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Rusic D, Kumric M, Seselja Perisin A, Leskur D, Bukic J, Modun D, Vilovic M, Vrdoljak J, Martinovic D, Grahovac M, Bozic J. Tackling the Antimicrobial Resistance "Pandemic" with Machine Learning Tools: A Summary of Available Evidence. Microorganisms 2024; 12:842. [PMID: 38792673 PMCID: PMC11123121 DOI: 10.3390/microorganisms12050842] [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: 03/16/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Antimicrobial resistance is recognised as one of the top threats healthcare is bound to face in the future. There have been various attempts to preserve the efficacy of existing antimicrobials, develop new and efficient antimicrobials, manage infections with multi-drug resistant strains, and improve patient outcomes, resulting in a growing mass of routinely available data, including electronic health records and microbiological information that can be employed to develop individualised antimicrobial stewardship. Machine learning methods have been developed to predict antimicrobial resistance from whole-genome sequencing data, forecast medication susceptibility, recognise epidemic patterns for surveillance purposes, or propose new antibacterial treatments and accelerate scientific discovery. Unfortunately, there is an evident gap between the number of machine learning applications in science and the effective implementation of these systems. This narrative review highlights some of the outstanding opportunities that machine learning offers when applied in research related to antimicrobial resistance. In the future, machine learning tools may prove to be superbugs' kryptonite. This review aims to provide an overview of available publications to aid researchers that are looking to expand their work with new approaches and to acquaint them with the current application of machine learning techniques in this field.
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Affiliation(s)
- Doris Rusic
- Department of Pharmacy, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (D.R.); (A.S.P.); (D.L.); (J.B.); (D.M.)
| | - Marko Kumric
- Department of Pathophysiology, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (M.K.); (M.V.); (J.V.); (D.M.)
- Laboratory for Cardiometabolic Research, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia
| | - Ana Seselja Perisin
- Department of Pharmacy, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (D.R.); (A.S.P.); (D.L.); (J.B.); (D.M.)
| | - Dario Leskur
- Department of Pharmacy, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (D.R.); (A.S.P.); (D.L.); (J.B.); (D.M.)
| | - Josipa Bukic
- Department of Pharmacy, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (D.R.); (A.S.P.); (D.L.); (J.B.); (D.M.)
| | - Darko Modun
- Department of Pharmacy, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (D.R.); (A.S.P.); (D.L.); (J.B.); (D.M.)
| | - Marino Vilovic
- Department of Pathophysiology, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (M.K.); (M.V.); (J.V.); (D.M.)
- Laboratory for Cardiometabolic Research, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia
| | - Josip Vrdoljak
- Department of Pathophysiology, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (M.K.); (M.V.); (J.V.); (D.M.)
- Laboratory for Cardiometabolic Research, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia
| | - Dinko Martinovic
- Department of Pathophysiology, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (M.K.); (M.V.); (J.V.); (D.M.)
- Department of Maxillofacial Surgery, University Hospital of Split, Spinciceva 1, 21000 Split, Croatia
| | - Marko Grahovac
- Department of Pharmacology, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia;
| | - Josko Bozic
- Department of Pathophysiology, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia; (M.K.); (M.V.); (J.V.); (D.M.)
- Laboratory for Cardiometabolic Research, University of Split School of Medicine, Soltanska 2A, 21000 Split, Croatia
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Kherabi Y, Thy M, Bouzid D, Antcliffe DB, Rawson TM, Peiffer-Smadja N. Machine learning to predict antimicrobial resistance: future applications in clinical practice? Infect Dis Now 2024; 54:104864. [PMID: 38355048 DOI: 10.1016/j.idnow.2024.104864] [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: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
INTRODUCTION Machine learning (ML) is increasingly being used to predict antimicrobial resistance (AMR). This review aims to provide physicians with an overview of the literature on ML as a means of AMR prediction. METHODS References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, ACM Digital Library, and IEEE Xplore Digital Library up to December 2023. RESULTS Thirty-six studies were included in this review. Thirty-two studies (32/36, 89 %) were based on hospital data and four (4/36, 11 %) on outpatient data. The vast majority of them were conducted in high-resource settings (33/36, 92 %). Twenty-four (24/36, 67 %) studies developed systems to predict drug resistance in infected patients, eight (8/36, 22 %) tested the performances of ML-assisted antibiotic prescription, two (2/36, 6 %) assessed ML performances in predicting colonization with carbapenem-resistant bacteria and, finally, two assessed national and international AMR trends. The most common inputs were demographic characteristics (25/36, 70 %), previous antibiotic susceptibility testing (19/36, 53 %) and prior antibiotic exposure (15/36, 42 %). Thirty-three (92 %) studies targeted prediction of Gram-negative bacteria (GNB) resistance as an output (92 %). The studies included showed moderate to high performances, with AUROC ranging from 0.56 to 0.93. CONCLUSION ML can potentially provide valuable assistance in AMR prediction. Although the literature on this topic is growing, future studies are needed to design, implement, and evaluate the use and impact of ML decision support systems.
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Affiliation(s)
- Yousra Kherabi
- Infectious and Tropical Disease Department, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris, France.
| | - Michaël Thy
- Medical and Infectious Diseases ICU (MI2) - Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France; EA 7323 - Pharmacology and Therapeutic Evaluation in Children and Pregnant Women, Université Paris Cité, Paris, France
| | - Donia Bouzid
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris, France; Emergency Department, Bichat Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - David B Antcliffe
- Division of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK; Department of Intensive Care Unit, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Timothy Miles Rawson
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK; Centre for Antimicrobial Optimisation Imperial College London, London, UK
| | - Nathan Peiffer-Smadja
- Infectious and Tropical Disease Department, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris, France; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
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Pinto-de-Sá R, Sousa-Pinto B, Costa-de-Oliveira S. Brave New World of Artificial Intelligence: Its Use in Antimicrobial Stewardship-A Systematic Review. Antibiotics (Basel) 2024; 13:307. [PMID: 38666983 PMCID: PMC11047419 DOI: 10.3390/antibiotics13040307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health problem in the One Health dimension. Artificial intelligence (AI) is emerging in healthcare, since it is helpful to deal with large amounts of data and as a prediction tool. This systematic review explores the use of AI in antimicrobial stewardship programs (ASPs) and summarizes the predictive performance of machine learning (ML) algorithms, compared with clinical decisions, in inpatients and outpatients who need antimicrobial prescriptions. This review includes eighteen observational studies from PubMed, Scopus, and Web of Science. The exclusion criteria comprised studies conducted only in vitro, not addressing infectious diseases, or not referencing the use of AI models as predictors. Data such as study type, year of publication, number of patients, study objective, ML algorithms used, features, and predictors were extracted from the included publications. All studies concluded that ML algorithms were useful to assist antimicrobial stewardship teams in multiple tasks such as identifying inappropriate prescribing practices, choosing the appropriate antibiotic therapy, or predicting AMR. The most extracted performance metric was AUC, which ranged from 0.64 to 0.992. Despite the risks and ethical concerns that AI raises, it can play a positive and promising role in ASP.
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Affiliation(s)
- Rafaela Pinto-de-Sá
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
| | - Bernardo Sousa-Pinto
- Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal;
- Center for Health Technology and Services Research—CINTESIS@RISE, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Sofia Costa-de-Oliveira
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
- Center for Health Technology and Services Research—CINTESIS@RISE, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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Giacobbe DR, Marelli C, Guastavino S, Mora S, Rosso N, Signori A, Campi C, Giacomini M, Bassetti M. Explainable and Interpretable Machine Learning for Antimicrobial Stewardship: Opportunities and Challenges. Clin Ther 2024:S0149-2918(24)00065-1. [PMID: 38519371 DOI: 10.1016/j.clinthera.2024.02.010] [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: 11/23/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
There is growing interest in exploiting the advances in artificial intelligence and machine learning (ML) for improving and monitoring antimicrobial prescriptions in line with antimicrobial stewardship principles. Against this background, the concepts of interpretability and explainability are becoming increasingly essential to understanding how ML algorithms could predict antimicrobial resistance or recommend specific therapeutic agents, to avoid unintended biases related to the "black box" nature of complex models. In this commentary, we review and discuss some relevant topics on the use of ML algorithms for antimicrobial stewardship interventions, highlighting opportunities and challenges, with particular attention paid to interpretability and explainability of employed models. As in other fields of medicine, the exponential growth of artificial intelligence and ML indicates the potential for improving the efficacy of antimicrobial stewardship interventions, at least in part by reducing time-consuming tasks for overwhelmed health care personnel. Improving our knowledge about how complex ML models work could help to achieve crucial advances in promoting the appropriate use of antimicrobials, as well as in preventing antimicrobial resistance selection and dissemination.
