010044] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
Accurate identification of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), commonly known as the Oriental fruit fly, is a significant challenge due to the morphological convergence and taxonomic uncertainties of species belonging to the same genus. This highly polyphagous species poses a significant threat to fruit crops. With its potential establishment in Europe becoming a growing concern, there is an urgent need for rapid and efficient diagnostic methods. The study presented here introduces a diagnostic protocol based on real-time PCR using a TaqMan probe for the early and reproducible identification of B. dorsalis. Specimens representing the genetic diversity of the Italian population were collected and analyzed. Specific primers and probe were designed based on the conserved regions and an in silico analysis confirmed their specificity. The assay conditions were optimized, and analytical sensitivity, specificity, repeatability, and reproducibility were evaluated. The protocol showed high sensitivity and specificity, accurately detecting low DNA concentrations of B. dorsalis. This standardized method provides a reliable tool for routine diagnostics, enhancing the accuracy and efficiency of identifying the Oriental fruit fly at all stages of its development, thereby facilitating effective pest management measures. The development of this diagnostic protocol is crucial for monitoring and supporting efforts to prevent the passive spread of B. dorsalis in Europe, particularly in light of the recent active infestations detected in Italy.
Collapse
Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (C.G.Z.); (A.M.)
| | - Claudia Gabriela Zubieta
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (C.G.Z.); (A.M.)
| | - Patrizia Sacchetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Piazzale delle Cascine, 18, 50144 Florence, Italy;
| | - Andrea Marrucci
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (C.G.Z.); (A.M.)
- Department of Agricultural Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Fortuna Miele
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
| | - Roberta Ascolese
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 21, 80126 Napoli, Italy
| | - Francesco Nugnes
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
| | - Umberto Bernardo
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), P.le Enrico Fermi 1, 80055 Portici, Italy; (F.M.); (R.A.); (F.N.)
| |
Collapse
|
38
|
Lee YJ, Jun LJ, Kim YJ, Han JE, Ko YJ, Oh YE, Lee EJ, Lee J, Jeong JB. Comparison of specificity and sensitivity of diagnostic methods for Enteromyxum leei and Enteromyxum fugu detected from cultured tiger puffer, Takifugu rubripes in Korea. J Fish Dis 2024; 47:e13865. [PMID: 37731267 DOI: 10.1111/jfd.13865] [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] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Enteromyxum leei and Enteromyxum fugu, which are myxosporean parasites, were first found in cultured tiger puffer Takifugu rubripes in Korea. We collected four tiger puffers that showed severe emaciation signs for our experiments. DNA sequencing was confirmed that the tiger puffers were coinfected with E. leei and E. fugu. Furthermore, similar amounts of E. leei and E. fugu were confirmed using real-time PCR in the intestine. To the best of our knowledge, there have been no reports of E. fugu infection in the olive flounder Paralichthys olivaceus. However, the diagnosis of inflowing water, discharged water and olive flounder samples using highly sensitive diagnostic methods confirmed the presence of E. fugu in water and fish samples from olive flounder farms near the tiger puffer farm. Therefore, the present study aimed to develop highly sensitive diagnostic methods such as real-time and two-step PCR for early diagnosis and follow-up of the emaciation disease and multiplex PCR for rapid diagnosis. The multiplex PCR method exhibited the same sensitivity as the one-step PCR method developed in this study, demonstrating its efficacy for rapid diagnosis. Therefore, the suggested methods can be utilized for the early diagnosis and rapid diagnosis of emaciation diseases and reduction of economic losses through rapid disease control.
