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Fernandes JRN, Teles AS, Fernandes TRS, Lima LDB, Balhara S, Gupta N, Teixeira S. Artificial Intelligence on Diagnostic Aid of Leprosy: A Systematic Literature Review. J Clin Med 2023; 13:180. [PMID: 38202187 PMCID: PMC10779723 DOI: 10.3390/jcm13010180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Leprosy is a neglected tropical disease that can cause physical injury and mental disability. Diagnosis is primarily clinical, but can be inconclusive due to the absence of initial symptoms and similarity to other dermatological diseases. Artificial intelligence (AI) techniques have been used in dermatology, assisting clinical procedures and diagnostics. In particular, AI-supported solutions have been proposed in the literature to aid in the diagnosis of leprosy, and this Systematic Literature Review (SLR) aims to characterize the state of the art. This SLR followed the preferred reporting items for systematic reviews and meta-analyses (PRISMA) framework and was conducted in the following databases: ACM Digital Library, IEEE Digital Library, ISI Web of Science, Scopus, and PubMed. Potentially relevant research articles were retrieved. The researchers applied criteria to select the studies, assess their quality, and perform the data extraction process. Moreover, 1659 studies were retrieved, of which 21 were included in the review after selection. Most of the studies used images of skin lesions, classical machine learning algorithms, and multi-class classification tasks to develop models to diagnose dermatological diseases. Most of the reviewed articles did not target leprosy as the study's primary objective but rather the classification of different skin diseases (among them, leprosy). Although AI-supported leprosy diagnosis is constantly evolving, research in this area is still in its early stage, then studies are required to make AI solutions mature enough to be transformed into clinical practice. Expanding research efforts on leprosy diagnosis, coupled with the advocacy of open science in leveraging AI for diagnostic support, can yield robust and influential outcomes.
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Affiliation(s)
- Jacks Renan Neves Fernandes
- PhD Program in Biotechnology—Northeast Biotechnology Network, Federal University of Piauí, Teresina 64049-550, Brazil;
| | - Ariel Soares Teles
- Postgraduate Program in Biotechnology, Parnaíba Delta Federal University, Parnaíba 64202-020, Brazil; (T.R.S.F.); (L.D.B.L.); (S.T.)
- Federal Institute of Maranhão, Araioses 65570-000, Brazil
| | - Thayaná Ribeiro Silva Fernandes
- Postgraduate Program in Biotechnology, Parnaíba Delta Federal University, Parnaíba 64202-020, Brazil; (T.R.S.F.); (L.D.B.L.); (S.T.)
| | - Lucas Daniel Batista Lima
- Postgraduate Program in Biotechnology, Parnaíba Delta Federal University, Parnaíba 64202-020, Brazil; (T.R.S.F.); (L.D.B.L.); (S.T.)
| | - Surjeet Balhara
- Department of Electronics & Communication Engineering, Bharati Vidyapeeth’s College of Engineering, New Delhi 110063, India;
| | - Nishu Gupta
- Department of Electronic Systems, Faculty of Information Technology and Electrical Engineering, Norwegian University of Science and Technology, 2815 Gjøvik, Norway;
| | - Silmar Teixeira
- Postgraduate Program in Biotechnology, Parnaíba Delta Federal University, Parnaíba 64202-020, Brazil; (T.R.S.F.); (L.D.B.L.); (S.T.)