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Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences, University of Genoa, Genoa, Italy; UO Clinica Malattie Infettive, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy.
| | - Cristina Marelli
- UO Clinica Malattie Infettive, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Sara Mora
- UO Information and Communication Technologies, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy
| | - Nicola Rosso
- UO Information and Communication Technologies, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy
| | - Alessio Signori
- Section of Biostatistics, Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Cristina Campi
- Department of Mathematics, University of Genoa, Genoa, Italy; Life Science Computational Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy
| | - Mauro Giacomini
- Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genoa, Genoa, Italy
| | - Matteo Bassetti
- Department of Health Sciences, University of Genoa, Genoa, Italy; UO Clinica Malattie Infettive, Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Policlinico San Martino, Genoa, Italy
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Berghea EC, Ionescu MD, Gheorghiu RM, Tincu IF, Cobilinschi CO, Craiu M, Bălgrădean M, Berghea F. Integrating Artificial Intelligence in Pediatric Healthcare: Parental Perceptions and Ethical Implications. CHILDREN (BASEL, SWITZERLAND) 2024; 11:240. [PMID: 38397353 PMCID: PMC10887612 DOI: 10.3390/children11020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
BACKGROUND Our study aimed to explore the way artificial intelligence (AI) utilization is perceived in pediatric medicine, examining its acceptance among patients (in this case represented by their adult parents), and identify the challenges it presents in order to understand the factors influencing its adoption in clinical settings. METHODS A structured questionnaire was applied to caregivers (parents or grandparents) of children who presented in tertiary pediatric clinics. RESULTS The most significant differentiations were identified in relation to the level of education (e.g., aversion to AI involvement was 22.2% among those with postgraduate degrees, 43.9% among those with university degrees, and 54.5% among those who only completed high school). The greatest fear among respondents regarding the medical use of AI was related to the possibility of errors occurring (70.1%). CONCLUSIONS The general attitude toward the use of AI can be considered positive, provided that it remains human-supervised, and that the technology used is explained in detail by the physician. However, there were large differences among groups (mainly defined by education level) in the way AI is perceived and accepted.
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Affiliation(s)
- Elena Camelia Berghea
- “Marie S. Curie” Emergency Children’s Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 041451 Bucharest, Romania; (E.C.B.); (M.B.)
| | - Marcela Daniela Ionescu
- “Marie S. Curie” Emergency Children’s Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 041451 Bucharest, Romania; (E.C.B.); (M.B.)
| | - Radu Marian Gheorghiu
- National Institute for Mother and Child Health “Alessandrescu-Rusescu”, Carol Davila University of Medicine and Pharmacy, 041249 Bucharest, Romania;
| | - Iulia Florentina Tincu
- Dr. Victor Gomoiu Clinical Children Hospital, Carol Davila University of Medicine and Pharmacy, 022102 Bucharest, Romania;
| | - Claudia Oana Cobilinschi
- Sfanta Maria Clinica Hospital, Carol Davila University of Medicine and Pharmacy, 011172 Bucharest, Romania; (C.O.C.); (F.B.)
| | - Mihai Craiu
- National Institute for Mother and Child Health “Alessandrescu-Rusescu”, Carol Davila University of Medicine and Pharmacy, 041249 Bucharest, Romania;
| | - Mihaela Bălgrădean
- “Marie S. Curie” Emergency Children’s Clinical Hospital, Carol Davila University of Medicine and Pharmacy, 041451 Bucharest, Romania; (E.C.B.); (M.B.)
| | - Florian Berghea
- Sfanta Maria Clinica Hospital, Carol Davila University of Medicine and Pharmacy, 011172 Bucharest, Romania; (C.O.C.); (F.B.)
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Tran Quoc V, Nguyen Thi Ngoc D, Nguyen Hoang T, Vu Thi H, Tong Duc M, Do Pham Nguyet T, Nguyen Van T, Ho Ngoc D, Vu Son G, Bui Duc T. Predicting Antibiotic Resistance in ICUs Patients by Applying Machine Learning in Vietnam. Infect Drug Resist 2023; 16:5535-5546. [PMID: 37638070 PMCID: PMC10460201 DOI: 10.2147/idr.s415885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Artificial Intelligence (AI) and machine learning (ML) are used extensively in HICs to detect and control antibiotic resistance (AMR) in laboratories and clinical institutions. ML is designed to predict outcome variables using an algorithm to enable "machines" to learn the "rules" from the data. ML is increasingly being applied in intensive care units to identify AMR and to assist empiric antibiotic therapy. This study aimed to evaluate the performance of ML models for predicting AMR bacteria and resistance to antibiotics in two Vietnamese hospitals. Patients and Methods A cross-sectional study combined with retrospective was conducted from 1st January 2020 to 30th June 2022. Five models were developed to predict antibiotic resistance of bacterial infections of ICU patients. Two datasets were prepared to predict AMR bacteria and antibiotics with ML models. The performance of the prediction models was evaluated by various indicators (sensitivity, specificity, precision, accuracy, F1-score, PRC, AuROC, and NormMCC) to determine the optimal time point for data selection. Python version 3.8 was used for statistical analyses. Results The accuracy, F1-score, AuROC, and normMMC of LightGBM, XGBoost, and Random Forest models were higher than those of other models in both datasets. In both datasets 1 and 2, accuracy, F1-score, AuROC and normMCC of the XGBoost model were the highest among five models (from 0.890 to 1.000). Only Random Forest models had specificity scores higher than 0.850. High scores of sensitivity, accuracy, precision, F1-score, and normMCC indicated that the models were making accurate predictions for datasets 1 and 2. Conclusion XGBoost, LightGBM, and Random Forest were the best-performed machine learning models to predict antibiotic resistance of bacterial infections of ICUs patients using the patients' EMRs.
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Affiliation(s)
- Viet Tran Quoc
- Intensive Care Unit, Military Hospital 175, Ho Chi Minh City, Vietnam
| | - Dung Nguyen Thi Ngoc
- Department of Military Science and Training, Military Hospital 175, Ho Chi Minh City, Vietnam
- Hanoi University of Public Health, Hanoi, Vietnam
| | - Trung Nguyen Hoang
- Department of Military Hygiene, Vietnam Military Medical University, Hanoi, Vietnam
| | - Hoa Vu Thi
- Department of Military Hygiene, Vietnam Military Medical University, Hanoi, Vietnam
| | - Minh Tong Duc
- Department of Military Hygiene, Vietnam Military Medical University, Hanoi, Vietnam
| | - Thanh Do Pham Nguyet
- Department of Military Science and Training, Military Hospital 175, Ho Chi Minh City, Vietnam
| | - Thanh Nguyen Van
- Department of General Planning, Military Hospital 175, Ho Chi Minh City, Vietnam
| | - Diep Ho Ngoc
- Department of Military Science and Training, Military Hospital 175, Ho Chi Minh City, Vietnam
| | - Giang Vu Son
- Department of Personnel, Military Hospital 175, Ho Chi Minh City, Vietnam
| | - Thanh Bui Duc
- Institute of Trauma and Orthopedics, Military hospital 175, Ho Chi Minh City, Vietnam
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Amin D, Garzόn-Orjuela N, Garcia Pereira A, Parveen S, Vornhagen H, Vellinga A. Artificial Intelligence to Improve Antibiotic Prescribing: A Systematic Review. Antibiotics (Basel) 2023; 12:1293. [PMID: 37627713 PMCID: PMC10451640 DOI: 10.3390/antibiotics12081293] [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: 06/08/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Introduction: The use of antibiotics leads to antibiotic resistance (ABR). Different methods have been used to predict and control ABR. In recent years, artificial intelligence (AI) has been explored to improve antibiotic (AB) prescribing, and thereby control and reduce ABR. This review explores whether the use of AI can improve antibiotic prescribing for human patients. Methods: Observational studies that use AI to improve antibiotic prescribing were retrieved for this review. There were no restrictions on the time, setting or language. References of the included studies were checked for additional eligible studies. Two independent authors screened the studies for inclusion and assessed the risk of bias of the included studies using the National Institute of Health (NIH) Quality Assessment Tool for observational cohort studies. Results: Out of 3692 records, fifteen studies were eligible for full-text screening. Five studies were included in this review, and a narrative synthesis was carried out to assess their findings. All of the studies used supervised machine learning (ML) models as a subfield of AI, such as logistic regression, random forest, gradient boosting decision trees, support vector machines and K-nearest neighbours. Each study showed a positive contribution of ML in improving antibiotic prescribing, either by reducing antibiotic prescriptions or predicting inappropriate prescriptions. However, none of the studies reported the engagement of AB prescribers in developing their ML models, nor their feedback on the user-friendliness and reliability of the models in different healthcare settings. Conclusion: The use of ML methods may improve antibiotic prescribing in both primary and secondary settings. None of the studies evaluated the implementation process of their models in clinical practices. Prospero Registration: (CRD42022329049).
