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Li H, Wang Y, Wan Y, Li M, Xu J, Wang Q, Wu D. Stimuli-responsive incremental DNA machine auto-catalyzed CRISPR-Cas12a feedback amplification permits ultrasensitive molecular diagnosis of esophageal cancer-related microRNA. Talanta 2024; 271:125675. [PMID: 38245957 DOI: 10.1016/j.talanta.2024.125675] [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: 11/28/2023] [Revised: 01/07/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Development of new diagnostic methods is essential for disease diagnosis and treatment. In this work, we present a stimuli-responsive incremental DNA machine auto-catalyzed CRISPR-Cas12a (SRI-DNA machine/CRISPR-Cas12a) feedback amplification for ultrasensitive molecular detection of miRNA-21, which is an important biomarker related closely to the initiation and development of cancers, such as esophageal cancer. Strategically, the powerful SRI-DNA machine and efficient trans-cleavage activity of the CRISPR-Cas12a system are ingeniously integrated via a rationally designed probe termed as stem-elongated functional hairpin probe (SEF-HP). The SRI-DNA machine begins with the target miRNA, the trigger of the reaction, binding complementarily to the SEF-HP, followed by autonomously performed mechanical strand replication, cleavage, and displacement circuit at multiple sites. This conversion process led to the amplified generation of numerous DNA activators that are complementary with CRISPR RNA (CrRNA). Once formed the DNA activator/CrRNA heteroduplex, the trans-cleavage activity of the CRISPR-Cas12a was activated to nonspecific cleavage of single-stranded areas of a reporter probe for fluorescence emission. Under optimal conditions, the target miRNA can be detected with a wide linear range and an excellent specificity. As a proof-of-concept, this SRI-DNA machine/CRISPR-Cas12a feedback amplification system is adaptable and scalable to higher-order artificial amplification circuits for biomarkers detection, highlighting its promising potential in early diagnosis and disease treatment.
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Affiliation(s)
- Hongxia Li
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Yi Wang
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Yu Wan
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Meimei Li
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China
| | - Jianguo Xu
- Jiaxing Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Zhejiang, Jiaxing, 314001, PR China; Engineering Research Center of Bio-Process, Ministry of Education, School of Food and Biological, Hefei University of Technology, Hefei, 230009, PR China.
| | - Qi Wang
- Key Laboratory of Embryo Development and Reproductive Regulation, Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, 236037, PR China.
| | - Donglei Wu
- Department of Oncology, Hefei First People's Hospital, Third Affiliated Hospital of Anhui Medical University, Hefei, 230032, PR China.
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Martins AV, Corrêa LL, Ribeiro MS, de Lima Coelho A, Lobão LF, Palmer JPS, Knackfuss FB, Molento MB, da Silva Barbosa A. Identification of third stage larvae of strongyles and molecular diagnosis of Strongylus vulgaris in the feces of Thoroughbred horses kept in training centers in Rio de Janeiro, Brazil. Vet Parasitol Reg Stud Reports 2024; 50:101019. [PMID: 38644042 DOI: 10.1016/j.vprsr.2024.101019] [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: 11/14/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
The aims of the present study were to identify strongyles in the feces of Thoroughbred horses based on larval morphology; to detect Strongylus vulgaris using molecular diagnosis and compare results to those of feces culture; and to determine the association between the presence of S. vulgaris with corresponding animal information (age range, gender, and anthelmintic use). Feces of horses kept in six Training Centers in Rio de Janeiro State, that showed the presence of ≥500 eggs per gram of feces (EPG) were subjected to strongyle identification. Of the 520 fecal samples collected, 35 had an EPG ≥ 500. After fecal culture for L3 larvae identification, DNA was extracted, subjected to PCR to amplify the ITS2 region DNA fragment of S. vulgaris, and sequenced. A total of 3500 larvae were analyzed. Most were classified as small strong (99.7%), with an emphasis on the type A subfamily of Cyathostominae. Forms of S. vulgaris only corresponded to 0.2%. In all, 25 samples showed amplified S. vulgaris DNA products and 11 showed nucleotide sequences with high sequence identity. Fecal culture and PCR results showed poor agreement (kappa = 0.105) for S. vulgaris diagnosis. Age, gender, anthelmintic use, and anthelmintic administration interval were not statistically significant. The present study showed the presence of S. vulgaris in the feces of horses kept in Rio de Janeiro Training Centers, mainly seen via PCR, which has emerged as the most effective tool for diagnosis. This study made it possible to identify strongyles that infect horses in the region, emphasizing upon the necessity for constant monitoring of the animals.
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Affiliation(s)
- André Vianna Martins
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil; Laboratório de Parasitologia e Doenças Parasitárias, Faculdade de Medicina Veterinária, Centro Universitário Serra dos Órgãos, Teresópolis, Rio de Janeiro, Brazil
| | - Laís Lisboa Corrêa
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Mariana Santos Ribeiro
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Aline de Lima Coelho
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Lucas Fernandes Lobão
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - João Pedro Siqueira Palmer
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | | | - Marcelo Beltrão Molento
- Laboratório de Parasitologia Clínica Veterinária, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Alynne da Silva Barbosa
- Laboratório de Bioagentes Ambientais, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil; Laboratório de Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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Tonen-Wolyec S, Otuli NL, Otsatre-Okuti M, Atenyi-Kasemire R, Dupont R, Bélec L. Analytical performances of a point-of-care loop-mediated isothermal amplification assay to detect Group B Streptococcus in intrapartum pregnant women living in the Democratic Republic of the Congo. Int J Infect Dis 2024; 142:106972. [PMID: 38387704 DOI: 10.1016/j.ijid.2024.02.015] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVES Group B Streptococcus (GBS) is the leading infectious cause of stillbirth and neonatal morbidity and mortality in sub-Saharan Africa. METHODS Vaginal and rectovaginal swab samples were obtained from 274 intrapartum pregnant women in the Democratic Republic of the Congo to be analyzed for GBS DNA detection in parallel by the point-of-care BIOSYNEX AMPLIFLASH® GBS assay (Biosynex SA, Illkirch-Graffenstaden, France) and by reference quantitative polymerase chain reaction (qPCR). RESULTS Rectovaginal swabbing, nearly two-fold more positive for GBS than vaginal swabbing alone, showed a high prevalence of GBS DNA positivity in 20.1% of eligible intrapartum pregnant women. In the event of significant bacterial carriage (i.e., cycle threshold ≤33 by reference qPCR), the AMPLIFLASH® GBS assay with rectovaginal swabbing showed high sensitivity (98.1%) and specificity (100.0%) for GBS DNA detection, with excellent concordance, reliability, and accuracy with the reference qPCR, and positive predictive values and negative predictive values above 99.0%. CONCLUSIONS The study demonstrates a high rate of female rectogenital GBS colonization in pregnant Congolese women. The AMPLIFLASH® GBS assay harbored excellent analytical performances in the field, which makes it suitable to be used as point-of-care molecular assay in various hospital and non-hospital settings where rapid diagnosis of GBS is necessary.
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Affiliation(s)
- Serge Tonen-Wolyec
- Faculté de Médecine et de Pharmacie, Université de Kisangani, Kisangani, Democratic Republic of the Congo; Faculté de Médecine, Université de Bunia, Bunia, Democratic Republic of the Congo.
| | - Noel Labana Otuli
- Faculté de Médecine et de Pharmacie, Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Monde Otsatre-Okuti
- Faculté de Médecine, Université de Bunia, Bunia, Democratic Republic of the Congo
| | | | - Raphael Dupont
- Laboratoire d'analyses médicales, Centre Cardiologique du Nord (CCN), Saint-Denis, France
| | - Laurent Bélec
- Laboratoire de virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, and Université Paris Cité, Paris, France
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Palmer JPS, Gazêta GS, André MR, Fialho PA, Corrêa LL, Damasceno JAL, Israel CB, Pereira RR, da Silva Barbosa A. Piroplasmid Infections Among Domestic Dogs in the Mountain City of Rio de Janeiro, Brazil. Acta Parasitol 2024:10.1007/s11686-024-00843-w. [PMID: 38602588 DOI: 10.1007/s11686-024-00843-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE The aim of the present study was to analyze the frequency of the piroplasmids in blood from dogs and ticks recovered from these animals in Teresópolis city, located in the mountain region of Rio de Janeiro state, Brazil. In addition to the clinical and hematological profile. METHODS A total of 400 dogs attended in a veterinary clinic in this city between 2020 and 2021 were included. The blood was collected from the dogs, along with ticks and information on these dogs was obtained through a questionnaire applied to the owners. Thin-smear analyses and complete blood counts were performed. All forms characteristic of piroplasmids were measured and classified morphologically. The blood was also subjected to PCR assays based on the genes 18S rRNA and hsp70. In addition, the ixodid ticks were classified morphologically and subjected to PCR for piroplasmids research. The amplified products were sent for gene sequencing. RESULTS Piroplasmids were detected in 2.3% of the dogs. The variables statistically associated with infections in these animals were hemorrhage/bleeding, jaundice, anisocytosis, activated monocytes and macroplatelets (p ≤ 0.05). Piriform, ring-shaped, oval and aberrant structures were viewed in erythrocytes, neutrophils and monocytes, with lengths greater than and less than 2.5 µm. The nine positive samples from these dogs were characterized as due to Rangelia vitalii. However, one sequence from B. vogeli was detected in a single adult specimen of R. sanguineus. CONCLUSION Although circulation of two species of piroplasmids potentially infective for domestic dogs has been observed in the mountain city of Rio de Janeiro, infection due to R. vitalii was mostly seen in the dogs of the present study.
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Affiliation(s)
- João Pedro Siqueira Palmer
- Parasite Molecular Biology Laboratory, Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, 24210-130, Brazil
- National Reference Laboratory on Vectors of Rickettsioses, Oswaldo Cruz Institute, Oswaldo Cruz Foudation, Rio de Janeiro, 21040-360, Brazil
| | - Gilberto Salles Gazêta
- National Reference Laboratory on Vectors of Rickettsioses, Oswaldo Cruz Institute, Oswaldo Cruz Foudation, Rio de Janeiro, 21040-360, Brazil
| | - Marcos Rogério André
- Vector-Borne Bioagents Laboratory (VBBL), Department of Pathology, Reproduction and One Health, São Paulo State University, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Priscila Alves Fialho
- Parasite Molecular Biology Laboratory, Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, 24210-130, Brazil
| | - Laís Lisboa Corrêa
- Parasite Molecular Biology Laboratory, Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, 24210-130, Brazil
| | | | - Carolina Bistritschan Israel
- Clinic School of Veterinary Medicine Luiz Cataldi de Souza, Serra Dos Órgãos University Center, Teresópolis, Rio de Janeiro, 25976-345, Brazil
| | - Rafael Rempto Pereira
- Clinic School of Veterinary Medicine Luiz Cataldi de Souza, Serra Dos Órgãos University Center, Teresópolis, Rio de Janeiro, 25976-345, Brazil
| | - Alynne da Silva Barbosa
- Parasite Molecular Biology Laboratory, Department of Microbiology and Parasitology, Biomedical Institute, Fluminense Federal University, Niterói, Rio de Janeiro, 24210-130, Brazil.
- Laboratory of Protozoology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, 21040-900, Brazil.
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Li H, Tie XJ. Exploring research progress in studying serum exosomal miRNA-21 as a molecular diagnostic marker for breast cancer. Clin Transl Oncol 2024:10.1007/s12094-024-03454-z. [PMID: 38602645 DOI: 10.1007/s12094-024-03454-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Breast cancer is one of the most prevalent malignancies affecting women globally and poses a significant public health challenge. Early clinical detection plays a pivotal role in providing optimal treatment opportunities and favorable prognoses, crucial for reducing breast cancer mortality and enhancing patients' quality of life. Therefore, the timely identification and diagnosis of breast cancer are imperative. Conventional tumor markers, such as carcinoembryonic antigen (CEA) and carbohydrate antigen 15-3 (CA15-3), serve as reliable methods for actively monitoring disease progression and have become a routine auxiliary diagnostic approach in clinical settings. However, these biomarkers exhibit limitations in sensitivity and specificity, particularly in the early screening and diagnosis of tumors, often yielding results inconsistent with clinical manifestations. In recent years, research has increasingly focused on exosomes released by tumor cells as potential new biomarkers for early stage breast cancer screening. Exosomes carry various components, including tumor-derived proteins, nucleic acids, and lipids. This paper delves into the specific utilization of serum exosomal microRNA-21 (miR-21) as a biomarker for early detection and diagnosis of breast cancer, evaluating its efficacy within this framework.
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Affiliation(s)
- Hang Li
- Department of Laboratory Medicine, Kaifeng Central Hospital, 85 HeDao Street, Kaifeng, 475000, China.
| | - Xiao-Jing Tie
- Department of Oncology, Kaifeng Central Hospital, Kaifeng, 475000, China
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Mao Z, Dong S, Yan Y, Wang C, Li W, Wang L, Qian C, Song Y, Tong L, Yu W. Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA. JCI Insight 2024; 9:e175482. [PMID: 38587071 DOI: 10.1172/jci.insight.175482] [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: 09/07/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDDifferentiating malignant from nonmalignant body fluids remains a clinical challenge because of the unsatisfying performance of conventional cytology. We aimed to improve the sensitivity and ubiquity of cancer cell detection by assaying universal cancer-only methylation (UCOM) markers in supernatant cell-free DNA (cfDNA).METHODSAn observational prospective cohort including 1,321 nonmalignant and malignant body fluids of multiple cancers was used to develop and validate a cfDNA UCOM methylation diagnostic assay. All samples were divided into 2 portions for cytology and supernatant cfDNA methylation analysis.RESULTSThe significant hypermethylation of a potentially novel UCOM marker, TAGMe, together with the formerly reported PCDHGB7, was identified in the cfDNA of malignant body fluid samples. The combined model, cell-free cancer-universal methylation (CUE), was developed and validated in a prospective multicancer cohort with markedly elevated sensitivity and specificity, and was further verified in a set containing additional types of malignant body fluids and metastases. In addition, it remained hypersensitive in detecting cancer cells in cytologically negative malignant samples.CONCLUSIONcfDNA methylation markers are robust in detecting tumor cells and are applicable to diverse body fluids and tumor types, providing a feasible complement to current cytology-based diagnostic analyses.TRIAL REGISTRATIONThis study was registered at Chictr.org.cn (ChiCTR2200060532).FUNDINGNational Natural Science Foundation of China (32270645, 31872814, 32000505, 82170088), the National Key R&D Program of Ningxia Hui Autonomous region (2022BEG01003), Shanghai Municipal Key Clinical Specialty (shslczdzk02201), Science and Technology Commission of Shanghai Municipality (20DZ2261200, 20DZ2254400), and Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101).