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Lopes-Luz L, Saavedra DP, Fogaça MBT, Bührer-Sékula S, Stefani MMDA. Challenges and advances in serological and molecular tests to aid leprosy diagnosis. Exp Biol Med (Maywood) 2023; 248:2083-2094. [PMID: 38059475 PMCID: PMC10800132 DOI: 10.1177/15353702231209422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
Leprosy is a neglected chronic infectious disease caused by obligate intracellular bacilli, Mycobacterium leprae and Mycobacterium lepromatosis. Despite multidrug therapy (MDT) success, leprosy accounts for more than 200,000 new cases yearly. Leprosy diagnosis remains based on the dermato-neurologic examination, but histopathology of skin biopsy and bacilloscopy of intradermal scraping are subsidiary diagnostic tests that require expertise and laboratory infrastructure. This minireview summarizes the state of the art of serologic tests to aid leprosy diagnosis, highlighting enzyme-linked immunosorbent assay (ELISA) and point-of-care tests (POCT) biotechnologies. Also, the impact of the postgenomic era on the description of new recombinantly expressed M. leprae-specific protein antigens, such as leprosy Infectious Disease Research Institute (IDRI) diagnostic (LID)-1 is summarized. Highly specific and sensitive molecular techniques to detect M. leprae DNA as the quantitative polymerase chain reaction (qPCR) and the loop-mediated isothermal amplification (LAMP) are briefly reviewed. Serology studies using phenolic glycolipid-I (PGL-I) semi-synthetic antigens, LID-1 fusion antigen, and the single fusion complex natural disaccharide-octyl (NDO)-LID show high sensitivity in multibacillary (MB) patients. However, serology is not applicable to paucibacillary patients, as they have weak humoral response and robust cell-mediated response, requiring tests for cellular biomarkers. Unlike ELISA-based tests, leprosy-specific POCT based on semi-synthetic PGL-I antigens and NDO-LID 1 antigen is easy to perform, cheaper, equipment-free, and can contribute to early diagnosis avoiding permanent incapacities and helping to interrupt M. leprae transmission. Besides its use to help diagnosis of household contacts or at-risk populations in endemic areas, potential applications of leprosy serology include monitoring MDT efficacy, identification of recent infection, especially in young children, as surrogate markers of disease progression to orient adult chemoprophylaxis and as a predictor of type 2 leprosy reactions. Advances in molecular biology techniques have reduced the complexity and execution time of qPCR confirming its utility to help diagnosis while leprosy-specific LAMP holds promise as an adjunct test to detect M. leprae DNA.
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Affiliation(s)
- Leonardo Lopes-Luz
- Laboratório de Desenvolvimento e Produção de Testes Rápidos, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brasil
- Innovation Hub in Point of Care Technologies, UFG-Merck S/A. Alliance, Goiânia 74690-900, Brasil
| | - Djairo Pastor Saavedra
- Laboratório de Desenvolvimento e Produção de Testes Rápidos, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brasil
- Innovation Hub in Point of Care Technologies, UFG-Merck S/A. Alliance, Goiânia 74690-900, Brasil
| | - Matheus Bernardes Torres Fogaça
- Laboratório de Desenvolvimento e Produção de Testes Rápidos, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brasil
- Innovation Hub in Point of Care Technologies, UFG-Merck S/A. Alliance, Goiânia 74690-900, Brasil
| | - Samira Bührer-Sékula
- Laboratório de Desenvolvimento e Produção de Testes Rápidos, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brasil
- Innovation Hub in Point of Care Technologies, UFG-Merck S/A. Alliance, Goiânia 74690-900, Brasil
| | - Mariane Martins de Araújo Stefani
- Laboratório de Desenvolvimento e Produção de Testes Rápidos, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia 74605-050, Brasil
- Innovation Hub in Point of Care Technologies, UFG-Merck S/A. Alliance, Goiânia 74690-900, Brasil
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Beltrame A, Fargnoli MC, Avanzi C, Sollima L, Pomari E, Mori A, Longoni SS, Moro L, Orza P, Jackson M, Perandin F. Leprosy in an Adopted Woman Diagnosed by Molecular Tools: A Case Report from a Non-Endemic Area. Pathogens 2023; 12:pathogens12020165. [PMID: 36839437 PMCID: PMC9963898 DOI: 10.3390/pathogens12020165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Coupled with its rarity in non-endemic areas, the clinical heterogeneity of leprosy makes diagnosis very challenging. We report a diagnosis of multibacillary leprosy in a 22-year-old Indian woman, adopted at the age of 10 and living in Italy. The patient presented with painful skin lesions on the face, trunk, and lower and upper extremities, associated with dysesthesia and a motor deficit in her left leg following corticosteroid therapy interruption. Histopathology results from the skin lesions suggested leprosy, but no acid-fast bacilli were identified. Molecular biology in a center specializing in tropical diseases confirmed the diagnosis, allowing prompt and adequate treatment. Genotype analysis allowed the identification of a genotype 1D of M. leprae, facilitating the epidemiological investigation of the plausible infection origin. No resistances to rifampicin, dapsone, or ofloxacin were detected. Leprosy will continue to exist in high-income nations, and the incidence may rise over time due to increasing migration and globalization. CARE guidelines were followed.
