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Tonks A, Harris T, Li B, Brown W, Smith R. Forecasting West Nile Virus With Graph Neural Networks: Harnessing Spatial Dependence in Irregularly Sampled Geospatial Data. GEOHEALTH 2024; 8:e2023GH000784. [PMID: 38962698 PMCID: PMC11220409 DOI: 10.1029/2023gh000784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Machine learning methods have seen increased application to geospatial environmental problems, such as precipitation nowcasting, haze forecasting, and crop yield prediction. However, many of the machine learning methods applied to mosquito population and disease forecasting do not inherently take into account the underlying spatial structure of the given data. In our work, we apply a spatially aware graph neural network model consisting of GraphSAGE layers to forecast the presence of West Nile virus in Illinois, to aid mosquito surveillance and abatement efforts within the state. More generally, we show that graph neural networks applied to irregularly sampled geospatial data can exceed the performance of a range of baseline methods including logistic regression, XGBoost, and fully-connected neural networks.
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Affiliation(s)
- Adam Tonks
- Department of StatisticsUniversity of Illinois at Urbana‐ChampaignChampaignILUSA
| | - Trevor Harris
- Department of StatisticsTexas A&M UniversityCollege StationTXUSA
| | - Bo Li
- Department of StatisticsUniversity of Illinois at Urbana‐ChampaignChampaignILUSA
| | - William Brown
- Department of PathobiologyUniversity of Illinois at Urbana‐ChampaignChampaignILUSA
| | - Rebecca Smith
- Department of PathobiologyUniversity of Illinois at Urbana‐ChampaignChampaignILUSA
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2
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Sikulu-Lord MT, Edstein MD, Goh B, Lord AR, Travis JA, Dowell FE, Birrell GW, Chavchich M. Rapid and non-invasive detection of malaria parasites using near-infrared spectroscopy and machine learning. PLoS One 2024; 19:e0289232. [PMID: 38527002 PMCID: PMC10962802 DOI: 10.1371/journal.pone.0289232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/26/2023] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Novel and highly sensitive point-of-care malaria diagnostic and surveillance tools that are rapid and affordable are urgently needed to support malaria control and elimination. METHODS We demonstrated the potential of near-infrared spectroscopy (NIRS) technique to detect malaria parasites both, in vitro, using dilutions of infected red blood cells obtained from Plasmodium falciparum cultures and in vivo, in mice infected with P. berghei using blood spotted on slides and non-invasively, by simply scanning various body areas (e.g., feet, groin and ears). The spectra were analysed using machine learning to develop predictive models for infection. FINDINGS Using NIRS spectra of in vitro cultures and machine learning algorithms, we successfully detected low densities (<10-7 parasites/μL) of P. falciparum parasites with a sensitivity of 96% (n = 1041), a specificity of 93% (n = 130) and an accuracy of 96% (n = 1171) and differentiated ring, trophozoite and schizont stages with an accuracy of 98% (n = 820). Furthermore, when the feet of mice infected with P. berghei with parasitaemia ≥3% were scanned non-invasively, the sensitivity and specificity of NIRS were 94% (n = 66) and 86% (n = 342), respectively. INTERPRETATION These data highlights the potential of NIRS technique as rapid, non-invasive and affordable tool for surveillance of malaria cases. Further work to determine the potential of NIRS to detect malaria in symptomatic and asymptomatic malaria cases in the field is recommended including its capacity to guide current malaria elimination strategies.
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Affiliation(s)
- Maggy T. Sikulu-Lord
- School of the Environment, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael D. Edstein
- Department of Drug Evaluation, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Queensland, Australia
| | - Brendon Goh
- School of the Environment, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Anton R. Lord
- Centre for Data Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jye A. Travis
- Department of Drug Evaluation, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Queensland, Australia
| | - Floyd E. Dowell
- Center for Grain and Animal Health Research, USDA Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Geoffrey W. Birrell
- Department of Drug Evaluation, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Queensland, Australia
| | - Marina Chavchich
- Department of Drug Evaluation, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Queensland, Australia
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Coelho BFO, Nunes SLP, de França CA, Costa DDS, do Carmo RF, Prates RM, Filho EFS, Ramos RP. On the feasibility of Vis-NIR spectroscopy and machine learning for real time SARS-CoV-2 detection. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123735. [PMID: 38064967 DOI: 10.1016/j.saa.2023.123735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 11/16/2023] [Accepted: 12/02/2023] [Indexed: 01/13/2024]
Abstract
The pandemic caused by Covid-19 is still present around the world. Despite advances in combating the disease, such as vaccine development, identifying infected individuals is still essential to optimize the control of human-to-human transmission of the virus. The main technique for detecting the virus is the RT-PCR method, which, despite its high relative cost, has a high accuracy in detecting the coronavirus. Given this, a method capable of performing the identification quickly, accurately, and inexpensively is necessary. Thus, this work aimed to analyze the feasibility of a new technique for identifying SARS-CoV-2 through the use of optical spectroscopy in the visible and near-infrared range (Vis-NIR) combined with machine learning algorithms. Spectral signals were obtained from nasopharyngeal swab samples previously analyzed using the RT-PCR method. The specimens were provided by the Molecular Diagnosis Laboratory of Covid-19 at Univasf. A total of 314 samples were analyzed, comprising 42 testing positive and 272 testing negative for Covid-19. Digital signal processing techniques, such as Savitzky-Golay filters and statistical methods were used to eliminate spurious elements from the original data and extract relevant features. Supervised machine learning algorithms such as SVM, Random Forest, and Naive Bayes classifiers were used to perform automatic sample identification. To evaluate the performance of the models, a 5-fold cross-validation technique was applied. With the proposed methodology, it was possible to achieve an accuracy of 75%, a sensitivity of 80%, and a specificity of 70%, in addition to an area under the ROC curve of 0.81, in the identification of nasopharyngeal swab samples from previously diagnosed individuals. From these results, it was possible to conclude that Vis-NIR spectroscopy is a promising, fast and relatively low cost technique to identify the SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | | | | | - Rodrigo Pereira Ramos
- Federal University of Sao Francisco Valley (Univasf), Petrolina, Pernambuco, Brazil.
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Cheng R, Bai X, Guo J, Huang L, Zhao D, Liu Z, Zhang W. Hyperspectral discrimination of ginseng variety and age from Changbai Mountain area. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123613. [PMID: 37976570 DOI: 10.1016/j.saa.2023.123613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The efficacy and market value of Panax ginseng Meyer are significantly influenced by its diversity and age. Traditional identification methods are prone to subjective biases and necessitate the use of destructive sample processing, leading to the loss and wastage of ginseng. Consequently, non-destructive in-situ identification has emerged as a crucial subject of interest for both researchers and the ginseng industry. The advancement of technology and the expansion of research have introduced spectral technology and image processing technology as novel approaches and concepts for non-destructive in-situ identification. METHODS Hyperspectral imaging (HSI) is a methodology that combines conventional spectroscopy and imaging to acquire comprehensive spectral and spatial data from various samples. In this study, we investigated the use of Support Vector Machine (SVM) and Spectral Angle Mapper (SAM) classifier algorithms, in conjunction with HSI classification technology, for quasi-Artificial Intelligence (quasi-AI) ginseng identification. To enhance the hyperspectral images prior to SVM classification, we compared the efficacy of Principal Component Analysis (PCA), Minimum Noise Fraction (MNF), and Independent Component Analysis (ICA). RESULTS The classification of ginseng based on age was accomplished through the utilization of Radial Basis Function (RBF) kernel SVM and SAM algorithm, which was trained on feature enhanced images. The classification of WMG, MCG, and GG is primarily based on age, with the endmember spectrum serving as the foundation for SAM and SVM. CONCLUSION The "endmember spectrum set" derived from the classification outcomes can serve as the "mutation point" for identifying ginseng of different ages.
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Affiliation(s)
- Ruiyang Cheng
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Xueyuan Bai
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jianying Guo
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Luqi Huang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Daqing Zhao
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Zhaojian Liu
- Department of Cell Biology, School of Basic Medical Science, Shandong University, Jinan, China.
| | - Wei Zhang
- Northeast Asia Research Institute of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.
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Ferreira TN, Santos LMB, Valladares V, Flanley CM, McDowell MA, Garcia GA, Mello-Silva CC, Maciel-de-Freitas R, Genta FA. Age, sex, and mating status discrimination in the sand fly Lutzomyia longipalpis using near infra-red spectroscopy (NIRS). Parasit Vectors 2024; 17:19. [PMID: 38217054 PMCID: PMC10787389 DOI: 10.1186/s13071-023-06097-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Understanding aspects related to the physiology and capacity of vectors is essential for effectively controlling vector-borne diseases. The sand fly Lutzomyia longipalpis has great importance in medical entomology for disseminating Leishmania parasites, the causative agent of Leishmaniasis, one of the main neglected diseases listed by the World Health Organization (WHO). In this respect, it is necessary to evaluate the transmission potential of this species and the success of vector control interventions. Near-infrared spectroscopy (NIRS) has been used to estimate the age of mosquitoes in different conditions (laboratory, semi-field, and conservation), taxonomic analysis, and infection detection. However, no studies are using NIRS for sand flies. METHODS In this study, we developed analytic models to estimate the age of L. longipalpis adults under laboratory conditions, identify their copulation state, and evaluate their gonotrophic cycle and diet. RESULTS Sand flies were classified with an accuracy of 58-82% in 3 age groups and 82-92% when separating them into young (<8 days) or old (>8 days) insects. The classification between mated and non-mated sandflies was 98-100% accurate, while the percentage of hits of females that had already passed the first gonotrophic cycle was only 59%. CONCLUSIONS We consider the age and copula estimation results very promising, as they provide essential aspects of vector capacity assessment, which can be obtained quickly and at a lower cost with NIRS.
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Affiliation(s)
- Tainá Neves Ferreira
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Lilha M B Santos
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Vanessa Valladares
- Malacology Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Catherine M Flanley
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Gabriela A Garcia
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - Rafael Maciel-de-Freitas
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
| | - Fernando Ariel Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil.
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Huang JD, Wang H, Power U, McLaughlin JA, Nugent C, Rahman E, Barabas J, Maguire P. Detecting Respiratory Viruses Using a Portable NIR Spectrometer-A Preliminary Exploration with a Data Driven Approach. SENSORS (BASEL, SWITZERLAND) 2024; 24:308. [PMID: 38203170 PMCID: PMC10781395 DOI: 10.3390/s24010308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/13/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
Respiratory viruses' detection is vitally important in coping with pandemics such as COVID-19. Conventional methods typically require laboratory-based, high-cost equipment. An emerging alternative method is Near-Infrared (NIR) spectroscopy, especially a portable one of the type that has the benefits of low cost, portability, rapidity, ease of use, and mass deployability in both clinical and field settings. One obstacle to its effective application lies in its common limitations, which include relatively low specificity and general quality. Characteristically, the spectra curves show an interweaving feature for the virus-present and virus-absent samples. This then provokes the idea of using machine learning methods to overcome the difficulty. While a subsequent obstacle coincides with the fact that a direct deployment of the machine learning approaches leads to inadequate accuracy of the modelling results. This paper presents a data-driven study on the detection of two common respiratory viruses, the respiratory syncytial virus (RSV) and the Sendai virus (SEV), using a portable NIR spectrometer supported by a machine learning solution enhanced by an algorithm of variable selection via the Variable Importance in Projection (VIP) scores and its Quantile value, along with variable truncation processing, to overcome the obstacles to a certain extent. We conducted extensive experiments with the aid of the specifically developed algorithm of variable selection, using a total of four datasets, achieving classification accuracy of: (1) 0.88, 0.94, and 0.93 for RSV, SEV, and RSV + SEV, respectively, averaged over multiple runs, for the neural network modelling of taking in turn 3 sessions of data for training and the remaining one session of an 'unknown' dataset for testing. (2) the average accuracy of 0.94 (RSV), 0.97 (SEV), and 0.97 (RSV + SEV) for model validation and 0.90 (RSV), 0.93 (SEV), and 0.91 (RSV + SEV) for model testing, using two of the datasets for model training, one for model validation and the other for model testing. These results demonstrate the feasibility of using portable NIR spectroscopy coupled with machine learning to detect respiratory viruses with good accuracy, and the approach could be a viable solution for population screening.