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Affiliation(s)
- Zhanrui Mao
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shihua Dong
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Yu Yan
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengyang Wang
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Wei Li
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengchen Qian
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Yuanlin Song
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Respiratory Research Institute, Shanghai, China
| | - Lin Tong
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Respiratory Research Institute, Shanghai, China
| | - Wenqiang Yu
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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Moghadam AA, Manafzadeh AR, Nikoonia MR, Dajliry K, Ramezan F, Tabibian S. Molecular and clinical profile of rare bleeding disorders: A single-center retrospective study. Transfus Apher Sci 2024:103921. [PMID: 38614915 DOI: 10.1016/j.transci.2024.103921] [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: 11/14/2023] [Revised: 03/22/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024]
Abstract
INTRODUCTION Due to their low frequency, there is little information on the molecular pathologies of rare bleeding disorders (RBD). Therefore, this study aimed to analyze the molecular and clinical profiles of patients with RBD. METHODS A retrospective single-center study was conducted among patients with factor (F) II, FVII, FX, and FXIII deficiencies between March 20, 2000, and June 31, 2023. Data on patient demographics, genetic analysis, and laboratory results were documented for all patients. The disease severity was classified according to the clotting factor activity (except FXIII) as follows: >5%: mild, 1-5%: moderate, and <1%: severe. RESULTS A total of 79 patients were enrolled in this study. Three of the cases had FII (3.7%), 40 had FVII (50.6%), 20 had FX (25.3%), and 16 had FXIII deficiency (20.2%). The median age of the patients at the time of diagnosis was six months for FII, 6.5 years for FVII, five months for FX, and 5.75 months for FXIII deficiencies, respectively. The major clinical manifestations were bruising, epistaxis, oral cavity bleeding, ecchymosis, and hemarthrosis. Consanguinity was present in 60 (76%) of patients. The majority of the patients had missense mutations. FVII mutations occurred primarily in exon 6, FX mutations affected mainly exons 2 and 7, and the majority of FXIII mutations occurred in exons 3 and 4. CONCLUSION The diagnosis of the causative mutations in patients with RBD provides an insight into the underlying molecular basis of these disorders and probably explains their variable clinical manifestations.
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Affiliation(s)
- Arash Ahmadfard Moghadam
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Reza Manafzadeh
- First Department of Internal Medicine, Division of Nephrology and Hypertension, University of Szeged, Szeged, Hungary
| | | | | | | | - Shadi Tabibian
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran.
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Jain R, Gupta G, Mitra DK, Guleria R. Diagnosis of extra pulmonary tuberculosis: An update on novel diagnostic approaches. Respir Med 2024; 225:107601. [PMID: 38513873 DOI: 10.1016/j.rmed.2024.107601] [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: 07/22/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/23/2024]
Abstract
Tuberculosis (TB) remains a major global public health problem worldwide. Though Pulmonary TB (PTB) is mostly discussed, one in five cases of TB present are extrapulmonary TB (EPTB) that manifests conspicuous diagnostic and management challenges with respect to the site of infection. The diagnosis of EPTB is often delayed or even missed due to insidious clinical presentation, pauci-bacillary nature of the disease, and lack of laboratory facilities in the resource limited settings. Culture, the classical gold standard for the diagnosis of tuberculosis, suffers from increased technical and logistical constraints in EPTB cases. Other than culture, several other tests are available but their feasibility and effciacy for the detection of EPTB is still the matter of interest. We need more specific and precise test/s for the various forms of EPTB diagnosis which can easily be applied in the routine TB control program is required. A test that can contribute remarkably towards improving EPTB case detection reducing the morbidity and mortality is the utmost requirement. In this review we described the scenario of molecular and other noval methods available for laboratory diagnosis of EPTB, and also discussed the challenges linked with each diagnostic method. This review will make the readers aware of new emerging diagnostic techniques in the field of EPTB diagnosis. They can make an informed decision to choose the appropriate one according to the test availability, their clinical settings and financial considerations.
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Affiliation(s)
- Rashi Jain
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gopika Gupta
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - D K Mitra
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Randeep Guleria
- Department of Pulmonary Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India; Institute of Internal Medicine & Respiratory and Sleep Medicine, Medanta-The Medicity, Gurugram, Haryana, 122033, India.
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Paim MG, Rivas BB, Sebastião GA, Kaefer K, Rodrigues RO, Mayer FQ, Nunes LN, Costa FVAD. Investigation of anti-Leptospira spp. antibodies and leptospiruria in cats attended to a veterinary teaching hospital in southern Brazil. Comp Immunol Microbiol Infect Dis 2024; 107:102138. [PMID: 38367297 DOI: 10.1016/j.cimid.2024.102138] [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: 11/13/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/19/2024]
Abstract
Leptospirosis is a bacterial zoonosis that affects both humans and animals worldwide. Currently, it is known that cats may be susceptible to infection. This study aims to investigate the presence of anti-Leptospira spp. antibodies and leptospiruria in cats, using Microscopic Agglutination Test (MAT) and Real-time Polymerase Chain Reaction (PCR) techniques, respectively. A total of 76 cats, undergoing comprehensive anamnesis, general physical examination, and complementary exams were included in the investigation. Among the 76 cats tested, 9.2% (7/76) exhibited the presence of anti-Leptospira spp. antibodies, while Leptospira spp. DNA was detected in at 1.3% (1/76) of the evaluated urine samples. No significant associations were observed between the serological and molecular diagnostic results and the assessed variables, including clinical data and laboratory results of cats testing positive. This study provides insight into the occurrence of Leptospira spp. infection and leptospiruria in cats treated at a veterinary teaching hospital in southern Brazil.
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Affiliation(s)
- Mirela Grünwalder Paim
- Hospital de Clínicas Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
| | - Bárbara Basseggio Rivas
- Hospital de Clínicas Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Grasiele Amorim Sebastião
- Hospital de Clínicas Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Kauana Kaefer
- Hospital de Clínicas Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rogério Oliveira Rodrigues
- Laboratório de Leptospirose, Instituto de Pesquisas Veterinárias Desidério Finamor, Fundação Estadual de Pesquisa Agropecuária, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor, Fundação Estadual de Pesquisa Agropecuária, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Luciana Neves Nunes
- Instituto de Matemática, Departamento de Estatística, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernanda Vieira Amorim da Costa
- Hospital de Clínicas Veterinárias, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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Poulain C, Launey Y, Bouras M, Lakhal K, Dargelos L, Crémet L, Gibaud SA, Corvec S, Seguin P, Rozec B, Asehnoune K, Feuillet F, Roquilly A. Clinical evaluation of the BioFire Respiratory Pathogen Panel for the guidance of empirical antimicrobial therapy in critically ill patients with hospital-acquired pneumonia: A multicenter, quality improvement project. Anaesth Crit Care Pain Med 2024; 43:101353. [PMID: 38355044 DOI: 10.1016/j.accpm.2024.101353] [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: 10/20/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND We aimed to determine whether implementing antimicrobial stewardship based on multiplex bacterial PCR examination of respiratory fluid can enhance outcomes of critically ill patients with hospital-acquired pneumonia (HAP). METHODS We conducted a quality improvement study in two hospitals in France. Adult patients requiring invasive mechanical ventilation with a diagnosis of HAP were included. In the pre-intervention period (August 2019 to April 2020), antimicrobial therapy followed European guidelines. In the «intervention» phase (June 2020 to October 2021), treatment followed a multiplex PCR-guided protocol. The primary endpoint was a composite endpoint made of mortality on day 28, clinical cure between days 7 and 10, and duration of invasive mechanical ventilation on day 28. The primary outcome was analyzed with a DOOR strategy. RESULTS A total of 443 patients were included in 3 ICUs from 2 hospitals (220 pre-intervention; 223 intervention). No difference in the ranking of the primary composite outcome was found (DOOR: 50.3%; 95%CI, 49.9%-50.8%). The number of invasive mechanical ventilation-free days at day 28 was 10.0 [0.0; 19.0] in the baseline period and 9.0 [0.0; 20.0] days during the intervention period (p = 0.95). The time-to-efficient antimicrobial treatment was 0.43 ± 1.29 days before versus 0.55 ± 1.13 days after the intervention (p = 0.56). CONCLUSION Implementation of Rapid Multiplex PCR to guide empirical antimicrobial therapy for critically ill patients with HAP was not associated with better outcomes. However, adherence to stewardship was low, and the study may have had limited power to detect a clinically important difference.
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Affiliation(s)
- Cécile Poulain
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France; Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France.
| | - Yoann Launey
- Univ Rennes, CHU Rennes, Department of Anaesthesia, Critical Care and Perioperative Medicine, F-35000 Rennes, France
| | - Marwan Bouras
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France; Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France
| | - Karim Lakhal
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France
| | - Laura Dargelos
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France
| | - Lise Crémet
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France; Nantes Université, CHU Nantes, Service de bactériologie-hygiène, pôle de biologie, Nantes, France
| | - Sophie-Anne Gibaud
- Nantes Université, CHU Nantes, Service de bactériologie-hygiène, pôle de biologie, Nantes, France
| | - Stéphane Corvec
- Nantes Université, CHU Nantes, Service de bactériologie-hygiène, pôle de biologie, Nantes, France
| | - Philippe Seguin
- Univ Rennes, CHU Rennes, Department of Anaesthesia, Critical Care and Perioperative Medicine, F-35000 Rennes, France
| | - Bertrand Rozec
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France
| | - Karim Asehnoune
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France; Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France
| | - Fanny Feuillet
- Nantes Université, CHU de Nantes, DRI, Département promotion, cellule vigilances, Nantes, France; Nantes Université, CHU de Nantes, DRI, Plateforme de Méthodologie et de Biostatistique, Nantes, France
| | - Antoine Roquilly
- Nantes Université, CHU Nantes, INSERM, Anesthesie Réanimation, CIC 0004, F-44000 Nantes, France; Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France
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Gaillard T, Dupieux-Chabert C, Roux AL, Tessier E, Boutet-Dubois A, Courboulès C, Corvec S, Bémer P, Lavigne JP, El Sayed F, Marchandin H, Munier C, Chanard E, Gazzano V, Loiez C, Laurent F. A prospective multicentre evaluation of BioFire® Joint Infection Panel for the rapid microbiological documentation of acute arthritis. Clin Microbiol Infect 2024:S1198-743X(24)00153-8. [PMID: 38522842 DOI: 10.1016/j.cmi.2024.03.022] [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: 09/14/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES To assess the performance of the rapid syndromic BioFire® Joint Infection Panel (BF-JIP) to detect bacterial and fungal pathogens, as well as antibiotic resistance genes, directly in synovial fluid specimens collected from patients with acute arthritis. METHODS The study was conducted in six French bacteriological laboratories. To assess the performances of BF-JIP, results were compared with those of synovial fluid 14-day culture and, in case of discrepancy, with those of complementary molecular methods and intraoperative samples. A total of 308 synovial fluid specimens were tested after collection from 308 adults and children presenting with clinical and biological suspicion of acute arthritis; patients presenting with acute periprosthetic joint infection were included according to the European Bone and Joint Infection Society 2021 criteria. RESULTS Only one specimen failed (no result). On the basis of the consolidated data, the BF-JIP was concordant with the 14-day culture in 280 (91.2%) of the 307 specimens finally included in the study. The positive percentage agreement was 84.9% (95% CI, 78.8-89.8%) and the negative percentage agreement was 100% (95% CI, 97.2-100%). The positive predictive value was extremely high (100%; 95% CI, 97.6-100%), whereas the negative predictive value was lower (82.6%; 95% CI, 75.7-88.2%), partially explained by the missing target species in the panel. DISCUSSION The BF-JIP showed high performances to detect pathogens involved in acute arthritis.
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Affiliation(s)
- Tiphaine Gaillard
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France.
| | - Céline Dupieux-Chabert
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France
| | - Anne-Laure Roux
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Eve Tessier
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Adeline Boutet-Dubois
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Camille Courboulès
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Stéphane Corvec
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Pascale Bémer
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Jean-Philippe Lavigne
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Faten El Sayed
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Hélène Marchandin
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Clément Munier
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Emmanuel Chanard
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Vincent Gazzano
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Caroline Loiez
- Centre Hospitalo-Universitaire de Lille, Institut de Microbiologie - Centre de Biologie Pathologie, Service Bactériologie, Lille, France
| | - Frédéric Laurent
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France
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12
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Bemanian MH, Shokouhi Shoormasti R, Arshi S, Jafari M, Shokri S, Fallahpour M, Nabavi M, Zaremehrjardi F. The role of molecular diagnosis in anaphylactic patients with dual or triple-sensitization to Hymenoptera venoms. Allergy Asthma Clin Immunol 2024; 20:22. [PMID: 38521942 PMCID: PMC10960983 DOI: 10.1186/s13223-024-00885-9] [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] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 02/29/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND The poly-sensitization to Hymenoptera venom makes it difficult to select genuine allergens for immunotherapy and increases patients' costs. The objective of this study was to determine the culprit allergen in dual or triple-sensitized patients to three Hymenoptera venoms through molecular diagnosis and evaluating the results of incorporating the molecular diagnosis with skin tests. METHODS Thirty-two patients with anaphylactic reactions and dual or triple-sensitization to Hymenoptera venoms in skin tests entered this study. IgE-sensitization to whole extracts and molecules of Apis mellifera (Api m), Vespula vulgaris (Ves v), and Polistes dominulus (Pol d) was evaluated utilizing ALEX or ImmunoCAP. RESULTS Twenty-nine patients (90.6%) were male. IgE-sensitization to at least one of the allergenic molecules related to Apis mellifera, Vespula vulgaris, and Polistes dominulus was seen in 59.4, 53.1, and 21.9%, respectively. Among 32 patients, 14 (43.8) and 8 (25%), were mono-sensitized to Api m and Ves v components in ALEX, respectively. Double sensitization to Hymenoptera was identified in 18.8% of patients in ALEX. Api m 1+/Api m 2-/Api m 10- and Ves v 1+/Ves v 5+ demonstrated the most prevalent sensitizations patterns in our patients. CONCLUSIONS The molecular diagnosis of IgE-sensitization to Hymenoptera venoms can be valuable, especially in patients who show dual or triple-sensitization in skin tests, as the ALEX results revealed mono and double-sensitization to Hymenoptera venoms in 22 and 6 patients, respectively. Regarding the high cost and adverse reactions of venom immunotherapy, especially for two or three venoms, incorporating the molecular diagnosis alongside skin tests for accurate diagnosis of the culprit venom could help decrease costs for patients.