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Affiliation(s)
- Anna Beltrame
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
- College of Public Health, University of South Florida, Tampa, FL 33612, USA
- Correspondence:
| | - Maria Concetta Fargnoli
- Dermatology Unit, Ospedale San Salvatore, 67100 L’Aquila, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Laura Sollima
- Pathology Unit, Ospedale San Salvatore, 67100 L’Aquila, Italy
| | - Elena Pomari
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Antonio Mori
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Silvia Stefania Longoni
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Lucia Moro
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Pierantonio Orza
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Francesca Perandin
- Department of Infectious—Tropical Diseases and Microbiology, I.R.C.C.S. Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
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Lima FR, de Paula NA, Simões MMR, Manso GMDC, Albertino GS, Felisbino GC, Antunes VMG, Perecin FAMC, Westin AT, Lugão HB, Frade MAC. Bacilloscopy and polymerase chain reaction of slit-skin smears and anti-phenolic glycolipid-I serology for Hansen’s disease diagnosis. Front Med (Lausanne) 2022; 9:972244. [PMID: 36035405 PMCID: PMC9399463 DOI: 10.3389/fmed.2022.972244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022] Open
Abstract
The bacilloscopy of the slit-skin smear (SSS) is the exclusive laboratory test associated with dermato-neurological evaluation for Hansen’s disease (HD) diagnosis; however, it is negative in the majority of PB or primary neural forms. Thus, a PCR technique involving different sequences and target genes has been performed with an aim to increase the sensitivity and specificity of M. leprae identification, especially in patients with low bacillary loads. Additionally, serological assays based on antibody response reflect infection levels and indicate that this could be a simpler, less invasive technique for estimating M. leprae exposure. Serological tests and PCR have been shown to be more sensitive and accurate than the SSS. Our study aimed to measure accuracy and performance among the SSS and PCR of dermal scrapings stored on filter paper and APGL-I serology for diagnosis in HD. A cross-sectional study analyzing the medical records (n = 345) of an HD outpatient-dermatology clinic from 2014 to 2021 was conducted. Accuracy performance parameters, correlation, and concordance were used to assess the value among the SSS, PCR, and APGL-I exams in HD. The SSS presented 24.5% sensitivity, 100% specificity, 37.4% accuracy, and the lowest negative predictive value (21.5%). The PCR assay had 41, 100, and 51% sensitivity, specificity, and accuracy, respectively. PCR and APGL-I serology increased the detection of HD cases by 16 and 20.6%, respectively. PCR was positive in 51.3% of patients when the SSS was negative. The SSS obtained moderate concordance with PCR [k-value: 0.43 (CI: 0.33–0.55)] and APGL-I [k-value: 0.41 (CI: 0.31–0.53)]. A moderate positive correlation was found between the APGL-I index and the bacillary index (r = 0.53; P < 0.0001). Thus, the use of the SSS is a low sensitivity and accuracy method due to its low performance in HD detection. The use of PCR and serological tests allows for a more sensitive and accurate diagnosis of patients.