Collapse
Affiliation(s)
- Young Juhn Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Lyu Jin Jun
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ye Ji Kim
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ji Eun Han
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Ye Jin Ko
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Yeong Eun Oh
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Eung Joon Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| | - Joon Bum Jeong
- Department of Marine Life Science, Jeju National University, Jeju City, Republic of Korea
| |
Collapse
|
39
|
Armenta-Leyva B, Munguía-Ramírez B, Cheng TY, Ye F, Henao-Díaz A, Giménez-Lirola LG, Zimmerman J. Normalizing real-time PCR results in routine testing. J Vet Diagn Invest 2024; 36:78-85. [PMID: 37919959 PMCID: PMC10734596 DOI: 10.1177/10406387231206080] [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] [Indexed: 11/04/2023] Open
Abstract
Normalization, the process of controlling for normal variation in sampling and testing, can be achieved in real-time PCR assays by converting sample quantification cycles (Cqs) to "efficiency standardized Cqs" (ECqs). We calculated ECqs as E-ΔCq, where E is amplification efficiency and ΔCq is the difference between sample and reference standard Cqs. To apply this approach to a commercial porcine reproductive and respiratory syndrome virus (PRRSV) RT-qPCR assay, we created reference standards by rehydrating and then diluting (1 × 10-4) a PRRSV modified-live vaccine (PRRS MLV; Ingelvac) with serum or oral fluid (OF) to match the sample matrix to be tested. Sample ECqs were calculated using the mean E and reference standard Cq calculated from the 4 reference standards on each plate. Serum (n = 132) and OF (n = 130) samples were collected from each of 12 pigs vaccinated with a PRRSV MLV from -7 to 42 d post-vaccination, tested, and sample Cqs converted to ECqs. Mean plate Es were 1.75-2.6 for serum and 1.7-2.3 for OF. Mean plate reference standard Cqs were 29.1-31.3 for serum and 29.2-31.5 for OFs. Receiver operating characteristic analysis calculated the area under the curve for serum and OF sample ECqs as 0.999 (95% CI: 0.997, 1.000) and 0.947 (0.890, 1.000), respectively. For serum, diagnostic sensitivity and specificity of the commercial PRRSV RT-qPCR assay were estimated as 97.9% and 100% at an ECq cutoff ≥ 0.20, and for OF, 82.6% and 100%, respectively, at an ECq cutoff ≥ 0.45.
Collapse
Affiliation(s)
- Betsy Armenta-Leyva
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| | - Berenice Munguía-Ramírez
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, the Ohio State University, Columbus, OH, USA
| | - Fangshu Ye
- Department of Statistics, College of Liberal Arts and Sciences, Iowa State University, Ames, IA, USA
| | | | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| | - Jeffrey Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Lloyd Veterinary Medical Center, Iowa State University, Ames, IA, USA
| |
Collapse
|
40
|
Kras K, Ropka-Molik K, Muszyński S, Arciszewski MB. Expression of Genes Encoding Selected Orexigenic and Anorexigenic Peptides and Their Receptors in the Organs of the Gastrointestinal Tract of Calves and Adult Domestic Cattle ( Bos taurus taurus). Int J Mol Sci 2023; 25:533. [PMID: 38203717 PMCID: PMC10779135 DOI: 10.3390/ijms25010533] [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: 10/02/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The regulation of food intake occurs at multiple levels, and two of the components of this process are orexigenic and anorexigenic peptides, which stimulate or inhibit appetite, respectively. The study of the function of these compounds in domestic cattle is essential for production efficiency, animal welfare, and health, as well as for economic benefits, environmental protection, and the contribution to a better understanding of physiological aspects that can be applied to other species. In this study, the real-time PCR method was utilized to determine the expression levels of GHRL, GHSR, SMIM20, GPR173, LEP, LEPR, and NUCB2 (which encode ghrelin, its receptor, phoenixin-14, its receptor, leptin, its receptor, and nesfatin-1, respectively) in the gastrointestinal tract (GIT) of Polish Holstein-Friesian breed cattle. In all analyzed GIT segments, mRNA for all the genes was present in both age groups, confirming their significance in these tissues. Gene expression levels varied distinctly across different GIT segments and between young and mature subjects. The differences between calves and adults were particularly pronounced in areas such as the forestomachs, ileum, and jejunum, indicating potential changes in peptides regulating food intake based on the developmental phase. In mature individuals, the forestomachs predominantly displayed an increase in GHRL expression, while the intestines had elevated levels of GHSR, GPR173, LEP, and NUCB2. In contrast, the forestomachs in calves showed upregulated expressions of LEP, LEPR, and NUCB2, highlighting the potential importance of peptides from these genes in bovine forestomach development.