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Affiliation(s)
- Jian-Dong Huang
- School of Computing, Ulster University, Belfast BT15 1AP, UK
| | - Hui Wang
- School of Computing, Ulster University, Belfast BT15 1AP, UK
| | - Ultan Power
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - James A. McLaughlin
- NIBEC Nanotechnology & Integrated Bio-Engineering Centre, School of Engineering, Ulster University, Belfast BT15 1AP, UK
| | - Chris Nugent
- School of Computing, Ulster University, Belfast BT15 1AP, UK
| | - Enayetur Rahman
- NIBEC Nanotechnology & Integrated Bio-Engineering Centre, School of Engineering, Ulster University, Belfast BT15 1AP, UK
| | - Judit Barabas
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Paul Maguire
- NIBEC Nanotechnology & Integrated Bio-Engineering Centre, School of Engineering, Ulster University, Belfast BT15 1AP, UK
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Menezes CA, Montresor LC, Jangola STG, de Mattos AC, Domingues ALC, Júnior AM, Silva CCM, Barbosa CS, de Mendonça CLF, Massara CL, Fonseca CT, de Oliveira EJ, Gomes ECDS, da Silva EF, Bezerra FSDM, Silva-Jr FP, de Siqueira IC, Silva JRME, Heller L, Farias LP, Beck LCNH, Santos MCS, Lima MG, Mourão MDM, Enk MJ, Fernandez MA, Katz N, Carvalho ODS, Parreiras PM, Neves RH, Gava SG, de Oliveira SA, Thiengo SC, Favre TC, Graeff-Teixeira C, Pieri OS, Caldeira RL, da Silva-Pereira RA, Rocha RS, Oliveira RR. FioSchisto's expert perspective on implementing WHO guidelines for schistosomiasis control and transmission elimination in Brazil. Front Immunol 2023; 14:1268998. [PMID: 38143743 PMCID: PMC10739458 DOI: 10.3389/fimmu.2023.1268998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
The World Health Organization (WHO) recognizes schistosomiasis as one of the Neglected Tropical Diseases targeted for global elimination in the 2030 Agenda of the Sustainable Development Goals. In Brazil, schistosomiasis mansoni is considered a public health problem, particularly prevalent among vulnerable populations living in areas with poor environmental and sanitary conditions. In 2022, the WHO published a Guideline encompassing recommendations to assist national programs in endemic countries in achieving morbidity control, eliminating schistosomiasis as a public health problem, and advancing towards interrupting transmission. The perspectives presented here, collectively prepared by members of the Oswaldo Cruz Foundation's (Fiocruz) Schistosomiasis Translational Program (FioSchisto), along with invited experts, examine the feasibility of the WHO recommendations for the Brazilian settings, providing appropriate recommendations for public health policies applicable to the epidemiological reality of Brazil, and suggests future research to address relevant issues. In Brazil, the provision of safe water and sanitation should be the key action to achieve schistosomiasis elimination goals. The agencies involved in measures implementation should act together with the Primary Care teams for planning, executing, monitoring, and evaluating actions in priority municipalities based on their epidemiological indicators. Host snails control should prioritize judicious ecological interventions at breeding sites. The Information, Education, and Communication (IEC) strategy should be associated with water and sanitation and other control actions, actively involving school community. To identify infected carriers, FioSchisto recommends a two-stage approach of immunological and molecular tests to verify transmission interruption during the intervention and beyond. Praziquantel administration should be done under medical supervision at the Primary Care level. MDA should be considered in exceptional settings, as a measure of initial attack strategy in locations presenting high endemicity, always integrated with water and sanitation, IEC, and snail control. To assist decision-making, as well as the monitoring and evaluation of strategic actions, there is a need for an Information System. FioSchisto considers this systematization essential to make investments in strategic research to support the improvement of schistosomiasis control actions. Efforts toward schistosomiasis elimination in Brazil will succeed with a paradigm shift from the vertical prescriptive framework to a community-centered approach involving intersectoral and interdisciplinary collaboration.
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Affiliation(s)
| | | | | | | | - Ana Lúcia Coutinho Domingues
- Centro de Ciências da Saúde, Departamento de Medicina Clínica, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Leo Heller
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, Brazil
| | | | | | | | - Mariana Gomes Lima
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | | | - Naftale Katz
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, Brazil
| | | | | | - Renata Heisler Neves
- Faculdade de Ciências Médicas, Universidade Estatual do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sandra Grossi Gava
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, Brazil
| | | | | | | | - Carlos Graeff-Teixeira
- Centro de Ciências da Saúde, Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | | | | | | | - Roberto Sena Rocha
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, Brazil
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Mshani IH, Siria DJ, Mwanga EP, Sow BB, Sanou R, Opiyo M, Sikulu-Lord MT, Ferguson HM, Diabate A, Wynne K, González-Jiménez M, Baldini F, Babayan SA, Okumu F. Key considerations, target product profiles, and research gaps in the application of infrared spectroscopy and artificial intelligence for malaria surveillance and diagnosis. Malar J 2023; 22:346. [PMID: 37950315 PMCID: PMC10638832 DOI: 10.1186/s12936-023-04780-3] [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] [Received: 03/04/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Studies on the applications of infrared (IR) spectroscopy and machine learning (ML) in public health have increased greatly in recent years. These technologies show enormous potential for measuring key parameters of malaria, a disease that still causes about 250 million cases and 620,000 deaths, annually. Multiple studies have demonstrated that the combination of IR spectroscopy and machine learning (ML) can yield accurate predictions of epidemiologically relevant parameters of malaria in both laboratory and field surveys. Proven applications now include determining the age, species, and blood-feeding histories of mosquito vectors as well as detecting malaria parasite infections in both humans and mosquitoes. As the World Health Organization encourages malaria-endemic countries to improve their surveillance-response strategies, it is crucial to consider whether IR and ML techniques are likely to meet the relevant feasibility and cost-effectiveness requirements-and how best they can be deployed. This paper reviews current applications of IR spectroscopy and ML approaches for investigating malaria indicators in both field surveys and laboratory settings, and identifies key research gaps relevant to these applications. Additionally, the article suggests initial target product profiles (TPPs) that should be considered when developing or testing these technologies for use in low-income settings.
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Affiliation(s)
- Issa H Mshani
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Doreen J Siria
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Emmanuel P Mwanga
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Bazoumana Bd Sow
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Roger Sanou
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Mercy Opiyo
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Malaria Elimination Initiative (MEI), Institute for Global Health Sciences, University of California, San Francisco, USA
| | - Maggy T Sikulu-Lord
- Faculty of Science, School of the Environment, The University of Queensland, Brisbane, QLD, Australia
| | - Heather M Ferguson
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Abdoulaye Diabate
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Klaas Wynne
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mario González-Jiménez
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Fredros Okumu
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
- School of Life Sciences and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania.
- School of Public Health, The University of the Witwatersrand, Park Town, South Africa.
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9
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Maia LJ, de Oliveira CH, Silva AB, Souza PAA, Müller NFD, Cardoso JDC, Ribeiro BM, de Abreu FVS, Campos FS. Arbovirus surveillance in mosquitoes: Historical methods, emerging technologies, and challenges ahead. Exp Biol Med (Maywood) 2023; 248:2072-2082. [PMID: 38183286 PMCID: PMC10800135 DOI: 10.1177/15353702231209415] [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: 01/08/2024] Open
Abstract
Arboviruses cause millions of infections each year; however, only limited options are available for treatment and pharmacological prevention. Mosquitoes are among the most important vectors for the transmission of several pathogens to humans. Despite advances, the sampling, viral detection, and control methods for these insects remain ineffective. Challenges arise with the increase in mosquito populations due to climate change, insecticide resistance, and human interference affecting natural habitats, which contribute to the increasing difficulty in controlling the spread of arboviruses. Therefore, prioritizing arbovirus surveillance is essential for effective epidemic preparedness. In this review, we offer a concise historical account of the discovery and monitoring of arboviruses in mosquitoes, from mosquito capture to viral detection. We then analyzed the advantages and limitations of these traditional methods. Furthermore, we investigated the potential of emerging technologies to address these limitations, including the implementation of next-generation sequencing, paper-based devices, spectroscopic detectors, and synthetic biosensors. We also provide perspectives on recurring issues and areas of interest such as insect-specific viruses.
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Affiliation(s)
- Luis Janssen Maia
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Laboratório de Baculovírus, Universidade de Brasília, Brasília 70910-900, Brasil
| | - Cirilo Henrique de Oliveira
- Laboratório de Comportamento de Insetos, Instituto Federal do Norte de Minas Gerais, Salinas 39560-000, Brasil
| | - Arthur Batista Silva
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins, Gurupi 77402-970, Brasil
| | - Pedro Augusto Almeida Souza
- Laboratório de Comportamento de Insetos, Instituto Federal do Norte de Minas Gerais, Salinas 39560-000, Brasil
| | - Nicolas Felipe Drumm Müller
- Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90035-003, Brasil
| | - Jader da Cruz Cardoso
- Divisão de Vigilância Ambiental em Saúde, Centro Estadual de Vigilância em Saúde, Secretaria Estadual de Saúde do Rio Grande do Sul, Porto Alegre 90610-000, Brasil
| | - Bergmann Morais Ribeiro
- Instituto de Ciências Biológicas, Departamento de Biologia Celular, Laboratório de Baculovírus, Universidade de Brasília, Brasília 70910-900, Brasil
| | | | - Fabrício Souza Campos
- Laboratório de Bioinformática e Biotecnologia, Universidade Federal do Tocantins, Gurupi 77402-970, Brasil
- Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 90035-003, Brasil
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10
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Gomez-Gonzalez E, Muñoz O, Gomez-Martin JC, Aceituno-Castro J, Fernandez-Muñoz B, Navas-Garcia JM, Barriga-Rivera A, Fernandez-Lizaranzu I, Munoz-Gonzalez FJ, Parrilla-Giraldez R, Requena-Lancharro D, Gil-Gamboa P, Ramos JL, Rosell-Valle C, Gomez-Gonzalez C, Martin-Lopez M, Relimpio-Lopez MI, Perales-Esteve MA, Puppo-Moreno A, Garcia-Cozar FJ, Olvera-Collantes L, de Los Santos-Trigo S, Gomez E, Sanchez-Pernaute R, Padillo-Ruiz J, Marquez-Rivas J. Polarimetric imaging for the detection of synthetic models of SARS-CoV-2: A proof of concept. JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER 2023; 302:108567. [PMID: 36945203 PMCID: PMC9987604 DOI: 10.1016/j.jqsrt.2023.108567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 03/04/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE To conduct a proof-of-concept study of the detection of two synthetic models of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using polarimetric imaging. APPROACH Two SARS-CoV-2 models were prepared as engineered lentiviruses pseudotyped with the G protein of the vesicular stomatitis virus, and with the characteristic Spike protein of SARS-CoV-2. Samples were prepared in two biofluids (saline solution and artificial saliva), in four concentrations, and deposited as 5-µL droplets on a supporting plate. The angles of maximal degree of linear polarization (DLP) of light diffusely scattered from dry residues were determined using Mueller polarimetry from87 samples at 405 nm and 514 nm. A polarimetric camera was used for imaging several samples under 380-420 nm illumination at angles similar to those of maximal DLP. Per-pixel image analysis included quantification and combination of polarization feature descriptors in 475 samples. MAIN RESULTS The angles (from sample surface) of maximal DLP were 3° for 405 nm and 6° for 514 nm. Similar viral particles that differed only in the characteristic spike protein of the SARS-CoV-2, their corresponding negative controls, fluids, and the sample holder were discerned at 10-degree and 15-degree configurations. SIGNIFICANCE Polarimetric imaging in the visible spectrum may help improve fast, non-contact detection and identification of viral particles, and/or other microbes such as tuberculosis, in multiple dry fluid samples simultaneously, particularly when combined with other imaging modalities. Further analysis including realistic concentrations of real SARS-CoV-2 viral particles in relevant human fluids is required. Polarimetric imaging under visible light may contribute to a fast, cost-effective screening of SARS-CoV-2 and other pathogens when combined with other imaging modalities.
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Affiliation(s)
- Emilio Gomez-Gonzalez
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Institute of Biomedicine of Seville, Spain
| | - Olga Muñoz
- Cosmic Dust Laboratory, Instituto de Astrofísica de Andalucía, CSIC, Granada 18008, Spain
| | | | - Jesus Aceituno-Castro
- Cosmic Dust Laboratory, Instituto de Astrofísica de Andalucía, CSIC, Granada 18008, Spain
- Centro Astronomico Hispano Alemán, Almeria 04550, Spain
| | - Beatriz Fernandez-Muñoz
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | | | - Alejandro Barriga-Rivera
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- School of Biomedical Engineering, The University of Sydney, NSW 2006, Australia
| | - Isabel Fernandez-Lizaranzu
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Institute of Biomedicine of Seville, Spain
| | - Francisco Javier Munoz-Gonzalez
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | | | - Desiree Requena-Lancharro
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | - Pedro Gil-Gamboa
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | - José Luis Ramos
- Cosmic Dust Laboratory, Instituto de Astrofísica de Andalucía, CSIC, Granada 18008, Spain
| | - Cristina Rosell-Valle
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | - Carmen Gomez-Gonzalez
- Service of Intensive Care, University Hospital 'Virgen del Rocio', Sevilla 41013, Spain
| | - Maria Martin-Lopez
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | - Maria Isabel Relimpio-Lopez
- Department of General Surgery, College of Medicine, Universidad de Sevilla, Seville 41009, Spain
- Department of Ophthalmology, University Hospital 'Virgen Macarena', Sevilla 41009, Spain
- OftaRed, Institute of Health 'Carlos III', Madrid 28029, Spain
| | - Manuel A Perales-Esteve
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Department of Electronic Engineering at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
| | - Antonio Puppo-Moreno
- Institute of Biomedicine of Seville, Spain
- Service of Intensive Care, University Hospital 'Virgen del Rocio', Sevilla 41013, Spain
| | - Francisco Jose Garcia-Cozar
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz, Cadiz 11003, Spain
- Instituto de Investigación e Innovación Biomedica de Cádiz (INIBICA), Cadiz 11009, Spain
| | - Lucia Olvera-Collantes
- Department of Biomedicine, Biotechnology and Public Health, University of Cadiz, Cadiz 11003, Spain
- Instituto de Investigación e Innovación Biomedica de Cádiz (INIBICA), Cadiz 11009, Spain
| | | | - Emilia Gomez
- Joint Research Centre, European Commission, Sevilla 41092, Spain
| | - Rosario Sanchez-Pernaute
- Unidad de Producción y Reprogramación Celular, Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Fundacion Publica Andaluza Progreso y Salud, Sevilla 41092, Spain
| | | | - Javier Marquez-Rivas
- Group of Interdisciplinary Physics, Department of Applied Physics III at the ETSI Engineering School, Universidad de Sevilla, Seville 41092, Spain
- Institute of Biomedicine of Seville, Spain
- Service of Neurosurgery, University Hospital 'Virgen del Rocío', Sevilla 41013, Spain
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Meireles ACA, Rios FGF, Feitoza LHM, da Silva LR, Julião GR. Nondestructive Methods of Pathogen Detection: Importance of Mosquito Integrity in Studies of Disease Transmission and Control. Pathogens 2023; 12:816. [PMID: 37375506 DOI: 10.3390/pathogens12060816] [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: 03/28/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Mosquitoes are vectors of many pathogens, including viruses, protozoans, and helminths, spreading these pathogens to humans as well as to wild and domestic animals. As the identification of species and the biological characterization of mosquito vectors are cornerstones for understanding patterns of disease transmission, and the design of control strategies, we conducted a literature review on the current use of noninvasive and nondestructive techniques for pathogen detection in mosquitoes, highlighting the importance of their taxonomic status and systematics, and some gaps in the knowledge of their vectorial capacity. Here, we summarized the alternative techniques for pathogen detection in mosquitoes based on both laboratory and field studies. Parasite infection and dissemination by mosquitoes can also be obtained via analyses of saliva- and excreta-based techniques or of the whole mosquito body, using a near-infrared spectrometry (NIRS) approach. Further research should be encouraged to seek strategies for detecting target pathogens while preserving mosquito morphology, especially in biodiversity hotspot regions, thus enabling the discovery of cryptic or new species, and the determination of more accurate taxonomic, parasitological, and epidemiological patterns.