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Affiliation(s)
- Filipe Rocha Lima
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Natália Aparecida de Paula
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Mateus Mendonça Ramos Simões
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gabriel Martins da Costa Manso
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Gustavo Sartori Albertino
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Giovani Cesar Felisbino
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Vanderson Mayron Granemann Antunes
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Fernanda André Martins Cruz Perecin
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Andrezza Telles Westin
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Helena Barbosa Lugão
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Marco Andrey Cipriani Frade
- Healing and Hansen’s Disease Laboratory, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- Dermatology Division, Department of Internal Medicine, National Referral Center for Sanitary Dermatology and Hansen’s Disease, Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- *Correspondence: Marco Andrey Cipriani Frade,
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Sharma M, Singh P. Advances in the Diagnosis of Leprosy. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.893653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Leprosy is a public health issue, and early detection is critical to avert disability. Despite the global attempt to eradicate this disease as a public health problem, it remains an important cause of global neurological disability. India, Brazil and Indonesia share more than 70% of the cases. The reduction of new cases is a priority in the WHO global strategy 2021-2030 which aims to reduce disease transmission in the community by diagnosing cases and identifying subclinical infection. The clinical manifestations of leprosy range from a few to several lesions. The identification remains difficult due to the limited sensitivity of traditional approaches based on bacillary counts of skin smears and histology. To aid in the diagnosis of this disease, molecular biology, and biotechnological technologies have been applied, each with its own set of benefits and downsides despite providing an essential tool to validate the clinical diagnosis of leprosy. Because of this, it is strongly recognized that specific, inexpensive point of care technologies should be developed, particularly to identify asymptomatic M. leprae infections or leprosy nearer to the suspected cases seeking medical attention. Thus, this review will provide an overview of the advancements in leprosy diagnosis over the world. The purpose of this review is to improve our understanding of the outcomes of current tests and technologies used in leprosy diagnosis and to emphasize critical aspects concerning the detection of leprosy bacilli.
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Zhu Y, Hua W, Liu Z, Zhang M, Wang X, Wu B, Wang Z, Chen J. Identification and characterization of nontuberculous mycobacteria isolated from suspected pulmonary tuberculosis patients in eastern china from 2009 to 2019 using an identification array system. Braz J Infect Dis 2022; 26:102346. [PMID: 35288106 PMCID: PMC9387452 DOI: 10.1016/j.bjid.2022.102346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/27/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022] Open
Abstract
Objective Nontuberculous mycobacteria (NTM) species are increasingly being isolated and have become a key factor affecting public health by causing pulmonary diseases. Most NTM species do not respond to conventional tuberculosis (TB) drugs. This study aimed to identify NTM isolated from suspected pulmonary TB patients from the Zhejiang province and analyze their distribution in the region. Methods A total of 1,113 NTM isolates from patients suspected to be suffering from acid-fast bacilli-positive tuberculosis were identified at the species level, using the CapitalBio Mycobacterium identification array and polymerase chain reaction amplification and sequencing of 16S-23S gene internal transcribed spacer (ITS), 16S rRNA, and hsp65. Results Of the 23,138 isolates, we identified 1,102 NTM (4.8%), mainly including Mycobacterium intracellulare (54.81%, 604/1,102), M. chelonae-M. abscessus (16.52%, 182/1,102), M. avium (13.16%, 145/1,102), M. kansasii (8.17%, 90/1,102), and M. gordonae (3.27%, 36/1,102). Conclusion The distribution of NTM species observed in patients with suspected pulmonary tuberculosis provides guidance for the diagnosis and treatment of NTM pulmonary diseases.
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Affiliation(s)
- Yelei Zhu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Wenya Hua
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhengwei Liu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Mingwu Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Xiaomeng Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Beibei Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhen Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.
