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Manescu P, Shaw MJ, Elmi M, Neary‐Zajiczek L, Claveau R, Pawar V, Kokkinos I, Oyinloye G, Bendkowski C, Oladejo OA, Oladejo BF, Clark T, Timm D, Shawe‐Taylor J, Srinivasan MA, Lagunju I, Sodeinde O, Brown BJ, Fernandez‐Reyes D. Expert-level automated malaria diagnosis on routine blood films with deep neural networks. Am J Hematol 2020; 95:883-891. [PMID: 32282969 DOI: 10.1002/ajh.25827] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 11/09/2022]
Abstract
Over 200 million malaria cases globally lead to half a million deaths annually. Accurate malaria diagnosis remains a challenge. Automated imaging processing approaches to analyze Thick Blood Films (TBF) could provide scalable solutions, for urban healthcare providers in the holoendemic malaria sub-Saharan region. Although several approaches have been attempted to identify malaria parasites in TBF, none have achieved negative and positive predictive performance suitable for clinical use in the west sub-Saharan region. While malaria parasite object detection remains an intermediary step in achieving automatic patient diagnosis, training state-of-the-art deep-learning object detectors requires the human-expert labor-intensive process of labeling a large dataset of digitized TBF. To overcome these challenges and to achieve a clinically usable system, we show a novel approach. It leverages routine clinical-microscopy labels from our quality-controlled malaria clinics, to train a Deep Malaria Convolutional Neural Network classifier (DeepMCNN) for automated malaria diagnosis. Our system also provides total Malaria Parasite (MP) and White Blood Cell (WBC) counts allowing parasitemia estimation in MP/μL, as recommended by the WHO. Prospective validation of the DeepMCNN achieves sensitivity/specificity of 0.92/0.90 against expert-level malaria diagnosis. Our approach PPV/NPV performance is of 0.92/0.90, which is clinically usable in our holoendemic settings in the densely populated metropolis of Ibadan. It is located within the most populous African country (Nigeria) and with one of the largest burdens of Plasmodium falciparum malaria. Our openly available method is of importance for strategies aimed to scale malaria diagnosis in urban regions where daily assessment of thousands of specimens is required.
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Affiliation(s)
- Petru Manescu
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Michael J. Shaw
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Muna Elmi
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Lydia Neary‐Zajiczek
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Remy Claveau
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Vijay Pawar
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Iasonas Kokkinos
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Gbeminiyi Oyinloye
- Department of Paediatrics, College of Medicine University of IbadanUniversity College Hospital Ibadan Nigeria
- Childhood Malaria Research GroupCollege of Medicine University of Ibadan, University College Hospital Ibadan Nigeria
| | - Christopher Bendkowski
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Olajide A. Oladejo
- Department of Computer ScienceUniversity of Ibadan Ibadan Nigeria
- African Computational Sciences Centre for Health and DevelopmentUniversity of Ibadan Ibadan Nigeria
| | - Bolanle F. Oladejo
- Department of Computer ScienceUniversity of Ibadan Ibadan Nigeria
- African Computational Sciences Centre for Health and DevelopmentUniversity of Ibadan Ibadan Nigeria
| | - Tristan Clark
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Denis Timm
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - John Shawe‐Taylor
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Mandayam A. Srinivasan
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
| | - Ikeoluwa Lagunju
- Department of Paediatrics, College of Medicine University of IbadanUniversity College Hospital Ibadan Nigeria
- Childhood Malaria Research GroupCollege of Medicine University of Ibadan, University College Hospital Ibadan Nigeria
- African Computational Sciences Centre for Health and DevelopmentUniversity of Ibadan Ibadan Nigeria
| | - Olugbemiro Sodeinde
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
- Department of Paediatrics, College of Medicine University of IbadanUniversity College Hospital Ibadan Nigeria
- Childhood Malaria Research GroupCollege of Medicine University of Ibadan, University College Hospital Ibadan Nigeria
| | - Biobele J. Brown
- Department of Paediatrics, College of Medicine University of IbadanUniversity College Hospital Ibadan Nigeria
- Childhood Malaria Research GroupCollege of Medicine University of Ibadan, University College Hospital Ibadan Nigeria
- African Computational Sciences Centre for Health and DevelopmentUniversity of Ibadan Ibadan Nigeria
| | - Delmiro Fernandez‐Reyes
- Department of Computer Science, Faculty of Engineering SciencesUniversity College London London UK
- Department of Paediatrics, College of Medicine University of IbadanUniversity College Hospital Ibadan Nigeria
- Childhood Malaria Research GroupCollege of Medicine University of Ibadan, University College Hospital Ibadan Nigeria
- African Computational Sciences Centre for Health and DevelopmentUniversity of Ibadan Ibadan Nigeria
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A Computer Modelling Approach To Evaluate the Accuracy of Microsatellite Markers for Classification of Recurrent Infections during Routine Monitoring of Antimalarial Drug Efficacy. Antimicrob Agents Chemother 2020; 64:AAC.01517-19. [PMID: 31932376 DOI: 10.1128/aac.01517-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/06/2020] [Indexed: 12/23/2022] Open
Abstract
Antimalarial drugs have long half-lives, so clinical trials to monitor their efficacy require long periods of follow-up to capture drug failure that may become patent only weeks after treatment. Reinfections often occur during follow-up, so robust methods of distinguishing drug failures (recrudescence) from emerging new infections are needed to produce accurate failure rate estimates. Molecular correction aims to achieve this by comparing the genotype of a patient's pretreatment (initial) blood sample with that of any infection that occurs during follow-up, with matching genotypes indicating drug failure. We use an in silico approach to show that the widely used match-counting method of molecular correction with microsatellite markers is likely to be highly unreliable and may lead to gross under- or overestimates of the true failure rates, depending on the choice of matching criterion. A Bayesian algorithm for molecular correction was previously developed and utilized for analysis of in vivo efficacy trials. We validated this algorithm using in silico data and showed it had high specificity and generated accurate failure rate estimates. This conclusion was robust for multiple drugs, different levels of drug failure rates, different levels of transmission intensity in the study sites, and microsatellite genetic diversity. The Bayesian algorithm was inherently unable to accurately identify low-density recrudescence that occurred in a small number of patients, but this did not appear to compromise its utility as a highly effective molecular correction method for analyzing microsatellite genotypes. Strong consideration should be given to using Bayesian methodology to obtain accurate failure rate estimates during routine monitoring trials of antimalarial efficacy that use microsatellite markers.