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Affiliation(s)
- Anne Caroline Alves Meireles
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Biodiversity and Health, PhD in Sciences-Fiocruz Rondônia/Oswaldo Cruz Institute, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
| | - Flávia Geovana Fontineles Rios
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Luiz Henrique Maciel Feitoza
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Lucas Rosendo da Silva
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
| | - Genimar Rebouças Julião
- Laboratory of Entomology, Oswaldo Cruz Foundation, Fiocruz Rondônia, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
- Postgraduate Program in Experimental Biology-PGBIOEXP, Fiocruz Rondônia-UNIR, BR-364, Km 9.5, Porto Velho 78900-550, RO, Brazil
- National Institute of Epidemiology of Western Amazônia-INCT-EpiAmO, Rua da Beira 7671, Lagoa, Porto Velho 76812-245, RO, Brazil
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12
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Li Y, Via BK, Han F, Li Y, Pei Z. Comparison of various chemometric methods on visible and near-infrared spectral analysis for wood density prediction among different tree species and geographical origins. FRONTIERS IN PLANT SCIENCE 2023; 14:1121287. [PMID: 36968398 PMCID: PMC10036815 DOI: 10.3389/fpls.2023.1121287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Visible and near-infrared (Vis-NIR) spectroscopy has been widely applied in many fields for the qualitative and quantitative analysis. Chemometric techniques including pre-processing, variable selection, and multivariate calibration models play an important role to better extract useful information from spectral data. In this study, a new de-noising method (lifting wavelet transform, LWT), four variable selection methods, as well as two non-linear machine learning models were simultaneously analyzed to compare the impact of chemometric approaches on wood density determination among various tree species and geographical locations. In addition, fruit fly optimization algorithm (FOA) and response surface methodology (RSM) were employed to optimize the parameters of generalized regression neural network (GRNN) and particle swarm optimization-support vector machine (PSO-SVM), respectively. As for various chemometric methods, the optimal chemometric method was different for the same tree species collected from different locations. FOA-GRNN model combined with LWT and CARS deliver the best performance for Chinese white poplar of Heilongjiang province. In contrast, PLS model showed a good performance for Chinese white poplar collected from Jilin province based on raw spectra. However, for other tree species, RSM-PSO-SVM models can improve the performance of wood density prediction compared to traditional linear and FOA-GRNN models. Especially for Acer mono Maxim, when compared to linear models, the coefficient of determination of prediction set ( R p 2 ) and relative prediction deviation (RPD) were increased by 47.70% and 44.48%, respectively. And the dimensionality of Vis-NIR spectral data was decreased from 2048 to 20. Therefore, the appropriate chemometric technique should be selected before building calibration models.
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Affiliation(s)
- Ying Li
- College of Energy and Transportation Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Brian K. Via
- Forest Products Development Center, School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, United States
| | - Feifei Han
- Laboratory Zhejiang Huadong Forestry Engineering Consulting and Design Corporation, Hangzhou, China
| | - Yaoxiang Li
- College of Engineering and Technology, Northeast Forestry University, Harbin, China
| | - Zhiyong Pei
- College of Energy and Transportation Engineering, Inner Mongolia Agricultural University, Hohhot, China
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13
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Garcia GA, Lord AR, Santos LMB, Kariyawasam TN, David MR, Couto-Lima D, Tátila-Ferreira A, Pavan MG, Sikulu-Lord MT, Maciel-de-Freitas R. Rapid and Non-Invasive Detection of Aedes aegypti Co-Infected with Zika and Dengue Viruses Using Near Infrared Spectroscopy. Viruses 2022; 15:11. [PMID: 36680052 PMCID: PMC9863061 DOI: 10.3390/v15010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
The transmission of dengue (DENV) and Zika (ZIKV) has been continuously increasing worldwide. An efficient arbovirus surveillance system is critical to designing early-warning systems to increase preparedness of future outbreaks in endemic countries. The Near Infrared Spectroscopy (NIRS) is a promising high throughput technique to detect arbovirus infection in Ae. aegypti with remarkable advantages such as cost and time effectiveness, reagent-free, and non-invasive nature over existing molecular tools for similar purposes, enabling timely decision making through rapid detection of potential disease. Our aim was to determine whether NIRS can differentiate Ae. aegypti females infected with either ZIKV or DENV single infection, and those coinfected with ZIKV/DENV from uninfected ones. Using 200 Ae. aegypti females reared and infected in laboratory conditions, the training model differentiated mosquitoes into the four treatments with 100% accuracy. DENV-, ZIKV-, and ZIKV/DENV-coinfected mosquitoes that were used to validate the model could be correctly classified into their actual infection group with a predictive accuracy of 100%, 84%, and 80%, respectively. When compared with mosquitoes from the uninfected group, the three infected groups were predicted as belonging to the infected group with 100%, 97%, and 100% accuracy for DENV-infected, ZIKV-infected, and the co-infected group, respectively. Preliminary lab-based results are encouraging and indicate that NIRS should be tested in field settings to evaluate its potential role to monitor natural infection in field-caught mosquitoes.
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Affiliation(s)
- Gabriela A. Garcia
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Anton R. Lord
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
- Spectroscopy and Data Consultants Pty Ltd., Brisbane, QLD 4035, Australia
| | - Lilha M. B. Santos
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | | | - Mariana R. David
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Dinair Couto-Lima
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Aline Tátila-Ferreira
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Márcio G. Pavan
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
| | - Maggy T. Sikulu-Lord
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Rafael Maciel-de-Freitas
- Laboratório de Mosquitos Transmissores de Hematozoários, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, Rio de Janeiro, Brazil
- Department of Arbovirology, Bernhard Nocht Institute of Tropical Medicine, 20359 Hamburg, Germany
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14
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Garcia GA, Kariyawasam TN, Lord AR, da Costa CF, Chaves LB, Lima-Junior JDC, Maciel-de-Freitas R, Sikulu-Lord MT. Malaria absorption peaks acquired through the skin of patients with infrared light can detect patients with varying parasitemia. PNAS NEXUS 2022; 1:pgac272. [PMID: 36712329 PMCID: PMC9802436 DOI: 10.1093/pnasnexus/pgac272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
To eliminate malaria, scalable tools that are rapid, affordable, and can detect patients with low parasitemia are required. Non-invasive diagnostic tools that are rapid, reagent-free, and affordable would also provide a justifiable platform for testing malaria in asymptomatic patients. However, non-invasive surveillance techniques for malaria remain a diagnostic gap. Here, we show near-infrared Plasmodium absorption peaks acquired non-invasively through the skin using a miniaturized hand-held near-infrared spectrometer. Using spectra from the ear, these absorption peaks and machine learning techniques enabled non-invasive detection of malaria-infected human subjects with varying parasitemia levels in less than 10 s.
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Affiliation(s)
- Gabriela A Garcia
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ 21040-900, Brazil
| | - Tharanga N Kariyawasam
- School of Biological Sciences, Faculty of Science, The University of Queensland, Brisbane, QLD 4072,, Australia
| | - Anton R Lord
- School of Computer Science, Centre for Data Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | | | - Lana Bitencourt Chaves
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ 21040-900, Brazil
| | - Josué da Costa Lima-Junior
- Laboratório de Imunoparasitologia, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ 21040-900, Brazil
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15
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Spectroscopic methods for COVID-19 detection and early diagnosis. Virol J 2022; 19:152. [PMID: 36138463 PMCID: PMC9502632 DOI: 10.1186/s12985-022-01867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
The coronavirus pandemic is a worldwide hazard that poses a threat to millions of individuals throughout the world. This pandemic is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which was initially identified in Wuhan, China's Hubei provincial capital, and has since spread throughout the world. According to the World Health Organization's Weekly Epidemiological Update, there were more than 250 million documented cases of coronavirus infections globally, with five million fatalities. Early detection of coronavirus does not only reduce the spread of the virus, but it also increases the chance of curing the infection. Spectroscopic techniques have been widely used in the early detection and diagnosis of COVID-19 using Raman, Infrared, mass spectrometry and fluorescence spectroscopy. In this review, the reported spectroscopic methods for COVID-19 detection were discussed with emphasis on the practical aspects, limitations and applications.
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16
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Rumaling MI, Chee FP, Bade A, Hasbi NH, Daim S, Juhim F, Duinong M, Rasmidi R. Methods of optical spectroscopy in detection of virus in infected samples: A review. Heliyon 2022; 8:e10472. [PMID: 36060463 PMCID: PMC9422564 DOI: 10.1016/j.heliyon.2022.e10472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 01/08/2023] Open
Affiliation(s)
- Muhammad Izzuddin Rumaling
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Fuei Pien Chee
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
- Corresponding author.
| | - Abdullah Bade
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Nur Hasshima Hasbi
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Sylvia Daim
- Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Floressy Juhim
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Mivolil Duinong
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Rosfayanti Rasmidi
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA Sabah Branch, Kota Kinabalu Campus, 88997 Kota Kinabalu, Sabah, Malaysia
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17
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Morgan J, Salcedo-Sora JE, Wagner I, Beynon RJ, Triana-Chavez O, Strode C. Rapid Evaporative Ionization Mass Spectrometry (REIMS): a Potential and Rapid Tool for the Identification of Insecticide Resistance in Mosquito Larvae. JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:5. [PMID: 36082679 PMCID: PMC9459442 DOI: 10.1093/jisesa/ieac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 06/15/2023]
Abstract
Insecticide resistance is a significant challenge facing the successful control of mosquito vectors globally. Bioassays are currently the only method for phenotyping resistance. They require large numbers of mosquitoes for testing, the availability of a susceptible comparator strain, and often insectary facilities. This study aimed to trial the novel use of rapid evaporative ionization mass spectrometry (REIMS) for the identification of insecticide resistance in mosquitoes. No sample preparation is required for REIMS and analysis can be rapidly conducted within hours. Temephos resistant Aedes aegypti (Linnaeus) larvae from Cúcuta, Colombia and temephos susceptible larvae from two origins (Bello, Colombia, and the lab reference strain New Orleans) were analyzed using REIMS. We tested the ability of REIMS to differentiate three relevant variants: population source, lab versus field origin, and response to insecticide. The classification of these data was undertaken using linear discriminant analysis (LDA) and random forest. Classification models built using REIMS data were able to differentiate between Ae. aegypti larvae from different populations with 82% (±0.01) accuracy, between mosquitoes of field and lab origin with 89% (±0.01) accuracy and between susceptible and resistant larvae with 85% (±0.01) accuracy. LDA classifiers had higher efficiency than random forest with this data set. The high accuracy observed here identifies REIMS as a potential new tool for rapid identification of resistance in mosquitoes. We argue that REIMS and similar modern phenotyping alternatives should complement existing insecticide resistance management tools.
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Affiliation(s)
- Jasmine Morgan
- Department of Biology, Edge Hill University, Ormskirk, Lancashire, L39 4QP, UK
| | | | - Iris Wagner
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Omar Triana-Chavez
- Instituto de Biología, Facultad de Ciencias Exactas y Naturales (FCEN), University of Antioquia, Medellín, Colombia
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18
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Mgaya JN, Siria DJ, Makala FE, Mgando JP, Vianney JM, Mwanga EP, Okumu FO. Effects of sample preservation methods and duration of storage on the performance of mid-infrared spectroscopy for predicting the age of malaria vectors. Parasit Vectors 2022; 15:281. [PMID: 35933384 PMCID: PMC9356448 DOI: 10.1186/s13071-022-05396-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Monitoring the biological attributes of mosquitoes is critical for understanding pathogen transmission and estimating the impacts of vector control interventions on the survival of vector species. Infrared spectroscopy and machine learning techniques are increasingly being tested for this purpose and have been proven to accurately predict the age, species, blood-meal sources, and pathogen infections in Anopheles and Aedes mosquitoes. However, as these techniques are still in early-stage implementation, there are no standardized procedures for handling samples prior to the infrared scanning. This study investigated the effects of different preservation methods and storage duration on the performance of mid-infrared spectroscopy for age-grading females of the malaria vector, Anopheles arabiensis. METHODS Laboratory-reared An. arabiensis (N = 3681) were collected at 5 and 17 days post-emergence, killed with ethanol, and then preserved using silica desiccant at 5 °C, freezing at - 20 °C, or absolute ethanol at room temperature. For each preservation method, the mosquitoes were divided into three groups, stored for 1, 4, or 8 weeks, and then scanned using a mid-infrared spectrometer. Supervised machine learning classifiers were trained with the infrared spectra, and the support vector machine (SVM) emerged as the best model for predicting the mosquito ages. RESULTS The model trained using silica-preserved mosquitoes achieved 95% accuracy when predicting the ages of other silica-preserved mosquitoes, but declined to 72% and 66% when age-classifying mosquitoes preserved using ethanol and freezing, respectively. Prediction accuracies of models trained on samples preserved in ethanol and freezing also reduced when these models were applied to samples preserved by other methods. Similarly, models trained on 1-week stored samples had declining accuracies of 97%, 83%, and 72% when predicting the ages of mosquitoes stored for 1, 4, or 8 weeks respectively. CONCLUSIONS When using mid-infrared spectroscopy and supervised machine learning to age-grade mosquitoes, the highest accuracies are achieved when the training and test samples are preserved in the same way and stored for similar durations. However, when the test and training samples were handled differently, the classification accuracies declined significantly. Protocols for infrared-based entomological studies should therefore emphasize standardized sample-handling procedures and possibly additional statistical procedures such as transfer learning for greater accuracy.
