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Jawad M, Adnan A, Rehman RA, Nazir S, Adeyemo OA, Amer SAM, Hadi S, Liu F, Wang CC, Rakha A. Evaluation of facial hair-associated SNPs: a pilot study on male Pakistani Punjabi population. Forensic Sci Med Pathol 2023; 19:293-302. [PMID: 35994154 DOI: 10.1007/s12024-022-00515-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 10/15/2022]
Abstract
Variation in facial hair is one of the most conspicuous features of facial appearance, particularly in South Asia and Middle East countries. A genome-wide association study in Latin Americans has identified multiple genetic variants at distinct loci being associated with facial hair traits including eyebrow thickness, beard thickness, and monobrow. In this pilot study, we have evaluated 16 SNPs associated with facial hair traits in 58 male individuals from the Punjabi population of Pakistan. In our sample, rs365060 in EDAR and rs12597422 in FTO showed significant association with monobrow, rs6684877 in MACF1 showed significant association with eyebrow thickness, and two SNPs in LOC105379031 (rs9654415 and rs7702331) showed significant association with beard thickness. Our results also suggest that genetic association may vary between ethnic groups and geographic regions. Although more data are needed to validate our results, our findings are of value in forensic molecular photofitting research in Pakistan.
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Affiliation(s)
- Muhammad Jawad
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Atif Adnan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia.
| | - Rahat Abdul Rehman
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Shahid Nazir
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan
| | - Oyenike A Adeyemo
- Department of Cell Biology and Genetics, Faculty of Science, University of Lagos, AkokaLagos, Yaba, Nigeria
| | - S A M Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
| | - Fan Liu
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, 11452, Kingdom of Saudi Arabia
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China.
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.
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Spruijtenburg B, Meijer EFJ, Xiao M, Shawky SM, Meis JF, de Groot T, El-Kholy MA. Genotyping and susceptibility testing uncovers large azole-resistant Candida tropicalis clade in Alexandria, Egypt. J Glob Antimicrob Resist 2023; 34:99-105. [PMID: 37419181 DOI: 10.1016/j.jgar.2023.06.012] [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: 04/25/2023] [Revised: 06/09/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVES Candida tropicalis is an emerging medically relevant Candida species. The yeast primarily causes opportunistic infections in intensive care units and is highly prevalent in tropical countries. The genetic diversity within this species is high, and nosocomial transmission has been reported. C. tropicalis genotyping of isolates from low- and middle-income countries is underrepresented when compared with that from high-income countries. Also, in Egypt, only limited genotyping has been conducted for C. tropicalis isolates, while antifungal resistance seems to increase, especially against azoles. METHODS Antifungal susceptibility testing was performed on 64 C. tropicalis isolates from ICU patients collected from multiple hospitals in Alexandria, Egypt. Genotyping by means of short tandem repeat (STR) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis was performed. RESULTS Using antifungal susceptibility testing, fluconazole resistance was observed in 24 isolates (38%), of which 23 harboured an ERG11 G464S substitution, previously shown to cause resistance in Candida albicans. STR genotyping showed that these 23 isolates were related, forming a distinct resistant clade. WGS SNP analysis subsequently confirmed this genetic relationship, although isolates within this clade differed in at least 429 SNPs, suggesting that these were independently introduced. CONCLUSION Overall, STR and WGS SNP analysis of this collection indicates limited C. tropicalis nosocomial transmission in Alexandria, while the presence of this large azole-resistant C. tropicalis clade within this city hampers the treatment of intensive care unit patients.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, People's Republic of China
| | - Sherine M Shawky
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Mohammed A El-Kholy
- Department of Microbiology and Biotechnology, Division of Clinical and Biological Sciences, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), Alexandria, Egypt.
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Capodanno D, Angiolillo DJ. Personalised antiplatelet therapies for coronary artery disease: what the future holds. Eur Heart J 2023; 44:3059-3072. [PMID: 37345589 DOI: 10.1093/eurheartj/ehad362] [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: 03/05/2023] [Revised: 05/07/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Coronary artery disease (CAD) is one of the leading causes of death globally, and antiplatelet therapy is crucial for both its prevention and treatment. Antiplatelet drugs such as aspirin and P2Y12 inhibitors are commonly used to reduce the risk of thrombotic events, including myocardial infarction, stroke, and stent thrombosis. However, the benefits associated with the use of antiplatelet drugs also come with a risk of bleeding complications. The ever-growing understanding of the poor prognostic implications associated with bleeding has set the foundations for defining strategies that can mitigate such safety concern without any trade-off in antithrombotic protection. To this extent, personalised antiplatelet therapy has emerged as a paradigm that optimizes the balance between safety and efficacy by customizing treatment to the individual patient's needs and risk profile. Accurate risk stratification for both bleeding and thrombosis can aid in selecting the optimal antiplatelet therapy and prevent serious and life-threatening outcomes. Risk stratification has traditionally included clinical and demographic characteristics and has expanded to incorporate angiographic features and laboratory findings. The availability of bedside platelet function testing as well as rapid genotyping assays has also allowed for a more individualized selection of antiplatelet therapy. This review provides a comprehensive overview of the current state of the art and future trends in personalised antiplatelet therapy for patients with CAD, with emphasis on those presenting with an acute coronary syndrome and undergoing percutaneous coronary revascularization. The aim is to provide clinicians with a comprehensive understanding of personalised antiplatelet therapy and facilitate informed clinical decision-making.
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Affiliation(s)
- Davide Capodanno
- Division of Cardiology, Azienda Ospedaliero-Universitaria 'G. Rodolico - San Marco', University of Catania, Via Santa Sofia, 78 - 95123 Catania, Italy
| | - Dominick J Angiolillo
- Division of Cardiology, University of Florida College of Medicine-Jacksonville, 655 West 8th Street, Jacksonville, FL 32209, USA
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Zhang J, Tu J, Chen Y, Jin X. Clinical characteristics and homology analysis of Staphylococcus aureus from would infection at a tertiary hospital in southern Zhejiang, China. BMC Microbiol 2023; 23:217. [PMID: 37573311 PMCID: PMC10422768 DOI: 10.1186/s12866-023-02921-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 01/28/2023] [Accepted: 06/28/2023] [Indexed: 08/14/2023] Open
Abstract
OBJECTIVE Staphylococcus aureus (S. aureus), especially Methicillin resistant S. aureus (MRSA), has been disseminated across communities and hospitals, associated with severe infections and organ failure. In order to understand the clinical epidemiological characteristics of S. aureus stains in the First Affiliated Hospital of Wenzhou Medical University in 2018, the prevalence and the drug resistance of S. aureus stains were investigated, for improving the clinical effective prevention and control of S. aureus infection. METHODS A total of 105 S. aureus isolates were separated from wound infection of inpatients in the First Affiliated Hospital of Wenzhou Medical University in 2018, and the department distributions and drug resistance of the isolates were analyzed. The genotyping homology analysis was conducted through the random amplified polymorphic DNA typing (RAPD-PCR) coupled with NTSYS cluster analysis. RESULTS Among the 105 strains of S. aureus, 31 isolates were MRSA. The prevalence of MRSA among inpatients in the Departments of Burn, Trauma, Orthopedics, Nephrology and Neurosurgery were 35.48%, 19.35%, 9.68%, 6.45%, and 29.03%, respectively. Among the 105 strains, 35.24% strains were the hospital-acquired infections (HAI) and 64.76% strains were community-acquired infections (CAI). DNA genotyping of the 105 S. aureus strains showed seventeen different groups, most of which were type I, type VII, type IX, and type VII, the others were scattered. CONCLUSION This study highlights the prevalence of S. aureus strains in the First Affiliated Hospital of Wenzhou Medical University in 2018. The emergence and mutation of the strains should be closely monitored for the prevention and control of the S. aureus infection and transmission in the nosocomial settings.
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Affiliation(s)
- Jiarong Zhang
- Department of Nosocomial Infection Prevention and Control, the First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325000, China
| | - Jingjing Tu
- The Key Laboratory of Diagnosis and Controlment for the Development of Chronic Liver Disease of Zhejiang Province, Ouhai District, Wenzhou, Zhejiang, 325000, China
| | - Yongping Chen
- The Key Laboratory of Diagnosis and Controlment for the Development of Chronic Liver Disease of Zhejiang Province, Ouhai District, Wenzhou, Zhejiang, 325000, China.
- Department of Infectious Diseases, the First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325000, China.
| | - Xiaoya Jin
- Department of Nosocomial Infection Prevention and Control, the First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325000, China.
- The Key Laboratory of Diagnosis and Controlment for the Development of Chronic Liver Disease of Zhejiang Province, Ouhai District, Wenzhou, Zhejiang, 325000, China.
- Department of Infectious Diseases, the First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, Zhejiang, 325000, China.
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Woyessa D, Morou E, Wipf N, Dada N, Mavridis K, Vontas J, Yewhalaw D. Species composition, infection rate and detection of resistant alleles in Anopheles funestus (Diptera: Culicidae) from Lare, a malaria hotspot district of Ethiopia. Malar J 2023; 22:233. [PMID: 37573300 PMCID: PMC10422748 DOI: 10.1186/s12936-023-04667-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 08/07/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND Anopheles funestus, which is considered as secondary vector of malaria in Ethiopia, is known to have several morphologically indistinguishable (sibling) species. Accurate identification of sibling species is crucial to understand their biology, behaviour and vector competence. In this study, molecular identification was conducted on the Ethiopian An. funestus populations. Moreover, insecticide resistance mechanism markers were detected, including ace N485I, kdr L1014F, L1014S, and CYP6P9a TaqMan qPCR was used to detect the infective stage of the parasite from field collected adult female An. funestus populations. METHODS Adult female mosquito collection was conducted from Lare, Gambella Regional State of Ethiopia between June 2018 to July 2020 using CDC light traps and HLC. Sub-samples of the morphologically identified An. funestus mosquitoes were molecularly identified using species-specific PCR, and the possible presence of insecticide resistance alleles was investigated using TaqMan qPCR (N485I-Ace-1), PCR-Sanger sequencing (L1014F-kdr), and PCR-RFLP (CYP6P9a resistance allele). Following head/thorax dissection, the TaqMan qPCR assay was used to investigate the presence of the infective stage Plasmodium parasite species. RESULTS A total of 1086 adult female An. funestus mosquitoes were collected during the study period. All sub-samples (N = 20) that were morphologically identified as An. funestus sensu lato (s.l.) were identified as An. funestus sensu stricto (s.s.) using species- specific PCR assay. The PCR-RFLP assay that detects the CYP6P9a resistance allele that confers pyrethroid resistance in An. funestus was applied in N = 30 randomly selected An. funestus s.l. SPECIMENS None of the specimens showed a digestion pattern consistent with the presence of the CYP6P9a resistance allele in contrast to what was observed in the positive control. Consequently, all samples were characterized as wild type. The qPCR TaqMan assay that detects the N485I acetylcholinesterase-1 mutation conferring resistance to organophosphates/carbamates in An. funestus was used in (N = 144) samples. All samples were characterized as wild type. The kdr L1014F and L1014S mutations in the VGSC gene that confer resistance to pyrethroids and DDT were analysed with direct Sanger sequencing after PCR and clean-up of the PCR products were also characterized as wild type. None of the samples (N = 169) were found positive for Plasmodium (P. falciparum/ovale/malariae/vivax) detection. CONCLUSION All An. funestus s.l. samples from Lare were molecularly identified as An. funestus s.s. No CYP6P9, N485I acetylcholinesterase 1, kdr L1014F or L1014S mutations were detected in the An. funestus samples. None of the An. funestus samples were positive for Plasmodium. Although the current study did not detect any insecticide resistant mechanism, it provides a reference for future vector monitoring programmes. Regular monitoring of resistance mechanisms covering wider geographical areas of Ethiopia where this vector is distributed is important for improving the efficacy of vector control programs.
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Affiliation(s)
- Delelegn Woyessa
- Department of Biology, College of Natural Sciences, Jimma University, P. O. Box 378, Jimma, Ethiopia.
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia.
- Tropical and Infectious Diseases Research Centre (TIDRC), P.O. Box 378, Jimma, Ethiopia.
| | - Evangelia Morou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | - Nadja Wipf
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Nsa Dada
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University, Tempe, USA
| | - Konstantinos Mavridis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | - Delenasaw Yewhalaw
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia
- Tropical and Infectious Diseases Research Centre (TIDRC), P.O. Box 378, Jimma, Ethiopia
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Wang Z, Yi J, Yu Q, Liu Y, Zhang R, Zhang D, Yang W, Xu Y, Chen Y. Performance evaluation of QuantStudio 1 plus real-time PCR instrument for clinical laboratory analysis: A proof-of-concept study. Pract Lab Med 2023; 36:e00330. [PMID: 37649547 PMCID: PMC10462677 DOI: 10.1016/j.plabm.2023.e00330] [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: 07/23/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 09/01/2023] Open
Abstract
Objective The real-time PCR system is one of the most powerful research tools available in the life sciences field. The aim of this study was to preliminarily evaluate the analytical performance of QuantStudio 1 Plus real-time PCR system (QS 1 plus) for clinical procedures. Methods The consistency of QS 1 plus with the reference system in terms of various clinical procedures was evaluated. For qualitative data, the Kappa test was used to analyze the agreement of the results. For the quantitative data, Passing-Bablok regression analysis and Bland-Altman plot analysis were used to assess the concordance between QS 1 plus and the reference instrument. Results Passing-Bablok regression showed an excellent agreement between the QS 1 plus and LC 480 systems for HBV DNA quantification (y = 0.928 + 0.970x), whereas Bland-Altman plot analysis showed very small mean deviations between the two systems. The QS 1 plus yielded perfectly consistent results with the reference instrument for methylenetetrahydrofolate reductase (MTHFR) C677T melting curve genotyping analysis, MTHFR C677T genotyping analysis, Norovirus RNA negative/positive analysis, influenza B virus (Flu B) RNA negative/positive analysis, Mycobacterium tuberculosis (MTB) DNA negative/positive analysis, Human Papillomavirus (HPV) genotyping analysis, epidermal growth factor receptor (EGFR) gene mutation analysis. Both the relative quantitative analysis and the relative quantitative analysis (standard curve) confirmed the satisfactory concordance between the QS 1 plus instrument and the ABI 7500 instrument by Passing-Bablok regression analysis (y = 0.180 + 0.817x and y = 0.012 + 1.000x, respectively) and Bland-Altman plot analysis. Conclusions Our research has proven that QS 1 plus is adaptable to most test procedures in the clinical laboratory. This may provide the basis for its further application.