| | - Jiazhen Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
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Manta FSDN, Jacomasso T, Rampazzo RDCP, Moreira SJM, Zahra NM, Cole ST, Avanzi C, Leal-Calvo T, Vasconcellos SEG, Suffys P, Ribeiro-Alves M, Krieger MA, Costa ADT, Moraes MO. Development and validation of a multiplex real-time qPCR assay using GMP-grade reagents for leprosy diagnosis. PLoS Negl Trop Dis 2022; 16:e0009850. [PMID: 35180224 PMCID: PMC8893668 DOI: 10.1371/journal.pntd.0009850] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/03/2022] [Accepted: 01/26/2022] [Indexed: 11/18/2022] Open
Abstract
Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae, an obligate intracellular bacterium. Timely detection is a challenge in leprosy diagnosis, relying on clinical examination and trained health professionals. Furthermore, adequate care and transmission control depend on early and reliable pathogen detection. Here, we describe a qPCR test for routine diagnosis of leprosy-suspected patients. The reaction simultaneously amplifies two specific Mycobacterium leprae targets (16S rRNA and RLEP), and the human 18S rRNA gene as internal control. The limit of detection was estimated to be 2.29 copies of the M. leprae genome. Analytical specificity was evaluated using a panel of 20 other skin pathogenic microorganisms and Mycobacteria, showing no cross-reactivity. Intra- and inter-operator Cp variation was evaluated using dilution curves of M. leprae DNA or a synthetic gene, and no significant difference was observed between three operators in two different laboratories. The multiplex assay was evaluated using 97 patient samples with clinical and histopathological leprosy confirmation, displaying high diagnostic sensitivity (91%) and specificity (100%). Validation tests in an independent panel of 50 samples confirmed sensitivity and specificity of 97% and 98%, respectively. Importantly, assay performance remained stable for at least five months. Our results show that the newly developed multiplex qPCR effectively and specifically detects M. leprae DNA in skin samples, contributing to an efficient diagnosis that expedites the appropriate treatment. Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae, an obligate intracellular bacterium. Diagnosis of leprosy often relies on skin examinations for clinical signs, bacilli staining from skin smears and invasive skin biopsies. However, the spectrum of clinical manifestations and, often, low bacilli numbers can hinder accurate diagnosis. Timely detection is a challenge in leprosy diagnosis, relying on clinical examination and requiring trained health professionals. Proper intervention for adequate care and transmission control depends on early and reliable pathogen detection. Quantitative PCR methods for detecting bacterial DNA are more sensitive and could aid in differentially diagnosing leprosy from other dermatological conditions. In this work, we present a new multiplex PCR that was assessed for quality control standards, and the data indicate that the assay is stable and reproducible. The results presented here are the basis of a novel and robust tool with potential to increase the accuracy of leprosy diagnosis in routine or reference laboratories.
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Affiliation(s)
| | - Thiago Jacomasso
- Instituto de Biologia Molecular do Paraná, FIOCRUZ, Curitiba, Brazil
| | | | | | - Najua M. Zahra
- Instituto de Biologia Molecular do Paraná, FIOCRUZ, Curitiba, Brazil
| | - Stewart T. Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, Colorado, United States of America
| | - Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Phillip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Marco Aurelio Krieger
- Instituto de Biologia Molecular do Paraná, FIOCRUZ, Curitiba, Brazil
- Laboratório de Ciências e Tecnologias Aplicadas à Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz/FIOCRUZ, Curitiba, Brazil
| | - Alexandre Dias Tavares Costa
- Instituto de Biologia Molecular do Paraná, FIOCRUZ, Curitiba, Brazil
- Laboratório de Ciências e Tecnologias Aplicadas à Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz/FIOCRUZ, Curitiba, Brazil
- * E-mail: (ADTC); (MOM)
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail: (ADTC); (MOM)
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Sevilha-Santos L, Cerqueira SRPS, Gomes CM. Standardization of SYBR Green-Based Real-Time PCR Through the Evaluation of Different Thresholds for Different Skin Layers: An Accuracy Study and Track of the Transmission Potential of Multibacillary and Paucibacillary Leprosy Patients. Front Microbiol 2022; 12:758222. [PMID: 35035383 PMCID: PMC8753983 DOI: 10.3389/fmicb.2021.758222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
The development of new molecular techniques is essential for the early diagnosis of leprosy. Studies in the field have failed to elucidate the performance of these tests in clinical practice. We aimed to design a new primer pair for the repetitive element (RLEP) target of Mycobacterium leprae and to test the accuracy of SYBR green-based real-time PCR through the evaluation of different thresholds for different skin layers. We also aimed to track the transmission potential of multibacillary and paucibacillary leprosy patients. The in vitro validation of our reaction resulted in a quantification limit of 0.03 bacilli. We then conducted a cross-sectional/cohort-based study of diagnostic accuracy. Patients were included, and skin samples were divided into four layers: epidermis, superior dermis, inferior dermis, and hypodermis. We also quantified M. leprae in nasal swabs of the included patients and compared the results to the number of household contacts also diagnosed with leprosy. One hundred patients with a clinical presentation compatible with leprosy were allocated to the leprosy or control group. Although the parasite load was greater in the superior and inferior dermis, M. leprae DNA was found in all skin layers. The best sensitivity was observed for the superior dermis using the presence of any quantifiable bacillus DNA as the threshold [sensitivity=59.26% (95% CI=45.97–71.32)]. In the epidermis, setting 1 quantifiable bacillus as the threshold resulted in 100% specificity (95% CI=92.29–100). The number of bacilli found in nasal swabs was not significantly related to the number of household contacts also diagnosed with leprosy. Paucibacillary patients tested positive only for bacillus fragments in nasal swabs but not for the entire bacilli. We can conclude that superficial biopsies might result in sensitivity loss, although different skin sample types will have little influence on the final accuracy. In contrast, threshold changes greatly influence these properties. Paucibacillary patients may not be a relevant source of disease transmission.