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Affiliation(s)
- Jacqueline N Mgaya
- Environmental Health and Ecological Science Department, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania.
- School of Life Science and Bioengineering, The Nelson Mandela African Institute of Science and Technology, P.O. Box 447, Arusha, Tanzania.
| | - Doreen J Siria
- Environmental Health and Ecological Science Department, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania
| | - Faraja E Makala
- Environmental Health and Ecological Science Department, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania
| | - Joseph P Mgando
- Environmental Health and Ecological Science Department, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania
| | - John-Mary Vianney
- School of Life Science and Bioengineering, The Nelson Mandela African Institute of Science and Technology, P.O. Box 447, Arusha, Tanzania
| | - Emmanuel P Mwanga
- Environmental Health and Ecological Science Department, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania.
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Fredros O Okumu
- Environmental Health and Ecological Science Department, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania.
- School of Life Science and Bioengineering, The Nelson Mandela African Institute of Science and Technology, P.O. Box 447, Arusha, Tanzania.
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
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19
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Infrared spectroscopy (NIRS and ATR-FTIR) together with multivariate classification for non-destructive differentiation between female mosquitoes of Aedes aegypti recently infected with dengue vs. uninfected females. Acta Trop 2022; 235:106633. [PMID: 35932844 DOI: 10.1016/j.actatropica.2022.106633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 08/03/2022] [Indexed: 11/23/2022]
Abstract
One of the most important steps in preventing arboviruses is entomological surveillance. The main entomological surveillance action is to detect vector foci in the shortest possible stages. In this work, near and medium infrared spectra collected from female Aedes aegypti mosquitoes recently infected and not infected with dengue were used in order to build chemometric models capable of differentiating the spectra of each class. For this, computational algorithms such as Successive Projection Algorithm (SPA) and Genetic Algorithm (GA) were used together with Linear Discriminant Analysis (LDA). The constructed models were evaluated with sensitivity and specificity calculations. It was observed that models based on near infrared (NIR) spectra have better classification results when compared to mid infrared (MIR) spectra, as well as models based on GA present better results when compared to those based on SPA. Thus, NIR-GA-LDA obtained the best results, reaching 100.00 % for sensitivity and specificity. NIR spectroscopy is 18 times faster and 116 times cheaper than RT-qPCR. The findings reported in this study may have important applications in the field of entomological surveillance, prevention and control of dengue vectors. In the future, mosquito traps equipped with portable NIR instruments capable of detecting infected mosquitoes may be used, in order to enable an action plan to prevent future outbreaks of the disease.
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20
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Yonar D, Severcan M, Gurbanov R, Sandal A, Yilmaz U, Emri S, Severcan F. Rapid diagnosis of malignant pleural mesothelioma and its discrimination from lung cancer and benign exudative effusions using blood serum. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166473. [PMID: 35753541 DOI: 10.1016/j.bbadis.2022.166473] [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: 12/19/2021] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023]
Abstract
Malignant pleural mesothelioma (MPM), an aggressive cancer associated with exposure to fibrous minerals, can only be diagnosed in the advanced stage because its early symptoms are also connected with other respiratory diseases. Hence, understanding the molecular mechanism and the discrimination of MPM from other lung diseases at an early stage is important to apply effective treatment strategies and for the increase in survival rate. This study aims to develop a new approach for characterization and diagnosis of MPM among lung diseases from serum by Fourier transform infrared spectroscopy (FTIR) coupled with multivariate analysis. The detailed spectral characterization studies indicated the changes in lipid biosynthesis and nucleic acids levels in the malignant serum samples. Furthermore, the results showed that healthy, benign exudative effusion, lung cancer, and MPM groups were successfully separated from each other by applying principal component analysis (PCA), support vector machine (SVM), and especially linear discriminant analysis (LDA) to infrared spectra.
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Affiliation(s)
- Dilek Yonar
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Yuksek Ihtisas University, Faculty of Medicine, Biophysics Department, Ankara, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronics Engineering, Ankara, Turkey
| | - Rafig Gurbanov
- Bilecik Seyh Edebali University, Department of Bioengineering, Bilecik, Turkey
| | - Abdulsamet Sandal
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Ankara Occupational and Environmental Diseases Hospital, Ankara, Turkey
| | - Ulku Yilmaz
- Atatürk Chest Diseases and Chest Surgery Training and Research Hospital, Ankara, Turkey
| | - Salih Emri
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Medicana Hospital, Department of Chest Diseases, Kadikoy, Istanbul, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Altinbas University, Faculty of Medicine, Biophysics Department, Istanbul, Turkey.
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21
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Raypah ME, Faris AN, Mohd Azlan M, Yusof NY, Suhailin FH, Shueb RH, Ismail I, Mustafa FH. Near-Infrared Spectroscopy as a Potential COVID-19 Early Detection Method: A Review and Future Perspective. SENSORS 2022; 22:s22124391. [PMID: 35746172 PMCID: PMC9229781 DOI: 10.3390/s22124391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/05/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a worldwide health anxiety. The rapid dispersion of the infection globally results in unparalleled economic, social, and health impacts. The pathogen that causes COVID-19 is known as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A fast and low-cost diagnosis method for COVID-19 disease can play an important role in controlling its proliferation. Near-infrared spectroscopy (NIRS) is a quick, non-destructive, non-invasive, and inexpensive technique for profiling the chemical and physical structures of a wide range of samples. Furthermore, the NIRS has the advantage of incorporating the internet of things (IoT) application for the effective control and treatment of the disease. In recent years, a significant advancement in instrumentation and spectral analysis methods has resulted in a remarkable impact on the NIRS applications, especially in the medical discipline. To date, NIRS has been applied as a technique for detecting various viruses including zika (ZIKV), chikungunya (CHIKV), influenza, hepatitis C, dengue (DENV), and human immunodeficiency (HIV). This review aims to outline some historical and contemporary applications of NIRS in virology and its merit as a novel diagnostic technique for SARS-CoV-2.
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Affiliation(s)
- Muna E. Raypah
- School of Physics, Universiti Sains Malaysia, George Town 11800, Pulau Pinang, Malaysia;
| | - Asma Nadia Faris
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
| | - Mawaddah Mohd Azlan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
| | - Fariza Hanim Suhailin
- Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia;
| | - Rafidah Hanim Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Irneza Ismail
- Advanced Devices & System (ADS) Research Group, Department of Electrical & Electronic Engineering, Faculty of Engineering and Built Environment, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai 71800, Negeri Sembilan, Malaysia
- Correspondence: (I.I.); (F.H.M.); Tel.: +60-7986569 (I.I.); +60-9-7672432 (F.H.M.)
| | - Fatin Hamimi Mustafa
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
- Correspondence: (I.I.); (F.H.M.); Tel.: +60-7986569 (I.I.); +60-9-7672432 (F.H.M.)
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22
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Sur UK, Santra C. Spectroscopy: a versatile sensing tool for cost-effective and rapid detection of novel coronavirus (COVID-19). EMERGENT MATERIALS 2022; 5:249-260. [PMID: 35252760 PMCID: PMC8883019 DOI: 10.1007/s42247-022-00358-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED The deadly novel coronavirus SARS-CoV-2 is responsible for COVID-19, which was first recognized in Wuhan, China, in December 2019. Rapid identification at primary stage of the novel coronavirus, SARS-CoV-2, is important to restrict it and prevent the pandemic. Real-time RT-PCR assays are the best diagnostic tests presently available for SARS-CoV-2 detection, which are highly sensitive, even though expensive equipment and trained technicians are necessary. Furthermore, the method has moderately long time bound. This deadly viral infection can also be detected by applying various spectroscopic techniques as spectroscopy can provide fast, precise identification and monitoring, leading to the overall understanding of its mutation rates, which will further facilitate antiviral drug development as well as vaccine development. It is an innovative and non-invasive technique for combating the spread of novel coronavirus. This review article demonstrates the application of various spectroscopic techniques to detect COVID-19 rapidly. Different spectroscopy-based detection protocols and additional development of new, novel sensors and biosensors along with diagnostic kits had been described here stressing the status of sensitive diagnostic systems to handle with the COVID-19 outbreak. GRAPHICAL ABSTRACT Spectroscopy: A versatile sensing tool for cost-effective and rapid detection of novel Coronavirus (COVID-19).
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Affiliation(s)
- Ujjal Kumar Sur
- Department of Chemistry, Behala College, University of Calcutta, Parnashree, Kolkata, 700060 West Bengal India
| | - Chittaranjan Santra
- Department of Chemistry (Ex), Netaji Nagar Day College, Kolkata, 700092 India
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23
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Gomez-Gonzalez E, Barriga-Rivera A, Fernandez-Muñoz B, Navas-Garcia JM, Fernandez-Lizaranzu I, Munoz-Gonzalez FJ, Parrilla-Giraldez R, Requena-Lancharro D, Gil-Gamboa P, Rosell-Valle C, Gomez-Gonzalez C, Mayorga-Buiza MJ, Martin-Lopez M, Muñoz O, Gomez-Martin JC, Relimpio-Lopez MI, Aceituno-Castro J, Perales-Esteve MA, Puppo-Moreno A, Garcia-Cozar FJ, Olvera-Collantes L, Gomez-Diaz R, de Los Santos-Trigo S, Huguet-Carrasco M, Rey M, Gomez E, Sanchez-Pernaute R, Padillo-Ruiz J, Marquez-Rivas J. Optical imaging spectroscopy for rapid, primary screening of SARS-CoV-2: a proof of concept. Sci Rep 2022; 12:2356. [PMID: 35181702 PMCID: PMC8857323 DOI: 10.1038/s41598-022-06393-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 12/24/2022] Open
Abstract
Effective testing is essential to control the coronavirus disease 2019 (COVID-19) transmission. Here we report a-proof-of-concept study on hyperspectral image analysis in the visible and near-infrared range for primary screening at the point-of-care of SARS-CoV-2. We apply spectral feature descriptors, partial least square-discriminant analysis, and artificial intelligence to extract information from optical diffuse reflectance measurements from 5 µL fluid samples at pixel, droplet, and patient levels. We discern preparations of engineered lentiviral particles pseudotyped with the spike protein of the SARS-CoV-2 from those with the G protein of the vesicular stomatitis virus in saline solution and artificial saliva. We report a quantitative analysis of 72 samples of nasopharyngeal exudate in a range of SARS-CoV-2 viral loads, and a descriptive study of another 32 fresh human saliva samples. Sensitivity for classification of exudates was 100% with peak specificity of 87.5% for discernment from PCR-negative but symptomatic cases. Proposed technology is reagent-free, fast, and scalable, and could substantially reduce the number of molecular tests currently required for COVID-19 mass screening strategies even in resource-limited settings.
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Affiliation(s)
- Emilio Gomez-Gonzalez
- Department of Applied Physics III, ETSI School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain. .,Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain.