Collapse
Affiliation(s)
- Katarzyna Kras
- Department of Animal Anatomy and Histology, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12 St., 20-950 Lublin, Poland;
| | - Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St., 32-083 Balice, Poland;
| | - Siemowit Muszyński
- Department of Biophysics, Faculty of Environmental Biology, University of Life Sciences in Lublin, 13 Akademicka St., 20-950 Lublin, Poland;
| | - Marcin B. Arciszewski
- Department of Animal Anatomy and Histology, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12 St., 20-950 Lublin, Poland;
| |
Collapse
|
41
|
Liu L, Xiang C, Zhang Y, He L, Meng F, Gong J, Liu J, Zhao F. A Novel Detection Procedure for Mutations in the 23S rRNA Gene of Macrolide-Resistant Mycoplasma pneumoniae with Two Non-Overlapping Probes Amplification Assay. Microorganisms 2023; 12:62. [PMID: 38257888 PMCID: PMC10820694 DOI: 10.3390/microorganisms12010062] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Mycoplasma pneumoniae is a significant cause of community-acquired pneumonia, which is often empirically treated with macrolides (MLs), but, presently, resistance to MLs has been a matter of close clinical concern. This assay is intended to contribute to resistance detection of M. pneumoniae in clinical practice. A novel real-time PCR assay with two non-overlapping probes on the same nucleic acid strand was designed in this study. It could effectively detect all mutation types of M. pneumoniae in 23S rRNA at loci 2063 and 2064. The results were determined by the following methods: ΔCT < 0.5 for MLs-sensitive M. pneumoniae; ΔCT > 2.0 for MLs-resistant M. pneumoniae; 10 copies as a limit of detection for all types. For detection of M. pneumoniae in 92 clinical specimens, the consistency between the results of this assay and the frequently used real-time PCR results was 95.65%. The consistency of MLs resistance results between PCR sequencing and this assay was 100% in all 43 specimens. The assay could not only cover a comprehensive range of targets and have high detection sensitivity but is also directly used for detection and MLs analysis of M. pneumoniae in specimens.
Collapse
Affiliation(s)
- Liyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
| | - Caixin Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
- School of Public Health, China Medical University, Shenyang 110122, China
| | - Yiwei Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
| | - Lihua He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
| | - Fanliang Meng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
| | - Jie Gong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
| | - Jie Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
- School of Public Health, China Medical University, Shenyang 110122, China
| | - Fei Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.L.); (C.X.); (Y.Z.); (L.H.); (F.M.); (J.G.); (J.L.)
| |
Collapse
|
42
|
Savicheva AM. Molecular Testing for the Diagnosis of Bacterial Vaginosis. Int J Mol Sci 2023; 25:449. [PMID: 38203620 PMCID: PMC10779368 DOI: 10.3390/ijms25010449] [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: 11/06/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Previously established diagnostic approaches for the diagnosis of bacterial vaginosis (BV), such as the Amsel criteria or the Nugent scoring system, do not always correspond to modern trends in understanding the etiology and pathogenesis of polymicrobial conditions. Inter-examiner variability and interpretation of data complicate the wet mount microscopy method. Gram staining of smears does not always provide reliable information regarding bacterial taxa, biofilms, or vaginal dysbiosis. Therefore, the introduction of molecular techniques into clinical practice is extremely relevant. Molecular approaches allow not only the diagnosis of BV but also provide an assessment of microbial composition, which is especially important in the differential diagnosis of vaginal infections. The current review represents an expert opinion on BV diagnosis and is based on extensive experience in the field of vaginal infection diagnosis and treatment.
Collapse
Affiliation(s)
- Alevtina M Savicheva
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductive Medicine, St. Petersburg 199034, Russia
| |
Collapse
|
43
|
Balić D, Dijanić T, Agičić M, Barić J, Kaltenbrunner M, Krajina H, Hochegger R, Škrivanko M, Kožul K. A Large-Scale Outbreak of Trichinellosis from Infected Wild Boar Meat in Croatia and the Role of Real-Time PCR Assays in Confirming the Source of the Disease. Microorganisms 2023; 11:2995. [PMID: 38138139 PMCID: PMC10745464 DOI: 10.3390/microorganisms11122995] [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: 11/28/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Trichinellosis in Croatia posed a significant health concern during the 1990s, followed by a notable improvement in the epidemiological situation. However, in 2017, there was a resurgence, with 37 recorded cases in 3 outbreaks and 3 sporadic cases. The source of this epidemic was homemade meat products derived from wild boar meat, leading to 26 infections. METHODS At the beginning of the outbreak and during the treatment of the patients, the medical and epidemiological records prepared throughout the investigation and over the course of patient treatment were reviewed. The recovery of the first-stage (L1) larvae from suspect meat products was achieved by artificial digestion. The molecular identification of the isolated larvae was performed by multiplex PCR. The molecular identification of the meat used to prepare the meat products was performed by real-time PCR assays. RESULTS The epidemic started in early 2017. In total, 71 exposed persons were documented: 26 with clinical symptoms and 3 hospitalised in two cities in different counties. The L1 burden in three different meat products was from 5.25 to 7.08 larvae per gram (LPG), and T. spiralis was determined as the aetiological agent of the outbreak. The molecular and biological identification confirmed that implicated meat products were made solely from wild boar meat. CONCLUSIONS Although trichinellosis is no longer a frequent occurrence in Croatia, several cases are still registered nearly every year. Wild boar meat poses an important risk factor for human health if compulsory testing is not conducted before consumption, especially if the meat products are consumed without proper thermal processing.