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Affiliation(s)
- Ziran Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Yi
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Qi Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yiwei Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Rui Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wenhang Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Chen
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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Karimi Z, Ranjbar R, Najafi A. CRISPR Typing of Clinical Strains of Salmonella spp. Isolated in Tehran, Iran. Iran J Public Health 2023; 52:1758-1763. [PMID: 37744550 PMCID: PMC10512146 DOI: 10.18502/ijph.v52i8.13415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/23/2022] [Indexed: 09/26/2023]
Abstract
Background Salmonella is one of the most leading causes of food-born infection and death among infants and people with the poor immunity system. Because Salmonella spp. have diversity in the genome composition and pathogenicity, access to rapid identification and genotyping is necessary to control of salmonellosis. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) typing is a genotyping method that checks these variable sequences in the bacterial genome in a specific species. This study aimed to differentiate Salmonella strains using CRISPR region. Methods Salmonella isolates, previously identified via standard microbiological and molecular tests, were subjected to the study. Bacterial DNA was extracted and PCR was done using specific primers. The different PCR products were sequenced and the repeats patterns were used to identify additional or degenerate repeat clusters in the CRISPR region. All different sequences were analyzed using CRISPRtionary tool for dendrogram generation using the binary file. Results Overall, 119 strains of various Salmonella serovars were used. The result showed unique CRISPR and diversity in spacer both in sequence and the number. Analysis of the extracted sequence and band patterns illustrated that, except for S. infantis, both S. enteritidis and S. typhimurium isolates were classified as a separate cluster. Conclusion CRISPR genotyping could provide serotype/spacers dictionary and it is performed at low cost and high speed in comparison to the other typing methods. Therefore, the assessment of CRISPR and spacer content can be considered as a powerful and practical discriminatory method for subtyping of Salmonella isolates.
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Affiliation(s)
- Zahra Karimi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Bakhshani A, Ganjali R, Tabatabaeizadeh SE. Prevalence of Human Papillomavirus (HPV) Genotypes among Women During 2015-2020 in Mashhad, Iran. Arch Iran Med 2023; 26:419-426. [PMID: 38301103 PMCID: PMC10685731 DOI: 10.34172/aim.2023.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/20/2022] [Indexed: 02/03/2024]
Abstract
BACKGROUND Cervical cancer is the fourth most common cancer in women, and human papillomavirus (HPV) is the leading cause of cervical cancer. Cervical cancer screening and HPV vaccination are important in the incidence of cervical cancer. METHODS This study was performed on Liquid Base Cytology (LBC) samples of 1214 women in Mashhad who were referred for cervical cancer screening in 2015-2020. Samples were examined by Single-Step PCR and Reverse Line Blot for HPV genotyping. RESULTS 386 women (31.8%) were HPV PCR positive. HPV genotyping of 277 samples showed that HPV 31 (3%), 16 (2.5%), 51 (2.2%), 18 (2%), and 66 (1.8%) were the most prevalent high-risk HPV (hrHPV) genotypes. Among low-risk HPV (lrHPV) genotypes, HPV 6 (9.2%), 53 (4.7%), and 42 (2.8%) were the most common genotypes. The range of multiple infections varied between two to eight genotypes and the prevalence of multiple HPV infections (12.4%) was higher than single infections (10.4%). For women with single HPV infections, HPV 31 and 66 were equally the most common hrHPV genotypes, followed by HPV 16 and 39. In women with multiple HPV infections, HPV 31 was the most common hrHPV genotype, followed by HPV 51 and 16. For both the single and multiple HPV infections, HPV 6 was the most common lrHPV genotype, followed by HPV 53 and 42. CONCLUSION In conclusion, due to the high prevalence of HPV single and multiple infections, the need for governmentally supported HPV vaccination and through cervical cancer screening should be emphasized to prevent cervical cancer.
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Affiliation(s)
- Anis Bakhshani
- Cellular and Molecular Biology Department, Razi University of Kermanshah, Kermanshah, Iran
- Norouzpour Pathobiology Laboratory, Mashhad, Iran
| | - Rashin Ganjali
- Norouzpour Pathobiology Laboratory, Mashhad, Iran
- Immunology Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed-Elias Tabatabaeizadeh
- Mashhad Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [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: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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Diallo A, Wonni I, Sicard A, Blondin L, Gagnevin L, Vernière C, Szurek B, Hutin M. Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations. Rice (N Y) 2023; 16:33. [PMID: 37523017 PMCID: PMC10390441 DOI: 10.1186/s12284-023-00648-x] [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: 01/27/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980's. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.
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Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso.
| | - A Sicard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Blondin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Gagnevin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Vernière
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - B Szurek
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - M Hutin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Saei H, Morinière V, Heidet L, Gribouval O, Lebbah S, Tores F, Mautret-Godefroy M, Knebelmann B, Burtey S, Vuiblet V, Antignac C, Nitschké P, Dorval G. VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data in autosomal dominant tubulointerstitial kidney disease. iScience 2023; 26:107171. [PMID: 37456840 PMCID: PMC10338300 DOI: 10.1016/j.isci.2023.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
The human genome comprises approximately 3% of tandem repeats with variable length (VNTR), a few of which have been linked to human rare diseases. Autosomal dominant tubulointerstitial kidney disease-MUC1 (ADTKD-MUC1) is caused by specific frameshift variants in the coding VNTR of the MUC1 gene. Calling variants from VNTR using short-read sequencing (SRS) is challenging due to poor read mappability. We developed a computational pipeline, VNtyper, for reliable detection of MUC1 VNTR pathogenic variants and demonstrated its clinical utility in two distinct cohorts: (1) a historical cohort including 108 families with ADTKD and (2) a replication naive cohort comprising 2,910 patients previously tested on a panel of genes involved in monogenic renal diseases. In the historical cohort all cases known to carry pathogenic MUC1 variants were re-identified, and a new 25bp-frameshift insertion in an additional mislaid family was detected. In the replication cohort, we discovered and validated 30 new patients.
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Affiliation(s)
- Hassan Saei
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Vincent Morinière
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Laurence Heidet
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Néphrologie Pédiatrique, Centre de Référence MARHEA, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Olivier Gribouval
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Said Lebbah
- Département de Santé Publique, Unité de Recherche Clinique, Hôpital Pitié-Salpêtrière, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Frederic Tores
- Plateforme Bio-informatique, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Manon Mautret-Godefroy
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Bertrand Knebelmann
- Service de Néphrologie, Centre de Référence MARHEA, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Stéphane Burtey
- Inserm, C2VN, INRAE, C2VN, Aix-Marseille Université, Marseille, France
- Centre de Néphrologie et Transplantation Rénale, AP-HM Hôpital de la Conception, Marseille, France
| | - Vincent Vuiblet
- Service de Néphrologie, CHU de Reims, Reims, France
- Service de Pathologie, CHU De Reims, Reims, France
- Institut d'Intelligence Artificielle en Santé, Université de Reims Champagne-Ardenne et CHU de Reims, Reims, France
| | - Corinne Antignac
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Patrick Nitschké
- Plateforme Bio-informatique, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Guillaume Dorval
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
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Reinoso-Arija R, Proaño C, Ruiz-Serrano R, Núñez Ollero D, Ruiz-Duque B, Ortega Ruiz F, Márquez Martín E, Carrasco Hernández L, López-Campos JL. [Results of the Implementation of a Case-Finding Program for Alpha-1 Antitrypsin Deficiency in COPD Patients]. Open Respir Arch 2023; 5:100251. [PMID: 37810428 PMCID: PMC10556779 DOI: 10.1016/j.opresp.2023.100251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/12/2023] [Indexed: 10/10/2023] Open
Abstract
Objectives Currently, the identification of new cases of alpha-1 antitrypsin deficiency (AATD) continues to be one of the great challenges facing the disease. The present study aims to perform an analysis of the results of the implementation of a systematic case detection program of AATD for patients with chronic obstructive pulmonary disease. Material and methods Cross-sectional observational study in which the results of AAT screening until December 2022 were analyzed. The cases studied were divided into three periods: (1) no systematic case detection until 2013; (2) systematic case detection of S and Z alleles for cases with AAT < 90 mg/dL until 2018, and (3) systematic case detection of 14 mutations for cases with AAT < 120 mg/dL since 2018. Results A total of 471 cases were studied, of which 306 (65.0%) were carriers of some mutation related to HAD. The number of detected cases of all mutations with their percentage against those studied in each period was respectively: 6 (100%), 48 (88.8%) and 253 (61.5%). If we limit to severe mutations (AAT < 57.2 mg/dL), the distribution by periods was respectively: 3 (50.0), 10 (18.5%) and 17 (4.1%). Conclusions The present study describes the changes in the detection of patients carrying DAAT-related alleles with three different case identification policies. The data support the use of systematic case detection system in the COPD patient population.
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Affiliation(s)
- Rocío Reinoso-Arija
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
| | - Carmen Proaño
- Departamento de Medicina, Universidad de Sevilla, Sevilla, España
| | - Rosario Ruiz-Serrano
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
| | - Dolores Núñez Ollero
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
| | - Borja Ruiz-Duque
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
| | - Francisco Ortega Ruiz
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, España
| | - Eduardo Márquez Martín
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, España
| | - Laura Carrasco Hernández
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, España
| | - José Luis López-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Sevilla, España
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, España
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Sofi OMUD, Godara R, Katoch R, Yadav A. Morphological and molecular evidence of sandfly (Diptera: Psychodidae: Phlebotomine) and its relevance to recent cases of leishmaniasis from Jammu region of North India. J Vector Borne Dis 2023; 60:328-332. [PMID: 37843245 DOI: 10.4103/0972-9062.374037] [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: 10/17/2023] Open
Abstract
Present study was conducted to carry out morphological and molecular confirmation of sandflies collected at the Department of Parasitology, Faculty of Veterinary and Animal Sciences, R.S. Pura, Jammu, India. Larva was maggot like with large head, thorax and abdomen with typical black head, 12 abdominal segments and last abdominal segment carried two pairs of caudal bristles with matchstick hairs on each segment. The adult fly possessed head, abdomen and thorax. Head consisted of pair of long, hairy and beaded antenna, proboscis and one pair of prominent black eyes. Thorax possessed a pair of wings and three pairs of legs, wings were hairy and pointed with 2nd longitudinal vein branched twice. The abdominal segments were covered with small hairs and last abdominal segment was having a pair of anal recti. These identification characteristics confirmed the fly under study as Phlebotomus argentipes that confirms its occurance in this region. Molecular characterization of identified flies was carried out on positive morophological flies. Confirmation of Phlebotomus species was ascertained by amplifying the 18S ribosomal RNA gene sequence using PCR. Clear amplification was observed for Phlebotomus argentipes (538 bp). After sequencing/genotyping, Phlebotomus argentipes (OP646634) isolate of present study was clustering in same clade with Phlebotomus argentipes sequences obtained from GeneBank from other locations across globe, irrespective of their geographical location, thus providing the molecular evidence of this species present in Jammu region of North India.
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Affiliation(s)
- Omer Mohi U Din Sofi
- Division of Veterinary Parasitology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu & Kashmir, India
| | - R Godara
- Division of Veterinary Parasitology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu & Kashmir, India
| | - R Katoch
- Division of Veterinary Parasitology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu & Kashmir, India
| | - A Yadav
- Division of Veterinary Parasitology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu & Kashmir, India
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Khorram M, Masjedi H, Tabrizi F, Rezaei M, Tabarsi P, Marjani M, Pourabdoullah M, Sheikholeslami FM. The Accuracy of Diagnosis and Genotyping of Leishmania Species Based on Spliced Leader Mini-Exon Gene by Nuclear Magnetic Resonance and Sequencing Assays. Iran J Parasitol 2023; 18:331-341. [PMID: 37886256 PMCID: PMC10597884 DOI: 10.18502/ijpa.v18i3.13756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/10/2023] [Indexed: 10/28/2023]
Abstract
Background We aimed to evaluate the accuracy of genotyping of Leishmania species by the spliced leader mini-exon gene. Methods Suspected leishmaniasis patients, referred to Masieh Daneshvary Hospital, Tehran, Iran were included from May 2017 to September 2021. The Leishmania species were genotyped by PCRRFLP based on the SL mini-exon gene and the ITS1 region of SSU-rRNA gene and compared with the sequencing results. The expressed metabolites of metacyclic promastigotes were evaluated by Proton nuclear magnetic resonance (1H-NMR). Results Out of 66 suspected cases, 36 (54.4%) were positive for Leishmania species based on the PCR assays. In 21 (31.8%) cases, promastigotes grew on culture tubes. Based on the RFLP of SL RNA profile, 13 (19.7%) L. tropica, 9 (13.6%) L. major, 3 (4.5%) L. infantum, and 8 (12.1%) C. fasciculata isolates, isolated from culture media, were identified; however, 3 (4.5%) cases were unidentifiable due to the low number of parasites. Seventeen metabolites were expressed by the metacyclic forms of L. major, L. tropica and C. fasciculata isolates. The top differential metabolites expressed more in C. fasciculata were FAD, p-Methoxybenzyl alcohol and S-b-G-5, 5-G-b-S (A = CH2) (P<0.005) whereas Veratryl glycerols and D-(+)-Mannose were significantly increased in L. major and Betulin, LTyrosine in L. tropica (P<0.01). Conclusion The invaluable techniques such as sequencing and 1H-NMR confirmed the results of genotyping of Leishmania species based on the SL mini-exon gene. SL mini exon gene can be used as a diagnostic tool to differentiate various Leishmania genotypes and detect contamination of culture media with C. fasciculata.