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Affiliation(s)
- Mohammad Hassan Bemanian
- Department of Allergy and Clinical Immunology, Rasool-E-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Raheleh Shokouhi Shoormasti
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Saba Arshi
- Department of Allergy and Clinical Immunology, Rasool-E-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Jafari
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Sima Shokri
- Department of Allergy and Clinical Immunology, Rasool-E-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Morteza Fallahpour
- Department of Allergy and Clinical Immunology, Rasool-E-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Nabavi
- Department of Allergy and Clinical Immunology, Rasool-E-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Zaremehrjardi
- Department of Allergy and Clinical Immunology, Rasool-E-Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Wu J, Lin Y, Yang K, Liu X, Wang H, Yu T, Tao R, Guo J, Chen L, Cheng H, Lou F, Cao S, Yu W, Hu H, Ye D. Clinical effectiveness of a multitarget urine DNA test for urothelial carcinoma detection: a double-blinded, multicenter, prospective trial. Mol Cancer 2024; 23:57. [PMID: 38504268 PMCID: PMC10949661 DOI: 10.1186/s12943-024-01974-4] [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: 10/26/2023] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
Urine-based testing is promising for noninvasive diagnosis of urothelial carcinoma (UC) but has suboptimal sensitivity for early-stage tumors. Herein, we developed a multitarget urine tumor DNA test, UI-Seek, for UC detection and evaluated its clinical feasibility. The prediction model was developed in a retrospective cohort (n = 382), integrating assays for FGFR3 and TERT mutations and aberrant ONECUT2 and VIM methylation to generate a UC-score. The test performance was validated in a double-blinded, multicenter, prospective trial (n = 947; ChiCTR2300076543) and demonstrated a sensitivity of 91.37% and a specificity of 95.09%. The sensitivity reached 75.81% for low-grade Ta tumors and exceeded 93% in high-grade Ta and higher stages (T1 to T4). Simultaneous identification of both bladder and upper urinary tract tumors was enabled with sensitivities exceeding 90%. No significant confounding effects were observed regarding benign urological diseases or non-UC malignancies. The test showed improved sensitivities over urine cytology, the NMP22 test, and UroVysion FISH alongside comparable specificities. The single-target accuracy was greater than 98% as confirmed by Sanger sequencing. Post-surgery UC-score decreased in 97.7% of subjects. Overall, UI-Seek demonstrated robust performance and considerable potential for the early detection of UC.
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Affiliation(s)
- Junlong Wu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuda Lin
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Hexi District, Tianjin, 300211, People's Republic of China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Kaiwei Yang
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Dajie, Xicheng District, Beijing, 100034, People's Republic of China
| | - Xiao Liu
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Tingting Yu
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Ran Tao
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Jing Guo
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Libin Chen
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Huanqing Cheng
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China.
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd, Beijing, 100176, People's Republic of China.
| | - Wei Yu
- Department of Urology, Peking University First Hospital, No. 8 Xishiku Dajie, Xicheng District, Beijing, 100034, People's Republic of China.
| | - Hailong Hu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, 23 Pingjiang Road, Hexi District, Tianjin, 300211, People's Republic of China.
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China.
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Li M, Jin Y, Xu Y, Sun Y, Yuan R, Zhang X, Qu S, Lv M, Liao M, Liang W, Zhang L, Chen X. From degraded to deciphered: ATAC-seq's application potential in forensic diagnosis. Int J Legal Med 2024:10.1007/s00414-024-03206-2. [PMID: 38491322 DOI: 10.1007/s00414-024-03206-2] [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: 10/25/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
In recent years, molecular biology-based diagnostic techniques have made remarkable strides and are now extensively utilized in clinical practice, providing invaluable insights for disease diagnosis and treatment. However, forensic medicine, especially forensic pathology, has witnessed relatively limited progress in the application of molecular biology technologies. A significant challenge in employing molecular techniques for forensic diagnoses lies in the quantitative and qualitative changes observed in diagnostic markers due to sample degradation-a recognized and formidable obstacle. Inspired by the success of DNA sequencing in forensic practices, which enables accurate individual identification even in cases involving degraded and deteriorated tissues and organs, we propose the application of the assay for transposase-accessible chromatin with sequencing (ATAC-seq) to identify targets at the transcriptional onset, exploring chromatin and DNA-level alterations for injury and disease inference in forensic samples. This study employs ATAC-seq to explore alterations in chromatin accessibility post-injury and their subsequent changes over a 2-h degradation period, employing traumatic brain injury (TBI) as a representative model. Our findings reveal high sensitivity of chromatin accessibility sites to injury, evidenced by shifts in thousands of peak positions post-TBI. Remarkably, these alterations remain largely unaffected by early degradation. Our results robustly endorse the notion that integrating and incorporating these specific loci for injury and disease diagnosis in forensic samples holds tremendous promise for practical application. We further validated the above results using human cortical tissue, which supported that early degradation did not significantly affect chromatin accessibility. This pioneering advancement in molecular diagnostic techniques may revolutionize the field of forensic science, especially forensic pathology.
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Affiliation(s)
- Manrui Li
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yuntian Jin
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yang Xu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yihan Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Ruixuan Yuan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Xiao Zhang
- Department of Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Xiameng Chen
- Department of Forensic Pathology and Forensic Clinical Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
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Tajadini H, Cornelissen JJLM, Zadegan R, Ravan H. An approach for state differentiation in nucleic acid circuits: Application to diagnostic DNA computing. Anal Chim Acta 2024; 1294:342266. [PMID: 38336407 DOI: 10.1016/j.aca.2024.342266] [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: 09/09/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Differentiating between different states in nucleic acid circuits is crucial for various biological applications. One approach, there is a requirement for complicated sequential summation, which can be excessive for practical purposes. By selectively labeling biologically significant states, this study tackles the issue and presents a more cost-effective and streamlined solution. The challenge is to efficiently distinguish between different states in a nucleic acid circuit. RESULTS An innovative method is introduced in this study to distinguish between states in a nucleic acid circuit, emphasizing the biologically relevant ones. The circuit comprises four DNA logic gates and two detection modules, one for determining fetal gender and the other for diagnosing X-linked genetic disorders. The primary module generates a G-quadruplex DNAzyme when activated by specific biomarkers, which leads to a distinct colorimetric signal. The secondary module responds to hemophilia and choroideremia biomarkers, generating one or two DNAzymes. The absence of female fetus indicators results in no DNAzyme or color change. The circuit can differentiate various fetal states by producing one to four active DNAzymes in response to male fetus biomarkers. A single-color solution for state differentiation is provided by this approach, which promises significant advancements in DNA computing and diagnostic applications. SIGNIFICANCE The innovative approach used in this study to distinguish states in nucleic acid circuits holds great significance. By selectively labeling biologically relevant states, circuit design is simplified and complexity is reduced. This advancement enables cost-effective and efficient diagnostic applications and contributes to DNA computing, providing a valuable solution to a fundamental problem.
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Affiliation(s)
- Hanie Tajadini
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Jeroen J L M Cornelissen
- Department of Molecules & Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, AE, 7500, the Netherlands
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran; Department of Molecules & Materials, MESA+ Institute for Nanotechnology, University of Twente, Enschede, AE, 7500, the Netherlands.
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16
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Xu Y, Wang Y, Zhang D, Zhang H, Wang Y, Wang W, Hu X. An autophagy-associated diagnostic signature based on peripheral blood for antibody-mediated rejection in renal transplantation. Transpl Immunol 2024; 84:102021. [PMID: 38452984 DOI: 10.1016/j.trim.2024.102021] [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: 10/04/2023] [Revised: 03/03/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Antibody-mediated rejection (ABMR) emerged as a major cause of graft loss in renal transplantation. Needle biopsy is the gold standard for diagnosis of ABMR in renal allografts. Thus, noninvasive diagnosis methods of ABMR with high accuracy are urgently needed to prevent unnecessary biopsies. METHODS We collected peripheral blood transcriptome data from two independent renal transplantation cohorts with patients with ABMR, stable well-functioning transplants (STA), and T-cell mediated rejection (TCMR). Differentially expressed genes (DEGs) were identified by comparing the ABMR group with the STA group. In addition, functional enrichment analysis and gene set enrichment analysis were performed to seek new key underlying mechanisms in ABMR. Subsequently, we utilized a Boruta algorithm and least absolute shrinkage and selection operator logistic algorithm to establish a diagnostic model which was then evaluated and validated in an independent cohort. RESULTS According to functional enrichment analysis, autophagy was found to be the primary upregulated biological process in ABMR. Based on algorithms, three autophagy-associated genes, ubiquitin specific peptidase 33 (USP33), Ras homolog mTORC1 binding (RHEB), and ABL proto-oncogene 2 (ABL2), were selected to establish the diagnostic model in the training cohort. This autophagy-related gene model possessed good diagnostic value in distinguishing ABMR from STA blood samples in the training cohort (AUC = 0.907) and in the validation cohort (AUC = 0.972). In addition, this model also showed good discernibility in distinguishing ABMR from TCMR in the training and validation cohorts (AUCs = 0.908 and 0.833). CONCLUSION We identified and validated an autophagy-associated diagnostic model with high accuracy for renal transplant patients with ABMR. Our study provided a new potential test for the non-invasive diagnosis of ABMR in clinical practice and highlighted the importance of autophagy in ABMR.
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Affiliation(s)
- Yue Xu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Yuxuan Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Di Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Hao Zhang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Yicun Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Wei Wang
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China; Institute of Urology, Capital Medical University, Beijing 100020, China.
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El Zakhem A, Mahmoud O, Bou Fakhreddine H, Mahfouz R, Bouakl I. Patterns and predictors of positive multiplex polymerase chain reaction respiratory panel among patients with acute respiratory infections in a single center in Lebanon. Mol Biol Rep 2024; 51:346. [PMID: 38401017 DOI: 10.1007/s11033-023-09133-6] [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: 07/26/2023] [Accepted: 12/08/2023] [Indexed: 02/26/2024]
Abstract
BACKGROUND Infectious agents associated with community-acquired acute respiratory infections (ARIs) remain understudied in Lebanon. We aim to assess the microbiological profiles of ARIs by employing polymerase chain reaction (PCR) and identifying predictors of positive PCR results among patients admitted for ARI. METHODS AND RESULTS We conducted a retrospective single-center study at the American University of Beirut Medical Center, including all respiratory PCR panels performed on pediatric (< 18) and adult (≥ 18) patients presenting with an ARI from January 2015 to March 2018, prior to the onset of the COVID-19 pandemic. We aimed to identify the epidemiological patterns of ARIs and the factors associated with positive PCRs in both adult and pediatric patients. Among 281 respiratory PCRs, 168 (59.7%) were positive for at least one pathogen, with 54.1% positive PCR for viruses, 7.8% for bacteria species, and 3.9% with virus-bacteria codetection. Almost 60% of the patients received antibiotics prior to PCR testing. PCR panels yielded more positive results in pediatric patients than in adults (P = 0.005). Bacterial detection was more common in adults compared to pediatrics (P < 0.001). The most common organism recovered in the entire population was Human Rhinovirus (RhV) (18.5%). Patients with pleural effusion on chest CT were less likely to have a positive PCR (95% Cl: 0.22-0.99). On multivariate analysis, pediatric age group (P < 0.001), stem cell transplant (P = 0.006), fever (P = 0.03) and UTRI symptoms (P = 0.004) were all predictive of a positive viral PCR. CONCLUSION Understanding the local epidemiology of ARI is crucial for proper antimicrobial stewardship. The identification of factors associated with positive respiratory PCR enhances our understanding of clinical characteristics and potential predictors of viral detection in our population.
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Affiliation(s)
- Aline El Zakhem
- Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, 110236, Lebanon
| | - Omar Mahmoud
- Division of Infectious Diseases, American University of Beirut Medical Center, Beirut, 110236, Lebanon
| | - Hisham Bou Fakhreddine
- Division of Pulmonary and Critical Care, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Imad Bouakl
- Division of Pulmonary and Critical Care, American University of Beirut Medical Center, Beirut, Lebanon.
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Liu J, Lin F, Sun Y, Liu X. Clinicopathological analysis of rosette-forming glioneuronal tumors. Diagn Pathol 2024; 19:39. [PMID: 38388383 PMCID: PMC10882769 DOI: 10.1186/s13000-024-01465-6] [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: 11/09/2023] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND This study aimed to investigate the clinicopathological characteristics, diagnostic indicators, and critical factors for the differential diagnosis of rosette-forming glioneuronal tumor (RGNT). PATIENTS AND METHODS This retrospective study included six surgically treated RGNT cases. We analyzed and summarized their clinical manifestations, radiological features, histological morphology, immunophenotype, and molecular genetic changes, supplemented with a literature review. RESULTS The patients comprised four males and two females with a mean age of 35 years. The tumors were located in the cerebellum (two cases); the fourth ventricle, quadrigeminal cistern, and third ventricle (one case each); and the fourth ventricle and brainstem (one case). Clinical manifestations included headaches in four cases, left eyelid ptosis in one case, and one asymptomatic case only identified during physical examination. Microscopically, the tumor cells were uniform in size and were marked by rosette-like or pseudorosette-like structures around the neuropil and blood vessels. Immunohistochemistry revealed biphasic patterns. The central neuropil components of the rosette-like structures around the neuropil and the pseudorosette structures of the perivascular regions expressed Syn, while the cells surrounding the rosettes expressed Olig2 and not GFAP. GFAP and S-100 were expressed in the glial components but not in the rosette or pseudorosette regions. The Ki-67 proliferation index was typically low. Molecular genetic analysis showed that the main molecular changes involved FGFR1 mutation accompanied by PIK3R1 mutation. None of the patients received chemoradiotherapy postoperatively. Follow-up durations varied between 4 and 23 months with no recorded recurrence or metastasis. CONCLUSION RGNT is a comparatively rare mixed glioneuronal tumor that occurs in the midline structures. Its morphology shows certain overlaps with other low-grade neuroepithelial tumors. Identifying the rosettes around the neuropil is critical for morphological diagnosis, and the molecular identification of FGFR1 mutations accompanied by PIK3R1 mutations can facilitate diagnosis.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Shenzhen Second People's Hospital, Shenzhen University 1st Affiliated Hospital, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Fan Lin
- Department of Radiology, Shenzhen Second People's Hospital, Shenzhen University 1st Affiliated Hospital, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Yanhua Sun
- Department of Pathology, Shenzhen Second People's Hospital, Shenzhen University 1st Affiliated Hospital, Shenzhen University School of Medicine, Shenzhen, 518035, China
| | - Xia Liu
- Department of Pathology, Shenzhen Second People's Hospital, Shenzhen University 1st Affiliated Hospital, Shenzhen University School of Medicine, Shenzhen, 518035, China.