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Assefa A, Ahmed AA, Deressa W, Wilson GG, Kebede A, Mohammed H, Sassine M, Haile M, Dilu D, Teka H, Murphy MW, Sergent S, Rogier E, Zhiyong Z, Wakeman BS, Drakeley C, Shi YP, Von Seidlein L, Hwang J. Assessment of subpatent Plasmodium infection in northwestern Ethiopia. Malar J 2020; 19:108. [PMID: 32131841 PMCID: PMC7057598 DOI: 10.1186/s12936-020-03177-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/22/2020] [Indexed: 12/30/2022] Open
Abstract
Background Ethiopia has set a goal for malaria elimination by 2030. Low parasite density infections may go undetected by conventional diagnostic methods (microscopy and rapid diagnostic tests) and their contribution to malaria transmission varies by transmission settings. This study quantified the burden of subpatent infections from samples collected from three regions of northwest Ethiopia. Methods Sub-samples of dried blood spots from the Ethiopian Malaria Indicator Survey 2015 (EMIS-2015) were tested and compared using microscopy, rapid diagnostic tests (RDTs), and nested polymerase chain reaction (nPCR) to determine the prevalence of subpatent infection. Paired seroprevalence results previously reported along with gender, age, and elevation of residence were explored as risk factors for Plasmodium infection. Results Of the 2608 samples collected, the highest positive rate for Plasmodium infection was found with nPCR 3.3% (95% CI 2.7–4.1) compared with RDT 2.8% (95% CI 2.2–3.5) and microscopy 1.2% (95% CI 0.8–1.7). Of the nPCR positive cases, Plasmodium falciparum accounted for 3.1% (95% CI 2.5–3.8), Plasmodium vivax 0.4% (95% CI 0.2–0.7), mixed P. falciparum and P. vivax 0.1% (95% CI 0.0–0.4), and mixed P. falciparum and Plasmodium malariae 0.1% (95% CI 0.0–0.3). nPCR detected an additional 30 samples that had not been detected by conventional methods. The majority of the nPCR positive cases (61% (53/87)) were from the Benishangul-Gumuz Region. Malaria seropositivity had significant association with nPCR positivity [adjusted OR 10.0 (95% CI 3.2–29.4), P < 0.001]. Conclusion Using nPCR the detection rate of malaria parasites increased by nearly threefold over rates based on microscopy in samples collected during a national cross-sectional survey in 2015 in Ethiopia. Such subpatent infections might contribute to malaria transmission. In addition to strengthening routine surveillance systems, malaria programmes may need to consider low-density, subpatent infections in order to accelerate malaria elimination efforts.
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Affiliation(s)
- Ashenafi Assefa
- Ethiopian Public Health Institute, Arbegnoch Street, Mail Box: 19922, Addis Ababa, Ethiopia. .,School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Ahmed Ali Ahmed
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wakgari Deressa
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - G Glenn Wilson
- Department of Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Amha Kebede
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Hussein Mohammed
- Ethiopian Public Health Institute, Arbegnoch Street, Mail Box: 19922, Addis Ababa, Ethiopia
| | - Maruon Sassine
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mebrahtom Haile
- Disease Prevention and Control Directorate, Federal Ministry of Health, Addis Ababa, Ethiopia
| | - Dereje Dilu
- Disease Prevention and Control Directorate, Federal Ministry of Health, Addis Ababa, Ethiopia
| | - Hiwot Teka
- U.S. President's Malaria Initiative, United States Agency for International Development, Addis Ababa, Ethiopia
| | - Matthew W Murphy
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, U.S. President's Malaria Initiative, Addis Ababa, Ethiopia
| | - Sheila Sergent
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Zhou Zhiyong
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian S Wakeman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ya Ping Shi
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jimee Hwang
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, U.S. President's Malaria Initiative, Atlanta, GA, USA
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