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Affiliation(s)
- Mahyar Khorram
- Department of New Sciences and Technologies, South Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Heidar Masjedi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Tabrizi
- Department of Parasitology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mitra Rezaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Marjani
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mihan Pourabdoullah
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh-Maryam Sheikholeslami
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Molecular Biology, Dr. Khosroshahi’s Pathobiology Laboratory, Tehran, Iran
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Ali Y, Khan A, Akhtar M, Khan S, Islam ZU, Farooqi N, Shah AA, Chen Y, Jalil F. Exploring the Associations and Molecular Impacts of miR-146a/rs2910164 and miR-196a2/rs185070757 with Rheumatoid Arthritis in a Pakistani Population. Lifestyle Genom 2023; 16:139-150. [PMID: 37369185 DOI: 10.1159/000526937] [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: 02/16/2022] [Accepted: 08/22/2022] [Indexed: 06/29/2023] Open
Abstract
INTRODUCTION MicroRNAs (miRNAs) are a new class of molecules that participate in post-transcriptional regulation of gene expression and hence have been reported to have a crucial role in the pathogenesis of rheumatoid arthritis (RA). We aimed to investigate the association of miR-146a rs2910164 (G/C) and miR-196a2 rs185070757 (T/G) with RA susceptibility in Pakistani patients and to bioinformatically predict the molecular function of these miRNAs. METHODS A case-control study on 600 individuals was conducted, including 300 RA patients and 300 matching healthy controls. Genotyping was performed by tetra-primer amplification of refractory mutation system-polymerase chain reaction, and the association between variants and RA was statistically determined using different models. RESULTS For the variant rs2910164 (G/C) in miR-146a, no difference in genotype distribution was observed between RA cases and controls, as determined using co-dominant (χ2 = 4.33; p = 0.114), homozygous dominant (C/C vs. G/G + C/G) (OR = 0.740 [0.531-1.032]; p = 0.091), homozygous recessive (G/G vs. C/C + G/C) (odds ratio [OR] = 01.432 [0.930-2.206]; p = 0.126), heterozygous (G/C vs. C/C + G/G) (OR = 1.084 [0.786-1.494]; p = 0.682), and additive (OR 0.778 [0.617-0.981]; p = 0.039) models. Similarly, the GT genotype in the rs185070757 (T/G) miR-196a2 variant did not differ between cases and controls with any models (p > 0.05). For the first time, we report no association of miR-146a rs2910164 (G/C) and miR-196a2 rs185070757 (T/G) with RA in a Pakistani population. A subsequent bioinformatic analysis revealed that the CC genotype of miR-146a rs2910164 might have a protective role against RA pathogenesis, with no effect observed with the miR-196a2 rs185070757. CONCLUSION Our findings suggest that these miRNAs might have little-to-no impact on the RA pathogenesis in the Pakistani population.
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Affiliation(s)
- Yasir Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Aamir Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Suleman Khan
- Consultant Rheumatologist, Lady Reading Hospital-MTI Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ul Islam
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Nadia Farooqi
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Aftab Ali Shah
- Department of Biotechnology, University of Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Yangchao Chen
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
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Winternitz J, Chakarov N, Rinaud T, Ottensmann M, Krüger O. High functional allelic diversity and copy number in both MHC classes in the common buzzard. BMC Ecol Evol 2023; 23:24. [PMID: 37355591 PMCID: PMC10290333 DOI: 10.1186/s12862-023-02135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC), which encodes molecules that recognize various pathogens and parasites and initiates the adaptive immune response in vertebrates, is renowned for its exceptional polymorphism and is a model of adaptive gene evolution. In birds, the number of MHC genes and sequence diversity varies greatly among taxa, believed due to evolutionary history and differential selection pressures. Earlier characterization studies and recent comparative studies suggest that non-passerine species have relatively few MHC gene copies compared to passerines. Additionally, comparative studies that have looked at partial MHC sequences have speculated that non-passerines have opposite patterns of selection on MHC class I (MHC-I) and class II (MHC-II) loci than passerines: namely, greater sequence diversity and signals of selection on MHC-II than MHC-I. However, new sequencing technology is revealing much greater MHC variation than previously expected while also facilitating full sequence variant detection directly from genomic data. Our study aims to take advantage of high-throughput sequencing methods to fully characterize both classes and domains of MHC of a non-passerine bird of prey, the common buzzard (Buteo buteo), to test predictions of MHC variation and differential selection on MHC classes. RESULTS Using genetic, genomic, and transcriptomic high-throughput sequencing data, we established common buzzards have at least three loci that produce functional alleles at both MHC classes. In total, we characterize 91 alleles from 113 common buzzard chicks for MHC-I exon 3 and 41 alleles from 125 chicks for MHC-IIB exon 2. Among these alleles, we found greater sequence polymorphism and stronger diversifying selection at MHC-IIB exon 2 than MHC-I exon 3, suggesting differential selection pressures on MHC classes. However, upon further investigation of the entire peptide-binding groove by including genomic data from MHC-I exon 2 and MHC-IIA exon 2, this turned out to be false. MHC-I exon 2 was as polymorphic as MHC-IIB exon 2 and MHC-IIA exon 2 was essentially invariant. Thus, comparisons between MHC-I and MHC-II that included both domains of the peptide-binding groove showed no differences in polymorphism nor diversifying selection between the classes. Nevertheless, selection analysis indicates balancing selection has been acting on common buzzard MHC and phylogenetic inference revealed that trans-species polymorphism is present between common buzzards and species separated for over 33 million years for class I and class II. CONCLUSIONS We characterize and confirm the functionality of unexpectedly high copy number and allelic diversity in both MHC classes of a bird of prey. While balancing selection is acting on both classes, there is no evidence of differential selection pressure on MHC classes in common buzzards and this result may hold more generally once more data for understudied MHC exons becomes available.
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Affiliation(s)
- Jamie Winternitz
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
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Pandey S, Singh A, Jaiswal P, Singh MK, Meena KR, Singh SK. The potentialities of omics resources for millet improvement. Funct Integr Genomics 2023; 23:210. [PMID: 37355501 DOI: 10.1007/s10142-023-01149-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
Millets are nutrient-rich (nutri-rich) cereals with climate resilience attributes. However, its full productive potential is not realized due to the lack of a focused yield improvement approach, as evidenced by the available literature. Also, the lack of well-characterized genomic resources significantly limits millet improvement. But the recent availability of genomic data and advancement in omics tools has shown its enormous potential to enhance the efficiency and precision faced by conventional breeding in millet improvement. The development of high throughput genotyping platforms based on next-generation sequencing (NGS) has provided a low-cost method for genomic information, specifically for neglected nutri-rich cereals with the availability of a limited number of reference genome sequences. NGS has created new avenues for millet biotechnological interventions such as mutation-based study, GWAS, GS, and other omics technologies. The simultaneous discovery of high-throughput markers and multiplexed genotyping platform has aggressively aided marker-assisted breeding for millet improvement. Therefore, omics technology offers excellent opportunities to explore and combine useful variations for targeted traits that could impart high nutritional value to high-yielding cultivars under changing climatic conditions. In millet improvement, an in-depth account of NGS, integrating genomics data with different biotechnology tools, is reviewed in this context.
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Affiliation(s)
- Saurabh Pandey
- Department of Agricultural, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Ashutosh Singh
- Centre for Advanced Studies on Climate Change, RPCAU, Pusa, Samastipur, Bihar, 848125, India.
| | - Priyanka Jaiswal
- Lovely Professional University, Jalandhar - Delhi G.T. Road, Phagwara, Punjab, 144411, India
| | - Mithilesh Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
| | - Khem Raj Meena
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Rajasthan, 305817, India
| | - Satish Kumar Singh
- Department of Genetics and Plant Breeding, RPCAU, Pusa, Samastipur, Bihar, 848125, India
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von Bredow B, Caldera JR, Cerón S, Chan JL, Gray HK, Garner OB, Yang S. Clinical next-generation sequencing assay combining full-length gene amplification and shotgun sequencing for the detection of CMV drug resistance mutations. J Clin Virol 2023; 165:105520. [PMID: 37336174 DOI: 10.1016/j.jcv.2023.105520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Cytomegalovirus (CMV) causes severe systemic and tissue-invasive disease in immunocompromised patients, particularly solid organ and hematopoietic stem cell transplant recipients. While antiviral drugs offer promising efficacy, clinical management is complicated by the high frequency of drug resistance-associated mutations. The most commonly encountered mutations occur in the genes encoding for the drug targets: UL54 (DNA polymerase), UL56 (terminase complex), and UL97 (phosphotransferase), conferring resistance to ganciclovir/cidofovir/foscarnet, letermovir, and ganciclovir/maribavir, respectively. Currently, standard practice for detecting drug resistance is sequencing-based genotypic analysis by commercial reference laboratories with strictly prescribed sample requirements and reporting parameters that can often restrict testing in a highly vulnerable population. In order to circumvent these limitations, we developed a dual-step next-generation sequencing (NGS)-based clinical assay that utilizes full-length gene amplification by long-range PCR followed by shotgun sequencing for mutation analysis. This laboratory-developed test (LDT) achieved satisfactory performance with 96.4% accuracy, 100% precision, and an analytical sensitivity of 300IU/mL with 20% allele frequency. Highlighted by two clinical cases, our NGS LDT was able to provide critical results from patient specimens with viral loads <500IU/mL and volumes <0.5 mL - conditions otherwise unacceptable by reference laboratories. Here, we describe the development and implementation of a robust NGS LDT that offers greater testing flexibility and sensitivity to accommodate a more diverse patient population.
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Affiliation(s)
- Benjamin von Bredow
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States; Department of Pathology, Oakland University William Beaumont School of Medicine, Rochester, MI, United States
| | - J R Caldera
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Stacey Cerón
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - June L Chan
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Hannah K Gray
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Omai B Garner
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States
| | - Shangxin Yang
- Department of Pathology and Laboratory Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA, United States.
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Baddal B, Oktay MN, Bostanci A, Yenen MC. Prevalence and genotype screening of human papillomavirus among women attending a private hospital in Northern Cyprus: an 11-year retrospective study. BMC Womens Health 2023; 23:297. [PMID: 37270608 DOI: 10.1186/s12905-023-02451-8] [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: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) is the most common sexually transmitted pathogen both in men and women. Accumulating epidemiological evidence supports a strong association between HPV infection and cancer of the cervix, vulva, vagina, anus, and penis. Currently, data on the HPV prevalence and genotyping is lacking in Northern Cyprus, a region in which HPV vaccination is not freely accessible via the national immunization program. The aim of this study was to evaluate the HPV type-specific prevalence in women with and without cytological abnormalities living in Northern Cyprus. METHODS A total of 885 women who presented to the Department of Gynecology and Obstetrics Clinic between January 2011 and December 2022 were included in the study. Samples were collected for cytology. Cervical specimens were investigated for the presence of HPV-DNA and genotyping of HPV was performed using real-time polymerase chain reaction (rtPCR). Cytological examination was interpreted according to the Bethesda system. RESULTS Among all patients, overall high-risk HPV DNA prevalence was 44.3%. HPV-16 and HPV-18 positivity was found in 10.4% and 3.7% of women respectively, while other high-risk HPV (OHR-HPV) was the most frequent type of HPV (30.2%). The highest frequency of HPV infection was observed in the 30-55 age group (51.0%), followed by the < 30 age group (45.7%). Co-infection with two or more HPV types was observed in 17.0% of all positive samples, in which the prevalence of HPV-16 + HPV-18 was 2.3%, HPV-16 + OHR-HPV and HPV-18 + OHR-HPV was 12.0% and 5.1%, respectively. Among the screened patients, 37.5% had abnormal and 62.5% had normal cytology results. HR-HPV positivity was 65.7% and 34.0% in patients with abnormal and normal cytology. The highest incidence of HRC-HPV was OHR-HPV types (44.7%) in positive cytology cases. Among women with a cytology result of ASCUS, L-SIL, H-SIL and unspecified dysplasia, 52.1%, 67.6%, 97.5% and 75.6% were respectively infected with HR-HPV. CONCLUSION The present study provides the latest epidemiological data related to HPV prevalence and genotype distribution among women living in Northern Cyprus. Considering the unavailability of free vaccination in the community, it is imperative to implement local HPV screening programs and provide guidelines on HPV prevention and measures during early school education.
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Affiliation(s)
- Buket Baddal
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus.
| | - Makbule Naz Oktay
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Eastern Mediterranean University, Famagusta, Cyprus
| | - Aysegul Bostanci
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, 99138, Cyprus
- Molecular Microbiology Laboratory, Near East University Hospital, Nicosia, 99138, Cyprus
| | - Mufit Cemal Yenen
- Department of Gynecology and Obstetrics, University of Kyrenia Hospital, Kyrenia, Cyprus
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Menezes KMF, Dábilla N, Souza M, Damasceno AD, Torres BBJ. Identification of a new polymorphism on the wild-type canine distemper virus genome: could this contribute to vaccine failures? Braz J Microbiol 2023; 54:665-678. [PMID: 37140816 PMCID: PMC10235312 DOI: 10.1007/s42770-023-00971-x] [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: 02/06/2023] [Accepted: 04/07/2023] [Indexed: 05/05/2023] Open
Abstract
The canine distemper virus (CDV) is responsible for a multisystem infectious disease with high prevalence in dogs and wild carnivores and has vaccination as the main control measure. However, recent studies show an increase in cases including vaccinated dogs in different parts of the world. There are several reasons for vaccine failures, including differences between vaccine strains and wild-type strains. In this study, a phylogenetic analysis of CDV strains from samples of naturally infected, vaccinated, and symptomatic dogs in Goiânia, Goiás, Brazil was performed with partial sequencing of the hemagglutinin (H) gene of CDV. Different sites of amino acid substitutions were found, and one strain had the Y549H mutation, typically present in samples from wild animals. Substitutions in epitopes (residues 367, 376, 379, 381, 386, and 388) that may interfere with the vaccine's ability to provide adequate protection against infection for CDV were observed. The identified strains were grouped in the South America 1/Europe lineage, with a significant difference from other lineages and vaccine strains. Twelve subgenotypes were characterized, considering a nucleotide identity of at least 98% among the strains. These findings highlight the relevance of canine distemper infection and support the need better monitoring of the circulating strains that contribute to elucidate if there is a need for vaccine update.