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19
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Mejías-Alpízar MJ, Porras-Silesky C, Rodríguez EJ, Quesada J, Alfaro-Segura MP, Robleto-Quesada J, Gutiérrez R, Rojas A. Mitochondrial and ribosomal markers in the identification of nematodes of clinical and veterinary importance. Parasit Vectors 2024; 17:77. [PMID: 38378676 PMCID: PMC10880205 DOI: 10.1186/s13071-023-06113-4] [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: 10/24/2023] [Accepted: 12/26/2023] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Nematodes of the Ascarididae, Ancylostomatidae and Onchocercidae families are parasites of human and veterinary importance causing infections with high prevalence worldwide. Molecular tools have significantly improved the diagnosis of these helminthiases, but the selection of genetic markers for PCR or metabarcoding purposes is often challenging because of the resolution these may show. METHODS Nuclear 18S rRNA, internal transcribed spacers 1 (ITS-1) and 2 (ITS-2), mitochondrial gene cytochrome oxidase 1 (cox1) and mitochondrial rRNA genes 12S and 16S loci were studied for 30 species of the mentioned families. Accordingly, their phylogenetic interspecies resolution, pairwise nucleotide p-distances and sequence availability in GenBank were analyzed. RESULTS The 18S rRNA showed the least interspecies resolution since separate species of the Ascaris, Mansonella, Toxocara or Ancylostoma genus were intermixed in phylogenetic trees as opposed to the ITS-1, ITS-2, cox1, 12S and 16S loci. Moreover, pairwise nucleotide p-distances were significantly different in the 18S compared to the other loci, with an average of 99.1 ± 0.1%, 99.8 ± 0.1% and 98.8 ± 0.9% for the Ascarididae, Ancylostomatidae and Onchocercidae families, respectively. However, ITS-1 and ITS-2 average pairwise nucleotide p-distances in the three families ranged from 72.7% to 87.3%, and the cox1, 12S and 16S ranged from 86.4% to 90.4%. Additionally, 2491 cox1 sequences were retrieved from the 30 analyzed species in GenBank, whereas 212, 1082, 994, 428 and 143 sequences could be obtained from the 18S, ITS-1, ITS-2, 12S and 16S markers, respectively. CONCLUSIONS The use of the cox1 gene is recommended because of the high interspecies resolution and the large number of sequences available in databases. Importantly, confirmation of the identity of an unknown specimen should always be complemented with the careful morphological examination of worms and the analysis of other markers used for specific parasitic groups.
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Affiliation(s)
- María José Mejías-Alpízar
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Catalina Porras-Silesky
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Esteban José Rodríguez
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Joban Quesada
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - María Paula Alfaro-Segura
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica
| | - Joby Robleto-Quesada
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica
| | - Ricardo Gutiérrez
- National Reference Center for Bacteriology, Costa Rican Institute for Research and Teaching in Nutrition and Health (INCIENSA), Tres Rios, Costa Rica
- Ross University School of Veterinary Medicine, West Farm, Basseterre, Saint Kitts and Nevis
| | - Alicia Rojas
- Laboratorio de Helmintología, Departamento de Parasitología, Facultad de Microbiología, University of Costa Rica, San José, Costa Rica.
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica.
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20
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Nazari-Vanani R, Negahdary M. Recent advances in electrochemical aptasensors and genosensors for the detection of pathogens. Environ Res 2024; 243:117850. [PMID: 38081349 DOI: 10.1016/j.envres.2023.117850] [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: 10/03/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
In recent years, pathogenic microorganisms have caused significant mortality rates and antibiotic resistance and triggered exorbitant healthcare costs. These pathogens often have high transmission rates within human populations. Rapid diagnosis is crucial in controlling and reducing the spread of pathogenic infections. The diagnostic methods currently used against individuals infected with these pathogens include relying on outward symptoms, immunological-based and, some biomolecular ones, which mainly have limitations such as diagnostic errors, time-consuming processes, and high-cost platforms. Electrochemical aptasensors and genosensors have emerged as promising diagnostic tools for rapid, accurate, and cost-effective pathogen detection. These bio-electrochemical platforms have been optimized for diagnostic purposes by incorporating advanced materials (mainly nanomaterials), biomolecular technologies, and innovative designs. This review classifies electrochemical aptasensors and genosensors developed between 2021 and 2023 based on their use of different nanomaterials, such as gold-based, carbon-based, and others that employed other innovative assemblies without the use of nanomaterials. Inspecting the diagnostic features of various sensing platforms against pathogenic analytes can identify research gaps and open new avenues for exploration.
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Affiliation(s)
- Razieh Nazari-Vanani
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Negahdary
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil.
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21
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Kim KH, Ryu E, Khaleel ZH, Seo SE, Kim L, Kim YH, Park HG, Kwon OS. Plasmonic digital PCR for discriminative detection of SARS-CoV-2 variants. Biosens Bioelectron 2024; 246:115859. [PMID: 38011776 DOI: 10.1016/j.bios.2023.115859] [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: 10/30/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
We developed a novel strategy for discriminative detection of SARS-CoV-2 variants based on the plasmonic photothermal effect of gold nanofilms and digital polymerase chain reaction (dPCR) technology. This method consists of the gold nanofilm-based dPCR chip fabrication for ultrafast heating and cooling cycles by the plasmonic photothermal effect, the LED quencher immobilization through the interfacing compound on the surface of the gold nanofilm to prevent photoquenching of PCR signaling dye, and the discriminative detection of the variant viruses from the COVID-19 clinical samples by photothermal cycles with fabricated dPCR chips and a portable plasmonic PCR device. Compared to conventional sequencing or RT-qPCR-based variant detection methods, this technology can be effectively applied to point-of-care testing by enabling ultrafast quantitative analysis with a small device. With this method, we successfully detected the delta variant and the omicron variant with a high sensitivity of 10 copies from COVID-19 patients' clinical samples within 25 min, including reverse transcription. This method can be applied universally to rapid and accurate point-of-care testing for various pandemic viruses as well as the coronavirus.
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Affiliation(s)
- Kyung Ho Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eunsu Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Zinah Hilal Khaleel
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sung Eun Seo
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Lina Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Oh Seok Kwon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Science and Technology, Sungkyunkwan University, Suwon, 16419, Republic of Korea; Department of Nano Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea.
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22
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Li T, Meng F, Fang Y, Luo Y, He Y, Dong Z, Tian B. Multienzymatic disintegration of DNA-scaffolded magnetic nanoparticle assembly for malarial mitochondrial DNA detection. Biosens Bioelectron 2024; 246:115910. [PMID: 38086308 DOI: 10.1016/j.bios.2023.115910] [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: 10/23/2023] [Revised: 11/20/2023] [Accepted: 12/02/2023] [Indexed: 12/30/2023]
Abstract
Early diagnosis of malaria can prevent the spread of disease and save lives, which, however, remains challenging in remote and less developed regions. Here we report a portable and low-cost optomagnetic biosensor for rapid amplification and detection of malarial mitochondrial DNA. Bioresponsive magnetic nanoparticle assemblies are constructed by using nucleic acid scaffolds containing endonucleolytic DNAzymes and their substrates, which can be activated by the presence of target DNA and self-disintegrated to release magnetic nanoparticles for optomagnetic quantification. Specifically, target molecules can induce padlock probe ligation and subsequent one-pot homogeneous cascade reactions consisting of nicking-enhanced rolling circle amplification, DNAzyme-assisted nucleic acid recycling, and strand-displacement-driven disintegration of the magnetic assembly. With an optimized magnetic actuation process for reaction acceleration, a detection limit of 1 fM can be achieved by the proposed biosensor with a total assay time of ca. 90 min and a dynamic detection range spanning 3 orders of magnitude. The robustness of the system was validated by testing target molecules spiked in 5% serum samples. Clinical sample validation was conducted by testing malaria-positive clinical blood specimens, obtaining quantitative results concordant with qPCR measurements.
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Affiliation(s)
- Tingting Li
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China
| | - Fanming Meng
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, China
| | - Yuan Fang
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; College of Biology, Hunan University, Changsha, 410082, China
| | - Yifei Luo
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China
| | - Yilong He
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China
| | - Zhuxin Dong
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; Furong Laboratory, Changsha, 410008, China
| | - Bo Tian
- School of Basic Medical Sciences, Central South University, Changsha, 410013, China; Furong Laboratory, Changsha, 410008, China.
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23
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Asees M, Jawabreh I, Hamarsheh O, Abdeen Z, Assi A, Azmi K. Molecular diagnosis of Taenia saginata from two patients in Palestine: two case reports. J Med Case Rep 2024; 18:96. [PMID: 38351027 PMCID: PMC10865552 DOI: 10.1186/s13256-024-04351-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Taeniasis, is a worldwide foodborne zoonotic disease caused by two principal species; Taenia saginata and Taenia solium. The tapeworm infects the intestine causing taeniasis in humans. Taeniasis is a very rare parasitic infection in Palestine with very few annual cases of unknown species. The infection rate and the disease status are not clear due to the lack of reports about the actual number of patients. CASE PRESENTATION Two Palestinian patients; one male of 22 years old from Hebron and the other is female of 33 years old from Ramallah were referred to Palestinian Health Services in the West Bank, Palestine, complained of weight loss, abdominal pain and presence of motile segments of creamy color in the their stool. Microscopic analysis of the stool samples from infected cases revealed Taenia eggs and proglottids, confirmed taeniasis infection. The parasite species was identified as T. saginata by polymerase chain reaction (PCR) amplification and sequencing of the cytochrome oxidase -1 (COX-1) gene. CONCLUSION Taeniasis is an unusual parasitic infection in Palestine, there is a growing concern that the actual numbers of infected individuals are much higher and the occurrence of human taeniasis is principally due to people's eating habits in consumption of raw or undercooked beef meat. This report highlighted for the first time the existence of taeniasis infection in the country; which necessitates the need to conduct further research and surveillance to reveal the actual infection rate and the available Taenia species.
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Affiliation(s)
- Mohammad Asees
- Hematology Department, Professional Labs, Ramallah, Palestine
| | - Issam Jawabreh
- Routine and Body Fluids Department, Professional Labs, Ramallah, Palestine
- Faculty of Medicine, Department of Biochemistry, Al-Quds University, Jerusalem, Palestine
| | - Omar Hamarsheh
- Department of Life Sciences, Al-Quds University, Jerusalem, Palestine
| | - Ziad Abdeen
- Al-Quds Public Health Society, Jerusalem, Palestine
| | - Ayoub Assi
- Routine and Body Fluids Department, Professional Labs, Ramallah, Palestine
| | - Kifaya Azmi
- Al-Quds Public Health Society, Jerusalem, Palestine.
- Faculty of Medicine, Department of Biochemistry, Al-Quds University, Jerusalem, Palestine.
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Martín Ramírez A, Barón Argos L, Lanza Suárez M, Carmona Rubio C, Pérez-Ayala A, Hisam SR, Rubio JM. Malaria diagnosis using a combined system of a simple and fast extraction method with a lyophilised Dual-LAMP assay in a non-endemic setting. Pathog Glob Health 2024; 118:80-90. [PMID: 37415348 PMCID: PMC10769111 DOI: 10.1080/20477724.2023.2232595] [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: 07/08/2023] Open
Abstract
Malaria is a parasitic disease distributed in tropical areas but with a high number of imported cases in non-endemic countries. The most specific and sensitive malaria diagnostic methods are PCR and LAMP. However, both require specific equipment, extraction procedures and a cold chain. This study aims to solve some limitations of LAMP method with the optimization and validation of six LAMP assays, genus and species-specific, using an easy and fast extraction method, the incorporation of a reaction control assay, two ways (Dual) of result reading and reagent lyophilization. The Dual-LAMP assays were validated against the Nested-Multiplex Malaria PCR. A conventional column and saline extraction methods, and the use of lyophilized reaction tubes were also assessed. A new reaction control Dual-LAMP-RC assay was designed. Dual-LAMP-Pspp assay showed no cross-reactivity with other parasites, repeatability and reproducibility of 100%, a significant correlation between parasite concentration and time to amplification and a LoD of 1.22 parasites/µl and 5.82 parasites/µl using column and saline extraction methods, respectively. Sensitivity and specificity of the six Dual-LAMP assays reach values of 100% or close to this, being lower for the Dual-LAMP-Pm. The Dual-LAMP-RC assay worked as expected. Lyophilized Dual-LAMP results were concordant with the reference method. Dual-LAMP malaria assays with the addition of a new reaction control LAMP assay and the use of a fast and easy saline extraction method, provided low limit of detection, no cross-reactivity, and good sensitivity and specificity. Furthermore, the reagent lyophilization and the dual result reading allow their use in most settings.
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Affiliation(s)
- Alexandra Martín Ramírez
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Lourdes Barón Argos
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Marta Lanza Suárez
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Claudia Carmona Rubio
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Pérez-Ayala
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Shamilah R. Hisam
- Parasitology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, Selangor, Malaysia
| | - José M. Rubio
- Malaria & Parasitic Emerging Diseases Laboratory. National Microbiology Center, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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25
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Carvalho LML, Jorge AADL, Bertola DR, Krepischi ACV, Rosenberg C. A Comprehensive Review of Syndromic Forms of Obesity: Genetic Etiology, Clinical Features and Molecular Diagnosis. Curr Obes Rep 2024:10.1007/s13679-023-00543-y. [PMID: 38277088 DOI: 10.1007/s13679-023-00543-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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 01/27/2024]
Abstract
Syndromic obesity refers to obesity occurring with additional clinical findings, such as intellectual disability/developmental delay, dysmorphic features, and congenital malformations. PURPOSE OF REVIEW: To present a narrative review regarding the genetic etiology, clinical description, and molecular diagnosis of syndromic obesity, which is a rare condition with high phenotypic variability and genetic heterogeneity. The following syndromes are presented in this review: Prader-Willi, Bardet-Biedl, Pseudohypoparathyroidism, Alström, Smith-Magenis, Cohen, Temple, 1p36 deletion, 16p11.2 microdeletion, Kleefstra, SIM1-related, Börjeson-Forssman-Lehmann, WAGRO, Carpenter, MORM, and MYT1L-related syndromes. RECENT FINDINGS: There are three main groups of mechanisms for syndromic obesity: imprinting, transcriptional activity regulation, and cellular cilia function. For molecular diagnostic, methods of genome-wide investigation should be prioritized over sequencing of panels of syndromic obesity genes. In addition, we present novel syndromic conditions that need further delineation, but evidences suggest they have a higher frequency of obesity. The etiology of syndromic obesity tends to be linked to disrupted neurodevelopment (central) and is associated with a diversity of genes and biological pathways. In the genetic investigation of individuals with syndromic obesity, the possibility that the etiology of the syndromic condition is independent of obesity should be considered. The accurate genetic diagnosis impacts medical management, treatment, and prognosis, and allows proper genetic counseling.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Alexander Augusto de Lima Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory (LIM/25), Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Débora Romeo Bertola
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
- Genetics Unit of Instituto da Criança, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Laboratory of Human Genetics - LGH, Institute of Biosciences, University of São Paulo (USP), Matão Street 277 - Room 350, São Paulo, SP, Brazil.