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Affiliation(s)
- Lais Sevilha-Santos
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | | | - Ciro Martins Gomes
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Medicina Tropcial, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
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Rampazzo RDCP, Zambenedetti MR, Alexandrino F, Jacomasso T, Tschá MK, de Fillipis AMB, Morello LG, Marchini FK. Development, verification, and validation of an RT-qPCR-based protocol for Yellow Fever diagnosis. Int J Infect Dis 2022; 119:34-37. [PMID: 34990800 DOI: 10.1016/j.ijid.2021.12.361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/10/2021] [Accepted: 12/27/2021] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Yellow fever (YF) is a public health threat with frequent outbreaks in tropical and subtropical areas, despite the existence of a safe and effective vaccine. The diagnosis of acute infection of the etiologic agent relies mainly on real-time reverse transcription-polymerase chain reaction (RT-qPCR)-based assays. OBJECTIVES The aim of this study was to evaluate and compare this novel protocol for yellow fever virus (YFV) diagnosis against assays developed in-house by reference laboratories for arboviruses. METHODS We developed a novel molecular protocol for the detection of YFV that includes an Internal Control to validate the reaction and an External Control to monitor the RNA extraction efficiency. RESULTS AND DISCUSSION Our assay detects one viral genome per reaction and displays no cross-reactions with dengue (1-4), Zika, or Chikungunya viruses. This novel assay yielded 95% of agreement with the reference method recommended by the Pan American Health Organization when analyzing 204 clinical samples and cultured viruses, these samples were analyzed in 3 different diagnosis centers for arboviruses in Brazil. The data suggest the use of the proposed multiplex assay protocol to do routine tests in a clinical laboratory. This product adds higher specificity and sensitivity in addition to reduced cost per test due to hands-on time and reagent spending.
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Affiliation(s)
- Rita de Cássia Pontello Rampazzo
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Miriam Ribas Zambenedetti
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Fabiana Alexandrino
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Thiago Jacomasso
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Marcel Kruchelski Tschá
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Ana Maria Bispo de Fillipis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Gustavo Morello
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil; Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil
| | - Fabricio Klerynton Marchini
- Instituto de Biologia Molecular do Paraná (IBMP), Rua Professor Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil; Instituto Carlos Chagas (ICC), FIOCRUZ-PR, Rua Prof. Algacyr Munhoz Mader, 3775 CIC, 81350-010, Curitiba, Paraná, Brazil.