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Affiliation(s)
- Doaa Amin
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin 4, Dublin, Ireland; (N.G.-O.); (S.P.); (A.V.)
| | - Nathaly Garzόn-Orjuela
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin 4, Dublin, Ireland; (N.G.-O.); (S.P.); (A.V.)
| | - Agustin Garcia Pereira
- Insight Centre for Data Analytics, University of Galway, H91 AEX4 Galway, Ireland; (A.G.P.); (H.V.)
| | - Sana Parveen
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin 4, Dublin, Ireland; (N.G.-O.); (S.P.); (A.V.)
| | - Heike Vornhagen
- Insight Centre for Data Analytics, University of Galway, H91 AEX4 Galway, Ireland; (A.G.P.); (H.V.)
| | - Akke Vellinga
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin 4, Dublin, Ireland; (N.G.-O.); (S.P.); (A.V.)
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O'Sullivan C, Tsai DHT, Wu ICY, Boselli E, Hughes C, Padmanabhan D, Hsia Y. Machine learning applications on neonatal sepsis treatment: a scoping review. BMC Infect Dis 2023; 23:441. [PMID: 37386442 DOI: 10.1186/s12879-023-08409-3] [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: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
INTRODUCTION Neonatal sepsis is a major cause of health loss and mortality worldwide. Without proper treatment, neonatal sepsis can quickly develop into multisystem organ failure. However, the signs of neonatal sepsis are non-specific, and treatment is labour-intensive and expensive. Moreover, antimicrobial resistance is a significant threat globally, and it has been reported that over 70% of neonatal bloodstream infections are resistant to first-line antibiotic treatment. Machine learning is a potential tool to aid clinicians in diagnosing infections and in determining the most appropriate empiric antibiotic treatment, as has been demonstrated for adult populations. This review aimed to present the application of machine learning on neonatal sepsis treatment. METHODS PubMed, Embase, and Scopus were searched for studies published in English focusing on neonatal sepsis, antibiotics, and machine learning. RESULTS There were 18 studies included in this scoping review. Three studies focused on using machine learning in antibiotic treatment for bloodstream infections, one focused on predicting in-hospital mortality associated with neonatal sepsis, and the remaining studies focused on developing machine learning prediction models to diagnose possible sepsis cases. Gestational age, C-reactive protein levels, and white blood cell count were important predictors to diagnose neonatal sepsis. Age, weight, and days from hospital admission to blood sample taken were important to predict antibiotic-resistant infections. The best-performing machine learning models were random forest and neural networks. CONCLUSION Despite the threat antimicrobial resistance poses, there was a lack of studies focusing on the use of machine learning for aiding empirical antibiotic treatment for neonatal sepsis.
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Affiliation(s)
| | - Daniel Hsiang-Te Tsai
- Centre for Neonatal and Paediatric Infection, St. George's, University of London, London, UK
- School of Pharmacy, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ian Chang-Yen Wu
- Centre for Neonatal and Paediatric Infection, St. George's, University of London, London, UK
- School of Pharmacy, Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Pharmacy, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Emanuela Boselli
- Department of Pediatrics, V. Buzzi Children's Hospital, University of Milan, Milan, Italy
| | - Carmel Hughes
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Deepak Padmanabhan
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Yingfen Hsia
- School of Pharmacy, Queen's University Belfast, Belfast, UK
- Centre for Neonatal and Paediatric Infection, St. George's, University of London, London, UK
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Wang X, Guo Z, Chai Y, Wang Z, Liao H, Wang Z, Wang Z. Application Prospect of the SOFA Score and Related Modification Research Progress in Sepsis. J Clin Med 2023; 12:jcm12103493. [PMID: 37240599 DOI: 10.3390/jcm12103493] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/05/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
In 2016, the SOFA score was proposed as the main evaluation system for diagnosis in the definition of sepsis 3.0, and the SOFA score has become a new research focus in sepsis. Some people are skeptical about diagnosing sepsis using the SOFA score. Experts and scholars from different regions have proposed different, modified versions of SOFA score to make up for the related problems with the use of the SOFA score in the diagnosis of sepsis. While synthesizing the different improved versions of SOFA proposed by experts and scholars in various regions, this paper also summarizes the relevant definitions of sepsis put forward in recent years to build a clear, improved application framework of SOFA score. In addition, the comparison between machine learning and SOFA scores related to sepsis is described and discussed in the article. Taken together, by summarizing the application of the improved SOFA score proposed in recent years in the related definition of sepsis, we believe that the SOFA score is still an effective means of diagnosing sepsis, but in the process of the continuous refinement and development of sepsis in the future, the SOFA score needs to be further refined and improved to provide more accurate coping strategies for different patient populations or application directions regarding sepsis. Against the big data background, machine learning has immeasurable value and significance, but its future applications should add more humanistic references and assistance.
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Affiliation(s)
- Xuesong Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China
| | - Zhe Guo
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China
| | - Yan Chai
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China
| | - Ziyi Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China
| | - Haiyan Liao
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China
| | - Ziwen Wang
- School of Clinical Medicine, Tsinghua University, Beijing 100190, China
| | - Zhong Wang
- Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing 100084, China
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Mintz I, Chowers M, Obolski U. Prediction of ciprofloxacin resistance in hospitalized patients using machine learning. COMMUNICATIONS MEDICINE 2023; 3:43. [PMID: 36977789 PMCID: PMC10050086 DOI: 10.1038/s43856-023-00275-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Ciprofloxacin is a widely used antibiotic that has lost efficiency due to extensive resistance. We developed machine learning (ML) models that predict the probability of ciprofloxacin resistance in hospitalized patients. METHODS Data were collected from electronic records of hospitalized patients with positive bacterial cultures, during 2016-2019. Susceptibility results to ciprofloxacin (n = 10,053 cultures) were obtained for Escherichia coli, Klebsiella pneumoniae, Morganella morganii, Pseudomonas aeruginosa, Proteus mirabilis and Staphylococcus aureus. An ensemble model, combining several base models, was developed to predict ciprofloxacin resistant cultures, either with (gnostic) or without (agnostic) information on the infecting bacterial species. RESULTS The ensemble models' predictions are well-calibrated, and yield ROC-AUCs (area under the receiver operating characteristic curve) of 0.737 (95%CI 0.715-0.758) and 0.837 (95%CI 0.821-0.854) on independent test-sets for the agnostic and gnostic datasets, respectively. Shapley additive explanations analysis identifies that influential variables are related to resistance of previous infections, where patients arrived from (hospital, nursing home, etc.), and recent resistance frequencies in the hospital. A decision curve analysis reveals that implementing our models can be beneficial in a wide range of cost-benefits considerations of ciprofloxacin administration. CONCLUSIONS This study develops ML models to predict ciprofloxacin resistance in hospitalized patients. The models achieve high predictive ability, are well calibrated, have substantial net-benefit across a wide range of conditions, and rely on predictors consistent with the literature. This is a further step on the way to inclusion of ML decision support systems into clinical practice.
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Affiliation(s)
- Igor Mintz
- School of Public Health, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Chowers
- Meir Medical Center, Kfar Saba, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel.
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel.