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26
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Alieva A, Di Costanzo A, Gazzotti M, Reutova O, Usova E, Bakaleiko V, Arca M, D'Erasmo L, Pellegatta F, Galimberti F, Olmastroni E, Catapano AL, Casula M. Genetic heterogeneity of familial hypercholesterolaemia in two populations from two different countries. Eur J Intern Med 2024:S0953-6205(24)00016-5. [PMID: 38245461 DOI: 10.1016/j.ejim.2024.01.010] [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: 11/13/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND Familial hypercholesterolemia (FH) is a genetically determined monogenic disorder of predominantly autosomal dominant inheritance. A number of studies on differences in the genetic profile of patients with FH have demonstrated the importance of a more substantive evaluation of genetic features. The aim of this study was to evaluate the genetic profile of patients with clinical FH among Italian and Russian patients. METHODS We included 144 Italian and 79 Russian FH patients; clinical diagnosis was based on the same criteria. Patients were divided in: positive to genetic test (one causative variant), inconclusive (only variants of uncertain clinical significance [VUS]), and negative (with likely benign/benign variants, heterozygous variants in LDLRAP1 gene, or without causative variants). RESULTS The genetic test was positive in 76.4 % of the Italian patients and in 49.4 % of the Russian patients. The presence of VUS alone was detected in 7.6 % and in 19.0 % (p < 0.001), respectively. Among patients with positive genetic diagnosis, pre-treatment LDL-C levels were higher in the Russian cohort (353.5 ± 111.3 vs. 302.7 ± 52.1 mg/dL, p = 0.009), as well as the percentage of treated patients (53.8 % vs. 14.5 %, p < 0.001) and the prevalence of premature coronary heart disease (12.8 % vs. 3.6 %, p = 0.039). Among patients carrying only VUS, mean pre-treatment LDL-C levels were similar between the cohorts (299.5 ± 68.1 vs. 295.3 ± 46.8 mg/dL, p = 0.863). Among pathogenic/likely pathogenic variants and VUS, only 5 % and 4 % was shared between the two cohorts, respectively. CONCLUSION The genetic background of patients clinically diagnosed with FH in two different countries is characterized by high variability.
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Affiliation(s)
- Asiiat Alieva
- Almazov National Medical Research Centre, Saint Petersburg, Russia.
| | - Alessia Di Costanzo
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Olga Reutova
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Elena Usova
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | | | - Marcello Arca
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura D'Erasmo
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | | | | | - Elena Olmastroni
- IRCCS MultiMedica, Sesto San Giovanni, Milan, Italy; Epidemiology and Preventive Pharmacology Service (SEFAP), Department of Pharmacological and Biomolecular Sciences (DisFeB), University of Milan, Milan, Italy
| | - Alberico L Catapano
- IRCCS MultiMedica, Sesto San Giovanni, Milan, Italy; Epidemiology and Preventive Pharmacology Service (SEFAP), Department of Pharmacological and Biomolecular Sciences (DisFeB), University of Milan, Milan, Italy
| | - Manuela Casula
- IRCCS MultiMedica, Sesto San Giovanni, Milan, Italy; Epidemiology and Preventive Pharmacology Service (SEFAP), Department of Pharmacological and Biomolecular Sciences (DisFeB), University of Milan, Milan, Italy
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Peng Y, Xue P, Wang R, Shang H, Yao B, Zheng Z, Yan C, Chen W, Xu J. Engineering of an adaptive tandem CRISPR/Cas12a molecular amplifier permits robust analysis of Vibrio parahaemolyticus. Talanta 2024; 266:125061. [PMID: 37567119 DOI: 10.1016/j.talanta.2023.125061] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Seeking new molecular diagnostic method for pathogenic bacteria detection is of utmost importance for ensuring food safety and protecting human health. Herein, we have engineered an adaptive tandem CRISPR/Cas12a molecular amplifier specifically designed for robust analysis of vibrio parahaemolyticus (V. parahaemolyticus), one of the most harmful pathogens. Our strategy involves the integration of three crucial processes: recombinase polymerase amplification (RPA) for copy number amplification, terminal deoxynucleotidyl transferase (TdT) for template-free strand elongation, and CRISPR/Cas12a-mediated trans-cleavage of a reporter molecule. By combining these processes, the target genomic DNA extracted from V. parahaemolyticus is able to activate many CRISPR/Cas12a units (CRISPR/Cas12an) simultaneously, resulting in a greatly amplified target signal to indicate the presence and concentration of V. parahaemolyticus. This unique model offers more advantages compared to traditional amplification models that use one RPA amplicon to activate one CRISPR/Cas12a unit. Under optimized conditions, our method enables the detection of target V. parahaemolyticus within a linear range of 1 × 102-1 × 107 CFU/mL, with an impressive limit of detection as low as 12.4 CFU/mL. It is conceivable that the adaptive tandem CRISPR/Cas12a molecular amplifier could be adapted as routine diagnostic kits in future for in-field detection of pathogens.
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Affiliation(s)
- Yubo Peng
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Pengpeng Xue
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Renjing Wang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Huijie Shang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Bangben Yao
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei, 230009, PR China; Anhui Province Institute of Product Quality Supervision & Inspection, Hefei, 230051, China
| | - Zhi Zheng
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei, 230009, PR China
| | - Chao Yan
- School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Wei Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China.
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China; Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei, 230009, PR China.
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Osorio-Peralta DC, Petano-Duque JM, Rondón-Barragán IS. Leishmania spp. diagnosis and therapeutic management in a cat from urban area in Ibagué (Colombia). Vet Parasitol Reg Stud Reports 2024; 47:100980. [PMID: 38199688 DOI: 10.1016/j.vprsr.2023.100980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Leishmania spp., a protozoan transmitted by sandflies, widely affects humans and dogs in Colombia, nevertheless feline leishmaniasis (FeL) remains understudied. OBJECTIVE This study reports a case of feline leishmaniasis in Colombia and its therapeutic management. METHODS Complete blood count, renal and hepatic serum biochemistry, nodular lesion cytology, FeLV/FIV snap test, abdominal ultrasound, and molecular diagnosis of Leishmania spp. 16 s rRNA gene amplification by real-time-PCR (qPCR), ITS-1 and hsp70 gene by endpoint-PCR and Sanger sequencing were performed. RESULTS The patient was negative for FIV/FeLV and showed leukocytosis, lymphocytosis, thrombocytopenia, neutrophilia, monocytosis, hypergammaglobulinemia, increased gamma-glutamyl-transferase, cortical nephrocalcinosis, diffuse heterogeneous splenic parenchyma, and cholangitis. Nodular lesion cytology, qPCR and Sanger sequencing confirmed the diagnosis of Leishmania spp. The patient was treated with allopurinol and miltefosine. After treatment, clinical signs disappeared. CONCLUSION Clinical examination, cytology, and molecular tests allowed a rapid and sensitive FeL diagnosis. Allopurinol and miltefosine improved the clinical condition of the cat.
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Affiliation(s)
- Diana Catalina Osorio-Peralta
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad of Tolima, Santa Helena Highs, 730006299 Ibagué, Tolima, Colombia
| | - Julieth Michel Petano-Duque
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad of Tolima, Santa Helena Highs, 730006299 Ibagué, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, Universidad of Tolima, Santa Helena Highs, 730006299 Ibagué, Tolima, Colombia.
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Dalal A, Kakker NK, Chaudhary D, Kumar A, Maan NS, Maan S. Co-infection of bluetongue virus serotypes 12 and 16 in sheep from Haryana, India. Vet Res Forum 2023; 14:635-641. [PMID: 38174092 PMCID: PMC10759771 DOI: 10.30466/vrf.2023.1990376.3796] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/17/2023] [Indexed: 01/05/2024]
Abstract
World Organization for Animal Health has listed bluetongue (BT) under notifiable diseases. The BT is an arboviral infectious disease of domestic and wild ruminants caused by the bluetongue virus (BTV). Southern states of India had remained the point of attention for BT since first presence in 1964 in Maharashtra. Recently, northern states of India have also been reported positive for BTV in small ruminants. The present study reported the dual infection of BTV serotypes, BTV-12 and -16 in sheep population from Sirsa district of Haryana in the year 2016. After detection and serotyping with Seg-2 specific real time polymerase chain reaction (PCR), the Seg-2 and Seg-6 of BTV were PCR amplified and sequenced. On phylogenetic analysis it was detected to be clustered in nucleotype G and nucleotype B specific for BTV-12 and BTV-16, respectively. This was the first report of BTV-16 from Haryana. The results signified the co-infection of two different serotypes in an animal from a single outbreak.
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Affiliation(s)
- Anita Dalal
- Department of Veterinary Microbiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India;
| | - Naresh Kumar Kakker
- Department of Veterinary Microbiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India;
| | - Deepika Chaudhary
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India;
| | - Aman Kumar
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India;
| | - Narender Singh Maan
- Department of Animal Nutrition College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India.
| | - Sushila Maan
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India;
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Gondard M, Lane M, Barratt J, Talundzic E, Qvarnstrom Y. Simultaneous targeted amplicon deep sequencing and library preparation for a time and cost-effective universal parasite diagnostic sequencing approach. Parasitol Res 2023; 122:3243-3256. [PMID: 37940706 PMCID: PMC10772880 DOI: 10.1007/s00436-023-07991-4] [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: 03/01/2023] [Accepted: 09/26/2023] [Indexed: 11/10/2023]
Abstract
We recently described a targeted amplicon deep sequencing (TADS) strategy that utilizes a nested PCR targeting the 18S rDNA gene of blood-borne parasites. The assay facilitates selective digestion of host DNA by targeting enzyme restriction sites present in vertebrates but absent in parasites. This enriching of parasite-derived amplicon drastically reduces the proportion of host-derived reads during sequencing and results in the sensitive detection of several clinically important blood parasites including Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes. Despite these promising results, high costs and the laborious nature of metagenomics sequencing are prohibitive to the routine use of this assay in most laboratories. We describe and evaluate a new metagenomic approach that utilizes a set of primers modified from our original assay that incorporates Illumina barcodes and adapters during the PCR steps. This modification makes amplicons immediately compatible with sequencing on the Illumina MiSeq platform, removing the need for a separate library preparation, which is expensive and time-consuming. We compared this modified assay to our previous nested TADS assay in terms of preparation speed, limit of detection (LOD), and cost. Our modifications reduced assay turnaround times from 7 to 5 days. The cost decreased from approximately $40 per sample to $11 per sample. The modified assay displayed comparable performance in the detection and differentiation of human-infecting Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes in clinical samples. The LOD of this modified approach was determined for malaria parasites and remained similar to that previously reported for our earlier assay (0.58 Plasmodium falciparum parasites/µL of blood). These modifications markedly reduced costs and turnaround times, making the assay more amenable to routine diagnostic applications.
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Affiliation(s)
- Mathilde Gondard
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Meredith Lane
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Synergy America Inc., Duluth, GA, USA
| | - Joel Barratt
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eldin Talundzic
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yvonne Qvarnstrom
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Xie X, Shen C, Zhang X, Wu G, Yang B, Qi Z, Tang Q, Wang Y, Ding H, Shi Z, Yu J. Rapid intraoperative multi- molecular diagnosis of glioma with ultrasound radio frequency signals and deep learning. EBioMedicine 2023; 98:104899. [PMID: 38041959 PMCID: PMC10711390 DOI: 10.1016/j.ebiom.2023.104899] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND Molecular diagnosis is crucial for biomarker-assisted glioma resection and management. However, some limitations of current molecular diagnostic techniques prevent their widespread use intraoperatively. With the unique advantages of ultrasound, this study developed a rapid intraoperative molecular diagnostic method based on ultrasound radio-frequency signals. METHODS We built a brain tumor ultrasound bank with 169 cases enrolled since July 2020, of which 43483 RF signal patches from 67 cases with a pathological diagnosis of glioma were a retrospective cohort for model training and validation. IDH1 and TERT promoter (TERTp) mutations and 1p/19q co-deletion were detected by next-generation sequencing. We designed a spatial-temporal integration model (STIM) to diagnose the three molecular biomarkers, thus establishing a rapid intraoperative molecular diagnostic system for glioma, and further analysed its consistency with the fifth edition of the WHO Classification of Tumors of the Central Nervous System (WHO CNS5). We tested STIM in 16-case prospective cohorts, which contained a total of 10384 RF signal patches. Two other RF-based classical models were used for comparison. Further, we included 20 cases additional prospective data for robustness test (ClinicalTrials.govNCT05656053). FINDINGS In the retrospective cohort, STIM achieved a mean accuracy and AUC of 0.9190 and 0.9650 (95% CI, 0.94-0.99) respectively for the three molecular biomarkers, with a total time of 3 s and a 96% match to WHO CNS5. In the prospective cohort, the diagnostic accuracy of STIM is 0.85 ± 0.04 (mean ± SD) for IDH1, 0.84 ± 0.05 for TERTp, and 0.88 ± 0.04 for 1p/19q. The AUC is 0.89 ± 0.02 (95% CI, 0.84-0.94) for IDH1, 0.80 ± 0.04 (95% CI, 0.71-0.89) for TERTp, and 0.85 ± 0.06 (95% CI, 0.73-0.98) for 1p/19q. Compared to the second best available method based on RF signal, the diagnostic accuracy of STIM is improved by 16.70% and the AUC is improved by 19.23% on average. INTERPRETATION STIM is a rapid, cost-effective, and easy-to-manipulate AI method to perform real-time intraoperative molecular diagnosis. In the future, it may help neurosurgeons designate personalized surgical plans and predict survival outcomes. FUNDING A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.
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Affiliation(s)
- Xuan Xie
- School of Information Science and Technology, Fudan University, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China
| | - Chao Shen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China
| | - Xiandi Zhang
- Department of Ultrasound, Huashan Hospital, Fudan University, Shanghai, China
| | - Guoqing Wu
- School of Information Science and Technology, Fudan University, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China
| | - Bojie Yang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China
| | - Zengxin Qi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China
| | - Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China
| | - Yuanyuan Wang
- School of Information Science and Technology, Fudan University, Shanghai, China
| | - Hong Ding
- Department of Ultrasound, Huashan Hospital, Fudan University, Shanghai, China.
| | - Zhifeng Shi
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China.
| | - Jinhua Yu
- School of Information Science and Technology, Fudan University, Shanghai, China; Neurosurgical Institute of Fudan University, Shanghai, China.