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10
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Wondimu A, Tassew H, Gelaye E, Hagos Y, Belay A, Teshome Y, Laiju S, Asebe G. Outbreak Investigation and Molecular Detection of Pox Virus Circulating in Sheep and Goats in Selected Districts of West Gojjam and Awi Zones Northwest, Ethiopia. VETERINARY MEDICINE (AUCKLAND, N.Z.) 2021; 12:303-315. [PMID: 34909409 PMCID: PMC8665829 DOI: 10.2147/vmrr.s318549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
INTRODUCTION Sheep and goat pox virus (SGPV) is a systemic contagious disease causing extreme illness and death in small ruminants. METHODS A cross-sectional study was conducted in West Gojjam and Awi zone of Amhara national regional state Northwest Ethiopia, from November 2018 to May 2019 with the objective of pox virus outbreak investigation and molecular detections in sheep and goats (shoats). The study included clinical examinations of lesions, laboratory analysis, and questionnaire survey. Study locations were selected randomly when an active outbreak was reported and observed. RESULTS A total of 485 small ruminants (303 sheep and 182 goats) suspected of shoat pox were examined for the presence of specific skin lesions, 71 (14.64%) showed pox lesions, 35 (11.55%) sheep and 36 (19.78%) goats, and 24 (4.95%) had died. The study revealed highest morbidity rate in Jawie (31.25%) and Gunagua (14.89%) districts in goats and sheep, respectively. Lowest morbidity rate was recorded in Dega Damot district in sheep (6.45%) and goats (7.14%), respectively. The mortality rate was >1% in all districts except Dega Damot for both species. From a total of 38 tissue samples, 19 samples were selected based on the geographical distribution. All 19 samples (6 sheep and 13 goats) were found to be positive for goat pox virus based on polymerase chain reaction results. The significant risk factors were free animal movements, age, flock size and composition, body condition, vaccination status, and season. The study showed that in the absence of free movement of animals, the disease was less likely to occur (OR = 0.05, CI 95%; 0.02, 0.15). CONCLUSION The disease was found in higher rate during the dry and short rainy season. Sheep were also found to be infected by goat pox virus. The study indicated that there was widespread sheep and goat pox in Northwest Ethiopia.
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Affiliation(s)
- Alemzewud Wondimu
- Debre Markos University, College of Agriculture and Natural Resources, Burie, Ethiopia
| | - Habtamu Tassew
- Bahir Dar University, College of Agriculture and Environmental Science, Bahir Dar, Ethiopia
| | | | | | | | - Yechale Teshome
- Bahir Dar University, College of Agriculture and Environmental Science, Bahir Dar, Ethiopia
| | - Sam Laiju
- Bahir Dar University, College of Agriculture and Environmental Science, Bahir Dar, Ethiopia
| | - Getahun Asebe
- Gambella University, College of Agriculture and Natural Resource, Gambella, Ethiopia
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Detection of six soil-transmitted helminths in human stool by qPCR- a systematic workflow. PLoS One 2021; 16:e0258039. [PMID: 34591904 PMCID: PMC8483301 DOI: 10.1371/journal.pone.0258039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
Soil-transmitted helminths (STH) infect up to one-quarter of the global population, with a significant associated disease burden. The main human STH are: Ancylostoma spp. and Necator americanus (hookworms); Ascaris lumbricoides, Trichuris trichiura, and Strongyloides stercoralis. The aim of this study was to establish a scalable system for stool STH multiplex quantitative real-time polymerase chain reactions (qPCR). Stool samples collected in Fiji and preserved in potassium dichromate were transferred to Melbourne at ambient temperature. Samples were washed to remove potassium dichromate and DNA was extracted with the Mini-Beadbeater-24 and a column-based kit. A SYBR green qPCR to detect the vertebrate mitochondrial gene was used as a DNA extraction control. Samples were tested using a probe-based multiplex qPCR targeting A. lumbricoides, T. trichiura and S. stercoralis, and in a second multiplex reaction to detect hookworms to the species level (A. duodenale, A. ceylanicum, N. americanus). An internal amplification control in both multiplex assays was included to prevent false-negative results due to PCR inhibitors. Samples were homogenised for a single cycle of 40 seconds to release STH DNA and washed stool was stored for up to 15 weeks at -30°C without compromising DNA. Our multiplex qPCR detected multiple species of STH without reduced sensitivity compared to singleplex. qPCR data from 40 stools was validated against STH-positive stools determined by microscopy. We have developed and validated an efficient and staged system for detecting six clinically important STH affecting humans that could be easily implemented without advanced automation in any qPCR-capable laboratory.