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Affiliation(s)
| | - Nathânia Dábilla
- Instituto de Patologia Tropical E Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Menira Souza
- Instituto de Patologia Tropical E Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Adilson Donizeti Damasceno
- Escola de Veterinária E Zootecnia, Universidade Federal de Goiás - UFG, Campus II CEP 74690900, Goiânia, GO, Brazil
| | - Bruno Benetti Junta Torres
- Escola de Veterinária E Zootecnia, Universidade Federal de Goiás - UFG, Campus II CEP 74690900, Goiânia, GO, Brazil
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Darabi A, Sarshari B, Vahdat K, Mousavi SA, Keshavarz M. Frequent detection and genotyping of human rhinovirus in SARS-CoV-2 negative patients; a study from south of Iran. Iran J Microbiol 2023; 15:462-467. [PMID: 37448684 PMCID: PMC10336278 DOI: 10.18502/ijm.v15i3.12908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Background and Objectives Human rhinovirus (HRV), a major cause of common cold, was associated to the hospitalization of children and adults. This cross-sectional study aimed to determine the prevalence, and genotype distribution of HRV in the patients with mild to severe respiratory infections who were negative for SARS-Cov-2. Materials and Methods Nasopharyngeal swab specimens (n = 356) from the patients aged 29 days to 82 years, received for the respiratory virus detection from January to December 2021, were analyzed for human rhinovirus (HRV) by RT-PCR. As a final step, genotyping was performed on obtained sequences. Results A total of 37 HRV infections were identified (37/356, 10%). The highest rates of positive HRV tests were observed in February (21.6%), and January (18.9%), compared with June and August (0%). HRV-positive cases mainly appeared in winter. Among the age groups, those 2-<5 years of age had the highest detection rate (21%), however, those >55 years of age had the lowest detection rate (3%). Among HRV-positive samples, 30 (81%) were identified as type HRV-A, 5 (13.5%) as HRV-B, and 2 (5.5%) as HRV-C. Conclusion Our results suggested that HRV frequency gradually decreased with the age of patients which is more active in Iran, especially in the cold months.
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Affiliation(s)
- Amirhossein Darabi
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Behrang Sarshari
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Katayoun Vahdat
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Seyed Alireza Mousavi
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohsen Keshavarz
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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Zhang J, Fu Y, Bian X, Han H, Dong H, Zhao G, Li J, Li X, Zhang L. Molecular identification and genotyping of Blastocystis sp. in sheep and goats from some areas in Inner Mongolia, Northern China. Parasitol Int 2023; 94:102739. [PMID: 36787864 DOI: 10.1016/j.parint.2023.102739] [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: 09/15/2022] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/14/2023]
Abstract
Blastocystis sp. is a kind of unicellular intestinal commensal which is widely distributed in humans and animals, and frequently found in the people who are in close contact with animals. To investigate the prevalence and evaluate the zoonotic potential of Blastocystis sp. in sheep and goats from Inner Mongolia, China, a total of 1037 samples were collected from them, and subjected to nested PCR amplification based on the small subunit ribosomal RNA (SSU rRNA) gene of Blastocystis sp. The sanger sequencing was used for Blastocystis sp. subtype identification. The results indicated that the average infection rate of Blastocystis sp. was 10.70% [95CI: 8.82%-12.58%] (111/1037), including 11.30% [95CI: 7.96%-14.64%] for sheep (39/345) and 10.40% [95CI: 8.13%-12.67%] for goats (72/692). Five Blastocystis subtypes (ST5, ST10, ST14, ST21 and ST26) were identified in the present study. Among them, ST10 was the most dominant subtype in sheep and goats, accounting for 70.27% (78/111) of the total identified positive samples. This is the first report regarding Blastocystis sp. subtypes ST21 and ST26 in goats in China. This study has provided a detail epidemiological data on the prevalence and subtypes distribution of Blastocystis sp. in sheep and goats in Inner Mongolia, China. Our results indicated that sheep and goats could be reservoir host for multiple Bastocystis subtypes, including the zoonotic subtypes. Further studies among humans, livestock and wild animals are needed to better understand their role in the spread of Blastocystis sp.
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Affiliation(s)
- Junchen Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, PR China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, PR China
| | - Yin Fu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, PR China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, PR China
| | - Xiaokun Bian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, PR China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, PR China
| | - Han Han
- Norman Bethune Health Science Center of Jilin University, Changchun 130021, Jinlin Province, PR China
| | - Heping Dong
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China.
| | - Guanghui Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, PR China.
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, PR China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, PR China.
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, PR China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, PR China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China; International Joint Research Laboratory for Zoonotic Diseases of Henan, Zhengzhou 450046, PR China; Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, PR China.
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Shawky A, Sabit H, Nazih M, Baraka K, El-Zawahry M. CYP2C19 Polymorphism in Ischemic Heart Disease Patients Taking Clopidogrel After Percutaneous Coronary Intervention in Egypt. J Epidemiol Glob Health 2023; 13:374-383. [PMID: 37202608 PMCID: PMC10272067 DOI: 10.1007/s44197-023-00113-4] [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: 01/13/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Cardiovascular diseases (CVDs) are considered a leading cause of death worldwide. Allelic variation in the CYP2C19 gene leads to a dysfunctional enzyme, and patients with this loss-of-function allele will have an impaired clopidogrel metabolism, which eventually results in major adverse cardiovascular events (MACE). Ischemic heart disease patients (n = 102) who underwent percutaneous cardiac intervention (PCI) followed by clopidogrel were enrolled in the present study. METHODS The genetic variations in the CYP2C19 gene were identified using the TaqMan chemistry-based qPCR technique. Patients were followed up for 1 year to monitor MACE, and the correlations between the allelic variations in CYP2C19 and MACE were recorded. RESULTS During the follow-up, we reported 64 patients without MACE (29 with unstable angina (UA), 8 with myocadiac infarction (MI), 1 patient with non-STEMI, and 1 patient with ischemic dilated cardiomyopathy (IDC)). Genotyping of CYP2C19 in the patients who underwent PCI and were treated with clopidogrel revealed that 50 patients (49%) were normal metabolizers for clopidogrel with genotype CYP2C19*1/*1 and 52 patients (51%) were abnormal metabolizers, with genotypes CYP2C19*1/*2 (n = 15), CYP2C19*1/*3 (n = 1), CYP2C19*1/*17 (n = 35), and CYP2C19*2/*17 (n = 1). Demographic data indicated that age and residency were significantly associated with abnormal clopidogrel metabolism. Moreover, diabetes, hypertension, and cigarette smoking were significantly associated with the abnormal metabolism of clopidogrel. These data shed light on the inter-ethnic variation in metabolizing clopidogrel based on the CYP2C19 allelic distribution. CONCLUSION This study, along with other studies that address genotype variation of clopidogrel-metabolizing enzymes, might pave the way for further understanding of the pharmacogenetic background of CVD-related drugs.
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Affiliation(s)
- Ahmed Shawky
- Department of Cardiology, College of Medicine, Helwan University, Cairo, Egypt
| | - Hussein Sabit
- Department of Medical Biotechnology, College of Biotechnology, Misr University for Science and Technology, P. O. Box 77, Giza, Egypt.
| | - Mahmoud Nazih
- Department of Clinical Pharmacy, Faculty of Pharmacy, Menoufia University, Shibin Al Kawm, Egypt
- Scientific Office, Egyptian Society of Pharmacogenomics and Personalized Medicine (ESPM), Cairo, Egypt
| | - Khalid Baraka
- Department of Cardiology, College of Medicine, Minia University, Minia, Egypt
| | - Mokhtar El-Zawahry
- Department of Medical Biotechnology, College of Biotechnology, Misr University for Science and Technology, P. O. Box 77, Giza, Egypt
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Kaba G, Stevenson A, Sakyi SA, Konney TO, Bhatia R, Titiloye NA, Oppong SA, Agyemang-Yeboah F, Cuschieri K, Graham SV. Diversity of cervicovaginal human papillomavirus (HPV) genotypes and naturally occurring E6/E7 DNA polymorphisms of HPV-16 in Ghana. Tumour Virus Res 2023; 15:200261. [PMID: 37179021 PMCID: PMC10209332 DOI: 10.1016/j.tvr.2023.200261] [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: 12/12/2022] [Revised: 04/12/2023] [Accepted: 05/10/2023] [Indexed: 05/15/2023] Open
Abstract
Human papillomavirus (HPV) E6 and E7 oncogene expression is essential for cervical carcinogenesis. Evidence exists that E6/E7 variants may have different transforming activities while the risk of HPV-16 variants (A/D) differs by race/ethnicity. We determined the type-specific diversity of HPV infection in women with high grade cervical disease or cervical cancer in Ghana and investigated naturally occurring E6/E7 DNA variants in this population. HPV genotyping was carried out on 207 cervical swab samples collected from women referred to a gynaecology clinic at two teaching hospitals in Ghana. HPV-16, HPV-18 and HPV-45 were detected in 41.9%, 23.3% and 16.3% of cases respectively. HPV-16 E6/E7 DNA sequencing was performed in 36 samples. Thirty samples contained E6/E7 variants of the HPV-16-B/C lineage. 21/36 samples were of the HPV-16C1 sublineage variant and all contained the E7 A647G(N29S) single nucleotide polymorphism (SNP). This study reveals the diversity of E6/E7 DNA and the dominance of HPV16 B/C variants in cervicovaginal HPV infection in Ghana. Type-specific HPV diversity analysis indicates that most Ghanaian cervical disease cases are vaccine preventable. The study provides an important baseline from which for the impact of vaccine and antivirals on clinically relevant HPV infection and associated disease can be measured.
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Affiliation(s)
- Gladys Kaba
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - Andrew Stevenson
- Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, Garscube Estate, University of Glasgow, Scotland, G61 1QH, UK
| | - Samuel Asamoah Sakyi
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Thomas Okpoti Konney
- Department of Obstetrics and Gynaecology, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ramya Bhatia
- Scottish HPV Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, University of Edinburgh, Scotland, EH16 4SA, UK
| | - Nicholas A Titiloye
- Department of Pathology, School of Medical Sciences, Kwame Nkrumah University of Science and Technology Kumasi, Ghana
| | - Samuel A Oppong
- Department of Obstetrics and Gynaecology, Korle-Bu Teaching Hospital and University of Ghana Medical School, Accra, Ghana
| | - Francis Agyemang-Yeboah
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kate Cuschieri
- Scottish HPV Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, University of Edinburgh, Scotland, EH16 4SA, UK
| | - Sheila V Graham
- Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, Garscube Estate, University of Glasgow, Scotland, G61 1QH, UK.
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Helenius G, Lillsunde-Larsson G, Bergengren L. Molecular triage of cervical screening samples in women 55-59 years of age: a pilot study. Infect Agent Cancer 2023; 18:31. [PMID: 37221548 DOI: 10.1186/s13027-023-00510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND With HPV screening the specificity of screening positives has decreased, even with a cytological triage test. Increases in colposcopies and detection of benign or low-grade dysplasia are reported, not least in older women. These results highlight the necessity to find other triage tests in HPV screening strategies, so that women can be more accurately selected for colposcopy, thus minimizing the clinically irrelevant findings. METHODS The study included 55- to 59-year-old women who exited the screening with normal cytology, but later in a follow-up test were positive for the HPV genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 and had a cervical cone biopsy done. To model a screening situation with hrHPV-positive women, three different triage strategies, namely, cytology, genotyping and methylation, were performed. The study considered the effect of direct referral to colposcopy for HPV genotypes 16, 18, 31, 33, 45, 52 and 58, and methylation for FAM19A4 and hsa-mir124-2 and/or any form of abnormal cytology. RESULTS Seven out of 49 women aged 55-59 years with hrHPV had a cone biopsy with high-grade squamous intraepithelial lesion. No triage method found all cases, and when comparing positive and negative predictive value and false negative rate, cytology showed better results than genotyping and methylation. CONCLUSION This study does not support a switch in triage strategies from cytology to hrHPV genotyping and methylation for women above 55 years of age yet, but demonstrates the need for more evidence on molecular triage strategies.
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Affiliation(s)
- Gisela Helenius
- School of Health Sciences, Örebro University, Örebro, Sweden
| | - Gabriella Lillsunde-Larsson
- School of Health Sciences, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Lovisa Bergengren
- Department of Women's Health, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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Fu L, Ma E, Okada M, Shibata Y, Shi YB. Competitive PCR with dual fluorescent primers enhances the specificity and reproducibility of genotyping animals generated from genome editing. Cell Biosci 2023; 13:83. [PMID: 37170319 PMCID: PMC10173569 DOI: 10.1186/s13578-023-01042-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
Targeted genome editing is a powerful tool for studying gene function in almost every aspect of biological and pathological processes. The most widely used genome editing approach is to introduce engineered endonucleases or CRISPR/Cas system into cells or fertilized eggs to generate double-strand DNA breaks within the targeted region, leading to DNA repair through homologous recombination or non-homologous end joining (NHEJ). DNA repair through NHEJ mechanism is an error-prone process that often results in point mutations or stretches of indels (insertions and deletions) within the targeted region. Such mutations in embryos are germline transmissible, thus providing an easy means to generate organisms with gene mutations. However, point mutations and short indels present difficulty for genotyping, often requiring labor intensive sequencing to obtain reliable results. Here, we developed a single-tube competitive PCR assay with dual fluorescent primers that allowed simple and reliable genotyping. While we used Xenopus tropicalis as a model organism, the approach should be applicable to genotyping of any organisms.