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11
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Mahalakshmi V, Balobaid A, Kanisha B, Sasirekha R, Ramkumar Raja M. Artificial Intelligence: A Next-Level Approach in Confronting the COVID-19 Pandemic. Healthcare (Basel) 2023; 11:healthcare11060854. [PMID: 36981511 PMCID: PMC10048108 DOI: 10.3390/healthcare11060854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/15/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus diseases (COVID-19) in late 2019 in China created a devastating economical loss and loss of human lives. To date, 11 variants have been identified with minimum to maximum severity of infection and surges in cases. Bacterial co-infection/secondary infection is identified during viral respiratory infection, which is a vital reason for morbidity and mortality. The occurrence of secondary infections is an additional burden to the healthcare system; therefore, the quick diagnosis of both COVID-19 and secondary infections will reduce work pressure on healthcare workers. Therefore, well-established support from Artificial Intelligence (AI) could reduce the stress in healthcare and even help in creating novel products to defend against the coronavirus. AI is one of the rapidly growing fields with numerous applications for the healthcare sector. The present review aims to access the recent literature on the role of AI and how its subfamily machine learning (ML) and deep learning (DL) are used to curb the pandemic’s effects. We discuss the role of AI in COVID-19 infections, the detection of secondary infections, technology-assisted protection from COVID-19, global laws and regulations on AI, and the impact of the pandemic on public life.
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Affiliation(s)
- V. Mahalakshmi
- Department of Computer Science, College of Computer Science & Information Technology, Jazan University, Jazan 45142, Saudi Arabia
- Correspondence: or
| | - Awatef Balobaid
- Department of Computer Science, College of Computer Science & Information Technology, Jazan University, Jazan 45142, Saudi Arabia
| | - B. Kanisha
- Department of Computer Science and Engineering, School of Computing, College of Engineering and Technology, SRM Institute of Science and Technology, Chengalpattu 603203, India
| | - R. Sasirekha
- Department of Computing Technologies, SRM Institute of Science and Technology, Kattankulathur Campus, Chengalpattu 603203, India
| | - M. Ramkumar Raja
- Department of Electrical Engineering, College of Engineering, King Khalid University, Abha 62529, Saudi Arabia
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12
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Sakagianni A, Koufopoulou C, Feretzakis G, Kalles D, Verykios VS, Myrianthefs P, Fildisis G. Using Machine Learning to Predict Antimicrobial Resistance-A Literature Review. Antibiotics (Basel) 2023; 12:antibiotics12030452. [PMID: 36978319 PMCID: PMC10044642 DOI: 10.3390/antibiotics12030452] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Machine learning (ML) algorithms are increasingly applied in medical research and in healthcare, gradually improving clinical practice. Among various applications of these novel methods, their usage in the combat against antimicrobial resistance (AMR) is one of the most crucial areas of interest, as increasing resistance to antibiotics and management of difficult-to-treat multidrug-resistant infections are significant challenges for most countries worldwide, with life-threatening consequences. As antibiotic efficacy and treatment options decrease, the need for implementation of multimodal antibiotic stewardship programs is of utmost importance in order to restrict antibiotic misuse and prevent further aggravation of the AMR problem. Both supervised and unsupervised machine learning tools have been successfully used to predict early antibiotic resistance, and thus support clinicians in selecting appropriate therapy. In this paper, we reviewed the existing literature on machine learning and artificial intelligence (AI) in general in conjunction with antimicrobial resistance prediction. This is a narrative review, where we discuss the applications of ML methods in the field of AMR and their value as a complementary tool in the antibiotic stewardship practice, mainly from the clinician's point of view.
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Affiliation(s)
| | - Christina Koufopoulou
- 1st Anesthesiology Department, Aretaieio Hospital, National and Kapodistrian University of Athens Medical School, 11528 Athens, Greece
| | - Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
- Department of Quality Control, Research and Continuing Education, Sismanogleio General Hospital, 15126 Marousi, Greece
| | - Dimitris Kalles
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Vassilios S Verykios
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece
| | - Pavlos Myrianthefs
- Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgios Fildisis
- Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
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13
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Tang R, Luo R, Tang S, Song H, Chen X. Machine learning in predicting antimicrobial resistance: a systematic review and meta-analysis. Int J Antimicrob Agents 2022; 60:106684. [PMID: 36279973 DOI: 10.1016/j.ijantimicag.2022.106684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Antimicrobial resistance (AMR) is a global health threat; rapid and timely identification of AMR improves patient prognosis and reduces inappropriate antibiotic use. METHODS Relevant literature in PubMed, Web of Science, Embase and Institute of Electrical and Electronics Engineers prior to 28 September 2021 was searched. Any study that deployed machine learning (ML) or a risk score as a tool to predict AMR was included in the final review; there were 25 studies that employed the ML algorithm to predict AMR. RESULTS Extended spectrum β-lactamases, methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem resistance were the most common outcomes in studies with a specific resistance pattern. The most common algorithms in ML prediction were logistic regression (n = 14 studies), decision tree (n = 14) and random forest (n = 7). The area under the curve (AUC) range for ML prediction was 0.48-0.93. The pooled AUC for ML prediction was 0.82 (0.78-0.85). Compared with risk score, higher specificity [87% (82-91) vs. 37% (25-51)] was indicated for ML prediction, but not sensitivity [67% (62-72) vs. 73% (67-79)]. CONCLUSIONS Machine learning might be a potential technology for AMR prediction; however, retrospective methodology for model development, nonstandard data processing and scarcity of validation in a randomised controlled trial or real-world study limit the application of these models in clinical practice.
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Affiliation(s)
- Rui Tang
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China.
| | - Rui Luo
- Department of Pain Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shiwei Tang
- Department of Pharmacy, People's Hospital of Xinjin District, Chengdu, China
| | - Haoxin Song
- Department of Pharmacy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiujuan Chen
- Department of Medical Big Data Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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14
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Sheu RK, Pardeshi MS. A Survey on Medical Explainable AI (XAI): Recent Progress, Explainability Approach, Human Interaction and Scoring System. SENSORS (BASEL, SWITZERLAND) 2022; 22:8068. [PMID: 36298417 PMCID: PMC9609212 DOI: 10.3390/s22208068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The emerging field of eXplainable AI (XAI) in the medical domain is considered to be of utmost importance. Meanwhile, incorporating explanations in the medical domain with respect to legal and ethical AI is necessary to understand detailed decisions, results, and current status of the patient's conditions. Successively, we will be presenting a detailed survey for the medical XAI with the model enhancements, evaluation methods, significant overview of case studies with open box architecture, medical open datasets, and future improvements. Potential differences in AI and XAI methods are provided with the recent XAI methods stated as (i) local and global methods for preprocessing, (ii) knowledge base and distillation algorithms, and (iii) interpretable machine learning. XAI characteristics details with future healthcare explainability is included prominently, whereas the pre-requisite provides insights for the brainstorming sessions before beginning a medical XAI project. Practical case study determines the recent XAI progress leading to the advance developments within the medical field. Ultimately, this survey proposes critical ideas surrounding a user-in-the-loop approach, with an emphasis on human-machine collaboration, to better produce explainable solutions. The surrounding details of the XAI feedback system for human rating-based evaluation provides intelligible insights into a constructive method to produce human enforced explanation feedback. For a long time, XAI limitations of the ratings, scores and grading are present. Therefore, a novel XAI recommendation system and XAI scoring system are designed and approached from this work. Additionally, this paper encourages the importance of implementing explainable solutions into the high impact medical field.
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Affiliation(s)
- Ruey-Kai Sheu
- Department of Computer Science, Tunghai University, No. 1727, Section 4, Taiwan Blvd, Xitun District, Taichung 407224, Taiwan
| | - Mayuresh Sunil Pardeshi
- AI Center, Tunghai University, No. 1727, Section 4, Taiwan Blvd, Xitun District, Taichung 407224, Taiwan
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15
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Kherabi Y, Messika J, Peiffer‐Smadja N. Machine learning, antimicrobial stewardship, and solid organ transplantation: Is this the future? Transpl Infect Dis 2022; 24:e13957. [DOI: 10.1111/tid.13957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Yousra Kherabi
- Infectious and Tropical Diseases Department Bichat‐Claude Bernard Hospital Assistance Publique‐Hôpitaux de Paris Paris France
| | - Jonathan Messika
- Université Paris Cité AP‐HP Bichat‐Claude Bernard Hospital Pneumologie B et Transplantation Pulmonaire Paris France
| | - Nathan Peiffer‐Smadja
- Infectious and Tropical Diseases Department Bichat‐Claude Bernard Hospital Assistance Publique‐Hôpitaux de Paris Paris France
- Université Paris Cité and Université Sorbonne Paris Nord Inserm IAME Paris France
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16
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Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2022. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2022. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901.