Collapse
Affiliation(s)
- Davor Balić
- Croatian Veterinary Institute, Department Vinkovci-National Reference Laboratory for Parasites (Genus Trichinella), 32100 Vinkovci, Croatia
| | - Tomislav Dijanić
- Public Health Institute of Osijek-Baranja County, 31000 Osijek, Croatia
| | - Marija Agičić
- Croatian Veterinary Institute, Department Vinkovci-National Reference Laboratory for Parasites (Genus Trichinella), 32100 Vinkovci, Croatia
| | - Josip Barić
- State Inspectorate of the Republic of Croatia, Osijek Regional Office-Vinkovci Branch Office, 32100 Vinkovci, Croatia
| | - Maria Kaltenbrunner
- AGES-Austrian Agency for Health and Food Safety, Institute for Food Safety Vienna, 1210 Vienna, Austria
| | - Hrvoje Krajina
- Croatian Veterinary Institute, Department Vinkovci-National Reference Laboratory for Parasites (Genus Trichinella), 32100 Vinkovci, Croatia
| | - Rupert Hochegger
- AGES-Austrian Agency for Health and Food Safety, Institute for Food Safety Vienna, 1210 Vienna, Austria
| | - Mario Škrivanko
- Croatian Veterinary Institute, Department Vinkovci-National Reference Laboratory for Parasites (Genus Trichinella), 32100 Vinkovci, Croatia
| | - Karlo Kožul
- Public Health Institute of Osijek-Baranja County, 31000 Osijek, Croatia
| |
Collapse
|
44
|
Pasquier G, Andreotti Q, Ravel C, Sterkers Y. Molecular diagnosis of visceral leishmaniasis: a French study comparing a reference PCR method targeting kinetoplast DNA and a commercial kit targeting ribosomal DNA. Microbiol Spectr 2023; 11:e0215423. [PMID: 37819127 PMCID: PMC10714885 DOI: 10.1128/spectrum.02154-23] [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: 05/22/2023] [Accepted: 08/23/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE PCR revolutionized the direct diagnosis of infectious diseases, especially protozooses, where the infectious load is usually low. Commercial PCR methods are available and offer many advantages, including convenience and batch tracking as part of a quality system. For most parameters, the performance of commercial methods is at least as good as that of finely optimized methods developed in expert laboratories. This comparison work has not been done for the molecular diagnosis of visceral leishmaniasis. Leishmania sp. has a unique organelle, the kinetoplast, which corresponds to the mitochondrial DNA. It is organized into a large number of minicircles, which has made it a target for the development of diagnostic PCR. The quanty Leishmaniae, Clonit kit targeting ribosomal DNA was compared to a widely used laboratory-developed method based on kinetoplast DNA. This reference method gave significantly better results, probably due to the difference in the number of repeats of the PCR targets.