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Affiliation(s)
- Liezhen Fu
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emily Ma
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Morihiro Okada
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yuki Shibata
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Bo Shi
- Section On Molecular Morphogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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Pratim Das P, Jyoti Kalita M, Jyoti Talukdar A, Mohd Khan F, Dutta K, Kalita S, Goswami N, Hazarika G, Samudrala G, Ghaznavi Idris M, Dutta S, Medhi S. Evaluation and analysis of novel germline variants in ethanol metabolism pathway genes predisposition to liver disease. Gene 2023; 873:147451. [PMID: 37150234 DOI: 10.1016/j.gene.2023.147451] [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: 01/24/2023] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
The pathogenetic events of liver disease are seemingly determined by factors linked to ethanol metabolism. The variations in genes encoding enzymes of the ethanol metabolic pathway can influence exposure to alcohol and thus may act as risk factors for the development of liver disease. The present study aimed to understand the genetic aspect of germline variations in ethanol metabolic pathway genes in two major categories of liver disease i.e. ALD and NAFLD. Targeted Re-sequencing was performed in the two disease categories along with healthy control followed by an assessment and evaluation of the variants in a case vs control manner. The pathogenicity prediction was evaluated using SIFT, PolyPhen, PROVEN, LRT, CADD, FATHMM, EIGEN, REVEL and VarSome, while MD simulation of a novel significant variant was performed using the GROMACS 5.1.4 package. The annotation of targeted re-sequencing results revealed 2172 variants in different locations of the genes. Upon recurrent assessment predominantly focusing on exonic missense variants from these genes of the alcohol metabolism pathway, the ALDH1L2 [c.337C>G, p.Pro113Ala, (rs199841702)] variant was found highly significant with comprehensive results. The amino acid substitution tool that predicted protein stability due to a point mutation showed a decrease in stability. The genotyping distribution of the identified novel variant in the population revealed that heterozygosity is significantly distributed in ALD patients. However, the predominant association between the inherited variant and the cause of developing disease needs further robust study.
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Affiliation(s)
- Partha Pratim Das
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Manash Jyoti Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Anjan Jyoti Talukdar
- Department of Medicine, Gauhati Medical College & Hospital, Guwahati, Assam-781032
| | - Faraz Mohd Khan
- School of Life sciences, Jawaharlal Nehru University, New Delhi, 110067
| | - Kalpajit Dutta
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Simanta Kalita
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Nabajyoti Goswami
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | - Gautam Hazarika
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014
| | | | | | - Sangit Dutta
- Department of Medicine, Gauhati Medical College & Hospital, Guwahati, Assam-781032
| | - Subhash Medhi
- Department of Bioengineering & Technology, Gauhati University, Guwahati, Assam-781014.
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128
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Oliveira CS, Silva MVGBD, Quintão CC, Otto PI, Alonso RV, Feres LF, Panetto JCDC, Machado MA, Camargo LSDA. Imputation accuracy for genomic selection using embryo biopsy samples in Gir. Reprod Biol 2023; 23:100765. [PMID: 37150127 DOI: 10.1016/j.repbio.2023.100765] [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: 09/13/2022] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023]
Abstract
The aim of this study was to establish a platform for genomic selection of in vitro-fertilized (IVF) Gir embryos. Multiple displacement amplification (MDA)-based embryo biopsy samples were genotyped, and genomic estimated breeding values (GEBV) for milk yield (305MY) were calculated. The concordance of GEBV and accuracy between embryo biopsies and the respective liveborn were assessed. Imputation was performed using two panels (Z-Chip and Bovine HD, Illumina) based on a database of 73,110 lactating cow's database and pedigree files from 147,131 animals. Biopsied embryos had similar pregnancy rates (39% vs 40%), pregnancy loss rates (18% vs 20%), and pregnancy length compared to Control embryos. After genotyping, low call rate means were detected for biopsy samples compared to the respective calf samples (0.80 vs 0.98). Imputation presented 0.83 (Z-Chip) and 0.96 (HD) accuracy (CORRanim). Embryo GEBV accuracy levels were higher in BovineHD imputation (0.82) than Z-Chip imputation (0.55) or no imputation (0.62), and the correlation between embryo/calf pairs' accuracy was 0.85 for BovineHD imputation, 0.11 for Z-Chip imputation, and 0.02 for no imputation. GEVB estimates correlation between embryo/calf pairs was 0.87 for BovineHD imputation, 0.80 for Z-Chip imputation, and 0.41 before imputation. The call rate of embryo samples did not affect the correlation between embryo/calf pairs for accuracy and GEBV before and after BovineHD imputation. Embryos obtained on the same farm presented GEBV 305MY differences of up to 800 kg, emphasizing the expected impact of embryo genomic selection for the Gir breed.
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Affiliation(s)
- Clara Slade Oliveira
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave., Juiz de Fora, MG 36038-330, Brazil.
| | | | | | - Pamela Itajara Otto
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave., Juiz de Fora, MG 36038-330, Brazil; Department of Animal Science, Universidade Federal de Santa Maria, 1000 Roraima Ave., Santa Maria, RS 97105-900, Brazil
| | | | - Luiz Fernando Feres
- Jose do Rosario Vellano University (UNIFENAS), MG 179Rd., Alfenas, MG 37132-440, Brazil
| | | | - Marco Antonio Machado
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave., Juiz de Fora, MG 36038-330, Brazil
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Abstract
We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt .
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Affiliation(s)
- Taher Mun
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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130
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Fan CC, Loughnan R, Wilson S, Hewitt JK. Genotype Data and Derived Genetic Instruments of Adolescent Brain Cognitive Development Study ® for Better Understanding of Human Brain Development. Behav Genet 2023; 53:159-168. [PMID: 37093311 PMCID: PMC10635818 DOI: 10.1007/s10519-023-10143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
The data release of Adolescent Brain Cognitive Development® (ABCD) Study represents an extensive resource for investigating factors relating to child development and mental wellbeing. The genotype data of ABCD has been used extensively in the context of genetic analysis, including genome-wide association studies and polygenic score predictions. However, there are unique opportunities provided by ABCD genetic data that have not yet been fully tapped. The diverse genomic variability, the enriched relatedness among ABCD subsets, and the longitudinal design of the ABCD challenge researchers to perform novel analyses to gain deeper insight into human brain development. Genetic instruments derived from the ABCD genetic data, such as genetic principal components, can help to better control confounds beyond the context of genetic analyses. To facilitate the use genomic information in the ABCD for inference, we here detail the processing procedures, quality controls, general characteristics, and the corresponding resources in the ABCD genotype data of release 4.0.
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Affiliation(s)
- Chun Chieh Fan
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, USA.
- Department of Radiology, School of Medicine, University of California, San Diego, San Diego, USA.
| | - Robert Loughnan
- Center for Human Development, University of California, San Diego, San Diego, USA
| | - Sylia Wilson
- Institute of Child Development, Univeristy of Minnesota, Minneapolis, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, USA
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Dashti A, Köster PC, Bailo B, de Las Matas AS, Habela MÁ, Rivero-Juarez A, Vicente J, Serrano E, Arnal MC, de Luco DF, Morrondo P, Armenteros JA, Balseiro A, Cardona GA, Martínez-Carrasco C, Ortiz JA, Carpio AJ, Calero-Bernal R, González-Barrio D, Carmena D. Occurrence and limited zoonotic potential of Cryptosporidium spp., Giardia duodenalis, and Balantioides coli infections in free-ranging and farmed wild ungulates in Spain. Res Vet Sci 2023; 159:189-197. [PMID: 37148738 DOI: 10.1016/j.rvsc.2023.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 05/08/2023]
Abstract
Little information is currently available on the occurrence and molecular diversity of the enteric protozoan parasites Cryptosporidium spp., Giardia duodenalis, and Balantioides coli in wild ungulates and the role of these host species as potential sources of environmental contamination and consequent human infections. The presence of these three pathogens was investigated in eight wild ungulate species present in Spain (genera Ammotragus, Capra, Capreolus, Cervus, Dama, Ovis, Rupicapra, and Sus) by molecular methods. Faecal samples were retrospectively collected from free-ranging (n = 1058) and farmed (n = 324) wild ungulates from the five Spanish bioregions. Overall infection rates were 3.0% (42/1382; 95% CI: 2.1-3.9%) for Cryptosporidium spp., 5.4% (74/1382; 95% CI: 4.2-6.5%) for G. duodenalis, and 0.7% (9/1382; 95% CI: 0.3-1.2%) for B. coli. Cryptosporidium infection was detected in roe deer (7.5%), wild boar (7.0%) and red deer (1.5%), and G. duodenalis in southern chamois (12.9%), mouflon (10.0%), Iberian wild goat (9.0%), roe deer (7.5%), wild boar (5.6%), fallow deer (5.2%) and red deer (3.8%). Balantioides coli was only detected in wild boar (2.5%, 9/359). Sequence analyses revealed the presence of six distinct Cryptosporidium species: C. ryanae in red deer, roe deer, and wild boar; C. parvum in red deer and wild boar; C. ubiquitum in roe deer; C. scrofarum in wild boar; C. canis in roe deer; and C. suis in red deer. Zoonotic assemblages A and B were detected in wild boar and red deer, respectively. Ungulate-adapted assemblage E was identified in mouflon, red deer, and southern chamois. Attempts to genotype samples positive for B. coli failed. Sporadic infections by canine- or swine-adapted species may be indicative of potential cross-species transmission, although spurious infections cannot be ruled out. Molecular evidence gathered is consistent with parasite mild infections and limited environmental contamination with (oo)cysts. Free-ranging wild ungulate species would not presumably play a significant role as source of human infections by these pathogens. Wild ruminants do not seem to be susceptible hosts for B. coli.
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Affiliation(s)
- Alejandro Dashti
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Ana Sánchez de Las Matas
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain
| | - Miguel Ángel Habela
- Department of Animal Health, Veterinary Sciences Faculty, Extremadura University, Caceres, Spain
| | - Antonio Rivero-Juarez
- Infectious Diseases Unit, Maimonides Institute for Biomedical Research (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Córdoba, Spain; Center for Biomedical Research Network in Infectious Diseases (CIBERINFEC), Health Institute Carlos III, Madrid, Spain
| | - Joaquín Vicente
- SaBio Group, Institute for Game and Wildlife Research, IREC (UCLM-CSIC-JCCM), Ciudad Real, Spain
| | - Emmanuel Serrano
- Wildlife Ecology & Health Group (WE&H), Wildlife Environmental Pathology Service (SEFaS), Department of Animal Medicine and Surgery, Autonomous University of Barcelona, Bellaterra, Spain
| | - Maria C Arnal
- Department of Animal Pathology, Veterinary Faculty, University of Zaragoza, Zaragoza, Spain
| | | | - Patrocinio Morrondo
- INVESAGA Group, Department of Animal Pathology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - José A Armenteros
- Council of Development, Territory Planning and the Environment of the Principado de Asturias, Oviedo, Spain
| | - Ana Balseiro
- Animal Health Department, Veterinary School, University of León, León, Spain; Animal Health Department, Mountain Livestock Institute (CSIC-University of León), León, Spain
| | | | - Carlos Martínez-Carrasco
- Animal Health Department, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", Espinardo, Murcia, Spain
| | - José Antonio Ortiz
- Medianilla S.L., Department of Veterinary and Research, Benalup-Casas Viejas, Spain
| | - Antonio José Carpio
- Institute for Research on Hunting Resources, IREC (UCLM-CSIC-JCCM), Ciudad Real, Spain; Department of Zoology, University of Cordoba, Campus de Rabanales, Cordoba, Spain
| | - Rafael Calero-Bernal
- SALUVET, Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid, Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain.
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Madrid, Spain; Center for Biomedical Research Network in Infectious Diseases (CIBERINFEC), Health Institute Carlos III, Madrid, Spain.
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da Moura AJF, Valadas V, Da Veiga Leal S, Montalvo Sabino E, Sousa CA, Pinto J. Screening of natural Wolbachia infection in mosquitoes (Diptera: Culicidae) from the Cape Verde islands. Parasit Vectors 2023; 16:142. [PMID: 37098535 PMCID: PMC10131387 DOI: 10.1186/s13071-023-05745-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/29/2022] [Accepted: 03/17/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Wolbachia pipientis is an endosymbiont bacterium that induces cytoplasmic incompatibility and inhibits arboviral replication in mosquitoes. This study aimed to assess Wolbachia prevalence and genetic diversity in different mosquito species from Cape Verde. METHODS Mosquitoes were collected on six islands of Cape Verde and identified to species using morphological keys and PCR-based assays. Wolbachia was detected by amplifying a fragment of the surface protein gene (wsp). Multilocus sequence typing (MLST) was performed with five housekeeping genes (coxA, gatB, ftsZ, hcpA, and fbpA) and the wsp hypervariable region (HVR) for strain identification. Identification of wPip groups (wPip-I to wPip-V) was performed using PCR-restriction fragment length polymorphism (RFLP) assay on the ankyrin domain gene pk1. RESULTS Nine mosquito species were collected, including the major vectors Aedes aegypti, Anopheles arabiensis, Culex pipiens sensu stricto, and Culex quinquefasciatus. Wolbachia was only detected in Cx. pipiens s.s. (100% prevalence), Cx. quinquefasciatus (98.3%), Cx. pipiens/quinquefasciatus hybrids (100%), and Culex tigripes (100%). Based on the results of MLST and wsp hypervariable region typing, Wolbachia from the Cx. pipiens complex was assigned to sequence type 9, wPip clade, and supergroup B. PCR/RFLP analysis revealed three wPip groups in Cape Verde, namely wPip-II, wPip-III, and wPip-IV. wPip-IV was the most prevalent, while wPip-II and wPip-III were found only on Maio and Fogo islands. Wolbachia detected in Cx. tigripes belongs to supergroup B, with no attributed MLST profile, indicating a new strain of Wolbachia in this mosquito species. CONCLUSIONS A high prevalence and diversity of Wolbachia was found in species from the Cx. pipiens complex. This diversity may be related to the mosquito's colonization history on the Cape Verde islands. To the best of our knowledge, this is the first study to detect Wolbachia in Cx. tigripes, which may provide an additional opportunity for biocontrol initiatives.