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Affiliation(s)
- Thomas De Corte
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium. .,Department of Intensive Care Medicine, Ghent University Hospital, Ghent, Belgium.
| | | | - Jan De Waele
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.,Department of Intensive Care Medicine, Ghent University Hospital, Ghent, Belgium
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17
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Rawson TM, Peiffer-Smadja N, Holmes A. Artificial Intelligence in Infectious Diseases. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Kovacs D, Msanga DR, Mshana SE, Bilal M, Oravcova K, Matthews L. Developing practical clinical tools for predicting neonatal mortality at a neonatal intensive care unit in Tanzania. BMC Pediatr 2021; 21:537. [PMID: 34852794 PMCID: PMC8638252 DOI: 10.1186/s12887-021-03012-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Neonatal mortality remains high in Tanzania at approximately 20 deaths per 1000 live births. Low birthweight, prematurity, and asphyxia are associated with neonatal mortality; however, no studies have assessed the value of combining underlying conditions and vital signs to provide clinicians with early warning of infants at risk of mortality. The aim of this study was to identify risk factors (including vital signs) associated with neonatal mortality in the neonatal intensive care unit (NICU) in Bugando Medical Centre (BMC), Mwanza, Tanzania; to identify the most accurate generalised linear model (GLM) or decision tree for predicting mortality; and to provide a tool that provides clinically relevant cut-offs for predicting mortality that is easily used by clinicians in a low-resource setting. METHODS In total, 165 neonates were enrolled between November 2019 and March 2020, of whom 80 (48.5%) died. We competed the performance of GLMs and decision trees by resampling the data to create training and test datasets and comparing their accuracy at correctly predicting mortality. RESULTS GLMs always outperformed decision trees. The best fitting GLM showed that (for standardised risk factors) temperature (OR 0.61, 95% CI 0.40-0.90), birthweight (OR 0.33, 95% CI 0.20-0.52), and oxygen saturation (OR 0.66, 95% CI 0.45-0.94) were negatively associated with mortality, while heart rate (OR 1.59, 95% CI 1.10-2.35) and asphyxia (OR 3.23, 95% 1.25-8.91) were risk factors. To identify the tool that balances accuracy and with ease of use in a low-resource clinical setting, we compared the best fitting GLM with simpler versions, and identified the three-variable GLM with temperature, heart rate, and birth weight as the best candidate. For this tool, cut-offs were identified using receiver operator characteristic (ROC) curves with the optimal cut-off for mortality prediction corresponding to 76.3% sensitivity and 68.2% specificity. The final tool is graphical, showing cut-offs that depend on birthweight, heart rate, and temperature. CONCLUSIONS Underlying conditions and vital signs can be combined into simple graphical tools that improve upon the current guidelines and are straightforward to use by clinicians in a low-resource setting.
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Affiliation(s)
- Dory Kovacs
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Delfina R Msanga
- Department of Paediatrics and Child Health, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Muhammad Bilal
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Katarina Oravcova
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health and Institute of Biodiversity, Animal health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
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19
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He S, Leanse LG, Feng Y. Artificial intelligence and machine learning assisted drug delivery for effective treatment of infectious diseases. Adv Drug Deliv Rev 2021; 178:113922. [PMID: 34461198 DOI: 10.1016/j.addr.2021.113922] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
In the era of antimicrobial resistance, the prevalence of multidrug-resistant microorganisms that resist conventional antibiotic treatment has steadily increased. Thus, it is now unquestionable that infectious diseases are significant global burdens that urgently require innovative treatment strategies. Emerging studies have demonstrated that artificial intelligence (AI) can transform drug delivery to promote effective treatment of infectious diseases. In this review, we propose to evaluate the significance, essential principles, and popular tools of AI in drug delivery for infectious disease treatment. Specifically, we will focus on the achievements and key findings of current research, as well as the applications of AI on drug delivery throughout the whole antimicrobial treatment process, with an emphasis on drug development, treatment regimen optimization, drug delivery system and administration route design, and drug delivery outcome prediction. To that end, the challenges of AI in drug delivery for infectious disease treatments and their current solutions and future perspective will be presented and discussed.
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Affiliation(s)
- Sheng He
- Boston Children's Hospital, Harvard Medical School, Harvard University, Boston, MA, USA.
| | - Leon G Leanse
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Yanfang Feng
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, USA.
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20
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Cook A, Sharland M, Yau Y, Bielicki J. Improving empiric antibiotic prescribing in pediatric bloodstream infections: a potential application of weighted-incidence syndromic combination antibiograms (WISCA). Expert Rev Anti Infect Ther 2021; 20:445-456. [PMID: 34424116 DOI: 10.1080/14787210.2021.1967145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Background: Increasing antibiotic resistance to WHO-recommended first- and second-line treatments of pediatric sepsis requires adaptation of prescribing guidelines. We discuss the potential and limitations of a weighted-incidence syndromic combination antibiogram (WISCA) as a practical tool for incorporating local microbiology data when assessing empiric coverage of commonly used antibiotics.Research design and methods: A brief questionnaire of 18 clinically significant isolates from pediatric blood cultures (Jan-Dec 2018) was sent to a global network of pediatric hospitals in July 2019. Weighted coverage estimates of non-antipseudomonal third-generation cephalosporins (3GC) and meropenem were estimated using Monte-Carlo simulation for each site reporting >100 isolates.Results: 52 hospitals in 23 countries in 5 WHO regions responded to the questionnaire; 13 sites met the sample size requirement. The most common isolates were S. aureus, Klebsiella spp., E. coli and Enterococcus spp. Coverage of 3GC ranged from 39% [95%CrI: 34-43%] to 73% (two sites: [95%CrI: 65-80%]; [95%CrI: 68-86%]) and meropenem coverage ranged from 54% [95%CrI: 47-60%] to 88% [95%CrI:84-91%].Conclusions: A WISCA is a data-driven, clinically intuitive tool that can be used to compare empiric antibiotic regimens for pediatric sepsis using existing large datasets. The estimates can be further refined using more complex meta-analytical methods and patient characteristics.
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Affiliation(s)
- Aislinn Cook
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Mike Sharland
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Yasmine Yau
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | | | - Julia Bielicki
- Paediatric Infectious Diseases Research Group, Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
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21
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Feretzakis G, Sakagianni A, Loupelis E, Kalles D, Skarmoutsou N, Martsoukou M, Christopoulos C, Lada M, Petropoulou S, Velentza A, Michelidou S, Chatzikyriakou R, Dimitrellos E. Machine Learning for Antibiotic Resistance Prediction: A Prototype Using Off-the-Shelf Techniques and Entry-Level Data to Guide Empiric Antimicrobial Therapy. Healthc Inform Res 2021; 27:214-221. [PMID: 34384203 PMCID: PMC8369050 DOI: 10.4258/hir.2021.27.3.214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/22/2021] [Accepted: 07/13/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE In the era of increasing antimicrobial resistance, the need for early identification and prompt treatment of multi-drug-resistant infections is crucial for achieving favorable outcomes in critically ill patients. As traditional microbiological susceptibility testing requires at least 24 hours, automated machine learning (AutoML) techniques could be used as clinical decision support tools to predict antimicrobial resistance and select appropriate empirical antibiotic treatment. METHODS An antimicrobial susceptibility dataset of 11,496 instances from 499 patients admitted to the internal medicine wards of a public hospital in Greece was processed by using Microsoft Azure AutoML to evaluate antibiotic susceptibility predictions using patients' simple demographic characteristics, as well as previous antibiotic susceptibility testing, without any concomitant clinical data. Furthermore, the balanced dataset was also processed using the same procedure. The datasets contained the attributes of sex, age, sample type, Gram stain, 44 antimicrobial substances, and the antibiotic susceptibility results. RESULTS The stack ensemble technique achieved the best results in the original and balanced dataset with an area under the curve-weighted metric of 0.822 and 0.850, respectively. CONCLUSIONS Implementation of AutoML for antimicrobial susceptibility data can provide clinicians useful information regarding possible antibiotic resistance and aid them in selecting appropriate empirical antibiotic therapy by taking into consideration the local antimicrobial resistance ecosystem.