| | - Alejandro Barriga-Rivera
- Department of Applied Physics III, ETSI School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain.,School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Beatriz Fernandez-Muñoz
- Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Consejería de Salud y Familias, Junta de Andalucía, 41092, Sevilla, Spain
| | | | - Isabel Fernandez-Lizaranzu
- Department of Applied Physics III, ETSI School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain.,Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain
| | - Francisco Javier Munoz-Gonzalez
- Department of Applied Physics III, ETSI School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | | | - Desiree Requena-Lancharro
- Department of Applied Physics III, ETSI School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | - Pedro Gil-Gamboa
- Department of Applied Physics III, ETSI School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | - Cristina Rosell-Valle
- Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain.,Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Consejería de Salud y Familias, Junta de Andalucía, 41092, Sevilla, Spain
| | - Carmen Gomez-Gonzalez
- Service of Intensive Care, University Hospital 'Virgen del Rocio', 41013, Sevilla, Spain.,Department of Medicine, College of Medicine, Universidad de Sevilla, 41009, Seville, Spain
| | - Maria Jose Mayorga-Buiza
- Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain.,Service of Anesthesiology, University Hospital 'Virgen del Rocio', 41013, Sevilla, Spain.,Department of Surgery, College of Medicine, Universidad de Sevilla, 41009, Seville, Spain
| | - Maria Martin-Lopez
- Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain.,Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Consejería de Salud y Familias, Junta de Andalucía, 41092, Sevilla, Spain
| | - Olga Muñoz
- Instituto de Astrofísica de Andalucía, CSIC, 18008, Granada, Spain
| | | | - Maria Isabel Relimpio-Lopez
- Department of Surgery, College of Medicine, Universidad de Sevilla, 41009, Seville, Spain.,Department of Ophthalmology, University Hospital 'Virgen Macarena', 41009, Sevilla, Spain.,OftaRed, Institute of Health 'Carlos III', 28029, Madrid, Spain
| | - Jesus Aceituno-Castro
- Instituto de Astrofísica de Andalucía, CSIC, 18008, Granada, Spain.,Centro Astronomico Hispano Alemán, 04550, Almeria, Spain
| | - Manuel A Perales-Esteve
- Department of Electronic Engineering, ETSI School of Engineering, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Antonio Puppo-Moreno
- Service of Intensive Care, University Hospital 'Virgen del Rocio', 41013, Sevilla, Spain.,Department of Medicine, College of Medicine, Universidad de Sevilla, 41009, Seville, Spain
| | | | - Lucia Olvera-Collantes
- Instituto de Investigación e Innovación Biomedica de Cádiz (INIBICA), 11009, Cadiz, Spain
| | | | | | | | | | - Emilia Gomez
- Joint Research Centre, European Commission, 41092, Sevilla, Spain
| | - Rosario Sanchez-Pernaute
- Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, Consejería de Salud y Familias, Junta de Andalucía, 41092, Sevilla, Spain
| | - Javier Padillo-Ruiz
- Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain.,Department of Surgery, College of Medicine, Universidad de Sevilla, 41009, Seville, Spain.,Department of General Surgery, University Hospital 'Virgen del Rocío', 41013, Sevilla, Spain
| | - Javier Marquez-Rivas
- Institute of Biomedicine of Seville (IBIS), 41013, Sevilla, Spain.,Department of Surgery, College of Medicine, Universidad de Sevilla, 41009, Seville, Spain.,Service of Neurosurgery, University Hospital 'Virgen del Rocío', 41013, Sevilla, Spain.,Centre for Advanced Neurology, 41013, Sevilla, Spain
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24
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Tátila-Ferreira A, Garcia GA, Dos Santos LMB, Pavan MG, de C Moreira CJ, Victoriano JC, da Silva-Junior R, Dos Santos-Mallet JR, Verly T, Britto C, Sikulu-Lord MT, Maciel-de-Freitas R. Near infrared spectroscopy accurately detects Trypanosoma cruzi non-destructively in midguts, rectum and excreta samples of Triatoma infestans. Sci Rep 2021; 11:23884. [PMID: 34903840 PMCID: PMC8668913 DOI: 10.1038/s41598-021-03465-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by Trypanosoma cruzi parasite with an estimated 70 million people at risk. Traditionally, parasite presence in triatomine vectors is detected through optical microscopy which can be low in sensitivity or molecular techniques which can be costly in endemic countries. The aim of this study was to evaluate the ability of a reagent-free technique, the Near Infrared Spectroscopy (NIRS) for rapid and non-invasive detection of T. cruzi in Triatoma infestans body parts and in wet/dry excreta samples of the insect. NIRS was 100% accurate for predicting the presence of T. cruzi infection Dm28c strain (TcI) in either the midgut or the rectum and models developed from either body part could predict infection in the other part. Models developed to predict infection in excreta samples were 100% accurate for predicting infection in both wet and dry samples. However, models developed using dry excreta could not predict infection in wet samples and vice versa. This is the first study to report on the potential application of NIRS for rapid and non-invasive detection of T. cruzi infection in T. infestans in the laboratory. Future work should demonstrate the capacity of NIRS to detect T. cruzi in triatomines originating from the field.
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Affiliation(s)
- Aline Tátila-Ferreira
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gabriela A Garcia
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lilha M B Dos Santos
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Márcio G Pavan
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carlos José de C Moreira
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Juliana C Victoriano
- Laboratório Interdisciplinar de Vigilância Entomológica de Diptera E Hemiptera, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Renato da Silva-Junior
- Laboratório Interdisciplinar de Vigilância Entomológica de Diptera E Hemiptera, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Universidade Iguaçu - UNIG, Rio de Janeiro, Brazil
| | - Jacenir R Dos Santos-Mallet
- Laboratório Interdisciplinar de Vigilância Entomológica de Diptera E Hemiptera, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Universidade Iguaçu - UNIG, Rio de Janeiro, Brazil
| | - Thaiane Verly
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Constança Britto
- Laboratório de Biologia Molecular e Doenças Endêmicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Maggy T Sikulu-Lord
- The School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia
| | - Rafael Maciel-de-Freitas
- Laboratório de Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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25
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Freitas DLD, Peres AFS, Silva LG, Mariz JVM, Santos MG, Morais RSP, Morais CLM, Martin FL, Pascoal DAV, de A S Camargo JD, Crispim JCO, Lima KMG. Near-infrared spectroscopy of blood plasma with chemometrics towards HIV discrimination during pregnancy. Sci Rep 2021; 11:22609. [PMID: 34799631 PMCID: PMC8604940 DOI: 10.1038/s41598-021-02105-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022] Open
Abstract
Prevention of mother-to-child transmission programs have been one of the hallmarks of success in the fight against HIV/AIDS. In Brazil, access to antiretroviral therapy (ART) during pregnancy has increased, leading to a reduction in new infections among children. Currently, lifelong ART is available to all pregnant, however yet challenges remain in eliminating mother-to-child transmission. In this paper, we focus on the role of near-infrared (NIR) spectroscopy to analyse blood plasma samples of pregnant women with HIV infection to differentiate pregnant women without HIV infection. Seventy-seven samples (39 HIV-infected patient and 38 healthy control samples) were analysed. Multivariate classification of resultant NIR spectra facilitated diagnostic segregation of both sample categories in a fast and non-destructive fashion, generating good accuracy, sensitivity and specificity. This method is simple and low-cost, and can be easily adapted to point-of-care screening, which can be essential to monitor pregnancy risks in remote locations or in the developing world. Therefore, it opens a new perspective to investigate vertical transmission (VT). The approach described here, can be useful for the identification and exploration of VT under various pathophysiological conditions of maternal HIV. These findings demonstrate, for the first time, the potential of NIR spectroscopy combined with multivariate analysis as a screening tool for fast and low-cost HIV detection.
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Affiliation(s)
- Daniel L D Freitas
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, 5072-970, Brazil
| | - Ana F S Peres
- Maternity School Januário Cicco, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Lidiane G Silva
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, 5072-970, Brazil
| | - João V M Mariz
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, 5072-970, Brazil
| | - Marcos G Santos
- Maternity School Januário Cicco, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
- Brain Institute, Federal University of Rio Grande do Norte, Natal, 59056-450, Brazil
| | - Rayanne S P Morais
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Camilo L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | | | - Daniel A V Pascoal
- Maternity School Januário Cicco, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Juliana D de A S Camargo
- Maternity School Januário Cicco, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Janaina C O Crispim
- Maternity School Januário Cicco, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Kassio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, 5072-970, Brazil.
- Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal, RN, 59012-310, Brazil.
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26
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Valladares V, Pasquini C, Thiengo SC, Mello-Silva CC. Feasibility of near-infrared spectroscopy for species identification and parasitological diagnosis of freshwater snails of the genus Biomphalaria (Planorbidae). PLoS One 2021; 16:e0259832. [PMID: 34762684 PMCID: PMC8584770 DOI: 10.1371/journal.pone.0259832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 10/27/2021] [Indexed: 11/19/2022] Open
Abstract
Near Infrared Spectroscopy (NIRS) has been applied in epidemiological surveillance studies of insect vectors of parasitic diseases, such as the Dengue's mosquitoes. However, regarding mollusks, vectors of important worldwide helminth diseases such as schistosomiasis, fascioliasis and angiostrongyliasis, NIRS studies are rare. This work proposes to establish and standardize the procedure of data collection and analysis using NIRS applied to medical malacology, i.e., to mollusk vectors identifications. Biomphalaria shells and live snails were analyzed regarding several operational aspects, such as: moisture, shell side and position of the live animal for acquisition of NIR spectra. Representative spectra of Biomphalaria shells and live snails were collected using an average of 50 scans per sample and resolution of 16 cm-1. For shells, the sample should first be dried for a minimum of 15 days at an average temperature of 26±1°C, and then placed directly in the equipment measurement window with its left side facing the light beam. Live animals should be dried with absorbent paper; placed into a glass jar, and analyzed similarly to the shells. Once standardized, the technique was applied aiming at two objectives: identification of Biomphalaria using only the shells and parasitological diagnosis for Schistosoma mansoni infection. The discrimination of the three Biomphalaria species intermediate hosts of S. mansoni only by shell has technical limit due to the scarcity of organic material. Nevertheless, it was possible to differentiate B. straminea from B. tenagophila and B. glabrata with 96% accuracy. As for the parasitological diagnosis, it was possible to differentiate infected mollusks shedding S. mansoni cercariae from the non-infected ones with 82, 5% accuracy. In conclusion, the Near Infrared Spectroscopy (NIR's) technique has proven to be an innovative and sound tool to detect infection by S. mansoni in the different species of Biomphalaria intermediate hosts.
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Affiliation(s)
- Vanessa Valladares
- Evaluation and Promotion of Environmental Health Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Célio Pasquini
- National Institute of Advanced Analytical Sciences and Technologies (INCTAA), State University of Campinas—UNICAMP / Chemistry Institute, Campinas, SP, Brazil
| | | | - Clélia Christina Mello-Silva
- Evaluation and Promotion of Environmental Health Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
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27
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A simple and fast spectroscopy-based technique for Covid-19 diagnosis. Sci Rep 2021; 11:16740. [PMID: 34408169 PMCID: PMC8373901 DOI: 10.1038/s41598-021-95568-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/22/2021] [Indexed: 12/24/2022] Open
Abstract
The coronavirus pandemic, which appeared in Wuhan, China, in December 2019, rapidly spread all over the world in only a few weeks. Faster testing techniques requiring less resources are key in managing the pandemic, either to enable larger scale testing or even just provide developing countries with limited resources, particularly in Africa, means to perform tests to manage the crisis. Here, we report an unprecedented, rapid, reagent-free and easy-to-use screening spectroscopic method for the detection of SARS-CoV-2 on RNA extracts. This method, validated on clinical samples collected from 280 patients with quantitative predictive scores on both positive and negative samples, is based on a multivariate analysis of FTIR spectra of RNA extracts. This technique, in agreement with RT-PCR, achieves 97.8% accuracy, 97% sensitivity and 98.3% specificity while reducing the testing time post RNA extraction from hours to minutes. Furthermore, this technique can be used in several laboratories with limited resources.
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28
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Gomez-Gonzalez E, Fernandez-Muñoz B, Barriga-Rivera A, Navas-Garcia JM, Fernandez-Lizaranzu I, Munoz-Gonzalez FJ, Parrilla-Giraldez R, Requena-Lancharro D, Guerrero-Claro M, Gil-Gamboa P, Rosell-Valle C, Gomez-Gonzalez C, Mayorga-Buiza MJ, Martin-Lopez M, Muñoz O, Martin JCG, Lopez MIR, Aceituno-Castro J, Perales-Esteve MA, Puppo-Moreno A, Cozar FJG, Olvera-Collantes L, de Los Santos-Trigo S, Gomez E, Pernaute RS, Padillo-Ruiz J, Marquez-Rivas J. Hyperspectral image processing for the identification and quantification of lentiviral particles in fluid samples. Sci Rep 2021; 11:16201. [PMID: 34376765 PMCID: PMC8355230 DOI: 10.1038/s41598-021-95756-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Optical spectroscopic techniques have been commonly used to detect the presence of biofilm-forming pathogens (bacteria and fungi) in the agro-food industry. Recently, near-infrared (NIR) spectroscopy revealed that it is also possible to detect the presence of viruses in animal and vegetal tissues. Here we report a platform based on visible and NIR (VNIR) hyperspectral imaging for non-contact, reagent free detection and quantification of laboratory-engineered viral particles in fluid samples (liquid droplets and dry residue) using both partial least square-discriminant analysis and artificial feed-forward neural networks. The detection was successfully achieved in preparations of phosphate buffered solution and artificial saliva, with an equivalent pixel volume of 4 nL and lowest concentration of 800 TU·\documentclass[12pt]{minimal}
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\begin{document}$$\upmu$$\end{document}μL−1. This method constitutes an innovative approach that could be potentially used at point of care for rapid mass screening of viral infectious diseases and monitoring of the SARS-CoV-2 pandemic.
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Affiliation(s)
- Emilio Gomez-Gonzalez
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain. .,Institute of Biomedicine of Seville, 41013, Sevilla, Spain.