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Affiliation(s)
- Aires Januário Fernandes da Moura
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL., Rua da Junqueira 100, 1349-008, Lisboa, Portugal.
- Unidade de Ciências da Natureza, da Vida E Do Ambiente, Universidade Jean Piaget de Cabo Verde, Praia, Cape Verde.
| | - Vera Valadas
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL., Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - Silvania Da Veiga Leal
- Laboratório de Entomologia Médica, Instituto Nacional de Saúde Pública, Praia, Cape Verde
| | - Eddyson Montalvo Sabino
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL., Rua da Junqueira 100, 1349-008, Lisboa, Portugal
- Laboratório de Simulidos, Universidad Nacional Hermilio Valdizan, Huánuco, Peru
| | - Carla A Sousa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL., Rua da Junqueira 100, 1349-008, Lisboa, Portugal
| | - João Pinto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL., Rua da Junqueira 100, 1349-008, Lisboa, Portugal
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Joeres M, Cardron G, Passebosc-Faure K, Plault N, Fernández-Escobar M, Hamilton CM, O'Brien-Anderson L, Calero-Bernal R, Galal L, Luttermann C, Maksimov P, Conraths FJ, Dardé ML, Ortega-Mora LM, Jokelainen P, Mercier A, Schares G. A ring trial to harmonize Toxoplasma gondii microsatellite typing: comparative analysis of results and recommendations for optimization. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04597-7. [PMID: 37093325 DOI: 10.1007/s10096-023-04597-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 02/06/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023]
Abstract
A ring trial among five European laboratories was organized to reach consistency in microsatellite (MS) typing of the zoonotic parasite Toxoplasma gondii. Three sample sets were circulated and analyzed by each laboratory following a previously published method that is based on fragment length polymorphism of 15 MS markers. The first sample set compared typing results in general and focused on effects of DNA concentration; the second sample set focused on the polymorphic fingerprinting markers that can differentiate T. gondii strains within the same archetypal lineage; and the third set focused on non-archetypal genotypes. Methodological variations between laboratories, including the software programs used to determine MS fragment length, were collated using a questionnaire. Overall, lineage-level typing results reached a high level of agreement, especially in samples with the highest DNA concentrations. However, laboratory-specific differences were observed for particular markers. Major median differences in fragment length, of up to 6 base pairs, were related to the fluorophore used to label fragment-specific primers. In addition, primer pairs with identical sequences obtained from different suppliers resulted in fragments of differing length. Furthermore, differences in the way the sequencing profiles were assessed and interpreted may have led to deviating results in fragment length determination. Harmonization of MS typing, for example, by using the same fluorophores or by numerical adjustments applied to the fragment-lengths determined, could improve the uniformity of the results across laboratories. This is the first interlaboratory comparison, providing guidelines (added as a supplement) for the optimization of this technique.
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Affiliation(s)
- M Joeres
- Institute of Epidemiology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - G Cardron
- Institute of Epidemiology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - K Passebosc-Faure
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
| | - N Plault
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of Chronic Diseases in Tropical Zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
| | - M Fernández-Escobar
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - C M Hamilton
- The Moredun Research Institute, Penicuik, Midlothian, UK
| | - L O'Brien-Anderson
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - R Calero-Bernal
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - L Galal
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of Chronic Diseases in Tropical Zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
| | - C Luttermann
- Institute of Immunology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, -Insel Riems, Greifswald, Germany
| | - P Maksimov
- Institute of Epidemiology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - F J Conraths
- Institute of Epidemiology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - M L Dardé
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of Chronic Diseases in Tropical Zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
| | - L M Ortega-Mora
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - P Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - A Mercier
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of Chronic Diseases in Tropical Zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
| | - G Schares
- Institute of Epidemiology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
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Bedhiaf-Romdhani S, Baazaoui I, Arari E, Lahmar M, Letaief N, Hemdène M, Rekik M, Haile A. Marker-assisted introgression of fecundity mutation into Barbarine sheep breed under low input production system. Trop Anim Health Prod 2023; 55:170. [PMID: 37093295 DOI: 10.1007/s11250-023-03520-8] [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: 12/09/2022] [Accepted: 02/11/2023] [Indexed: 04/25/2023]
Abstract
Fecundity gene introgression has become an economical method to improve sheep prolificacy in developing countries. The FecXBar and FecGH mutations are variants of the BMP15 and GDF9 sheep genes, respectively, identified in Tunisian Barbarine sheep prolific line "W-INRAT," created through a prolificacy-based selection program. The first mutation caused increased prolificacy in heterozygous state and sterility in homozygous ewes. The aim of this work was to increase the number of effective carriers by the introgression of fecundity mutation into non-carrier conventional flocks based on a marker-assisted breeding program. The genotyping was carried out to follow up on the segregation of prolificacy mutation. The conventional ewes, raised in state farms of Tunisia and inseminated by "W-INRAT" rams, yielded 100% carriers females at heterozygous state. These females were selected to be inseminated with conventional rams and produced carriers' lambs with 66.7% males and 33.3% females. The prolific males will be kept in breeding centers to disseminate the fecundity mutation in commercial flocks. This approach facilitates the dissemination of fecundity genes and contributes to livelihood improvement in communities raising Barbarine sheep.
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Affiliation(s)
- Sonia Bedhiaf-Romdhani
- National Agricultural Research Institute of Tunisia, Laboratory of Animal and forage Production, University of Carthage, 1004, Ariana, Tunisia.
| | - Imen Baazaoui
- National Agricultural Research Institute of Tunisia, Laboratory of Animal and forage Production, University of Carthage, 1004, Ariana, Tunisia
| | - Emna Arari
- National Agricultural Research Institute of Tunisia, Laboratory of Animal and forage Production, University of Carthage, 1004, Ariana, Tunisia
- National Agronomic Institute of Tunisia, 43 Avenue Charles Nicolle, 1082, Tunis-Mahrajène, Tunisia
| | - Mustapha Lahmar
- Livestock and Pasture Agency-OEP, Ministry of Agriculture, Water Resources and Fisheries, Tunis, Tunisia
| | - Neyrouz Letaief
- National Agricultural Research Institute of Tunisia, Laboratory of Animal and forage Production, University of Carthage, 1004, Ariana, Tunisia
- National Agronomic Institute of Tunisia, 43 Avenue Charles Nicolle, 1082, Tunis-Mahrajène, Tunisia
| | - Mounir Hemdène
- Livestock and Pasture Agency-OEP, Ministry of Agriculture, Water Resources and Fisheries, Tunis, Tunisia
| | - Mourad Rekik
- International Center for Agricultural Research in the Dry Areas, Amman, Jordan
| | - Aynalem Haile
- International Center for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
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135
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Aljubouri TRS, Al-Shuhaib MBS. The identification of a novel SNP in the resistin (RETN) gene associated with growth traits in Karakul and Awassi sheep. Trop Anim Health Prod 2023; 55:165. [PMID: 37084102 DOI: 10.1007/s11250-023-03595-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023]
Abstract
Resistin is one of the most important adipocytokines in mammalian cells due to its involvement in insulin resistance, obesity, and autoimmune diseases. Resistin is encoded by RETN gene that is primarily expressed in adipose tissues. Mutations in this gene have been associated with several productive traits in animals. This study was conducted to assess the possible biomarker capacity of RETN by evaluating its association with growth traits in two economically important sheep in the Middle East. Genotyping was conducted using PCR-single strand conformation polymorphism (SSCP), and the polymorphism of RETN was associated with several growth traits for three months intervals starting from birth until one year of age. In a total of 190 Karakul sheep and 245 Awassi sheep, only one SNP (233A > C) was detected in the RETN gene. The identified novel SNP showed significant associations with all growth traits at the ages of six, nine, and twelve months. At the age of six months onward, lambs with AC and CC genotypes showed respectively lower body weight and length, chest and abdominal circumferences, and wither and rump heights than those with AA genotype. Due to the remarkable association between RETN;233A > C and lower growth traits, this genotype is suggested as a promising marker to assess growth traits in Karakul and Awassi sheep. This is the first study that demonstrated the importance of RETN as a possible tool for evaluating growth traits in two breeds of sheep with a possibility to be applied to other breeds via large-scale association analysis.
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Affiliation(s)
- Thamer R S Aljubouri
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
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136
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Chen SL, Kang YT, Liang YH, Qiu XT, Li ZJ. A Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis. Biomed Environ Sci 2023; 36:343-352. [PMID: 37105909 DOI: 10.3967/bes2023.040] [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] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/30/2022] [Indexed: 06/19/2023]
Abstract
OBJECTIVE A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis. METHODS In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation. RESULTS We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks. CONCLUSION This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis.
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Affiliation(s)
- Sheng Lin Chen
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China;State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yu Tong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yi He Liang
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Xiao Tong Qiu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zhen Jun Li
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China;State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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137
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Wu J, Chang R, Liu Y. Key Mutant Genes and Biological Pathways Involved in Aspirin Resistance in the Residents of the Chinese Plateau Area. Comb Chem High Throughput Screen 2023:CCHTS-EPUB-131084. [PMID: 37076463 DOI: 10.2174/1386207326666230418113637] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/30/2023] [Accepted: 02/08/2023] [Indexed: 04/21/2023]
Abstract
INTRODUCTION Aspirin is used to prevent and treat cardiovascular diseases; however, some patients develop aspirin resistance. AIM We aimed to explore the potential molecular mechanisms underlying aspirin resistance in people living in the Chinese plateau area. METHODS In total, 91 participants receiving aspirin treatment from the Qinghai plateau area were divided into the aspirin resistance and aspirin sensitivity groups. Genotyping was performed using the Sequence MASSarray. Differentially mutated genes between the two groups were analyzed using MAfTools. The annotation of differentially mutated genes was conducted based on the Metascape database. RESULTS AND DISCUSSION In total, 48 differential SNP and 22 differential InDel mutant genes between the aspirin resistance and aspirin sensitivity groups were screened using Fisher's exact test (P < 0.05). After the χ2 test, a total of SNP mutant genes, including ZFPL1 and TLR3, and 19 InDel mutant genes were found to be differentially expressed between the two groups (P < 0.05). Functional analysis revealed that these differential SNP mutations were mainly enriched in aspirin resistance pathways, such as the Wnt signaling pathway. Furthermore, these genes were related to many diseases, including various aspirin indications. CONCLUSION This study identified several genes and pathways that could be involved in arachidonic acid metabolic processes and aspirin resistance progression, which will provide a theoretical understanding of the molecular mechanism of aspirin resistance.
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Affiliation(s)
- Jinchun Wu
- Department of Cardiology, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, China
| | - Rong Chang
- Department of Cardiology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, Guangdong, 518109, China
| | - Yanmin Liu
- Department of Cardiology, Qinghai Provincial People's Hospital, Xining, Qinghai, 810007, China
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138
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Zarei A, Pourmand MR, Amin Harati F, Zolfaghari P, Dehghan A, Emamie A, Movahedi S. Multilocus VNTR analysis-ompA typing of Chlamydia trachomatis isolates in Tehran, Iran. J Infect Chemother 2023:S1341-321X(23)00098-3. [PMID: 37062413 DOI: 10.1016/j.jiac.2023.04.007] [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: 09/14/2022] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023]
Abstract
INTRODUCTION This study is the first to describe the genetic diversity of C. trachomatis strains derived from patients with signs and symptoms of genitourinary infections admitted to Tehran health centers and hospitals using the high-resolution genotyping method, multilocus variable-number tandem-repeat analysis with ompA sequencing (MLVA)-ompA. METHODS One hundred and sixty-seven urogenital specimens were collected from October 2019 to July 2020. Specimens were inoculated to cell culture and examined for the presence of C. trachomatis isolates by microscopic valuation. Out of 167 samples, 19 (11.3%) viable C. trachomatis organisms were isolated in cell culture. Eighteen isolates were successfully genotyped by MLVA-ompA analysis. RESULTS The most prevalent ompA genotypes were E, D, F and G, comprising 42%, 26.3% and 21% and 10.5% of isolates, respectively. Other genotypes were not detected from any of the samples. Out of the 18 fully genotyped isolates, 10 different MLVA-ompA genotypes were obtained. The most prevalent MLVA-ompA genotypes were 8.6.1-E (33.3%) and 8.5.2-D (16.6%). Genotype 8.6.1-E was common in both females and males. CONCLUSIONS Our results showed that MLVA-ompA analysis was more discriminatory than ompA typing alone and, therefore, a suitable complement to ompA. Using this method, dominant genotypes in the community and transmission patterns in sexual networks could be identified. The high diversity of C. trachomatis strains in Tehran may be due to the low level of public health and awareness, and future studies are needed.