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Affiliation(s)
- Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, Patras,
Greece
- IT Department, Sismanogleio General Hospital, Marousi,
Greece
- Independent Department of Quality Control, Research and Continuing Education, Sismanogleio General Hospital, Marousi,
Greece
| | | | | | - Dimitris Kalles
- School of Science and Technology, Hellenic Open University, Patras,
Greece
| | | | - Maria Martsoukou
- Clinical Microbiology Laboratory, Sismanogleio General Hospital, Marousi,
Greece
| | | | - Malvina Lada
- Internal Medicine Department, Sismanogleio General Hospital, Marousi,
Greece
| | | | - Aikaterini Velentza
- Clinical Microbiology Laboratory, Sismanogleio General Hospital, Marousi,
Greece
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22
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Moran E, Robinson E, Green C, Keeling M, Collyer B. Towards personalized guidelines: using machine-learning algorithms to guide antimicrobial selection. J Antimicrob Chemother 2021; 75:2677-2680. [PMID: 32542387 DOI: 10.1093/jac/dkaa222] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Electronic decision support systems could reduce the use of inappropriate or ineffective empirical antibiotics. We assessed the accuracy of an open-source machine-learning algorithm trained in predicting antibiotic resistance for three Gram-negative bacterial species isolated from patients' blood and urine within 48 h of hospital admission. METHODS This retrospective, observational study used routine clinical information collected between January 2010 and October 2016 in Birmingham, UK. Patients from whose blood or urine cultures Escherichia coli, Klebsiella pneumoniae or Pseudomonas aeruginosa was isolated were identified. Their demographic, microbiology and prescribing data were used to train an open-source machine-learning algorithm-XGBoost-in predicting resistance to co-amoxiclav and piperacillin/tazobactam. Multivariate analysis was performed to identify predictors of resistance and create a point-scoring tool. The performance of both methods was compared with that of the original prescribers. RESULTS There were 15 695 admissions. The AUC of the receiver operating characteristic curve for the point-scoring tools ranged from 0.61 to 0.67, and performed no better than medical staff in the selection of appropriate antibiotics. The machine-learning system performed statistically but marginally better (AUC 0.70) and could have reduced the use of unnecessary broad-spectrum antibiotics by as much as 40% among those given co-amoxiclav, piperacillin/tazobactam or carbapenems. A validation study is required. CONCLUSIONS Machine-learning algorithms have the potential to help clinicians predict antimicrobial resistance in patients found to have a Gram-negative infection of blood or urine. Prospective studies are required to assess performance in an unselected patient cohort, understand the acceptability of such systems to clinicians and patients, and assess the impact on patient outcome.
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Affiliation(s)
- Ed Moran
- Southmead Hospital, North Bristol NHS Trust, Bristol BS10 5NB, UK
| | - Esther Robinson
- Birmingham Public Health Laboratory, Public Health England, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK
| | - Christopher Green
- Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Bordesley Green East, Birmingham B9 5SS, UK.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matt Keeling
- Zeeman Institute, Mathematics Institute and School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Benjamin Collyer
- Zeeman Institute, Mathematics Institute and School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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23
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Kanjilal S, Oberst M, Boominathan S, Zhou H, Hooper DC, Sontag D. A decision algorithm to promote outpatient antimicrobial stewardship for uncomplicated urinary tract infection. Sci Transl Med 2021; 12:12/568/eaay5067. [PMID: 33148625 DOI: 10.1126/scitranslmed.aay5067] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/11/2019] [Accepted: 10/16/2020] [Indexed: 11/02/2022]
Abstract
Antibiotic resistance is a major cause of treatment failure and leads to increased use of broad-spectrum agents, which begets further resistance. This vicious cycle is epitomized by uncomplicated urinary tract infection (UTI), which affects one in two women during their life and is associated with increasing antibiotic resistance and high rates of prescription for broad-spectrum second-line agents. To address this, we developed machine learning models to predict antibiotic susceptibility using electronic health record data and built a decision algorithm for recommending the narrowest possible antibiotic to which a specimen is susceptible. When applied to a test cohort of 3629 patients presenting between 2014 and 2016, the algorithm achieved a 67% reduction in the use of second-line antibiotics relative to clinicians. At the same time, it reduced inappropriate antibiotic therapy, defined as the choice of a treatment to which a specimen is resistant, by 18% relative to clinicians. For specimens where clinicians chose a second-line drug but the algorithm chose a first-line drug, 92% (1066 of 1157) of decisions ended up being susceptible to the first-line drug. When clinicians chose an inappropriate first-line drug, the algorithm chose an appropriate first-line drug 47% (183 of 392) of the time. Our machine learning decision algorithm provides antibiotic stewardship for a common infectious syndrome by maximizing reductions in broad-spectrum antibiotic use while maintaining optimal treatment outcomes. Further work is necessary to improve generalizability by training models in more diverse populations.
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Affiliation(s)
- Sanjat Kanjilal
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA 02215, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Michael Oberst
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sooraj Boominathan
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Helen Zhou
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David Sontag
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Applications of Machine Learning to the Problem of Antimicrobial Resistance: an Emerging Model for Translational Research. J Clin Microbiol 2021; 59:e0126020. [PMID: 33536291 DOI: 10.1128/jcm.01260-20] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antimicrobial resistance (AMR) remains one of the most challenging phenomena of modern medicine. Machine learning (ML) is a subfield of artificial intelligence that focuses on the development of algorithms that learn how to accurately predict outcome variables using large sets of predictor variables that are typically not hand selected and are minimally curated. Models are parameterized using a training data set and then applied to a test data set on which predictive performance is evaluated. The application of ML algorithms to the problem of AMR has garnered increasing interest in the past 5 years due to the exponential growth of experimental and clinical data, heavy investment in computational capacity, improvements in algorithm performance, and increasing urgency for innovative approaches to reducing the burden of disease. Here, we review the current state of research at the intersection of ML and AMR with an emphasis on three domains of work. The first is the prediction of AMR using genomic data. The second is the use of ML to gain insight into the cellular functions disrupted by antibiotics, which forms the basis for understanding mechanisms of action and developing novel anti-infectives. The third focuses on the application of ML for antimicrobial stewardship using data extracted from the electronic health record. Although the use of ML for understanding, diagnosing, treating, and preventing AMR is still in its infancy, the continued growth of data and interest ensures it will become an important tool for future translational research programs.
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25
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Artificial Intelligence in Infectious Diseases. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_103-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Singh SR, Mao B, Evdokimov K, Tan P, Leab P, Ong R, Vonthanak S, Tam CC, Hsu LY, Turner P. Prevalence of MDR organism (MDRO) carriage in children and their household members in Siem Reap Province, Cambodia. JAC Antimicrob Resist 2020; 2:dlaa097. [PMID: 34223049 PMCID: PMC8210010 DOI: 10.1093/jacamr/dlaa097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The rising incidence of infections caused by MDR organisms (MDROs) poses a significant public health threat. However, little has been reported regarding community MDRO carriage in low- and middle-income countries. METHODS We conducted a cross-sectional study in Siem Reap, Cambodia comparing hospital-associated households, in which an index child (age: 2-14 years) had been hospitalized for at least 48 h in the preceding 2-4 weeks, with matched community households on the same street, in which no other child had a recent history of hospitalization. Participants were interviewed using a survey questionnaire and tested for carriage of MRSA, ESBL-producing Enterobacterales (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) by culture followed by antibiotic susceptibility testing. We used logistic regression analysis to analyse associations between collected variables and MDRO carriage. RESULTS Forty-two pairs of households including 376 participants with 376 nasal swabs and 290 stool specimens were included in final analysis. MRSA was isolated from 26 specimens (6.9%). ESBL-producing Escherichia coli was detected in 269 specimens (92.8%) whereas ESBL-producing Klebsiella pneumoniae was isolated from 128 specimens (44.1%), of which 123 (42.4%) were co-colonized with ESBL-producing E. coli. Six (2.1%) specimens tested positive for CPE (4 E. coli and 2 K. pneumoniae). The prevalence ratios for MRSA, ESBL-producing E. coli and ESBL-producing K. pneumoniae carriage did not differ significantly in hospital-associated households and hospitalized children compared with their counterparts. CONCLUSIONS The high prevalence of ESBL-E across both household types suggests that MDRO reservoirs are common in the community. Ongoing genomic analyses will help to understand the epidemiology and course of MDRO spread.