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Akbaba TH, Ekici M, Çolpak Aİ, Brown KL, Karadağ Ö, Balci-Peynircioglu B. Behçet's syndrome: recent advances to aid diagnosis. Clin Exp Med 2023; 23:4079-4090. [PMID: 37897656 DOI: 10.1007/s10238-023-01226-7] [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: 09/19/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023]
Abstract
Behçet's syndrome is a recurring inflammatory multiorgan disorder affecting the skin, mucosa, eyes, joints, stomach, and central nervous system. Behçet's syndrome epidemiology varies greatly among populations (0.64-420/100,000), and Behçet's syndrome has gained increasing international acclaim in the recent 50 years due to raising awareness of the syndrome, although it is rare in most population. In addition to the unclear etiology of the syndrome, the diagnosis of Behçet's syndrome is complicated by a vague clinical presentation, phenotypic heterogeneity and/or incomplete representation, and the lack of any specific laboratory, radiographic, or histological findings. There exists a dire need to elucidate factors that contribute to disease pathogenesis and/or are associated with clinical features of Behçet's syndrome and the classification of different forms of the syndrome. The identification of such molecular, cellular, and/or clinical factors are crucial for timely diagnosis and efficacious management of Behçet's syndrome. We discuss recent advances in the clinical diagnosis of Behçet's syndrome and related contributions of genetics, epigenetics, microbiome, inflammasomes, and autoantibodies to the improved diagnosis, management, and understanding of Behçet's syndrome.
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Affiliation(s)
- Tayfun Hilmi Akbaba
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- BC Children's Hospital Research Institute, Vancouver, Canada
- Division of Rheumatology, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mustafa Ekici
- Division of Rheumatology, Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Ayşe İlksen Çolpak
- Department of Neurology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Kelly L Brown
- BC Children's Hospital Research Institute, Vancouver, Canada
- Division of Rheumatology, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Ömer Karadağ
- Division of Rheumatology, Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Lee J, Moon K, Cho S, Lim Y, Kim S, Kim SB, Han SM, Kim YH, Lee SH. Establishment and application of bioassay- and molecular marker-based methods for monitoring fluvalinate resistance of Varroa mites. Pestic Biochem Physiol 2023; 197:105655. [PMID: 38072530 DOI: 10.1016/j.pestbp.2023.105655] [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: 09/05/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023]
Abstract
The Varroa mite, Varroa destructor, is an ectoparasite that infests honey bees. The extensive use of acaricides, including fluvalinate, has led to the emergence of resistance in Varroa mite populations worldwide. This study's objective is to monitor fluvalinate resistance in field populations of Varroa mites in Korea through both bioassay-based and molecular marker-based methods. To achieve this, a residual contact vial (RCV) bioassay was established for on-site resistance monitoring. A diagnostic dose of 200 ppm was determined based on the bioassay using a putative susceptible population. In the RCV bioassay, early mortality evaluation was effective for accurately discriminating mites with the knockdown resistance (kdr) genotype, while late evaluation was useful for distinguishing mites with additional resistance factors. The RCV bioassay of 14 field mite populations collected in 2021 indicated potential resistance development in four populations. As an alternative approach, quantitative sequencing was employed to assess the frequency of the L925I/M mutation in the voltage-gated sodium channel (VGSC), associated with fluvalinate kdr trait. While the mutation was absent in 2020 Varroa mite populations, it emerged in 2021, increased in frequency in 2022, and became nearly widespread across the country by 2023. This recent emergence and rapid spread of fluvalinate resistance within a span of three years demonstrate the Varroa mite's significant potential for developing resistance. This situation further underscores the urgent need to replace fluvalinate with alternative acaricides. A few novel VGSC mutations potentially involved in resistance were identified. Potential factors driving the rapid expansion of resistance were further discussed.
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Affiliation(s)
- Joonhee Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - KyungHwan Moon
- Department of Vector Entomology, Kyungpook National University, Sangju, Republic of Korea
| | - SuSie Cho
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Youngcheon Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghyeon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Su-Bae Kim
- Apiculture Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Wanju, Republic of Korea
| | - Sang-Mi Han
- Apiculture Division, Department of Agricultural Biology, National Institute of Agricultural Sciences, Wanju, Republic of Korea.
| | - Young Ho Kim
- Department of Vector Entomology, Kyungpook National University, Sangju, Republic of Korea; Research Institute of Invertebrate Vector, Kyungpook National University, Sangju, Republic of Korea.
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Muñoz-Ramírez CP, Colin N, Canales-Aguirre CB, Manosalva A, López-Rodríguez R, Sukumaran J, Górski K. Species tree analyses and speciation-based species delimitation support new species in the relict catfish family Diplomystidae and provide insights on recent glacial history in Patagonia. Mol Phylogenet Evol 2023; 189:107932. [PMID: 37751827 DOI: 10.1016/j.ympev.2023.107932] [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: 03/10/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 09/28/2023]
Abstract
Diplomystidae is an early-diverged family of freshwater catfish endemic to southern South America. We have recently collected five juvenile specimens belonging to this family from the Bueno River Basin, a basin which the only previous record was a single juvenile specimen collected in 1996. This finding confirms the distribution of the family further South in northern Patagonia, but poses new questions about the origin of this population in an area with a strong glacial history. We used phylogenetic analyses to evaluate three different hypotheses that could explain the origin of this population in the basin. First, the population could have originated in Atlantic basins (East of the Andes) and dispersed to the Bueno Basin after the Last Glacial Maximum (LGM) via river reversals, as it has been proposed for other population of Diplomystes as well as for other freshwater species from Patagonia. Second, the population could have originated in the geographically close Valdivia Basin (West of the Andes) and dispersed south to its current location in the Bueno Basin. Third, regardless of its geographic origin (West or East of the Andes), the Bueno Basin population could have a longer history in the basin, surviving in situ through the LGM. In addition, we conducted species delimitation analyses using a recently developed method that uses a protracted model of speciation. Our goal was to test the species status of the Bueno Basin population along with another controversial population in Central Chile (Biobío Basin), which appeared highly divergent in previous studies with mtDNA. The phylogenetic analyses showed that the population from the Bueno Basin is more related to Atlantic than to Pacific lineages, although with a deep divergence that predated the LGM, supporting in situ survival rather than postglacial dispersal. In addition, these analyses also showed that the species D. nahuelbutaensis is polyphyletic, supporting the need for a taxonomic reevaluation. The species delimitation analyses supported two new species which are described using molecular diagnostic characters: Diplomystes arratiae sp. nov. from the Biobío, Carampangue, and Laraquete basins, maintaining D. nahuelbutaensis valid only for the Imperial Basin, and Diplomystes habitae sp. nov. from the Bueno Basin. This study greatly increases the number of species within both the family Diplomystidae and Patagonia, and contributes substantially to the knowledge of the evolution of southern South American freshwater biodiversity during its glacial history. Given the important contribution to the phylogenetic diversity of the family, we recommend a high conservation priority for both new species. Finally, this study highlights an exemplary scenario where species descriptions based only on DNA data are particularly valuable, bringing additional elements to the ongoing debate on DNA-based taxonomy.
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Affiliation(s)
- Carlos P Muñoz-Ramírez
- Instituto de Entomología, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - Nicole Colin
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Cristian B Canales-Aguirre
- Centro i∼mar, Universidad de Los Lagos, Camino a Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio INVASAL, Concepción, Chile
| | - Aliro Manosalva
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA, Universidad de Concepción, Chile
| | - Ruby López-Rodríguez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Konrad Górski
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile.
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Hassanpour P, Spotin A, Morovati H, Aghebati-Maleki L, Raeisi M, Rezaee MA, Hasani A, Aghebati-Maleki A, Abdollahzadeh H, Nami S. Molecular diagnosis, phylogenetic analysis, and antifungal susceptibility profiles of Candida species isolated from neutropenic oncological patients. BMC Infect Dis 2023; 23:765. [PMID: 37932679 PMCID: PMC10629196 DOI: 10.1186/s12879-023-08774-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Neutropenia is the most important cause of life-threatening invasive fungal infections (IFIs). Here, we studied the frequency and antifungal susceptibility profiles of Candida species that colonized or caused infections among neutropenic patients with solid or hematological malignancies. METHODS A total of 362 clinical samples were collected from 138 patients. After initial isolation using a mix of mycological methods, isolates were screened using chromogenic culture media. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was applied for molecular identification. Positive or suspected cases were confirmed using the reference method of sequencing. Antifungal susceptibility testing for voriconazole and caspofungin was carried out using the microbroth dilution method. An in-silico assay was applied for phylogenetic analysis. RESULTS Thirty-four Candida strains were isolated. C. albicans (47.06%) and C. glabrata (29.41%) were the most frequent strains. Antifungal treatment reduced the chance of Candida colonization by almost 76% in neutropenic patients (OR: 1.759; 95% CI: 1.349 to 2.390; p value: 0.000). An unusual and non-resistant strain, C. lambica, was reported from the bloodstream of a 56-year-old man with hematologic malignancy (HM). Eight isolates were non-susceptible, and one isolate was resistant to voriconazole. Also, four isolates were non-susceptible to caspofungin. CONCLUSION We can conclude that there is a cause-and-effect relationship between neutropenia, HM background, and Candida species separated from neutropenic patients, which can lead to possible infections. Further and repetitive studies are recommended using different molecular methods for better prediction and management of fungal infections in neutropenic patients.
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Affiliation(s)
- Parviz Hassanpour
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Adel Spotin
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Morovati
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Alka Hasani
- Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Aghebati-Maleki
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Abdollahzadeh
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sanam Nami
- Department of Parasitology and Mycology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Portanti O, Thabet S, Abenza E, Ciarrocchi E, Pisciella M, Irelli R, Savini G, Hammami S, Pulsoni S, Casaccia C, Coetzee L, Marcacci M, Di Domenico M, Lorusso A. Development and validation of an RT-qPCR for detection and quantitation of emerging epizootic hemorrhagic disease virus serotype 8 RNA from field samples. J Virol Methods 2023; 321:114808. [PMID: 37690747 DOI: 10.1016/j.jviromet.2023.114808] [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: 07/19/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
Epizootic hemorrhagic disease virus (EHDV) is a Culicoides-transmitted virus circulating in multiple serotypes. It has become a concern in the European Union as a novel strain of the serotype 8 (EHDV-8) of clear Northern African origin, has been recently discovered in symptomatic cattle in Italy (islands of Sardinia and Sicily), Spain, and Portugal. Current molecular typing methods targeting the S2 nucleotide sequences -coding for the outermost protein of the virion VP2- are not able to detect the novel emerging EHDV-8 strain as they enrolled the S2 sequence of the unique EHDV-8 reference strain isolated in Australia in 1982. Thus, in this study, we developed and validated a novel typing assay for the detection and quantitation of the novel EHDV-8 RNA from field samples, including blood of ruminants and insects. This molecular tool will certainly support EHDV-8 surveillance and control.
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Affiliation(s)
- Ottavio Portanti
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Sarah Thabet
- Service de Microbiologie, Immunologie et Pathologie Générale, École Nationale de Médecine Vétérinaire de Sidi Thabet, IRESA, Université de la Manouba, Tunisia
| | - Elena Abenza
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Eugenia Ciarrocchi
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Maura Pisciella
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Roberta Irelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Salah Hammami
- Service de Microbiologie, Immunologie et Pathologie Générale, École Nationale de Médecine Vétérinaire de Sidi Thabet, IRESA, Université de la Manouba, Tunisia
| | - Simone Pulsoni
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Claudia Casaccia
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Lauren Coetzee
- Central Veterinary Laboratory (CVL), 24 Goethe Street, Private Bag 18137 Windhoek, Namibia; Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise, Campo Boario, 64100 Teramo, Italy.
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Pereira DCA, Teixeira-Neto RG, Lopes VV, Pena HP, Paz GF, Custodio CHX, Belo VS, da Fonseca Júnior AA, da Silva ES. Development of quantitative PCR and digital PCR for the quantification of Leishmania infantum in dogs. Mol Cell Biochem 2023; 478:2445-2450. [PMID: 36790551 DOI: 10.1007/s11010-023-04672-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Abstract
Leishmaniasis is a zoonotic disease with worldwide distribution. In the Americas, the causative agent of the visceral form is the protozoa Leishmania (Leishmania) infantum. Transmission to the host or vertebrate reservoir occurs through the bite of infected arthropod females like Lutzomyia longipalpis. The epidemiological connection between the infection in dogs and humans generate constant studies about the relationship between the parasite and the canine host, including the development of methods and tests for the detection and quantification ofLeishmania (L.) infantum. Both conventional PCR (cPCR) and quantitative PCR (qPCR) can be used in the diagnosis of the parasite. Dropet Digital PCR (ddPCR) is another useful tool. Knowing the parasite load and its relationship with the clinical signs of naturally infected dogs is useful in research development and for establishing treatments that reduce the transmission of the disease. In this study, thirty-nine clinical samples of spleen from dogs naturaly infected by L. infantum were collected after necropsy. Two molecular tools were used to quantify the parasite load (qPCR and ddPCR) and there was 100% agreement in the results of the them. The tools developed in this work are important for the detection of L. infantum in dogs and humans. Droplet Digital PCR does not require a standard curve and is easy to standardize. In such manner, this new tool can generate more in-depth information in the broad debate about parasitic loads and the pathogenesis of leishmaniasis.
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Affiliation(s)
| | | | - Valeriana Valadares Lopes
- Universidade Federal de São João Del Rei (UFSJ), Campus Centro-Oeste Dona Lindu, Divinópolis, Brazil
| | - Héber Paulino Pena
- Universidade Federal de São João Del Rei (UFSJ), Campus Centro-Oeste Dona Lindu, Divinópolis, Brazil
| | | | | | - Vinícius Silva Belo
- Universidade Federal de São João Del Rei (UFSJ), Campus Centro-Oeste Dona Lindu, Divinópolis, Brazil
| | | | - Eduardo Sérgio da Silva
- Universidade Federal de São João Del Rei (UFSJ), Campus Centro-Oeste Dona Lindu, Divinópolis, Brazil.