Collapse
Affiliation(s)
- Grégoire Pasquier
- Department of Parasitology-Mycology, National Reference Center for Leishmaniasis, University of Montpellier, CNRS, IRD, University Hospital Center (CHU) of Montpellier, Montpellier, France
| | - Quentin Andreotti
- Department of Parasitology-Mycology, National Reference Center for Leishmaniasis, University of Montpellier, CNRS, IRD, University Hospital Center (CHU) of Montpellier, Montpellier, France
| | - Christophe Ravel
- Department of Parasitology-Mycology, National Reference Center for Leishmaniasis, University of Montpellier, CNRS, IRD, University Hospital Center (CHU) of Montpellier, Montpellier, France
| | - Yvon Sterkers
- Department of Parasitology-Mycology, National Reference Center for Leishmaniasis, University of Montpellier, CNRS, IRD, University Hospital Center (CHU) of Montpellier, Montpellier, France
| |
Collapse
|
45
|
Ghosh P, Chowdhury R, Faisal K, Khan MAA, Hossain F, Rahat MA, Chowdhury MAA, Mithila NT, Kamal M, Maruf S, Nath R, Kobialka RM, Ceruti A, Cameron M, Duthie MS, Wahed AAE, Mondal D. Evaluation of a Point-of-Need Molecular Diagnostic Tool Coupled with Rapid DNA Extraction Methods for Visceral Leishmaniasis. Diagnostics (Basel) 2023; 13:3639. [PMID: 38132223 PMCID: PMC10742398 DOI: 10.3390/diagnostics13243639] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
A rapid, cost-effective, and simple nucleic acid isolation technique coupled with a point-of-need DNA amplification assay is a desirable goal for programmatic use. For diagnosis of Visceral Leishmaniasis (VL), Recombinase Polymerase Amplification (RPA) rapid tests for the detection of Leishmania DNA are versatile and have operational advantages over qPCR. To facilitate the delivery of the RPA test at point-of-need for VL diagnosis, we compared two rapid DNA extraction methods, SwiftDx (SX) and an in-house Boil and Spin (BS) method, coupled with RPA amplification, versus more widely used methods for DNA extraction and amplification, namely Qiagen (Q) kits and qPCR, respectively. A total of 50 confirmed VL patients and 50 controls, matched for age and gender, were recruited from Mymensingh, Bangladesh, a region highly endemic for VL. Blood samples were collected from each participant and DNA was extracted using Q, SX and BS methods. Following DNA extraction, qPCR and RPA assays were performed to detect L. donovani in downstream analysis. No significant differences in sensitivity of the RPA assay were observed between DNA extraction methods, 94.00% (95% CI: 83.45-98.75%), 90% (95% CI: 78.19-96.67%), and 88% (95% CI: 75.69-95.47%) when using Q, SX, and BS, respectively. Similarly, using qPCR, no significant differences in sensitivity were obtained when using Q or SX for DNA extraction, 94.00% (95% CI: 83.45-98.75%) and 92.00% (80.77-97.78%), respectively. It is encouraging that RPA and qPCR showed excellent agreement (k: 0.919-0.980) when different extraction methods were used and that the DNA impurities using BS had no inhibitory effect on the RPA assay. Furthermore, significantly higher DNA yields were obtained using SX and BS versus Q; however, a significantly higher parasite load was detected using qPCR when DNA was extracted using Q versus SX. Considering the cost, execution time, feasibility, and performance of RPA assay, rapid extraction methods such as the Boil and Spin technique appear to have the potential for implementation in resource-limited endemic settings. Further clinical research is warranted prior to broader application.
Collapse
Affiliation(s)
- Prakash Ghosh
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rajashree Chowdhury
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Khaledul Faisal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Anik Ashfaq Khan
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Faria Hossain
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Abu Rahat
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Md. Arko Ayon Chowdhury
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Nishad Tasnim Mithila
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Mostafa Kamal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Shomik Maruf
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rupen Nath
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| | - Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Mary Cameron
- London School of Hygiene and Tropical Medicine, University of London, London WC1E 7HT, UK;
| | | | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany; (M.A.A.K.); (R.M.K.); (A.C.)
| | - Dinesh Mondal
- Nutrition Research Division (NRD), International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.C.); (K.F.); (F.H.); (M.A.R.); (M.A.A.C.).; (N.T.M.); (M.K.); (S.M.); (R.N.); (D.M.)
| |
Collapse
|
46
|
Boyte ME, Benkowski A, Pane M, Shehata HR. Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques. Front Microbiol 2023; 14:1304621. [PMID: 38192285 PMCID: PMC10773886 DOI: 10.3389/fmicb.2023.1304621] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.