| | - Beatriz Fernandez-Muñoz
- Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, 41092, Sevilla, Spain
| | - Alejandro Barriga-Rivera
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain.,School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | | | - Isabel Fernandez-Lizaranzu
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain.,Institute of Biomedicine of Seville, 41013, Sevilla, Spain
| | - Francisco Javier Munoz-Gonzalez
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | | | - Desiree Requena-Lancharro
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | - Manuel Guerrero-Claro
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | - Pedro Gil-Gamboa
- Department of Applied Physics III, School of Engineering, Universidad de Sevilla, Camino de los Descubrimientos s/n, 41092, Sevilla, Spain
| | - Cristina Rosell-Valle
- Institute of Biomedicine of Seville, 41013, Sevilla, Spain.,Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, 41092, Sevilla, Spain
| | - Carmen Gomez-Gonzalez
- Service of Intensive Care, University Hospital 'Virgen del Rocio', 41013, Sevilla, Spain
| | - Maria Jose Mayorga-Buiza
- Institute of Biomedicine of Seville, 41013, Sevilla, Spain.,Service of Anaesthesiology, University Hospital 'Virgen del Rocio', 41013, Sevilla, Spain
| | - Maria Martin-Lopez
- Institute of Biomedicine of Seville, 41013, Sevilla, Spain.,Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, 41092, Sevilla, Spain
| | - Olga Muñoz
- Instituto de Astrofísica de Andalucía, CSIC, 18008, Granada, Spain
| | | | - Maria Isabel Relimpio Lopez
- Department of Ophthalmology, University Hospital 'Virgen Macarena', 41009, Sevilla, Spain.,OftaRed, Institute of Health 'Carlos III', 28029, Madrid, Spain
| | - Jesus Aceituno-Castro
- Instituto de Astrofísica de Andalucía, CSIC, 18008, Granada, Spain.,Centro Astronomico Hispano Alemán, 04550, Almeria, Spain
| | - Manuel A Perales-Esteve
- Department of Electronic Engineering, School of Engineering, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Antonio Puppo-Moreno
- Service of Intensive Care, University Hospital 'Virgen del Rocio', 41013, Sevilla, Spain
| | | | - Lucia Olvera-Collantes
- Instituto de Investigación E Innovación Biomedica de Cádiz (INIBICA), 11009, Cadiz, Spain
| | | | - Emilia Gomez
- Joint Research Centre, European Commission, 41092, Sevilla, Spain
| | - Rosario Sanchez Pernaute
- Unidad de Producción y Reprogramación Celular (UPRC), Red Andaluza de Diseño y Traslación de Terapias Avanzadas, 41092, Sevilla, Spain
| | - Javier Padillo-Ruiz
- Institute of Biomedicine of Seville, 41013, Sevilla, Spain.,Department of General Surgery, University Hospital 'Virgen del Rocío', 41013, Sevilla, Spain
| | - Javier Marquez-Rivas
- Institute of Biomedicine of Seville, 41013, Sevilla, Spain.,Service of Neurosurgery, University Hospital 'Virgen del Rocío', 41013, Sevilla, Spain.,Centre for Advanced Neurology, 41013, Sevilla, Spain
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29
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Wei C, Wang J, Ji J. Forensic Classification of Pigments by Attenuated Total Reflectance – Fourier Transform Infrared Spectroscopy and Chemometrics. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1801712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Chenjie Wei
- School of investigation, People’s Public Security University of China, Beijing, China
| | - Jifen Wang
- School of investigation, People’s Public Security University of China, Beijing, China
| | - Jiahua Ji
- School of investigation, People’s Public Security University of China, Beijing, China
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30
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Detection of Plasmodium falciparum in laboratory-reared and naturally infected wild mosquitoes using near-infrared spectroscopy. Sci Rep 2021; 11:10289. [PMID: 33986416 PMCID: PMC8119679 DOI: 10.1038/s41598-021-89715-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 11/18/2022] Open
Abstract
There is an urgent need for high throughput, affordable methods of detecting pathogens inside insect vectors to facilitate surveillance. Near-infrared spectroscopy (NIRS) has shown promise to detect arbovirus and malaria in the laboratory but has not been evaluated in field conditions. Here we investigate the ability of NIRS to identify Plasmodium falciparum in Anopheles coluzzii mosquitoes. NIRS models trained on laboratory-reared mosquitoes infected with wild malaria parasites can detect the parasite in comparable mosquitoes with moderate accuracy though fails to detect oocysts or sporozoites in naturally infected field caught mosquitoes. Models trained on field mosquitoes were unable to predict the infection status of other field mosquitoes. Restricting analyses to mosquitoes of uninfectious and highly-infectious status did improve predictions suggesting sensitivity and specificity may be better in mosquitoes with higher numbers of parasites. Detection of infection appears restricted to homogenous groups of mosquitoes diminishing NIRS utility for detecting malaria within mosquitoes.
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31
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Goh B, Ching K, Soares Magalhães RJ, Ciocchetta S, Edstein MD, Maciel-de-Freitas R, Sikulu-Lord MT. The application of spectroscopy techniques for diagnosis of malaria parasites and arboviruses and surveillance of mosquito vectors: A systematic review and critical appraisal of evidence. PLoS Negl Trop Dis 2021; 15:e0009218. [PMID: 33886567 PMCID: PMC8061870 DOI: 10.1371/journal.pntd.0009218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
CONCLUSIONS/SIGNIFICANCE The potential of RS as a surveillance tool for malaria and arbovirus vectors and MIRS for the diagnosis and surveillance of arboviruses is yet to be assessed. NIRS capacity as a surveillance tool for malaria and arbovirus vectors should be validated under field conditions, and its potential as a diagnostic tool for malaria and arboviruses needs to be evaluated. It is recommended that all 3 techniques evaluated simultaneously using multiple machine learning techniques in multiple epidemiological settings to determine the most accurate technique for each application. Prior to their field application, a standardised protocol for spectra collection and data analysis should be developed. This will harmonise their application in multiple field settings allowing easy and faster integration into existing disease control platforms. Ultimately, development of rapid and cost-effective point-of-care diagnostic tools for malaria and arboviruses based on spectroscopy techniques may help combat current and future outbreaks of these infectious diseases.
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Affiliation(s)
- Brendon Goh
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Koek Ching
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Ricardo J Soares Magalhães
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Brisbane, Australia
- Children's Health Research Centre, Children's Health and Environment Program, The University of Queensland, Brisbane, Australia
| | - Silvia Ciocchetta
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- UQ Spatial Epidemiology Laboratory, School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - Michael D Edstein
- Australian Defence Force, Malaria and Infectious Disease Institute, Brisbane, Australia
| | | | - Maggy T Sikulu-Lord
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, Australia
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32
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Costa J, Ferreira EC, Santos C. COVID-19, Chikungunya, Dengue and Zika Diseases: An Analytical Platform Based on MALDI-TOF MS, IR Spectroscopy and RT-qPCR for Accurate Diagnosis and Accelerate Epidemics Control. Microorganisms 2021; 9:microorganisms9040708. [PMID: 33808104 PMCID: PMC8066533 DOI: 10.3390/microorganisms9040708] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 and arboviruses (ARBOD) epidemics co-occurrence is a great concern. In tropical and subtropical regions, ARBOD diseases such as chikungunya, dengue, and Zika are frequent. In both COVID-19 and ARBOD cases, an accurate diagnosis of infected patients is crucial to promote adequate treatment and isolation measures in COVID-19 cases. Overlap of clinical symptoms and laboratory parameters between COVID-19 and ARBOD present themselves as an extra challenge during diagnosis. COVID-19 diagnosis is mainly performed by quantitative reverse polymerase chain reaction (RT-qPCR), while ARBOD diagnosis is performed by serology, detection of antigen or antibody, and molecular diagnosis. In this review, the epidemiologic profile of arboviruses and SARS-CoV-2 is analyzed, and potential risks of symptom overlap is addressed. The implementation of an analytical platform based on infrared (IR) spectroscopy, MALDI-TOF mass spectrometry, and RT-qPCR is discussed as an efficient strategy for a fast, robust, reliable, and cost-effective diagnosis system even during the co-occurrence of virus outbreaks. The spectral data of IR spectroscopy and MALDI-TOF MS obtained from COVID-19 infected and recovered patients can be used to build up an integrated spectral database. This approach can enable us to determine quickly the groups that have been exposed and have recovered from COVID-19 or ARBOD, avoiding misdiagnoses.
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Affiliation(s)
- Jéssica Costa
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811-230, Chile;
| | - Eugénio C. Ferreira
- CEB-Centre of Biological Engineering, Universidade do Minho, Campus of Gualtar, 4710-057 Braga, Portugal;
| | - Cledir Santos
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco 4811-230, Chile
- Correspondence: ; Tel.: +56-45-259-6726
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33
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Valladares V, Pasquini C, Thiengo SC, Fernandez MA, Mello-Silva CC. Field Application of NIR Spectroscopy for the Discrimination of the Biomphalaria Species That Are Intermediate Hosts of Schistosoma mansoni in Brazil. Front Public Health 2021; 9:636206. [PMID: 33777886 PMCID: PMC7994760 DOI: 10.3389/fpubh.2021.636206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Near Infrared Spectroscopy (NIRS) is a spectroscopic technique that evaluates the vibrational energy levels of the chemical bonds of molecules within a wavelength range of 750–2,500 nm. This simple method acquires spectra that provide qualitative and quantitative data on the chemical components of the biomass of living organisms through the interaction between the electromagnetic waves and the sample. NIRS is an innovative, rapid, and non-destructive technique that can contribute to the differentiation of species based on their chemical phenotypes. Chemical profiles were obtained by NIRS from three snail species (Biomphalaria glabrata, Biomphalaria straminea, and Biomphalaria tenagophila) that are intermediate hosts of Schistosoma mansoni in Brazil. The correct identification of these species is important from an epidemiological viewpoint, given that each species has distinct biological and physiological characteristics. The present study aimed to develop a chemometric model for the interspecific and intra-specific classification of the three species, focusing on laboratory and field populations. The data were obtained from 271 live animals, including 150 snails recently collected from the field, with the remainder being raised in the laboratory. Populations were sampled at three localities in the Brazilian state of Rio de Janeiro, in the municipalities of Sumidouro (B. glabrata) and Paracambi (B. straminea), and the borough of Jacarepaguá in the Rio de Janeiro city (B. tenagophila). The chemometric analysis was run in the Unscrambler® software. The intra-specific classification of the field and laboratory populations obtained accuracy rates of 72.5% (B. tenagophila), 77.5% (B. straminea), and 85.0% (B. glabrata). The interspecific differentiation had a hit rate of 75% for the field populations and 80% for the laboratory populations. The results indicate chemical and metabolic differences between populations of the same species from the field and the laboratory. The chemical phenotype, which is closely related to the metabolic profile of the snails, varied between environments. Overall, the NIRS technique proved to be a potentially valuable tool for medical malacology, enabling the systematic discrimination of the Biomphalaria snails that are the intermediate hosts of S. mansoni in Brazil.
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Affiliation(s)
- Vanessa Valladares
- Environmental Health Monitoring and Prevention Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - Célio Pasquini
- Chemistry Institute, Universidade Estadual de Campinas/UNICAMP, Campinas, Brazil
| | - Silvana C Thiengo
- Malacology Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - Monica A Fernandez
- Malacology Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - Clélia C Mello-Silva
- Environmental Health Monitoring and Prevention Laboratory, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
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34
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Zhang X, Li G, Chen G, Zhu N, Wu D, Wu Y, James TD. Recent progresses and remaining challenges for the detection of Zika virus. Med Res Rev 2021; 41:2039-2108. [PMID: 33559917 DOI: 10.1002/med.21786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
Abstract
Zika virus (ZIKV) has emerged as a particularly notorious mosquito-borne flavivirus, which can lead to a devastating congenital syndrome in the fetuses of pregnant mothers (e.g., microcephaly, spasticity, craniofacial disproportion, miscarriage, and ocular abnormalities) and cause the autoimmune disorder Guillain-Barre' syndrome of adults. Due to its severity and rapid dispersal over several continents, ZIKV has been acknowledged to be a global health concern by the World Health Organization. Unfortunately, the ZIKV has recently resurged in India with the potential for devastating effects. Researchers from all around the world have worked tirelessly to develop effective detection strategies and vaccines for the prevention and control of ZIKV infection. In this review, we comprehensively summarize the most recent research into ZIKV, including the structural biology and evolution, historical overview, pathogenesis, symptoms, and transmission. We then focus on the detection strategies for ZIKV, including viral isolation, serological assays, molecular assays, sensing methods, reverse transcription loop mediated isothermal amplification, transcription-mediated amplification technology, reverse transcription strand invasion based amplification, bioplasmonic paper-based device, and reverse transcription isothermal recombinase polymerase amplification. To conclude, we examine the limitations of currently available strategies for the detection of ZIKV, and outline future opportunities and research challenges.
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Affiliation(s)
- Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guang Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Niu Zhu
- Department of Public Health, Xi'an Medical University, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath, UK.,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, China
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35
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Santos LMB, Mutsaers M, Garcia GA, David MR, Pavan MG, Petersen MT, Corrêa-Antônio J, Couto-Lima D, Maes L, Dowell F, Lord A, Sikulu-Lord M, Maciel-de-Freitas R. High throughput estimates of Wolbachia, Zika and chikungunya infection in Aedes aegypti by near-infrared spectroscopy to improve arbovirus surveillance. Commun Biol 2021; 4:67. [PMID: 33452445 PMCID: PMC7810739 DOI: 10.1038/s42003-020-01601-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
Deployment of Wolbachia to mitigate dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) transmission is ongoing in 12 countries. One way to assess the efficacy of Wolbachia releases is to determine invasion rates within the wild population of Aedes aegypti following their release. Herein we evaluated the accuracy, sensitivity and specificity of the Near Infrared Spectroscopy (NIRS) in estimating the time post death, ZIKV-, CHIKV-, and Wolbachia-infection in trapped dead female Ae. aegypti mosquitoes over a period of 7 days. Regardless of the infection type, time post-death of mosquitoes was accurately predicted into four categories (fresh, 1 day old, 2–4 days old and 5–7 days old). Overall accuracies of 93.2, 97 and 90.3% were observed when NIRS was used to detect ZIKV, CHIKV and Wolbachia in dead Ae. aegypti female mosquitoes indicating NIRS could be potentially applied as a rapid and cost-effective arbovirus surveillance tool. However, field data is required to demonstrate the full capacity of NIRS for detecting these infections under field conditions. Santos et al. demonstrate that the Near Infrared Spectroscopy (NIRS) can accurately estimate the death time of trapped female Aedes aegypti and vector infection with Zika virus, Chikungunya virus, or Wolbachia in a 7-day trapping period. This study suggests that NIRS may provide an accurate and inexpensive tool that improves arbovirus surveillance systems.
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Affiliation(s)
- Lilha M B Santos
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Mathijs Mutsaers
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil.,Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2000, Antwerp, Belgium
| | - Gabriela A Garcia
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Mariana R David
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Márcio G Pavan
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Martha T Petersen
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Jessica Corrêa-Antônio
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Dinair Couto-Lima
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2000, Antwerp, Belgium
| | - Floyd Dowell
- USDA-ARS, Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA
| | - Anton Lord
- The School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia.,QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Maggy Sikulu-Lord
- The School of Public Health, The University of Queensland, Herston, QLD, 4006, Australia
| | - Rafael Maciel-de-Freitas
- Laboratório de Transmissores de Hematozoários, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil. .,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
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36
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Rutkowski N, Dong Y, Dimopoulos G. Field-deployable molecular diagnostic platform for arbovirus detection in Aedes aegypti. Parasit Vectors 2020; 13:489. [PMID: 32972453 PMCID: PMC7513541 DOI: 10.1186/s13071-020-04357-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/11/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Surveillance of mosquito infection status is critical for planning and deployment of proper mosquito control initiatives. Point-of-care (POC) detection assays are necessary for monitoring the infection prevalence and geographical range of viruses in mosquito vector populations. We therefore assessed the novel real-time PCR (qPCR) bCUBE (Hyris, London, UK) molecular diagnostic system as a tool for virus detection. METHODS Aedes aegypti Rps17 was used to validate and determine correlation coefficient for the novel bCUBE qPCR system to a laboratory standard StepOnePlus real-time PCR system (Applied Biosystems, Waltham, MA, USA). Experimentally infected Ae. aegypti were quantified for Zika (ZIKV) and dengue virus serotype 2 (DENV2) viral genomic RNA. Infection prevalence was compared to plaque assay. RESULTS We developed and validated a novel qPCR system for the detection of ZIKV and DENV2 using the real-time qPCR system bCUBE. With bCUBE-based qRT-PCR, viral genomic RNA could be detected in individually infected Ae. aegypti mosquitoes and in pools of 5, 10 or 15 mosquitoes. CONCLUSIONS The portable qPCR bCUBE diagnostic system is capable of detecting Zika and dengue virus in mosquitoes and therefore has potential as a practical field-deployable diagnostic test for vector-borne disease surveillance programmes.