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Hermsen MA, Lechner M, Oliveira Ferrer L, Trama A, Eriksen PRG, Martinez-Balibrea E, von Buchwald C. EUSICA/COST IMMUNO-model workshop fostering collaboration to advance sinonasal cancer research: A meeting report. Oral Oncol 2023; 146:106543. [PMID: 37573683 DOI: 10.1016/j.oraloncology.2023.106543] [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: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
Sinonasal cancer is a clinically and histologically heterogeneous group of rare tumors with generally poor clinical outcomes. Their low incidence hampers the advancement of clinical management as well as translational research, and calls for multicenter and multinational collaboration between physicians and researchers. This report describes the proceedings of a two-day conference organized by the European Network for Sinonasal Cancer Research (EUSICA) and COST Action 'IMMUNO-model', fostering such collaboration and focusing on preclinical tumor and immuno models, surgical and radio-oncological treatments, core facilities for genetic characterization and molecular tumor classification, and cancer registry.
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Affiliation(s)
- Mario A Hermsen
- Dept Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain.
| | - Matt Lechner
- CL Division of Surgery and Interventional Science and UCL Cancer Institute, University College London, London, UK
| | | | - Annalisa Trama
- Fondazione IRCCS Istituto Nazionale dei Tumori di milano, Milan, Italy
| | - Patrick René Gerhard Eriksen
- Dept Otorhinolaryngology, Head and Neck Surgery & Audiology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Eva Martinez-Balibrea
- Procure Program, Catalan Institue of Oncology and CARE Program, Germans Trias I Pujol Research Institute, Badalona, Spain
| | - Christian von Buchwald
- Dept Otorhinolaryngology, Head and Neck Surgery & Audiology, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
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Andargie TE, Roznik K, Redekar N, Hill T, Zhou W, Apalara Z, Kong H, Gordon O, Meda R, Park W, Johnston TS, Wang Y, Brady S, Ji H, Yanovski JA, Jang MK, Lee CM, Karaba AH, Cox AL, Agbor-Enoh S. Cell-free DNA reveals distinct pathology of multisystem inflammatory syndrome in children. J Clin Invest 2023; 133:e171729. [PMID: 37651206 PMCID: PMC10617770 DOI: 10.1172/jci171729] [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: 05/01/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare but life-threatening hyperinflammatory condition induced by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes pediatric COVID-19 (pCOVID-19). The relationship of the systemic tissue injury to the pathophysiology of MIS-C is poorly defined. We leveraged the high sensitivity of epigenomics analyses of plasma cell-free DNA (cfDNA) and plasma cytokine measurements to identify the spectrum of tissue injury and glean mechanistic insights. Compared with pediatric healthy controls (pHCs) and patients with pCOVID-19, patients with MIS-C had higher levels of cfDNA primarily derived from innate immune cells, megakaryocyte-erythroid precursor cells, and nonhematopoietic tissues such as hepatocytes, cardiac myocytes, and kidney cells. Nonhematopoietic tissue cfDNA levels demonstrated significant interindividual variability, consistent with the heterogenous clinical presentation of MIS-C. In contrast, adaptive immune cell-derived cfDNA levels were comparable in MIS-C and pCOVID-19 patients. Indeed, the cfDNA of innate immune cells in patients with MIS-C correlated with the levels of innate immune inflammatory cytokines and nonhematopoietic tissue-derived cfDNA, suggesting a primarily innate immunity-mediated response to account for the multisystem pathology. These data provide insight into the pathogenesis of MIS-C and support the value of cfDNA as a sensitive biomarker to map tissue injury in MIS-C and likely other multiorgan inflammatory conditions.
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Affiliation(s)
- Temesgen E. Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
- Department of Biology, Howard University, Washington DC, USA
| | - Katerina Roznik
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Neelam Redekar
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Tom Hill
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Oren Gordon
- Infectious Diseases Unit, Department of Pediatrics, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rohan Meda
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Woojin Park
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Trevor S. Johnston
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Yi Wang
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sheila Brady
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, Maryland, USA
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jack A. Yanovski
- Section on Growth and Obesity, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, Maryland, USA
| | - Moon K. Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
| | - Clarence M. Lee
- Department of Biology, Howard University, Washington DC, USA
| | - Andrew H. Karaba
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA. GFAfT is detailed in Supplemental Acknowledgments
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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Welch CL, Aldred MA, Balachandar S, Dooijes D, Eichstaedt CA, Gräf S, Houweling AC, Machado RD, Pandya D, Prapa M, Shaukat M, Southgate L, Tenorio-Castano J, Chung WK. Defining the clinical validity of genes reported to cause pulmonary arterial hypertension. Genet Med 2023; 25:100925. [PMID: 37422716 PMCID: PMC10766870 DOI: 10.1016/j.gim.2023.100925] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE Pulmonary arterial hypertension (PAH) is a rare, progressive vasculopathy with significant cardiopulmonary morbidity and mortality. Genetic testing is currently recommended for adults diagnosed with heritable, idiopathic, anorexigen-, hereditary hemorrhagic telangiectasia-, and congenital heart disease-associated PAH, PAH with overt features of venous/capillary involvement, and all children diagnosed with PAH. Variants in at least 27 genes have putative evidence for PAH causality. Rigorous assessment of the evidence is needed to inform genetic testing. METHODS An international panel of experts in PAH applied a semi-quantitative scoring system developed by the NIH Clinical Genome Resource to classify the relative strength of evidence supporting PAH gene-disease relationships based on genetic and experimental evidence. RESULTS Twelve genes (BMPR2, ACVRL1, ATP13A3, CAV1, EIF2AK4, ENG, GDF2, KCNK3, KDR, SMAD9, SOX17, and TBX4) were classified as having definitive evidence and 3 genes (ABCC8, GGCX, and TET2) with moderate evidence. Six genes (AQP1, BMP10, FBLN2, KLF2, KLK1, and PDGFD) were classified as having limited evidence for causal effects of variants. TOPBP1 was classified as having no known PAH relationship. Five genes (BMPR1A, BMPR1B, NOTCH3, SMAD1, and SMAD4) were disputed because of a paucity of genetic evidence over time. CONCLUSION We recommend that genetic testing includes all genes with definitive evidence and that caution be taken in the interpretation of variants identified in genes with moderate or limited evidence. Genes with no known evidence for PAH or disputed genes should not be included in genetic testing.
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Affiliation(s)
- Carrie L Welch
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, IN
| | - Srimmitha Balachandar
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Indiana University School of Medicine, IN
| | - Dennis Dooijes
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Christina A Eichstaedt
- Center for Pulmonary Hypertension, Thoraxklinik-Heidelberg gGmbH, at Heidelberg University Hospital and Translational Lung Research Center, German Center for Lung Research, Heidelberg, Germany; Laboratory for Molecular Genetic Diagnostics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Stefan Gräf
- NIHR BioResource for Translational Research - Rare Diseases, Department of Haemotology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom; Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Arjan C Houweling
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rajiv D Machado
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom
| | - Divya Pandya
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Matina Prapa
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom; St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Memoona Shaukat
- Center for Pulmonary Hypertension, Thoraxklinik-Heidelberg gGmbH, at Heidelberg University Hospital and Translational Lung Research Center, German Center for Lung Research, Heidelberg, Germany; Laboratory for Molecular Genetic Diagnostics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Laura Southgate
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, United Kingdom
| | - Jair Tenorio-Castano
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IDiPAZ, Universidad Autonoma de Madrid, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; ITHACA, European Reference Network, Brussels, Belgium
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY; Department of Medicine, Columbia University Irving Medical Center, New York, NY.
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Pascual-Vázquez G, Alonso-Sardón M, Rodríguez-Alonso B, Pardo-Lledías J, Romero Alegría A, Fernández-Soto P, Muñoz Bellido JL, Muro A, Belhassen-García M. Molecular diagnosis of Chagas disease: a systematic review and meta-analysis. Infect Dis Poverty 2023; 12:95. [PMID: 37845734 PMCID: PMC10577976 DOI: 10.1186/s40249-023-01143-7] [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: 03/20/2023] [Accepted: 08/20/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND The complexity of the Chagas disease and its phases is impossible to have a unique test for both phases and a lot of different epidemiological scenarios. Currently, serology is the reference standard technique; occasionally, results are inconclusive, and a different diagnostic technique is needed. Some guidelines recommend molecular testing. A systematic review and meta-analysis of available molecular tools/techniques for the diagnosis of Chagas disease was performed to measure their heterogeneity and efficacy in detecting Trypanosoma cruzi infection in blood samples. METHODS A systematic review was conducted up to July 27, 2022, including studies published in international databases. Inclusion and exclusion criteria were defined to select eligible studies. Data were extracted and presented according to PRISMA 2020 guidelines. Study quality was assessed using Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2). A random-effects model was used to calculate pooled sensitivity, specificity, and diagnostic odds ratio (DOR). Forest plots and a summary of the receiving operating characteristics (SROC) curves displayed the outcomes. Heterogeneity was determined by I2 and Tau2 statistics and P values. Funnel plots and Deek's test were used to assess publication bias. A quantitative meta-analysis of the different outcomes in the two different clinical phases was performed. RESULTS We identified 858 records and selected 32 papers. Studies pertained to endemic countries and nonendemic areas with adult and paediatric populations. The sample sizes ranged from 17 to 708 patients. There were no concerns regarding the risk of bias and applicability of all included studies. A positive and nonsignificant correlation coefficient (S = 0.020; P = 0.992) was obtained in the set of studies that evaluated diagnostic tests in the acute phase population (ACD). A positive and significant correlation coefficient (S = 0.597; P < 0.000) was obtained in the case of studies performed in the chronic phase population (CCD). This resulted in high heterogeneity between studies, with the master mix origin and guanidine addition representing significant sources. INTERPRETATION/CONCLUSIONS AND RELEVANCE The results described in this meta-analysis (qualitative and quantitative analyses) do not allow the selection of the optimal protocol of molecular method for the study of Trypanosoma cruzi infection in any of its phases, among other reasons due to the complexity of this infection. Continuous analysis and optimization of the different molecular techniques is crucial to implement this efficient diagnosis in endemic areas.
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Affiliation(s)
- Guillermo Pascual-Vázquez
- Infectious and Tropical Diseases Group (E-INTRO), Biomedical Research Institute of Salamanca (IBSAL), Tropical Diseases Research Center of the University of Salamanca (CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Montserrat Alonso-Sardón
- Area of Preventive Medicine, Epidemiology and Public Health, Department of Biomedical and Diagnostic Sciences, Faculty of Medicine, E-INTRO, IBSAL, CIETUS, University of Salamanca, Salamanca, Spain
| | - Beatriz Rodríguez-Alonso
- Internal Medicine Service, University Health Care Complex of Salamanca (CAUSA), E-INTRO, IBSAL, CIETUS, Salamanca, Spain
| | - Javier Pardo-Lledías
- Internal Medicine Department, Hospital Marqués de Valdecilla, University of Cantabria, IDIVAL (Valdecilla Research Institute), Santander, Spain
| | | | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Group (E-INTRO), IBSAL. CIETUS. Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Juan Luis Muñoz Bellido
- Microbiology and Parasitology Service, CAUSA, IBSAL, CIETUS, CSIC, Department of Biomedical and Diagnostic Sciences, University of Salamanca, Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Group (E-INTRO), IBSAL. CIETUS. Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - Moncef Belhassen-García
- Internal Medicine Service. Infectious Diseases Section, CAUSA, IBSAL, CIETUS, University of Salamanca, Paseo San Vicente 58-182, 37007, Salamanca, Spain.
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Hwu WL. Deciphering the diagnostic dilemma: A comprehensive review of the Taiwanese cardiac variant in Fabry disease. J Formos Med Assoc 2023:S0929-6646(23)00402-3. [PMID: 37833114 DOI: 10.1016/j.jfma.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/21/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Molecular diagnosis has undergone rapid and significant advancements in recent years. But because molecular diagnosis can be conducted independently of phenotype, it can engender ambiguity and potential misinterpretations in disease diagnosis. Fabry disease, an X-linked lysosomal storage disorder, arises from a deficiency in α-galactosidase A. In 2002, Ishii and colleagues uncovered a variant (IVS4+919G > A) deep within intron 4 of the GLA gene that could lead to aberrant splicing of the GLA mRNA. This variant is present in 1:875 males in Taiwan, and many patients with hypertrophic cardiomyopathy and the IVS4+919G > A variant are currently treated by enzyme replacement therapy, an expensive treatment. Unfortunately, till now only one article published in 2013 described the outcome of treatment. This review summarized the conflicting evidence about the clinical relevance of the IVS4+919G > A variant, and suggest a multifactorial model, rather than a monogenic model, for the involvement of the IVS4+919G > A variant in hypertrophic cardiomyopathy. The diagnostic dilemma for this Taiwanese cardiac variant in Fabry disease clearly emphasizes the need for precise interpretation and application of molecular diagnostic results.
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Affiliation(s)
- Wuh-Liang Hwu
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
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Li Y, Kang T, Park HG. One-pot, ultrasensitive, and multiplex detection of SARS-CoV-2 genes utilizing self-priming hairpin-mediated isothermal amplification. Biosens Bioelectron 2023; 237:115522. [PMID: 37437457 DOI: 10.1016/j.bios.2023.115522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
The global pandemic resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its emerging variants highlights the need for convenient and accurate detection protocols to facilitate timely prevention and management of the disease. Herein, we propose a new self-priming hairpin-mediated isothermal amplification (SIAM) protocol enabling one-pot and ultrasensitive identification of SARS-CoV-2 in a multiplexed way. This approach works by targeting a specific RNA sequence with a self-priming hairpin (SP) probe and promoting continuously repeated extension and nicking reactions to produce numerous trigger molecules, which could specifically bind to molecular beacons (MBs) and produce fluorescent signals. Under an isothermal condition of 37 °C, this technique allowed for the simultaneous identification of the spike (S) and nucleocapsid (N) genes of SARS-CoV-2 down to single copy/μL levels. We further validated the practical diagnostic capabilities of the SIAM method by accurately testing 20 clinical samples with 100% sensitivity and specificity. The SIAM method has a lot of potential to be a reliable nucleic acid testing protocol to identify infections caused by a wide range of pathogens.