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Affiliation(s)
- Shweta R Singh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Bunsoth Mao
- University of Health Sciences, Phnom Penh, Cambodia
| | - Konstantin Evdokimov
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Pisey Tan
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Phana Leab
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Rick Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | - Clarence C Tam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Li Yang Hsu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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Wong JG, Aung AH, Lian W, Lye DC, Ooi CK, Chow A. Risk prediction models to guide antibiotic prescribing: a study on adult patients with uncomplicated upper respiratory tract infections in an emergency department. Antimicrob Resist Infect Control 2020; 9:171. [PMID: 33138859 PMCID: PMC7605344 DOI: 10.1186/s13756-020-00825-3] [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: 07/08/2020] [Accepted: 09/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Appropriate antibiotic prescribing is key to combating antimicrobial resistance. Upper respiratory tract infections (URTIs) are common reasons for emergency department (ED) visits and antibiotic use. Differentiating between bacterial and viral infections is not straightforward. We aim to provide an evidence-based clinical decision support tool for antibiotic prescribing using prediction models developed from local data. METHODS Seven hundred-fifteen patients with uncomplicated URTI were recruited and analysed from Singapore's busiest ED, Tan Tock Seng Hospital, from June 2016 to November 2018. Confirmatory tests were performed using the multiplex polymerase chain reaction (PCR) test for respiratory viruses and point-of-care test for C-reactive protein. Demographic, clinical and laboratory data were extracted from the hospital electronic medical records. Seventy percent of the data was used for training and the remaining 30% was used for validation. Decision trees, LASSO and logistic regression models were built to predict when antibiotics were not needed. RESULTS The median age of the cohort was 36 years old, with 61.2% being male. Temperature and pulse rate were significant factors in all 3 models. The area under the receiver operating curve (AUC) on the validation set for the models were similar. (LASSO: 0.70 [95% CI: 0.62-0.77], logistic regression: 0.72 [95% CI: 0.65-0.79], decision tree: 0.67 [95% CI: 0.59-0.74]). Combining the results from all models, 58.3% of study participants would not need antibiotics. CONCLUSION The models can be easily deployed as a decision support tool to guide antibiotic prescribing in busy EDs.
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Affiliation(s)
- Joshua Guoxian Wong
- Department of Clinical Epidemiology, Office of Clinical Epidemiology, Analytics and Knowledge, Tan Tock Seng Hospital, Singapore, Singapore
| | - Aung-Hein Aung
- Department of Clinical Epidemiology, Office of Clinical Epidemiology, Analytics and Knowledge, Tan Tock Seng Hospital, Singapore, Singapore
| | - Weixiang Lian
- Department of Clinical Epidemiology, Office of Clinical Epidemiology, Analytics and Knowledge, Tan Tock Seng Hospital, Singapore, Singapore
| | - David Chien Lye
- Infectious Disease Research and Training Office, National Centre for Infectious Diseases, Singapore, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chee-Kheong Ooi
- Department of Emergency Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Angela Chow
- Department of Clinical Epidemiology, Office of Clinical Epidemiology, Analytics and Knowledge, Tan Tock Seng Hospital, Singapore, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
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Fanelli U, Pappalardo M, Chinè V, Gismondi P, Neglia C, Argentiero A, Calderaro A, Prati A, Esposito S. Role of Artificial Intelligence in Fighting Antimicrobial Resistance in Pediatrics. Antibiotics (Basel) 2020; 9:antibiotics9110767. [PMID: 33139605 PMCID: PMC7692722 DOI: 10.3390/antibiotics9110767] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
Artificial intelligence (AI) is a field of science and engineering concerned with the computational understanding of what is commonly called intelligent behavior. AI is extremely useful in many human activities including medicine. The aim of our narrative review is to show the potential role of AI in fighting antimicrobial resistance in pediatric patients. We searched for PubMed articles published from April 2010 to April 2020 containing the keywords “artificial intelligence”, “machine learning”, “antimicrobial resistance”, “antimicrobial stewardship”, “pediatric”, and “children”, and we described the different strategies for the application of AI in these fields. Literature analysis showed that the applications of AI in health care are potentially endless, contributing to a reduction in the development time of new antimicrobial agents, greater diagnostic and therapeutic appropriateness, and, simultaneously, a reduction in costs. Most of the proposed AI solutions for medicine are not intended to replace the doctor’s opinion or expertise, but to provide a useful tool for easing their work. Considering pediatric infectious diseases, AI could play a primary role in fighting antibiotic resistance. In the pediatric field, a greater willingness to invest in this field could help antimicrobial stewardship reach levels of effectiveness that were unthinkable a few years ago.
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Affiliation(s)
- Umberto Fanelli
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
| | - Marco Pappalardo
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
| | - Vincenzo Chinè
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
| | - Pierpacifico Gismondi
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
| | - Cosimo Neglia
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
| | - Alberto Argentiero
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
| | - Adriana Calderaro
- Microbiology and Virology Unit, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;
| | - Andrea Prati
- Department of Engineering and Architecture, University of Parma, 43126 Parma, Italy;
| | - Susanna Esposito
- Pediatric Clinic, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (U.F.); (M.P.); (V.C.); (P.G.); (C.N.); (A.A.)
- Correspondence: ; Tel.: +39-0521-704790
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McCann-Pineo M, Ruskin J, Rasul R, Vortsman E, Bevilacqua K, Corley SS, Schwartz RM. Predictors of emergency department opioid administration and prescribing: A machine learning approach. Am J Emerg Med 2020; 46:217-224. [PMID: 33071093 DOI: 10.1016/j.ajem.2020.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION The opioid epidemic has altered normative clinical perceptions on addressing both acute and chronic pain, particularly within the Emergency Department (ED) setting, where providers are now confronted with balancing pain management and potential abuse. This study aims to examine patient sociodemographic and ED clinical characteristics to comprehensively determine predictors of opioid administration during an ED visit (ED-RX) and prescribing upon discharge (DC-RX). METHODS ED visit data of patients ≥18 years old from the National Hospital Ambulatory Medical Care Survey (NHAMCS) from 2014 to 2017 were used. Opioid prescriptions were determined utilizing Lexicon narcotic drug classifications. Visit characteristics studied included sociodemographic variables, and ED clinical variables, such as chief complaint, and discharge diagnosis. Machine learning methods were used to determine predictors of ED-RX and DC-RX and weighted logistic regressions were performed using selected predictors. RESULTS Of the 44,227 ED visits identified, patients tended to be female (57.4%), and White (74.2%) with an average age of 46.4 years (SE = 0.3). Weighted proportions of ED-RX and DC-RX were 23.2% and 18.9%, respectively. The strongest predictors of ED-RX were CT scan ordered (OR = 2.18, 95% CI = 1.84-2.58), abdominal pain (OR = 1.93, 95% CI:1.59-2.34) and back pain (OR = 1.81, 95% CI:1.45-2.27). Tooth pain (OR = 6.94, 95% CI = 4.40-10.94) and fracture injury diagnoses (OR = 3.76, 95% CI = 2.72-5.19) were the strongest predictors of DC-RX. CONCLUSIONS These findings demonstrate the utility of machine learning for understanding clinical predictors of opioid administration and prescribing in the ED, and its potential in informing standardized prescribing recommendations and guidelines.
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Affiliation(s)
- Molly McCann-Pineo
- Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; The Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY 11030, USA; Joint Center for Disaster Health, Trauma and Resilience at Mount Sinai, Stony Brook University and Northwell Health, New York, USA.
| | - Julia Ruskin
- Department of Computer Science, Princeton University, 35 Olden St, Princeton, NJ 08540, USA.
| | - Rehana Rasul
- Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; The Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY 11030, USA; Joint Center for Disaster Health, Trauma and Resilience at Mount Sinai, Stony Brook University and Northwell Health, New York, USA.
| | - Eugene Vortsman
- Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; Department of Emergency Medicine, Long Island Jewish Medical Center, Northwell Health, 270-05 76th Ave, Queens, NY 11040, USA,.
| | - Kristin Bevilacqua
- Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA.
| | - Samantha S Corley
- Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; The Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY 11030, USA; Joint Center for Disaster Health, Trauma and Resilience at Mount Sinai, Stony Brook University and Northwell Health, New York, USA.
| | - Rebecca M Schwartz
- Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; Department of Occupational Medicine, Epidemiology and Prevention, Northwell Health, 175 Community Drive, 2nd floor, Great Neck, NY 11021, USA; The Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY 11030, USA; Joint Center for Disaster Health, Trauma and Resilience at Mount Sinai, Stony Brook University and Northwell Health, New York, USA; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, USA; Institute for Translational Epidemiology and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 2-70A, New York, NY 10029, USA.