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Affiliation(s)
- Natalie Rutkowski
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD USA
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Near-Infrared Spectroscopy Evaluations for the Differentiation of Carbapenem-Resistant from Susceptible Enterobacteriaceae Strains. Diagnostics (Basel) 2020; 10:diagnostics10100736. [PMID: 32977503 PMCID: PMC7598181 DOI: 10.3390/diagnostics10100736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial Resistance (AMR) caused by Carbapenem-Resistant Enterobacteriaceae (CRE) is a global threat. Accurate identification of these bacterial species with associated AMR is critical for their management. While highly accurate methods to detect CRE are available, they are costly, timely and require expert skills, making their application infeasible in low-resource settings. Here, we investigated the potential of Near-Infrared Spectroscopy (NIRS) for a range of applications: (i) the detection and differentiation of isolates of two pathogenic Enterobacteriaceae species, Klebsiella pneumoniae and Escherichia coli, and (ii) the differentiation of carbapenem resistant and susceptible K. pneumoniae. NIRS has successfully differentiated between K. pneumoniae and E. coli isolates with a predictive accuracy of 89.04% (95% CI; 88.7–89.4%). K. pneumoniae isolates harbouring carbapenem-resistance determinants were differentiated from susceptible K. pneumoniae strains with an accuracy of 85% (95% CI; 84.2–86.1%). To our knowledge, this is the largest proof of concept demonstration for the utility and feasibility of NIRS to rapidly differentiate between K. pneumoniae and E. coli as well as carbapenem-resistant K. pneumoniae from susceptible strains.
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Seabourn P, Spafford H, Yoneishi N, Medeiros M. The Aedes albopictus (Diptera: Culicidae) microbiome varies spatially and with Ascogregarine infection. PLoS Negl Trop Dis 2020; 14:e0008615. [PMID: 32813707 PMCID: PMC7437863 DOI: 10.1371/journal.pntd.0008615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/20/2020] [Indexed: 12/30/2022] Open
Abstract
The mosquito microbiome alters the physiological traits of medically important mosquitoes, which can scale to impact how mosquito populations sustain disease transmission. The mosquito microbiome varies significantly within individual mosquitoes and among populations, however the ecological and environmental factors that contribute to this variation are poorly understood. To further understand the factors that influence variation and diversity of the mosquito microbiome, we conducted a survey of the bacterial microbiome in the medically important mosquito, Aedes albopictus, on the high Pacific island of Maui, Hawai'i. We detected three bacterial Phyla and twelve bacterial families: Proteobacteria, Acitinobacteria, and Firmicutes; and Anaplasmataceae, Acetobacteraceae, Enterobacteriaceae, Burkholderiaceae, Xanthobacteraceae, Pseudomonadaceae, Streptomycetaceae, Staphylococcaceae, Xanthomonadaceae, Beijerinckiaceae, Rhizobiaceae, and Sphingomonadaceae. The Ae. albopictus bacterial microbiota varied among geographic locations, but temperature and rainfall were uncorrelated with this spatial variation. Infection status with an ampicomplexan pathosymbiont Ascogregarina taiwanensis was significantly associated with the composition of the Ae. albopictus bacteriome. The bacteriomes of mosquitoes with an A. taiwanensis infection were more likely to include several bacterial symbionts, including the most abundant lineage of Wolbachia sp. Other symbionts like Asaia sp. and several Enterobacteriaceae lineages were less prevalent in A. taiwanensis-infected mosquitoes. This highlights the possibility that inter- and intra-domain interactions may structure the Ae. albopictus microbiome.
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Affiliation(s)
- Priscilla Seabourn
- Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, Hawai’i, United States of America
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, Hawai’i, United States of America
| | - Helen Spafford
- Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, Hawai’i, United States of America
| | - Nicole Yoneishi
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, Hawai’i, United States of America
| | - Matthew Medeiros
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, Hawai’i, United States of America
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Kading RC, Cohnstaedt LW, Fall K, Hamer GL. Emergence of Arboviruses in the United States: The Boom and Bust of Funding, Innovation, and Capacity. Trop Med Infect Dis 2020; 5:E96. [PMID: 32517268 PMCID: PMC7345222 DOI: 10.3390/tropicalmed5020096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022] Open
Abstract
Mosquito-borne viruses will continue to emerge and generate a significant public health burden around the globe. Here, we provide a longitudinal perspective on how the emergence of mosquito-borne viruses in the Americas has triggered reactionary funding by sponsored agencies, stimulating a number of publications, innovative development of traps, and augmented capacity. We discuss the return on investment (ROI) from the oscillation in federal funding that influences demand for surveillance and control traps and leads to innovation and research productivity.
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Affiliation(s)
- Rebekah C. Kading
- Department of Microbiology, Colorado State University, Immunology and Pathology, Fort Collins, Colorado, CO 80523, USA
| | - Lee W. Cohnstaedt
- United States Department of Agriculture, Arthropod-borne Animal Diseases Research Unit, Agricultural Research Service, Manhattan, Kansas, KS 66502, USA;
| | - Ken Fall
- BioQuip Products, Rancho Dominguez, California, CA 90220, USA;
| | - Gabriel L. Hamer
- Department of Entomology, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, TX 77843, USA;
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Gupta N, Yadav PD, Patil DY, Sapkal G. Preparedness of public health-care system for Zika virus outbreak: An Indian perspective. J Infect Public Health 2020; 13:949-955. [PMID: 32340832 DOI: 10.1016/j.jiph.2020.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 11/20/2022] Open
Abstract
Zika virus is a mosquito-borne flavivirus that has emerged recently and affected in many countries. Since its discovery in Uganda in 1947, two major outbreaks were reported from Yap Islands in 2007 and French Polynesia in 2013. In 2015, the first case of ZIKV infection was confirmed from Brazil followed by a report of cases from American and Caribbean countries. In February 2016, the World Health Organization declared ZIKV infection a Public Health Emergency of International Concern. India reported the first Zika case in 2017. Subsequently, 157 laboratory-confirmed cases of ZIKV including 63 pregnant women were reported from Rajasthan, India in 2018. Since 2014, many countries took initiatives to boost their public health system to combat ZIKV. However, there is still scope for the improvement. This review describes ZIKV outbreaks, diagnostic challenges, surveillance and control measures in India and the future perspective to deal with the ZIKV outbreak in India.
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Affiliation(s)
- Nivedita Gupta
- Epidemiology and Communicable Diseases, Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi 110029, India.
| | - Pragya D Yadav
- ICMR-National Institute of Virology, Sus-Pashan Road, Pune, Maharashtra 411021, India
| | - Deepak Y Patil
- ICMR-National Institute of Virology, Sus-Pashan Road, Pune, Maharashtra 411021, India
| | - Gajanan Sapkal
- ICMR-National Institute of Virology, Sus-Pashan Road, Pune, Maharashtra 411021, India
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Ovitraps Provide a Reliable Estimate of Wolbachia Frequency during wMelBr Strain Deployment in a Geographically Isolated Aedes aegypti Population. INSECTS 2020; 11:insects11020092. [PMID: 32024068 PMCID: PMC7074419 DOI: 10.3390/insects11020092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023]
Abstract
Deployment of Aedes aegypti mosquitoes carrying the endosymbiont bacterium Wolbachia has been identified as a promising strategy to reduce dengue, chikungunya, and Zika transmission. We investigated whether sampling larvae from ovitraps can provide reliable estimates on Wolbachia frequency during releases, as compared to the expensive adult-based BG-Sentinel. We conducted pilot releases in a semi-field system (SFS) divided into six cages of 21 m2, each with five ovitraps. Five treatments were chosen to represent different points of a hypothetical invasion curve: 10%, 25%, 50%, 75%, and 90% of Wolbachia frequency. Collected eggs were counted and hatched, and the individuals from a net sample of 27% of larvae per treatment were screened for Wolbachia presence by RT-qPCR. Ovitrap positioning had no effect on egg hatching rate. Treatment strongly affected the number of eggs collected and also the hatching rate, especially when Wolbachia was at a 10% frequency. A second observation was done during the release of Wolbachia in Rio under a population replacement approach when bacterium frequency was estimated using 30 BG-Sentinel traps and 45 ovitraps simultaneously. By individually screening 35% (N = 3904) of larvae collected by RT-qPCR, we were able to produce a similar invasion curve to the one observed when all adults were individually screened. If sampling is reduced to 20%, monitoring Wolbachia frequency with 45 ovitraps would be roughly half the cost of screening all adult mosquitoes captured by 30 BG-Sentinels. Our findings support the scale-up of Wolbachia releases, especially in areas with limited resources to afford massive trapping with BG-Sentinel traps.
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Bramhachari PV. Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges. DYNAMICS OF IMMUNE ACTIVATION IN VIRAL DISEASES 2020. [PMCID: PMC7121190 DOI: 10.1007/978-981-15-1045-8_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Diagnosis and identification of viruses is an important component of diagnostic virology laboratory. Although various modes of diagnostic methods are now available at disposal, a vast majority of the diseases across the globe remain undiagnosed. This is largely due to the overlapping undifferentiated set of symptoms across myriad set of RNA and DNA viral diseases. As such, it becomes critical to take into consideration several factors for viral diagnosis ranging from the type and quality of specimen collected, time of specimen collection, mode of transport, accuracy, specificity, sensitivity, and the type of diagnostic method used. This chapter broadly emphasizes various methods on diagnostic virology ranging from the classical methods of diagnosis to the most recently developed molecular methods of detection of virus.
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Mwanga EP, Minja EG, Mrimi E, Jiménez MG, Swai JK, Abbasi S, Ngowo HS, Siria DJ, Mapua S, Stica C, Maia MF, Olotu A, Sikulu-Lord MT, Baldini F, Ferguson HM, Wynne K, Selvaraj P, Babayan SA, Okumu FO. Detection of malaria parasites in dried human blood spots using mid-infrared spectroscopy and logistic regression analysis. Malar J 2019; 18:341. [PMID: 31590669 PMCID: PMC6781347 DOI: 10.1186/s12936-019-2982-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/28/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Epidemiological surveys of malaria currently rely on microscopy, polymerase chain reaction assays (PCR) or rapid diagnostic test kits for Plasmodium infections (RDTs). This study investigated whether mid-infrared (MIR) spectroscopy coupled with supervised machine learning could constitute an alternative method for rapid malaria screening, directly from dried human blood spots. METHODS Filter papers containing dried blood spots (DBS) were obtained from a cross-sectional malaria survey in 12 wards in southeastern Tanzania in 2018/19. The DBS were scanned using attenuated total reflection-Fourier Transform Infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra in the range 4000 cm-1 to 500 cm-1. The spectra were cleaned to compensate for atmospheric water vapour and CO2 interference bands and used to train different classification algorithms to distinguish between malaria-positive and malaria-negative DBS papers based on PCR test results as reference. The analysis considered 296 individuals, including 123 PCR-confirmed malaria positives and 173 negatives. Model training was done using 80% of the dataset, after which the best-fitting model was optimized by bootstrapping of 80/20 train/test-stratified splits. The trained models were evaluated by predicting Plasmodium falciparum positivity in the 20% validation set of DBS. RESULTS Logistic regression was the best-performing model. Considering PCR as reference, the models attained overall accuracies of 92% for predicting P. falciparum infections (specificity = 91.7%; sensitivity = 92.8%) and 85% for predicting mixed infections of P. falciparum and Plasmodium ovale (specificity = 85%, sensitivity = 85%) in the field-collected specimen. CONCLUSION These results demonstrate that mid-infrared spectroscopy coupled with supervised machine learning (MIR-ML) could be used to screen for malaria parasites in human DBS. The approach could have potential for rapid and high-throughput screening of Plasmodium in both non-clinical settings (e.g., field surveys) and clinical settings (diagnosis to aid case management). However, before the approach can be used, we need additional field validation in other study sites with different parasite populations, and in-depth evaluation of the biological basis of the MIR signals. Improving the classification algorithms, and model training on larger datasets could also improve specificity and sensitivity. The MIR-ML spectroscopy system is physically robust, low-cost, and requires minimum maintenance.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
| | - Elihaika G Minja
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Emmanuel Mrimi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | | | - Johnson K Swai
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Said Abbasi
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Halfan S Ngowo
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Doreen J Siria
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Salum Mapua
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
- School of Life Sciences, University of Keele, Keele, Staffordshire, ST5 5BG, UK
| | - Caleb Stica
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania
| | - Marta F Maia
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Ally Olotu
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Interventions and Clinical Trials Department, Ifakara Health Institute, Bagamoyo, Tanzania
| | - Maggy T Sikulu-Lord
- School of Public Health, University of Queensland, Saint Lucia, Australia
- Department of Mathematics, Statistics and Computer Science, Marquette University, Wisconsin, USA
| | - Francesco Baldini
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Morogoro, Tanzania.