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Leal-Calvo T, Avanzi C, Mendes MA, Benjak A, Busso P, Pinheiro RO, Sarno EN, Cole ST, Moraes MO. A new paradigm for leprosy diagnosis based on host gene expression. PLoS Pathog 2021; 17:e1009972. [PMID: 34695167 PMCID: PMC8568100 DOI: 10.1371/journal.ppat.1009972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/04/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional profiling is a powerful tool to investigate and detect human diseases. In this study, we used bulk RNA-sequencing (RNA-Seq) to compare the transcriptomes in skin lesions of leprosy patients or controls affected by other dermal conditions such as granuloma annulare, a confounder for paucibacillary leprosy. We identified five genes capable of accurately distinguishing multibacillary and paucibacillary leprosy from other skin conditions. Indoleamine 2,3-dioxygenase 1 (IDO1) expression alone was highly discriminatory, followed by TLR10, BLK, CD38, and SLAMF7, whereas the HS3ST2 and CD40LG mRNA separated multi- and paucibacillary leprosy. Finally, from the main differentially expressed genes (DEG) and enriched pathways, we conclude that paucibacillary disease is characterized by epithelioid transformation and granuloma formation, with an exacerbated cellular immune response, while multibacillary leprosy features epithelial-mesenchymal transition with phagocytic and lipid biogenesis patterns in the skin. These findings will help catalyze the development of better diagnostic tools and potential host-based therapeutic interventions. Finally, our data may help elucidate host-pathogen interplay driving disease clinical manifestations.
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Affiliation(s)
- Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mayara Abud Mendes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Roberta Olmo Pinheiro
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Euzenir Nunes Sarno
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Stewart Thomas Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
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Demonstration of a fast and easy sample-to-answer protocol for tuberculosis screening in point-of-care settings: A proof of concept study. PLoS One 2020; 15:e0242408. [PMID: 33315885 PMCID: PMC7735633 DOI: 10.1371/journal.pone.0242408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/03/2020] [Indexed: 11/22/2022] Open
Abstract
We sought to develop a smooth and low cost sample preparation and DNA extraction protocol, streamlined with a ready-to-use qPCR in a portable instrument to overcome some of the existing hurdles. Several solutions were evaluated as to their ability to liquefy a mucin-based matrix. Each liquefied matrix, supplemented with either Mycobacterium tuberculosis (MTB) H37Rv strain DNA or intact cells, was aliquoted onto a filter paper embedded with solubilizing agents, and was subsequently dried up. Most of the nucleic acids, including genomic DNA from the bacilli and the host, binds to the filter paper. Next, several protocols were evaluated to elute the DNA from the paper, using qPCR to detect the insertion sequence IS6110, a M. tuberculosis complex genomic marker. The limit of detection (LOD) of the best protocol was then evaluated using parallel seeding and colony counting. The protocol was also evaluated using seventeen sputum samples, previously characterized by the GeneXpert or culture. Two instruments (the ABI7500 Standard and the Q3-Plus system) and two reagents storage formats (frozen or ready-to-use) were evaluated. Solutions containing guanidine isothiocyanate exerted the best liquefying effect on the mucin-based matrix extracted from one 6-mm punches, followed by a brief incubation at 95°C. The resulting DNA contained impurities, but a simple 1:10 dilution elicited the detection of MTB and human genomic targets. The described protocol presented an apparent LOD of 02 CFU/mL of MTB. Challenging the protocol with previously characterized samples showed substantial agreement with GeneXpert MTB/RIF results (sensitivity of 90%, agreement of 88.9%, kappa coefficient of 0.77), and moderate agreement with culture results (sensitivity of 100%, agreement of 78.9%, kappa coefficient of 0.58). This work presents a sensitive proof–of-concept protocol for sputum liquefaction and decontamination followed by a simple DNA extraction procedure, in which the extraction steps are streamlined with a ready-to-use qPCR in a portable instrument that can be employed in low infrastructure settings.
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