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Affiliation(s)
- Atefe Zarei
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Farzaneh Amin Harati
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pouria Zolfaghari
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Dehghan
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Emamie
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shohreh Movahedi
- Department of Obstetrics and Gynecology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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139
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Blin M, Dametto S, Agniwo P, Webster BL, Angora E, Dabo A, Boissier J. A duplex tetra-primer ARMS-PCR assay to discriminate three species of the Schistosoma haematobium group: Schistosoma curassoni, S. bovis, S. haematobium and their hybrids. Parasit Vectors 2023; 16:121. [PMID: 37029440 PMCID: PMC10082484 DOI: 10.1186/s13071-023-05754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND The use of applications involving single nucleotide polymorphisms (SNPs) has greatly increased since the beginning of the 2000s, with the number of associated techniques expanding rapidly in the field of molecular research. Tetra-primer amplification refractory mutation system-PCR (T-ARMS-PCR) is one such technique involving SNP genotyping. It has the advantage of amplifying multiple alleles in a single reaction with the inclusion of an internal molecular control. We report here the development of a rapid, reliable and cost-effective duplex T-ARMS-PCR assay to distinguish between three Schistosoma species, namely Schistosoma haematobium (human parasite), Schistosoma bovis and Schistosoma curassoni (animal parasites), and their hybrids. This technique will facilitate studies of population genetics and the evolution of introgression events. METHODS During the development of the technique we focused on one of the five inter-species internal transcribed spacer (ITS) SNPs and one of the inter-species 18S SNPs which, when combined, discriminate between all three Schistosoma species and their hybrid forms. We designed T-ARMS-PCR primers to amplify amplicons of specific lengths for each species, which in turn can then be visualized on an electrophoresis gel. This was further tested using laboratory and field-collected adult worms and field-collected larval stages (miracidia) from Spain, Egypt, Mali, Senegal and Ivory Coast. The combined duplex T-ARMS-PCR and ITS + 18S primer set was then used to differentiate the three species in a single reaction. RESULTS The T-ARMS-PCR assay was able to detect DNA from both species being analysed at the maximum and minimum levels in the DNA ratios (95/5) tested. The duplex T-ARMS-PCR assay was also able to detect all hybrids tested and was validated by sequencing the ITS and the 18S amplicons of 148 of the field samples included in the study. CONCLUSIONS The duplex tetra-primer ARMS-PCR assay described here can be applied to differentiate between Schistosoma species and their hybrid forms that infect humans and animals, thereby providing a method to investigate the epidemiology of these species in endemic areas. The addition of several markers in a single reaction saves considerable time and is of long-standing interest for investigating genetic populations.
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Affiliation(s)
- Manon Blin
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
- SAS ParaDev®, 66860, Perpignan, France
| | - Sarah Dametto
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
| | - Privat Agniwo
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France
- Department of Epidemiology of Infectious Diseases, Faculty of Pharmacy, IRL 3189, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Bonnie L Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Science, Natural History Museum, London, SW7 5BD, UK
- London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London, W2 1PG, UK
| | - Etienne Angora
- Swiss Tropical and Public Health Institute, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- Unité de Formation et de Recherche Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, BPV 34, Abidjan, Côte d'Ivoire
| | - Abdoulaye Dabo
- Department of Epidemiology of Infectious Diseases, Faculty of Pharmacy, IRL 3189, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jérôme Boissier
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan Via Domitia, Perpignan, 66860, France.
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140
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Erndwein L, Kawash J, Knowles S, Vorsa N, Polashock J. Cranberry fruit epicuticular wax benefits and identification of a wax-associated molecular marker. BMC Plant Biol 2023; 23:181. [PMID: 37020185 PMCID: PMC10074888 DOI: 10.1186/s12870-023-04207-w] [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] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND As the global climate changes, periods of abiotic stress throughout the North American cranberry growing regions will become more common. One consequence of high temperature extremes and drought conditions is sunscald. Scalding damages the developing berry and reduces yields through fruit tissue damage and/or secondary pathogen infection. Irrigation runs to cool the fruit is the primary approach to controlling sunscald. However, it is water intensive and can increase fungal-incited fruit rot. Epicuticular wax functions as a barrier to various environmental stresses in other fruit crops and may be a promising feature to mitigate sunscald in cranberry. In this study we assessed the function of epicuticular wax in cranberries to attenuate stresses associated with sunscald by subjecting high and low epicuticular wax cranberries to controlled desiccation and light/heat exposure. A cranberry population that segregates for epicuticular wax was phenotyped for epicuticular fruit wax levels and genotyped using GBS. Quantitative trait loci (QTL) analyses of these data identified a locus associated with epicuticular wax phenotype. A SNP marker was developed in the QTL region to be used for marker assisted selection. RESULTS Cranberries with high epicuticular wax lost less mass percent and maintained a lower surface temperature following heat/light and desiccation experiments as compared to fruit with low wax. QTL analysis identified a marker on chromosome 1 at position 38,782,094 bp associated with the epicuticular wax phenotype. Genotyping assays revealed that cranberry selections homozygous for a selected SNP have consistently high epicuticular wax scores. A candidate gene (GL1-9), associated with epicuticular wax synthesis, was also identified near this QTL region. CONCLUSIONS Our results suggest that high cranberry epicuticular wax load may help reduce the effects of heat/light and water stress: two primary contributors to sunscald. Further, the molecular marker identified in this study can be used in marker assisted selection to screen cranberry seedlings for the potential to have high fruit epicuticular wax. This work serves to advance the genetic improvement of cranberry crops in the face of global climate change.
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Affiliation(s)
- Lindsay Erndwein
- ORISE Postdoctoral Research Associate, Chatsworth, NJ, 08019, USA
| | - Joseph Kawash
- Genetic Improvement of Fruit and Vegetables Laboratory, Agricultural Research Service, USDA-ARS, Chatsworth, NJ, 08019, USA
| | - Sara Knowles
- P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ, 08019, USA
| | - Nicholi Vorsa
- P.E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ, 08019, USA
| | - James Polashock
- Genetic Improvement of Fruit and Vegetables Laboratory, Agricultural Research Service, USDA-ARS, Chatsworth, NJ, 08019, USA.
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141
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Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 2023; 25:100006. [PMID: 36621880 PMCID: PMC10085845 DOI: 10.1016/j.gim.2023.100006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [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: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk. METHODS To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results. RESULTS GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022. CONCLUSION Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Harris T Bland
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pedro J Caraballo
- Department of Internal Medicine and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ozan Dikilitas
- Mayo Clinician Investigator Training Program, Department of Internal Medicine and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alanna DiVietro
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Sophie Forman
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Adam S Gordon
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Richard Green
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | | | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sofia Labrecque
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Lori Orlando
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL
| | | | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Konrad Teodor Sawicki
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David Veenstra
- School of Pharmacy, University of Washington, Seattle, WA
| | - Digna R Velez Edwards
- Division of Quantitative Science, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - James Booth
- Department of Emergency Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - James J Cimino
- Division of General Internal Medicine and the Informatics Institute, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Patrick Davis
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Beth Devine
- School of Pharmacy, University of Washington, Seattle, WA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | | | - Melissa L Habrat
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Christin Hoell
- Department of Obstetrics & Gynecology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Martha Horike-Pyne
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eimear E Kenny
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Bruce Korf
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | | | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Thomas May
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA
| | | | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Brenda Mutai
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bahram Namjou
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Mass General Brigham Personalized Medicine, Boston, MA
| | - Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | | | - Maya Sabatello
- Division of Nephrology, Department of Medicine & Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York, NY
| | - Dan J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Baergen Schultz
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Lynn Seabolt
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Gabriel Q Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, AZ
| | - Richard R Sharp
- Biomedical Ethics Program, Department of Quantitative Health Science, Mayo Clinic, Rochester, MN
| | - Brian Shirts
- Department of Laboratory Medicine & Pathology, University of Washington Medical Center, Seattle, WA
| | - Maureen E Smith
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Jordan W Smoller
- Department of Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeritt Thayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Theresa Walunas
- Department of Medicine and Center for Health Information Partnerships, Northwestern University, Chicago, IL
| | - Wei-Qi Wei
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN.
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Georgiou M, Robson AG, Jovanovic K, Guimarães TACD, Ali N, Pontikos N, Uwaydat SH, Mahroo OA, Cheetham ME, Webster AR, Hardcastle AJ, Michaelides M. RP2-Associated X-linked Retinopathy: Clinical Findings, Molecular Genetics, and Natural History. Ophthalmology 2023; 130:413-422. [PMID: 36423731 PMCID: PMC10567581 DOI: 10.1016/j.ophtha.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/23/2022] Open
Abstract
PURPOSE To review and describe in detail the clinical course, functional and anatomic characteristics of RP2-associated retinal degeneration. DESIGN Retrospective case series. PARTICIPANTS Male participants with disease-causing variants in the RP2 gene. METHODS Review of all case notes and results of molecular genetic testing, retinal imaging (fundus autofluorescence [FAF] imaging, OCT), and electrophysiology assessment. MAIN OUTCOME MEASURES Molecular genetic testing, clinical findings including best-corrected visual acuity (BCVA), qualitative and quantitative retinal imaging analysis, and electrophysiology parameters. RESULTS Fifty-four molecularly confirmed patients were identified from 38 pedigrees. Twenty-eight disease-causing variants were identified, with 20 not previously clinically characterized. Fifty-three patients (98.1%) presented with retinitis pigmentosa. The mean age of onset (range ± standard deviation [SD]) was 9.6 years (1-57 ± 9.2 years). Forty-four patients (91.7%) had childhood-onset disease, with mean age of onset of 7.6 years. The most common first symptom was night blindness (68.8%). Mean BCVA (range ± SD) was 0.91 logarithm of the minimum angle of resolution (logMAR) (0-2.7 ± 0.80) and 0.94 logMAR (0-2.7 ± 0.78) for right and left eyes, respectively. On the basis of the World Health Organization visual impairment criteria, 18 patients (34%) had low vision. The majority (17/22) showed electroretinogram (ERG) evidence of a rod-cone dystrophy. Pattern ERG P50 was undetectable in all but 2 patients. A range of FAF findings was observed, from normal to advanced atrophy. There were no statistically significant differences between right and left eyes for ellipsoid zone width (EZW) and outer nuclear layer (ONL) thickness. The mean annual rate of EZW loss was 219 μm/year, and the mean annual decrease in ONL thickness was 4.93 μm/year. No patient with childhood-onset disease had an identifiable ellipsoid zone (EZ) after the age of 26 years at baseline or follow-up. Four patients had adulthood-onset disease and a less severe phenotype. CONCLUSIONS This study details the clinical phenotype of RP2 retinopathy in a large cohort. The majority presented with early-onset severe retinal degeneration, with early macular involvement and complete loss of the foveal photoreceptor layer by the third decade of life. Full-field ERGs revealed rod-cone dystrophy in the vast majority, but with generalized (peripheral) cone system involvement of widely varying severity in the first 2 decades of life. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Michalis Georgiou
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom; Jones Eye Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Anthony G Robson
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Katarina Jovanovic
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Thales A C de Guimarães
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Naser Ali
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Nikolas Pontikos
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Sami H Uwaydat
- Jones Eye Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Omar A Mahroo
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom.
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143
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Diel R, Meywald-Walter K, Schwarzbach C, Voss K, Dreyer V, Niemann S. Risk of tuberculosis transmission by children in Hamburg, Germany. Respir Med 2023; 209:107152. [PMID: 36781053 DOI: 10.1016/j.rmed.2023.107152] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
BACKGROUND Data from a prospective molecular-epidemiologic study (1997-2021) in Hamburg, Germany, were evaluated to assess the transmission risk of Mycobacterium tuberculosis complex (Mtbc) by children <15 years in a low-incidence setting. METHODS Isolates of Mtbc were genotyped whole genome sequencing, applying a core genome multilocus sequence typing scheme. Close contacts of culture-confirmed children were examined for latent Mtbc infections (LTBI) with particular focus on IGRA testing. RESULTS Out of 3154 culture-confirmed tuberculosis (TB) cases, 79 (2.5%) were children <15 years. Of those, 52 (58%) had pulmonary TB. Genotyping revealed that 35 of the 52 children (67%) were epidemiologically confirmed secondary cluster members; all of their source cases were adults. Six immigrant children presented without a presumed source case; their TB diagnoses came on average 48 weeks (interquartile range [IQR] 71) after their arrival in Germany. Three German-born children were determined to have been infected by adult relatives while visiting their parents' home country. Of the 317 children's close contacts tested with QuantiFERON-TB Gold-In Tube for LTBI, only 21 (6.6%) were positive. Absent a history of prior exposure or immigration from a high-incidence country, none of the contacts of younger (<10 years) TB-afflicted children was latently infected, whereas 2 older children infected 12 of their contacts, children and adults. During a mean observational period of 551 weeks (IQR 735) on average, no secondary TB cases appeared. CONCLUSIONS Children with pulmonary TB disease, especially those aged below 10 years, rarely transmit Mtbc to their close contacts in a low-incidence setting.
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Affiliation(s)
- Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany; LungClinic Grosshansdorf, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Germany.
| | | | | | - Klaas Voss
- Public Health Department Hamburg-Central, Hamburg, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology Group, National Reference Laboratory for Mycobacteria, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology Group, National Reference Laboratory for Mycobacteria, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Borstel, Germany
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Firouzeh N, Borj HF, Ziaali N, Kareshk AT, Ahmadinejad M, Shafiei R. Genetic Diversity of Toxoplasma gondii by Serological and Molecular Analyzes in Different Sheep and Goat Tissues in Northeastern Iran. Iran J Parasitol 2023; 18:217-228. [PMID: 37583631 PMCID: PMC10423913 DOI: 10.18502/ijpa.v18i2.13188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/25/2023] [Indexed: 08/17/2023]
Abstract
Background Toxoplasmosis is a parasitic disease caused by compilation protozoan agent Toxoplasma gondii, leading to significant financial and quality-adjusted life-year losses. Overcooked or raw meat consumption has been a considerable transmission route. The present study was conducted to determine the seropositivity rate of T. gondii in sheep and goats by serological and molecular tests and genotyping of obtained isolates in northeast Iran. Methods Blood and tissue samples (diaphragm, heart) of 296 animals (including 168 sheep and 128 goats) were collected from the slaughterhouse in Quchan Country from august 2016 to April 2017. Modified agglutination test (MAT) and the PCR method performed to detect parasite DNA on tissues.PCR-RFLP method of GRA6 gene was used to determine the genotype of T. gondii. In addition, sequencing analysis was performed to evaluate the Toxoplasma type strains. Results Serum positive for MAT results were found in 27.4% of sheep and 23.4% of goats. Positive PCR of B1 gene results in diaphragm and heart tissues of sheep and goats was 47.8% and 26.1%, 40% and 23.3%, respectively. PCR of GRA6 gene results were positive in 10 samples that RFLP technique results using MseI enzyme revealed genotype I. Sequencing and phylogenetic analysis revealed DNA of all samples was closely related to Toxoplasma type I. Conclusion Concerning the high seropositivity rate of toxoplasmosis, undertaking an appropriate preventive program for reducing the prevalence of T. gondii infection by raw or undercooked meat consumption of livestock is recommended. Our study supports the notion that these animals' consumption of raw and undercooked meat can be a probable source of human toxoplasmosis.