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa.
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González Jiménez M, Babayan SA, Khazaeli P, Doyle M, Walton F, Reedy E, Glew T, Viana M, Ranford-Cartwright L, Niang A, Siria DJ, Okumu FO, Diabaté A, Ferguson HM, Baldini F, Wynne K. Prediction of mosquito species and population age structure using mid-infrared spectroscopy and supervised machine learning. Wellcome Open Res 2019; 4:76. [PMID: 31544155 PMCID: PMC6753605 DOI: 10.12688/wellcomeopenres.15201.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 11/20/2022] Open
Abstract
Despite the global efforts made in the fight against malaria, the disease is resurging. One of the main causes is the resistance that Anopheles mosquitoes, vectors of the disease, have developed to insecticides. Anopheles must survive for at least 10 days to possibly transmit malaria. Therefore, to evaluate and improve malaria vector control interventions, it is imperative to monitor and accurately estimate the age distribution of mosquito populations as well as their population sizes. Here, we demonstrate a machine-learning based approach that uses mid-infrared spectra of mosquitoes to characterise simultaneously both age and species identity of females of the African malaria vector species Anopheles gambiae and An. arabiensis, using laboratory colonies. Mid-infrared spectroscopy-based prediction of mosquito age structures was statistically indistinguishable from true modelled distributions. The accuracy of classifying mosquitoes by species was 82.6%. The method has a negligible cost per mosquito, does not require highly trained personnel, is rapid, and so can be easily applied in both laboratory and field settings. Our results indicate this method is a promising alternative to current mosquito species and age-grading approaches, with further improvements to accuracy and expansion for use with wild mosquito vectors possible through collection of larger mid-infrared spectroscopy data sets.
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Affiliation(s)
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pegah Khazaeli
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret Doyle
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Elliott Reedy
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Thomas Glew
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mafalda Viana
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdoulaye Niang
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Doreen J. Siria
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Fredros O. Okumu
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Abdoulaye Diabaté
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Heather M. Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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González Jiménez M, Babayan SA, Khazaeli P, Doyle M, Walton F, Reedy E, Glew T, Viana M, Ranford-Cartwright L, Niang A, Siria DJ, Okumu FO, Diabaté A, Ferguson HM, Baldini F, Wynne K. Prediction of mosquito species and population age structure using mid-infrared spectroscopy and supervised machine learning. Wellcome Open Res 2019; 4:76. [PMID: 31544155 PMCID: PMC6753605 DOI: 10.12688/wellcomeopenres.15201.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 01/14/2023] Open
Abstract
Despite the global efforts made in the fight against malaria, the disease is resurging. One of the main causes is the resistance that Anopheles mosquitoes, vectors of the disease, have developed to insecticides. Anopheles must survive for at least 10 days to possibly transmit malaria. Therefore, to evaluate and improve malaria vector control interventions, it is imperative to monitor and accurately estimate the age distribution of mosquito populations as well as their population sizes. Here, we demonstrate a machine-learning based approach that uses mid-infrared spectra of mosquitoes to characterise simultaneously both age and species identity of females of the African malaria vector species Anopheles gambiae and An. arabiensis, using laboratory colonies. Mid-infrared spectroscopy-based prediction of mosquito age structures was statistically indistinguishable from true modelled distributions. The accuracy of classifying mosquitoes by species was 82.6%. The method has a negligible cost per mosquito, does not require highly trained personnel, is rapid, and so can be easily applied in both laboratory and field settings. Our results indicate this method is a promising alternative to current mosquito species and age-grading approaches, with further improvements to accuracy and expansion for use with wild mosquito vectors possible through collection of larger mid-infrared spectroscopy data sets.
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Affiliation(s)
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pegah Khazaeli
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret Doyle
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Elliott Reedy
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Thomas Glew
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mafalda Viana
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdoulaye Niang
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Doreen J. Siria
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Fredros O. Okumu
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Abdoulaye Diabaté
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Heather M. Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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Mwanga EP, Mapua SA, Siria DJ, Ngowo HS, Nangacha F, Mgando J, Baldini F, González Jiménez M, Ferguson HM, Wynne K, Selvaraj P, Babayan SA, Okumu FO. Using mid-infrared spectroscopy and supervised machine-learning to identify vertebrate blood meals in the malaria vector, Anopheles arabiensis. Malar J 2019; 18:187. [PMID: 31146762 PMCID: PMC6543689 DOI: 10.1186/s12936-019-2822-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/25/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The propensity of different Anopheles mosquitoes to bite humans instead of other vertebrates influences their capacity to transmit pathogens to humans. Unfortunately, determining proportions of mosquitoes that have fed on humans, i.e. Human Blood Index (HBI), currently requires expensive and time-consuming laboratory procedures involving enzyme-linked immunosorbent assays (ELISA) or polymerase chain reactions (PCR). Here, mid-infrared (MIR) spectroscopy and supervised machine learning are used to accurately distinguish between vertebrate blood meals in guts of malaria mosquitoes, without any molecular techniques. METHODS Laboratory-reared Anopheles arabiensis females were fed on humans, chickens, goats or bovines, then held for 6 to 8 h, after which they were killed and preserved in silica. The sample size was 2000 mosquitoes (500 per host species). Five individuals of each host species were enrolled to ensure genotype variability, and 100 mosquitoes fed on each. Dried mosquito abdomens were individually scanned using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectrometer to obtain high-resolution MIR spectra (4000 cm-1 to 400 cm-1). The spectral data were cleaned to compensate atmospheric water and CO2 interference bands using Bruker-OPUS software, then transferred to Python™ for supervised machine-learning to predict host species. Seven classification algorithms were trained using 90% of the spectra through several combinations of 75-25% data splits. The best performing model was used to predict identities of the remaining 10% validation spectra, which had not been used for model training or testing. RESULTS The logistic regression (LR) model achieved the highest accuracy, correctly predicting true vertebrate blood meal sources with overall accuracy of 98.4%. The model correctly identified 96% goat blood meals, 97% of bovine blood meals, 100% of chicken blood meals and 100% of human blood meals. Three percent of bovine blood meals were misclassified as goat, and 2% of goat blood meals misclassified as human. CONCLUSION Mid-infrared spectroscopy coupled with supervised machine learning can accurately identify multiple vertebrate blood meals in malaria vectors, thus potentially enabling rapid assessment of mosquito blood-feeding histories and vectorial capacities. The technique is cost-effective, fast, simple, and requires no reagents other than desiccants. However, scaling it up will require field validation of the findings and boosting relevant technical capacity in affected countries.
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Affiliation(s)
- Emmanuel P Mwanga
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania.
| | - Salum A Mapua
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Doreen J Siria
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Halfan S Ngowo
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francis Nangacha
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Joseph Mgando
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
| | - Francesco Baldini
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Science Thematic Group, Ifakara Health Institute, Morogoro, Tanzania
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Public Health, University of Witwatersrand, Johannesburg, South Africa
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González Jiménez M, Babayan SA, Khazaeli P, Doyle M, Walton F, Reedy E, Glew T, Viana M, Ranford-Cartwright L, Niang A, Siria DJ, Okumu FO, Diabaté A, Ferguson HM, Baldini F, Wynne K. Prediction of mosquito species and population age structure using mid-infrared spectroscopy and supervised machine learning. Wellcome Open Res 2019; 4:76. [PMID: 31544155 PMCID: PMC6753605 DOI: 10.12688/wellcomeopenres.15201.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2019] [Indexed: 01/17/2023] Open
Abstract
Despite the global efforts made in the fight against malaria, the disease is resurging. One of the main causes is the resistance that Anopheles mosquitoes, vectors of the disease, have developed to insecticides. Anopheles must survive for at least 10 days to possibly transmit malaria. Therefore, to evaluate and improve malaria vector control interventions, it is imperative to monitor and accurately estimate the age distribution of mosquito populations as well as their population sizes. Here, we demonstrate a machine-learning based approach that uses mid-infrared spectra of mosquitoes to characterise simultaneously both age and species identity of females of the African malaria vector species Anopheles gambiae and An. arabiensis. mid-infrared spectroscopy-based prediction of mosquito age structures was statistically indistinguishable from true modelled distributions. The accuracy of classifying mosquitoes by species was 82.6%. The method has a negligible cost per mosquito, does not require highly trained personnel, is rapid, and so can be easily applied in both laboratory and field settings. Our results indicate this method is a promising alternative to current mosquito species and age-grading approaches, with further improvements to accuracy and expansion for use with other mosquito vectors possible through collection of larger mid-infrared spectroscopy data sets.
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Affiliation(s)
| | - Simon A. Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pegah Khazaeli
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret Doyle
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Finlay Walton
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Elliott Reedy
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Thomas Glew
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mafalda Viana
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Abdoulaye Niang
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Doreen J. Siria
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Fredros O. Okumu
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Environmental Health & Ecological Sciences Department, Ifakara Health Institute, Off Mlabani Passage, PO Box 53, Ifakara, Tanzania
| | - Abdoulaye Diabaté
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Heather M. Ferguson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Klaas Wynne
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
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48
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Maia MF, Kapulu M, Muthui M, Wagah MG, Ferguson HM, Dowell FE, Baldini F, Ranford-Cartwright L. Detection of Plasmodium falciparum infected Anopheles gambiae using near-infrared spectroscopy. Malar J 2019; 18:85. [PMID: 30890179 PMCID: PMC6423776 DOI: 10.1186/s12936-019-2719-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Large-scale surveillance of mosquito populations is crucial to assess the intensity of vector-borne disease transmission and the impact of control interventions. However, there is a lack of accurate, cost-effective and high-throughput tools for mass-screening of vectors. METHODS A total of 750 Anopheles gambiae (Keele strain) mosquitoes were fed Plasmodium falciparum NF54 gametocytes through standard membrane feeding assay (SMFA) and afterwards maintained in insectary conditions to allow for oocyst (8 days) and sporozoite development (14 days). Thereupon, each mosquito was scanned using near infra-red spectroscopy (NIRS) and processed by quantitative polymerase chain reaction (qPCR) to determine the presence of infection and infection load. The spectra collected were randomly assigned to either a training dataset, used to develop calibrations for predicting oocyst- or sporozoite-infection through partial least square regressions (PLS); or to a test dataset, used for validating the calibration's prediction accuracy. RESULTS NIRS detected oocyst- and sporozoite-stage P. falciparum infections with 88% and 95% accuracy, respectively. This study demonstrates proof-of-concept that NIRS is capable of rapidly identifying laboratory strains of human malaria infection in African mosquito vectors. CONCLUSIONS Accurate, low-cost, reagent-free screening of mosquito populations enabled by NIRS could revolutionize surveillance and elimination strategies for the most important human malaria parasite in its primary African vector species. Further research is needed to evaluate how the method performs in the field following adjustments in the training datasets to include data from wild-caught infected and uninfected mosquitoes.
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Affiliation(s)
- Marta F Maia
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4020, Basel, Switzerland.
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland.
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK.
| | - Melissa Kapulu
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Michelle Muthui
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
| | - Martin G Wagah
- KEMRI Wellcome Trust Research Programme, P.O. Box 230, Kilifi, 80108, Kenya
- Department of Public Health, School of Human and Health Sciences, Pwani University, Kilifi, Kenya
| | - Heather M Ferguson
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Floyd E Dowell
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Francesco Baldini
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
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49
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Development and Validation of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for Rapid Detection of ZIKV in Mosquito Samples from Brazil. Sci Rep 2019; 9:4494. [PMID: 30872672 PMCID: PMC6418238 DOI: 10.1038/s41598-019-40960-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
The rapid spread of Zika virus (ZIKV) represents a global public health problem, especially in areas that harbor several mosquito species responsible for virus transmission, such as Brazil. In these areas, improvement in mosquito control needs to be a top priority, but mosquito viral surveillance occurs inefficiently in ZIKV-endemic countries. Quantitative reverse transcription PCR (qRT-PCR) is the gold standard for molecular diagnostic of ZIKV in both human and mosquito samples. However, the technique presents high cost and limitations for Point-of-care (POC) diagnostics, which hampers its application for a large number of samples in entomological surveillance programs. Here, we developed and validated a one-step reverse transcription LAMP (RT-LAMP) platform for detection of ZIKV in mosquito samples. The RT-LAMP assay was highly specific for ZIKV and up to 10,000 times more sensitive than qRT-PCR. Assay validation was performed using 60 samples from Aedes aegypti and Culex quinquefasciatus mosquitoes collected in Pernambuco State, Brazil, which is at the epicenter of the Zika epidemic. The RT-LAMP had a sensitivity of 100%, specificity of 91.18%, and overall accuracy of 95.24%. Thus, our POC diagnostics is a powerful and inexpensive tool to monitor ZIKV in mosquito populations and will allow developing countries to establish better control strategies for this devastating pathogen.
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50
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Abstract
Most reported optical recorders of the wingbeat of insects are based on the so-called extinction light, which is the variation of light in the receiver due to the cast shadow of the insect’s wings and main body. In this type of recording devices, the emitter uses light and is placed opposite to the receiver, which is usually a single (or multiple) photodiode. In this work, we present a different kind of wingbeat sensor and its associated recorder that aims to extract a deeper representational signal of the wingbeat event and color characterization of the main body of the insect, namely: a) we record the backscattered light that is richer in harmonics than the extinction light, b) we use three different spectral bands, i.e., a multispectral approach that aims to grasp the melanization and microstructural and color features of the wing and body of the insects, and c) we average at the receiver’s level the backscattered signal from many LEDs that illuminate the wingbeating insect from multiple orientations and thus offer a smoother and more complete signal than one based on a single snapshot. We present all the necessary details to reproduce the device and we analyze many insects of interest like the bee Apis mellifera, the wasp Polistes gallicus, and some insects whose wingbeating characteristics are pending in the current literature, like Drosophila suzukii and Zaprionus, another member of the drosophilidae family.
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