Collapse
Affiliation(s)
- Marie-Eve Boyte
- NutraPharma Consulting Services Inc., Sainte-Anne-des-Plaines, QC, Canada
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
| | | |
Collapse
|
47
|
Soto Brito Y, Fonseca Castro DA, Guilarte Garcia E, Kouri Cardellá V, Ramirez Cardentey C, Mondeja Rodriguez BA, Concepción López JJ, Sánchez Alvarez MDL, López Pérez M, Gutierrez Coronado T, Torres Mosqueda K, Suárez Licor G. Chlamydia trachomatis infection in Cuban adolescent and young populations. Int J STD AIDS 2023; 34:1024-1033. [PMID: 37607391 DOI: 10.1177/09564624231191568] [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: 08/24/2023]
Abstract
BACKGROUND In Cuba, little is known regarding the prevalence of Chlamydia trachomatis (CT) infection in adolescents and young people. We study the frequency of CT infection in these populations, and its association with clinical-epidemiological variables. METHODS A total of 496 individuals aged 12 to 24 were recruited from November 2018 to November 2019. Of them, 302 were patients attending at sexually transmitted infections (STI) services and 194 were young volunteers. CT detections were carried out by real-time PCR and IgG serology. RESULTS The prevalence of CT using PCR was 9.1% (45/496); 12.3% (37/302) for subjects attending STI service and 4.1% (8/194) for young volunteers, being significantly higher in the first group (OR=3.25; p=.001). CT IgG antibodies was detected in 38.6% (81/210). Individuals from 12 to 17 years old were more likely infected with CT (OR=2.21; p=.010). Infection was associated with the early onset of sexual intercourse, the frequent changing of sexual partners and black ethnicity. CONCLUSIONS The results suggest that Cuban adolescents and young populations are at highest risk of acquiring CT infection and developing reproductive complications. The data obtained advise the needs of implementation of a routine CT screening strategy, for timely diagnosis, detection and treatment at the earliest ages.
Collapse
Affiliation(s)
- Yudira Soto Brito
- Sexually Transmitted Infections Laboratory, Department of Virology, "Pedro Kourí" Tropical Medicine Institute (IPK), Havana, Cuba
| | - Darien Alejandro Fonseca Castro
- Sexually Transmitted Infections Laboratory, Department of Virology, "Pedro Kourí" Tropical Medicine Institute (IPK), Havana, Cuba
| | - Elias Guilarte Garcia
- Sexually Transmitted Infections Laboratory, Department of Virology, "Pedro Kourí" Tropical Medicine Institute (IPK), Havana, Cuba
| | - Vivian Kouri Cardellá
- Sexually Transmitted Infections Laboratory, Department of Virology, "Pedro Kourí" Tropical Medicine Institute (IPK), Havana, Cuba
| | - Celeste Ramirez Cardentey
- Sexually Transmitted Infections Laboratory, Department of Virology, "Pedro Kourí" Tropical Medicine Institute (IPK), Havana, Cuba
| | | | | | | | - Maida López Pérez
- Mariana Grajales" Gyneco-obstetric University Hospital, Santa Clara, Cuba
| | | | | | | |
Collapse
|
48
|
Maleki AR, Tabatabaei RR, Aminian F, Ranjbar S, Ashrafi F, Ranjbar R. Antibacterial and antibiofilm effects of green synthesized selenium nanoparticles on clinical Klebsiella pneumoniae isolates. J Basic Microbiol 2023; 63:1373-1382. [PMID: 37699755 DOI: 10.1002/jobm.202300332] [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: 06/12/2023] [Revised: 08/24/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023]
Abstract
Nanotechnology covers many disciplines, including the biological sciences. In this study, selenium nanoparticles (Se-NPs) were synthesized using Artemisia annua extract and investigated against clinical strains of klebsiella pneumoniae (K. pneumoniae) for their anti-biofilm effects. In this experimental study, from May 1998 to September 1998, 50 clinical samples of blood, urine, and sputum were collected, and K. pneumoniae strains were isolated using microbiological methods. Subsequently, the antibacterial effects of Se-NPs at concentrations of 12-25-50-100/5-6/3-25/125 μg/mL were studied. Finally, biofilm-producing strains were isolated, and the expression of mrkA biofilm gene was studied in real-time strains treated with Se-NPs using real-time polymerase chain reaction (PCR). Out of 50 clinical samples, 20 strains of K. pneumoniae were isolated. Minimum inhibitory concentration (MIC) results of Se-NPs showed that Se-NPs were capable of significant cell killing. Real-time PCR results also showed that mrkA gene expression was significantly reduced in strains treated with Se-NPs. According to this study, Se-NPs could reduce bacterial growth and biofilm formation, therefore, could be considered a candidate drug in the medical application for infections caused by K. pneumoniae.