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Affiliation(s)
- Yan Li
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Levy M, Bazak L, Lev-El N, Greenberg R, Kropach N, Basel-Salmon L, Maya I. Potential Founder Variants in COL4A4 Identified in Bukharian Jews Linked to Autosomal Dominant and Autosomal Recessive Alport Syndrome. Genes (Basel) 2023; 14:1854. [PMID: 37895203 PMCID: PMC10606019 DOI: 10.3390/genes14101854] [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: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Alport syndrome is a hereditary disorder caused by pathogenic variants in the COL4A gene, which can be inherited in an autosomal recessive, dominant, or X-linked pattern. In the Bukharian Jewish population, no founder pathogenic variant has been reported in COL4A4. METHODS The cohort included 38 patients from 22 Bukharian Jewish families with suspected Alport syndrome who were referred the nephrogenetics clinic between 2012 and 2022. The study collected demographic, clinical, and genetic data from electronic medical records, which were used to evaluate the molecular basis of the disease using Sanger sequencing, and next-generation sequencing. RESULTS Molecular diagnosis was confirmed in 20/38 patients, with each patient having at least one of the three disease-causing COL4A4 variants detected: c.338G A (p.Gly1008Arg), and c.871-6T>C. In addition, two patients were obligate carriers. Overall, there were 17 heterozygotes, 2 compound heterozygotes, and 3 homozygotes. Each variant was detected in more than one unrelated family. All patients had hematuria with/without proteinuria at referral, and the youngest patient with proteinuria (age 5 years) was homozygous for the c.338G>A variant. End-stage renal disease was diagnosed in two patients at the age of 38 years, a compound heterozygote for c.338G>A and c.871-6T>C. Hearing deterioration was detected in three patients, the youngest aged 40 years, all of whom were heterozygous for c.338G>A. CONCLUSION This study unveils three novel disease-causing variants, c.3022G>A, c.871-6T>C, and c.338G>A, in the COL4A4 gene that are recurrent among Jews of Bukharian ancestry, and cause Alport syndrome in both dominant and recessive autosomal inheritance patterns.
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Affiliation(s)
- Michal Levy
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
| | - Lily Bazak
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Noa Lev-El
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Rotem Greenberg
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Nesia Kropach
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva 4920235, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Felsenstein Medical Research Center, Petach Tikva 4920235, Israel
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
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Sato M, Neufeld EB, Playford MP, Lei Y, Sorokin AV, Aponte AM, Freeman LA, Gordon SM, Dey AK, Jeiran K, Hamasaki M, Sampson ML, Shamburek RD, Tang J, Chen MY, Kotani K, Anderson JL, Dullaart RP, Mehta NN, Tietge UJ, Remaley AT. Cell-free, high-density lipoprotein-specific phospholipid efflux assay predicts incident cardiovascular disease. J Clin Invest 2023; 133:e165370. [PMID: 37471145 PMCID: PMC10503808 DOI: 10.1172/jci165370] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/18/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUNDCellular cholesterol efflux capacity (CEC) is a better predictor of cardiovascular disease (CVD) events than HDL-cholesterol (HDL-C) but is not suitable as a routine clinical assay.METHODSWe developed an HDL-specific phospholipid efflux (HDL-SPE) assay to assess HDL functionality based on whole plasma HDL apolipoprotein-mediated solubilization of fluorescent phosphatidylethanolamine from artificial lipid donor particles. We first assessed the association of HDL-SPE with prevalent coronary artery disease (CAD): study I included NIH severe-CAD (n = 50) and non-CAD (n = 50) participants, who were frequency matched for sex, BMI, type 2 diabetes mellitus, and smoking; study II included Japanese CAD (n = 70) and non-CAD (n = 154) participants. We also examined the association of HDL-SPE with incident CVD events in the Prevention of Renal and Vascular End-stage Disease (PREVEND) study comparing 340 patients with 340 controls individually matched for age, sex, smoking, and HDL-C levels.RESULTSReceiver operating characteristic curves revealed stronger associations of HDL-SPE with prevalent CAD. The AUCs in study I were as follows: HDL-SPE, 0.68; apolipoprotein A-I (apoA-I), 0.62; HDL-C, 0.63; and CEC, 0.52. The AUCs in study II were as follows: HDL-SPE, 0.83; apoA-I, 0.64; and HDL-C, 0.53. Also longitudinally, HDL-SPE was significantly associated with incident CVD events independent of traditional risk factors with ORs below 0.2 per SD increment in the PREVEND study (P < 0.001).CONCLUSIONHDL-SPE could serve as a routine clinical assay for improving CVD risk assessment and drug discovery.TRIAL REGISTRATIONClinicalTrials.gov NCT01621594.FUNDINGNHLBI Intramural Research Program, NIH (HL006095-06).
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Affiliation(s)
- Masaki Sato
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
- Division of Community and Family Medicine and Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke-City, Tochigi, Japan
- Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimotsuga-gun, Tochigi, Japan
| | - Edward B. Neufeld
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Martin P. Playford
- Section of Inflammation and Cardiometabolic Diseases, NHLBI, NIH, Bethesda, Maryland, USA
| | - Yu Lei
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Alexander V. Sorokin
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
- Section of Inflammation and Cardiometabolic Diseases, NHLBI, NIH, Bethesda, Maryland, USA
| | - Angel M. Aponte
- Proteomics Core Facility, NHLBI, NIH, Bethesda, Maryland, USA
| | - Lita A. Freeman
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Scott M. Gordon
- Saha Cardiovascular Research Center and Department of Physiology, University of Kentucky, Lexington, Kentucky, USA
| | - Amit K. Dey
- Section of Inflammation and Cardiometabolic Diseases, NHLBI, NIH, Bethesda, Maryland, USA
| | - Kianoush Jeiran
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Masato Hamasaki
- Division of Community and Family Medicine and Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke-City, Tochigi, Japan
- Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., Shimotsuga-gun, Tochigi, Japan
| | | | - Robert D. Shamburek
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Jingrong Tang
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Marcus Y. Chen
- Laboratory of Cardiovascular CT, NHLBI, NIH, Bethesda, Maryland, USA
| | - Kazuhiko Kotani
- Division of Community and Family Medicine and Department of Clinical Laboratory Medicine, Jichi Medical University, Shimotsuke-City, Tochigi, Japan
| | - Josephine L.C. Anderson
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Robin P.F. Dullaart
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Nehal N. Mehta
- Section of Inflammation and Cardiometabolic Diseases, NHLBI, NIH, Bethesda, Maryland, USA
| | - Uwe J.F. Tietge
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alan T. Remaley
- Lipoprotein Metabolism Laboratory, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
- The NIH Clinical Center and
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Sharma K, Sharma M, Gupta N, Modi T, Joshi H, Shree R, Sharma A. Determining the diagnostic potential of Truenat MTB Plus for Tubercular lymphadenitis and detection of drug resistance and a comparison with GeneXpert Ultra. Tuberculosis (Edinb) 2023; 142:102379. [PMID: 37480632 DOI: 10.1016/j.tube.2023.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
SETTING Tubercular lymphadenitis (TBLA), the most common form of extrapulmonary tuberculosis, is a diagnostic challenge. OBJECTIVE Truenat MTB Plus (TruPlus) along with Truenat Rif assay (TruRif) was evaluated for detection of TBLA and rifampicin resistance and compared with GeneXpert Ultra (Xpert Ultra). DESIGN 100 fine-needle aspirated specimens [50 confirmed by culture/smear/cytology, 20 clinically suspected, and 30 controls], processed in the mycobacteriology division of department of microbiology were subjected to TruPlus and TruRif, Xpert Ultra and multiplex PCR. The results of TBLA detection were compared against composite reference standard (CRS) and those of rifampicin resistance were compared against phenotypic drug susceptibility testing and rpoB gene sequencing. RESULTS In comparison to CRS, the diagnostic yield of TruPlus, Xpert Ultra and MPCR was 77.14%, 59.18% and 84.28%, respectively; with substantial agreement for TruPlus (k = 0.66) and MPCR (k = 0.76) and moderate for Xpert Ultra (k = 0.60). TruRif reported four cases as RifR and Xpert Ultra reported two. On comparing with phenotypic DST and gene sequencing, only two cases of RifR were confirmed, hence TruRif reported false-RifR in two cases. CONCLUSION TruPlus could be used as a reliable tool for diagnosing TBLA. The reporting of RifR by TruRif should be confirmed by phenotypic DST or gene sequencing.
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Affiliation(s)
- Kusum Sharma
- Department of Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Megha Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Bilaspur, Himachal Pradesh, India
| | - Nalini Gupta
- Department of Cytology and Gynaecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Tanish Modi
- Government Medical College and Hospital, Sector 32, Chandigarh, India
| | - Himanshu Joshi
- Department of Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ritu Shree
- Department of Neurology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aman Sharma
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Řehulka J, Kubátová A, Hubka V. A visceral mycosis in farmed rainbow trout ( Oncorhynchus mykiss) caused by Neopyrenochaeta submersa. Med Mycol Case Rep 2023; 41:4-7. [PMID: 37274730 PMCID: PMC10232464 DOI: 10.1016/j.mmcr.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
A mycotic infection manifesting as abdominal distension with free serous fluid accumulation in the coelomic cavity is documented in farmed rainbow trout. Histological examination using PAS and silver staining revealed the presence of numerous fungal hyphae in the spleen and gastrointestinal wall. The isolated fungus was sterile and identified by using phylogenetic analysis based on four loci as Neopyrenochaeta submersa. This is the first time this fungus has been reported as pathogen.
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Affiliation(s)
- Jiří Řehulka
- Department of Zoology, Silesian Museum, 746 01, Opava, Czech Republic
| | - Alena Kubátová
- Department of Botany, Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic
| | - Vit Hubka
- Department of Botany, Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, v.v.i., 142 20, Prague 4, Czech Republic
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Henriques AM, Neto A, Fagulha T, Almeida V, Fevereiro M. Molecular characterization and phylogenetic analysis of Newcastle disease viruses isolated in southern Angola, 2016-2018. Infect Genet Evol 2023; 113:105481. [PMID: 37442285 DOI: 10.1016/j.meegid.2023.105481] [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: 12/26/2022] [Revised: 06/02/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Newcastle disease (ND) is a highly contagious viral disease that affects many bird species worldwide. This study presents the results of the molecular characterization and phylogenetic analysis of 15 virulent ND viruses (NDV) isolated from chickens during outbreaks reported in 2016 and 2018, in the provinces of Namibe and Huíla, in southern Angola. A 561-nucleotide fragment of the F gene was amplified by RT-PCR and sequenced for molecular characterization. Results showed that in all isolates the amino acid sequence comprising the cleavage site of fusion protein is characteristic of virulent viruses (RRQKR/F). Blast analysis revealed high similarity (99.2%) between two isolates from Huíla province, HLA4 and HLA6, and strain 5620 (GenBank accession number KY747479) isolated from chickens in the neighboring country Namibia, in 2016. The other isolates investigated are more related (97.0%) with strain 6195 (GenBank accession number KY747480), also isolated in Namibia in 2016. Phylogenetic analysis performed by Maximum Likelihood, Neighbor-joining and Bayesian methods revealed that like the strains isolated in Namibia, the isolates from southern Angola also belong to subgenotype 2 of genotype VII (VII.2). The network analysis revealed that NBA1 isolate from Angola is closer to a common ancestor than the isolates from Namibia, suggesting that transmission of ND viruses occurred from Angola to Namibia.
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Affiliation(s)
- Ana M Henriques
- Laboratory of Virology, National Institute of Agricultural and Veterinary Research, Lisbon, Portugal.
| | - António Neto
- Laboratory for the Production of Veterinary Vaccines, Veterinary Research Institute, Lubango, Angola
| | - Teresa Fagulha
- Laboratory of Virology, National Institute of Agricultural and Veterinary Research, Lisbon, Portugal
| | - Virgílio Almeida
- Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal; Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Miguel Fevereiro
- Laboratory of Virology, National Institute of Agricultural and Veterinary Research, Lisbon, Portugal
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De La Fuente Villar BB, Gomes LHF, Portari EA, Ramos CNP, Rocha DN, Pereira JP, Neves EDS, Guida LDC. Real-time PCR in the diagnosis of congenital toxoplasmosis. Braz J Infect Dis 2023; 27:102804. [PMID: 37743041 PMCID: PMC10539865 DOI: 10.1016/j.bjid.2023.102804] [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: 04/06/2023] [Revised: 08/09/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023] Open
Abstract
The diagnosis of congenital toxoplasmosis presents limitations and therefore new options are necessary. The analysis of amniotic fluid by real-time PCR has already proved effective for confirmation of fetal infection. However, its performance in other biological samples is not clear yet. The aim of this study is to better understand the role of real-time PCR in the blood of the mother and newborn as well as in the amniotic fluid and placenta in the diagnosis of congenital toxoplasmosis. This is a descriptive cohort study of pregnant women with toxoplasmosis followed up in Rio de Janeiro, Brazil. Real-time PCR was performed in samples of maternal blood, amniotic fluid, placenta, and blood of newborns. In addition, histopathological examination of placentas was performed, and data collected from babies were collected. 116 pregnant women were followed up and 298 samples were analyzed. One (0.9%) pregnant woman presented positive PCR in the blood, 3 (3.5%) in the amniotic fluid, 1 (2.3%) in the placenta and no newborn had positive PCR in the blood. Histopathological study was suggestive of toxoplasmosis infection in 24 (49%) placentas. Six (5.2%) newborns were diagnosed with congenital toxoplasmosis, and only cases with positive PCR in the amniotic fluid had correlation of the PCR result with the diagnosis of congenital infection. Both maternal and blood samples of newborns and placenta did not prove to be promising in the diagnosis of congenital toxoplasmosis. Further studies are needed to evaluate the real role of molecular diagnosis in other biological materials rather than the amniotic fluid.
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Affiliation(s)
| | | | - Elyzabeth Avvad Portari
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Carla Nasser Patrocinio Ramos
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Danielle Nascimento Rocha
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - José Paulo Pereira
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Elizabeth de Souza Neves
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Letícia da Cunha Guida
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil.
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Curtin K, Wang J, Fike BJ, Binkley B, Li P. A 3D printed microfluidic device for scalable multiplexed CRISPR-cas12a biosensing. Biomed Microdevices 2023; 25:34. [PMID: 37642743 DOI: 10.1007/s10544-023-00675-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Accurate, rapid, and multiplexed nucleic acid detection is critical for environmental and biomedical monitoring. In recent years, CRISPR-Cas12a has shown great potential in improving the performance of DNA biosensing. However, the nonspecific trans-cleavage activity of Cas12a complicates the multiplexing capability of Cas12a biosensing. We report a 3D-printed composable microfluidic plate (cPlate) device that utilizes miniaturized wells and microfluidic loading for a multiplexed CRISPR-Cas12a assay. The device easily combines loop-mediated isothermal amplification (LAMP) and CRISPR-Cas12a readout in a simple and high-throughput workflow with low reagent consumption. To ensure the maximum performance of the device, the concentration of Cas12a and detection probe was optimized, which yielded a four-fold sensitivity improvement. Our device demonstrates sensitive detection to the fg mL- 1 level for four waterborne pathogens including shigella, campylobacter, cholera, and legionella within 1 h, making it suitable for low-resource settings.
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Affiliation(s)
- Kathrine Curtin
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV, USA
| | - Jing Wang
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Bethany J Fike
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Brandi Binkley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA.
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