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Affiliation(s)
- Nima Firouzeh
- Vector-Borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnourd, Iran
| | - Hamid Foroughi Borj
- Department of Medical Parasitology and Mycology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Naser Ziaali
- Department of Medical Parasitology and Mycology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Amir Tavakoli Kareshk
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohammad Ahmadinejad
- Department of Medical Parasitology and Mycology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Shafiei
- Vector-Borne Diseases Research Center, North Khorasan University of Medical Sciences, Bojnourd, Iran
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Fulvio F, Righetti L, Minervini M, Moschella A, Paris R. The B1080/B1192 molecular marker identifies hemp plants with functional THCA synthase and total THC content above legal limit. Gene 2023; 858:147198. [PMID: 36641078 DOI: 10.1016/j.gene.2023.147198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
In Cannabis sativa L. the presence of delta 9-tetrahydrocannabinolic acid (THCA) above legal limit is a challenging issue that still restricts the industrial exploitation of this promising crop. In recent years, the interest of entrepreneurs and growers who see hemp as a dynamic and profitable crop was joined by the growing knowledge on C. sativa genetics and genomics, accelerated by the application of high throughput tools. Despite the renewed interest in the species, much remains to be clarified, especially about the long-standing problem of THCA in hemp inflorescences, which could even result in the seizure of the whole harvest. Although several hypotheses have been formulated on the accumulation of this metabolite in industrial varieties, none is conclusive yet. In this work, individuals of a population of the hemp cultivar 'FINOLA' obtained from commercial seeds were investigated for total THC level and examined at molecular level. A marker linked to THCA synthase was found at a high incidence in both male and female plants, suggesting a considerable genetic variability within the seed batch. Full-length sequences encoding for putatively functional THCA synthases were isolated for the first time from the genome of both female and male plants of an industrial hemp variety and, using transcriptional analysis, the THCA synthase expression was quantified in mature inflorescences of individuals identified by the marker. Biochemical analyses finally demonstrated for these plants a 100% association between the predicted and actual chemotype.
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Zabihi Rizi F, Ghorbani A, Zahtab P, Darbaghshahi NN, Ataee N, Pourhamzeh P, Hamzei B, Dolatabadi NF, Zamani A, Hooshmand M. TYK2 single-nucleotide variants associated with the severity of COVID-19 disease. Arch Virol 2023; 168:119. [PMID: 36959416 PMCID: PMC10035968 DOI: 10.1007/s00705-023-05729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/31/2023] [Indexed: 03/25/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a lethal disease caused by the coronavirus SARS-CoV-2, which can result in a broad clinical spectrum of respiratory symptoms. While many clinical risk factors such as concomitant chronic diseases play roles in the pathophysiology of COVID-19, genetic predisposition factors have not been widely studied. The aim of this study was, therefore, to evaluate the relationship between some singlenucleotide polymorphisms (SNPs) of the human genes TYK2 and ACE2 and the severity of SARS-CoV-2 infection. Genomic DNA was isolated from 200 SARS-CoV-2-infected individuals with severe (n = 100) or mild (n = 100) disease. Owing to the importance of ACE2 and TYK2 genes in regulating the immune response to SARS-CoV-2 infection, TYK2 gene SNPs, i.e. rs2304255, rs2304256, rs12720270, and rs12720354 and ACE2 rs382746 variants, were genotyped in the samples. To confirm the results, the expression of different TYK2 genotypes was investigated using real-time PCR. The presence of the nucleotide T at the locus rs2304255 was shown to be a risk factor linked to disease severity (OR [95% CI] = 3.2485 [2.1554-4.8961]). Similarly, the presence of A at the locus rs12720354 increased the risk of severity (OR [95% CI]) = 3.9721 [2.6075-6.0509]). In contrast, the presence of A at the loci rs2304256 and rs12720270 was observed to reduce the severity risk (OR [95% CI] = 0.2495 [0.1642-0.3793] and 0.1668 [0.1083-0.2569], respectively). Real-time PCR results also demonstrated that the expression level of TYK2 in samples with the TT genotype of rs2304255 and the AA genotype of rs12720354 and in samples with the GG genotype of rs12720207 was significantly lower than in those with other genotypes. The results of this study suggest that TYK2 SNPs might be utilized to identify individuals who are at risk for severe COVID-19, in order to better manage their health care. It is predicted that the presence of some alleles (T in rs2304255, A in rs12720354, and G in rs12720207) of TYK2 can affect COVID-19 severity by reducing TYK2 expression and thereby affecting the regulatory role of TYK2 in the immune response.
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Affiliation(s)
- Fateme Zabihi Rizi
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Atousa Ghorbani
- Department of Biology, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Parnia Zahtab
- Department of Biological Sciences and Technology, Faculty of Materials Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Niloufar Naderi Darbaghshahi
- Department of Genetics, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Esfahan, Iran
| | - Nioosha Ataee
- Department of Genetics, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Esfahan, Iran
| | | | - Behnaz Hamzei
- Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | - Nasrin Fatahi Dolatabadi
- Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran.
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran.
| | - Atefeh Zamani
- Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | - Masoud Hooshmand
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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Vicente J, Navascués E, Benito S, Marquina D, Santos A. Microsatellite typing of Lachancea thermotolerans for wine fermentation monitoring. Int J Food Microbiol 2023; 394:110186. [PMID: 36963240 DOI: 10.1016/j.ijfoodmicro.2023.110186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023]
Abstract
Climate change is causing a lack of acidity during winemaking and oenologists use several solutions to cope with such a problem. Lachancea thermotolerans, which has the potential to tolerate the harsh physicochemical conditions of wine, has emerged as a promising alternative for pH management during winemaking and, currently, it is the most valuable yeast used for acidity control in wine. In this work a manageable method for L. thermotolerans genotyping based on a multiplexed microsatellite amplification in 6 different loci was developed. The proposed method was used to distinguish between 103 collection strains obtained from different geographical and isolation sources, and then challenged against a 429 L. thermotolerans isolates from several wineries and harvests. The procedure was also tested for fermentation monitoring and strain implantation. This approach was conceived to simplify the methodology available for L. thermotolerans genotyping, making it easy for applying in wine-related laboratories. This method can be applied to distinguish between L. thermotolerans strains in selection programs and to follow implantation of inoculated strains during winemaking with optimal results.
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Affiliation(s)
- Javier Vicente
- Department of Genetics, Physiology and Microbiology, Unit of Microbiology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Eva Navascués
- Pago de Carraovejas, S.L.U., 47300 Peñafiel, Valladolid, Spain; Department of Chemistry and Food Technology, Polytechnic University of Madrid, 28040 Madrid, Spain
| | - Santiago Benito
- Department of Chemistry and Food Technology, Polytechnic University of Madrid, 28040 Madrid, Spain
| | - Domingo Marquina
- Department of Genetics, Physiology and Microbiology, Unit of Microbiology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Antonio Santos
- Department of Genetics, Physiology and Microbiology, Unit of Microbiology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain.
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148
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Wang Y, Chen H, Gao H, Wei H, Wang Y, Mu K, Liu L, Dai E, Rong Z, Wang S. CESSAT: A chemical additive-enhanced single-step accurate CRISPR/Cas13 testing system for field-deployable ultrasensitive detection and genotyping of SARS-CoV-2 variants of concern. Biosens Bioelectron 2023; 229:115238. [PMID: 36958206 PMCID: PMC10027308 DOI: 10.1016/j.bios.2023.115238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/22/2023]
Abstract
The continued emergence of SARS-CoV-2 variants of concern (VOCs) has raised great challenges for epidemic prevention and control. A rapid, sensitive, and on-site SARS-CoV-2 genotyping technique is urgently needed for individual diagnosis and routine surveillance. Here, a field-deployable ultrasensitive CRISPR-based diagnostics system, called Chemical additive-Enhanced Single-Step Accurate CRISPR/Cas13 Testing system (CESSAT), for simultaneous screening of SARS-CoV-2 and its five VOCs (Alpha, Beta, Gamma, Delta, and Omicron) within 40 min was reported. In this system, a single-step reverse transcription recombinase polymerase amplification-CRISPR/Cas13a assay was incorporated with optimized extraction-free viral lysis and reagent lyophilization, which could eliminate complicated sample processing steps and rigorous reagent storage conditions. Remarkably, 10% glycine as a chemical additive could improve the assay sensitivity by 10 times, making the limit of detection as low as 1 copy/μL (5 copies/reaction). A compact optic fiber-integrated smartphone-based device was developed for sample lysis, assay incubation, fluorescence imaging, and result interpretation. CESSAT could specifically differentiate the synthetic pseudovirus of SARS-CoV-2 and its five VOCs. The genotyping results for 40 clinical samples were in 100% concordance with standard method. We believe this simple but efficient enhancement strategy can be widely incorporated with existing Cas13a-based assays, thus leading a substantial progress in the development and application of rapid, ultrasensitive, and accurate nucleic acid analysis technology.
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Affiliation(s)
- Yunxiang Wang
- Bioinformatics Center of AMMS, Beijing, 100850, PR China
| | - Hong Chen
- Bioinformatics Center of AMMS, Beijing, 100850, PR China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, PR China
| | - Hongjuan Wei
- Bioinformatics Center of AMMS, Beijing, 100850, PR China
| | - Yuling Wang
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, PR China
| | - Kai Mu
- Bioinformatics Center of AMMS, Beijing, 100850, PR China
| | - Liyan Liu
- Bioinformatics Center of AMMS, Beijing, 100850, PR China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, 050021, PR China.
| | - Zhen Rong
- Bioinformatics Center of AMMS, Beijing, 100850, PR China.
| | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing, 100850, PR China.
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149
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Grillova L, Cokelaer T, Mariet JF, da Fonseca JP, Picardeau M. Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing. BMC Infect Dis 2023; 23:157. [PMID: 36918832 PMCID: PMC10012794 DOI: 10.1186/s12879-023-08126-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited. METHODS Here, we carried out hybridization capture followed by Illumina sequencing of the core genome directly from 20 clinical samples that were PCR positive for pathogenic Leptospira to elucidate the genetic diversity of currently circulating Leptospira strains in mainland France. RESULTS Capture with RNA probes covering the L. interrogans core genome resulted in a 72 to 13,000-fold increase in pathogen reads relative to standard sequencing without capture. Variant analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genomes was then carried out to determine the genotype of the infecting strain. For samples with sufficient coverage (19/20 samples with coverage > 8×), we could unambiguously identify L. interrogans serovars Icterohaemorrhagiae and Copenhageni (14 samples), L. kirschneri serovar Grippotyphosa (4 samples), and L. interrogans serovar Pyrogenes (1 sample) as the infecting strains. CONCLUSIONS We obtained high-quality genomic data with suitable coverage for confident core genome genotyping of the agent of leptospirosis for most of our clinical samples. The recovery of the genome of the serovars Icterohaemorrhagiae and Copenhageni directly from multiple clinical samples revealed low adaptive diversification of the core genes during human infection. The ability to generate culture-free genomic data opens new opportunities for better understanding of the epidemiology of this fastidious pathogen and pathogenesis of this neglected disease.
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Affiliation(s)
- Linda Grillova
- Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, 75015, Paris, France.,Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France.,Département Biologie Computationnelle, Institut Pasteur, Université Paris Cité, Hub de Bioinformatique et Biostatistique, 75015, Paris, France
| | - Jean-François Mariet
- Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | | | - Mathieu Picardeau
- Biology of Spirochetes Unit, French National Reference Centre for Leptospirosis, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, 75015, Paris, France.
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Rosić I, Nikolić I, Ranković T, Anteljević M, Medić O, Berić T, Stanković S. Genotyping-driven diversity assessment of biocontrol potent Bacillus spp. strain collection as a potential method for the development of strain-specific biomarkers. Arch Microbiol 2023; 205:114. [PMID: 36907935 DOI: 10.1007/s00203-023-03460-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/01/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023]
Abstract
Bacillus species are among the most researched and frequently applied biocontrol agents. To estimate their potential as environmentally friendly microbial-based products, reliable and rapid plant colonization monitoring methods are essential. We evaluated repetitive element-based (rep) and Random Amplified Polymorphic DNA (RAPD) PCR (Polymerase Chain Reaction) genotyping in a diversity assessment of 251 strains from bulk soil, straw, and manure samples across Serbia, highlighting their discriminative force and the presence of unique bands. RAPD 272, OPG 5, and (GTG)5 primers were most potent in revealing the high diversity of a sizable environmental Bacillus spp. collection. RAPD 272 also amplified a unique band for a proven biocontrol strain, opening the possibility of Sequence Characterized Amplified Region (SCAR) marker design. That will enable colonization studies using the SCAR marker for its specific detection. This study provides a guide for primer selection for diversity and monitoring studies of environmental Bacillus spp. isolates.
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Affiliation(s)
- Iva Rosić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia.
| | - Ivan Nikolić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Tamara Ranković
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Marina Anteljević
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Olja Medić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Tanja Berić
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
| | - Slaviša Stanković
- University of Belgrade - Faculty of Biology, Center for Biological Control and Plant Growth Promotion, University of Belgrade, Studentski Trg 16, 11000, Belgrade, Serbia
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