Collapse
Affiliation(s)
- Ali Reza Maleki
- Depatment of Microbiology, School of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Robab Rafiei Tabatabaei
- Depatment of Microbiology, School of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Fatemeh Aminian
- Department of Molecular Cell Biology and Genetics, Bushehr Branch, Islamic Azad University, Bushehr, Iran
| | - Sina Ranjbar
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Ashrafi
- Depatment of Microbiology, School of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
49
|
Bouike Y, Sakima M, Taninishi Y, Matsutani T, Noguchi Y, Bo R, Awano H, Nishio H. Real-Time PCR-Based Screening for Homozygous SMN2 Deletion Using Residual Dried Blood Spots. Genes (Basel) 2023; 14:2159. [PMID: 38136980 PMCID: PMC10742981 DOI: 10.3390/genes14122159] [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: 11/09/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The survival motor neuron 2 (SMN2) gene is a recognized modifier gene of spinal muscular atrophy (SMA). However, our knowledge about the role of SMN2-other than its modification of SMA phenotypes-is very limited. Discussions regarding the relationship between homozygous SMN2 deletion and motor neuron diseases, including amyotrophic lateral sclerosis, have been mainly based on retrospective epidemiological studies of the diseases, and the precise relationship remains inconclusive. In the present study, we first estimated that the frequency of homozygous SMN2 deletion was ~1 in 20 in Japan. We then established a real-time polymerase chain reaction (PCR)-based screening method using residual dried blood spots to identify infants with homozygous SMN2 deletion. This method can be applied to a future prospective cohort study to clarify the relationship between homozygous SMN2 deletion and motor neuron diseases. In our real-time PCR experiment, both PCR (low annealing temperatures) and blood (high hematocrit values and low white blood cell counts) conditions were associated with incorrect results (i.e., false negatives and positives). Together, our findings not only help to elucidate the role of SMN2, but also aid in our understanding of the pitfalls of current SMA newborn screening programs for detecting homozygous SMN1 deletions.
Collapse
Affiliation(s)
- Yoshihiro Bouike
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Makoto Sakima
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Yuya Taninishi
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Takanori Matsutani
- Division of Physiology, Shinko Hospital, 1-4-47 Wakinohama-cho, Chuo-ku, Kobe 651-0072, Japan;
| | - Yoriko Noguchi
- Department of Clinical Laboratory, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan;
| | - Ryosuke Bo
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan;
| | - Hiroyuki Awano
- Organization for Research Initiative and Promotion, Research Initiative Center, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan;
| | - Hisahide Nishio
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan
| |
Collapse
|
50
|
Vinje MA, Friedman DA. Exogenous spike-in mouse RNAs for accurate differential gene expression analysis in barley using RT-qPCR. Biol Methods Protoc 2023; 8:bpad034. [PMID: 38116324 PMCID: PMC10728042 DOI: 10.1093/biomethods/bpad034] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) followed by the 2-ΔΔCt method is the most common way to measure transcript levels for relative gene expression assays. The quality of an RT-qPCR assay is dependent upon the identification and validation of reference genes to normalize gene expression data. The so-called housekeeping genes are commonly used as internal reference genes because they are assumed to be ubiquitously expressed at stable levels. Commonly, researchers do not validate their reference genes but rely on historical reference genes or previously validated genes from an unrelated experiment. Using previously validated reference genes to assess gene expression changes occurring during malting resulted in extensive variability. Therefore, a new method was tested and validated to circumvent the use of internal reference genes. Total mouse RNA was chosen as the external reference RNA and a suite of primer sets to putatively stable mouse genes was created to identify stably expressed genes for use as an external reference gene. cDNA was created by co-amplifying total mouse RNA, as an RNA spike-in, and barley RNA. When using the external reference genes to normalize malting gene expression data, standard deviations were significantly reduced and significant differences in transcript abundance were observed, whereas when using the internal reference genes, standard deviations were larger with no significant differences seen. Furthermore, external reference genes were more accurate at assessing expression levels in malting and developing grains, whereas the internal reference genes overestimated abundance in developing grains and underestimated abundance in malting grains.
Collapse
Affiliation(s)
- Marcus A Vinje
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI 53726, United States
| | - David A Friedman
- USDA, Agricultural Research Service, Cereal Crops Research Unit, Madison, WI 53726, United States
| |
Collapse
|