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Lewin-Epstein O, Baruch S, Hadany L, Stein GY, Obolski U. Predicting antibiotic resistance in hospitalized patients by applying machine learning to electronic medical records. Clin Infect Dis 2020; 72:e848-e855. [PMID: 33070171 DOI: 10.1093/cid/ciaa1576] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Computerized decision support systems are becoming increasingly prevalent with advances in data collection and machine learning algorithms. However, they are scarcely used for empiric antibiotic therapy. Here we accurately predict the antibiotic resistance profiles of bacterial infections of hospitalized patients using machine learning algorithms applied to patients' electronic medical records (EMR). METHODS The data included antibiotic resistance results of bacterial cultures from hospitalized patients, alongside their electronic medical records. Five antibiotics were examined: Ceftazidime (n=2942), Gentamicin (n=4360), Imipenem (n=2235), Ofloxacin (n=3117) and Sulfamethoxazole-Trimethoprim (n=3544). We applied lasso logistic regression, neural networks, gradient boosted trees, and an ensemble combining all three algorithms, to predict antibiotic resistance. Variable influence was gauged by permutation tests and Shapely Additive Explanations analysis. RESULTS The ensemble model outperformed the separate models and produced accurate predictions on a test set data. When no knowledge regarding the infecting bacterial species was assumed, the ensemble model yielded area under the receiver-operating-characteristic (auROC) scores of 0.73-0.79, for different antibiotics. Including information regarding the bacterial species improved the auROCs to 0.8-0.88. The effects of different variables on the predictions were assessed and found consistent with previously identified risk factors for antibiotic resistance. CONCLUSIONS Our study demonstrates the potential of machine learning models to accurately predict antibiotic resistance of bacterial infections of hospitalized patients. Moreover, we show that rapid information regarding the infecting bacterial species can improve predictions substantially. The implementation of such systems should be seriously considered by clinicians to aid correct empiric therapy and to potentially reduce antibiotic misuse.
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Affiliation(s)
- Ohad Lewin-Epstein
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv
| | - Shoham Baruch
- School of Public Health, Tel-Aviv University, Tel-Aviv
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv
| | - Gideon Y Stein
- Internal Medicine "A", Meir Medical Center, Kfar Saba.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv
| | - Uri Obolski
- School of Public Health, Tel-Aviv University, Tel-Aviv.,Porter School of Environmental and Earth Sciences, Tel-Aviv University, Tel-Aviv
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Islam MT, Im J, Ahmmed F, Kim DR, Khan AI, Zaman K, Ali M, Marks F, Qadri F, Kim JH, Clemens JD. Use of Typhoid Vi-Polysaccharide Vaccine as a Vaccine Probe to Delineate Clinical Criteria for Typhoid Fever. Am J Trop Med Hyg 2020; 103:665-671. [PMID: 32588803 PMCID: PMC7410438 DOI: 10.4269/ajtmh.19-0968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Blood cultures (BCs) detect an estimated 50% of typhoid fever cases. There is need for validated clinical criteria to define cases that are BC negative, both to help direct empiric antibiotic treatment and to better evaluate the magnitude of protection conferred by typhoid vaccines. To derive and validate a clinical rule for defining BC-negative typhoid fever, we assessed, in a cluster-randomized effectiveness trial of Vi-polysaccharide (ViPS) typhoid vaccine in Kolkata, India, 14,797 episodes of fever lasting at least 3 days during 4 years of comprehensive, BC-based surveillance of 70,865 persons. A recursive partitioning algorithm was used to develop a decision rule to predict BC-proven typhoid cases with a diagnostic specificity of 97–98%. To validate this rule as a definition for BC-negative typhoid fever, we assessed whether the rule defined culture-negative syndromes prevented by ViPS vaccine. In a training subset of individuals, we identified the following two rules: rule 1: patients aged < 15 years with prolonged fever accompanied by a measured body temperature ≥ 100°F, headache, and nausea; rule 2: patients aged ≥ 15 years with prolonged fever accompanied by nausea and palpable liver but without constipation. The adjusted protective efficacy of ViPS against clinical typhoid defined by these rules in persons aged ≥ 2 years in a separate validation subset was 33% (95% CI: 4–53%). We have defined and validated a clinical rule for predicting BC-negative typhoid fever using a novel vaccine probe approach. If validated in other settings, this rule may be useful to guide clinical care and to enhance typhoid vaccine evaluations.
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Affiliation(s)
- Md Taufiqul Islam
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | - Faisal Ahmmed
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Deok Ryun Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Ashraful Islam Khan
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Khalequ Zaman
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Florian Marks
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,International Vaccine Institute, Seoul, Republic of Korea
| | - Firdausi Qadri
- International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Jerome H Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - John D Clemens
- Korea University College of Medicine, Seoul, South Korea.,UCLA Fielding School of Public Health, Los Angeles, California.,International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh
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Bielicki JA, Sharland M, Heath PT, Walker AS, Agarwal R, Turner P, Cromwell DA. Evaluation of the Coverage of 3 Antibiotic Regimens for Neonatal Sepsis in the Hospital Setting Across Asian Countries. JAMA Netw Open 2020; 3:e1921124. [PMID: 32049298 DOI: 10.1001/jamanetworkopen.2019.21124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE High levels of antimicrobial resistance in neonatal bloodstream isolates are being reported globally, including in Asia. Local hospital antibiogram data may include too few isolates to meaningfully examine the expected coverage of antibiotic regimens. OBJECTIVE To assess the coverage offered by 3 antibiotic regimens for empirical treatment of neonatal sepsis in Asian countries. DESIGN, SETTING, AND PARTICIPANTS A decision analytical model was used to estimate coverage of 3 prespecified antibiotic regimens according to a weighted-incidence syndromic combination antibiogram. Relevant data to parameterize the models were identified from a systematic search of Ovid MEDLINE and Embase. Data from Asian countries published from 2014 onward were of interest. Only data on blood culture isolates from neonates with sepsis, bloodstream infection, or bacteremia reported from the relevant setting were included. Data analysis was performed from April 2019 to July 2019. EXPOSURES The prespecified regimens of interest were aminopenicillin-gentamicin, third-generation cephalosporins (cefotaxime or ceftriaxone), and meropenem. The relative incidence of different bacteria and their antimicrobial susceptibility to antibiotics relevant for determining expected concordance with these regimens were extracted. MAIN OUTCOMES AND MEASURES Coverage was calculated on the basis of a decision-tree model incorporating relative bacterial incidence and antimicrobial susceptibility of relevant isolates. Data on 7 bacteria most commonly reported in the included studies were used for estimating coverage, which was reported at the country level. RESULTS Data from 48 studies reporting on 10 countries and 8376 isolates were used. Individual countries reported 51 (Vietnam) to 6284 (India) isolates. Coverage varied considerably between countries. Meropenem was generally estimated to provide the highest coverage, ranging from 64.0% (95% credible interval [CrI], 62.6%-65.4%) in India to 90.6% (95% CrI, 86.2%-94.4%) in Cambodia, followed by aminopenicillin-gentamicin (from 35.9% [95% CrI, 27.7%-44.0%] in Indonesia to 81.0% [95% CrI, 71.1%-89.7%] in Laos) and cefotaxime or ceftriaxone (from 17.9% [95% CrI, 11.7%-24.7%] in Indonesia to 75.0% [95% CrI, 64.8%-84.1%] in Laos). Aminopenicillin-gentamicin coverage was lower than that of meropenem in all countries except Laos (81.0%; 95% CrI, 71.1%-89.7%) and Nepal (74.3%; 95% CrI, 70.3%-78.2%), where 95% CrIs for aminopenicillin-gentamicin and meropenem were overlapping. Third-generation cephalosporin coverage was lowest of the 3 regimens in all countries. The coverage difference between aminopenicillin-gentamicin and meropenem for countries with nonoverlapping 95% CrIs ranged from -15.9% in China to -52.9% in Indonesia. CONCLUSIONS AND RELEVANCE This study's findings suggest that noncarbapenem antibiotic regimens may provide limited coverage for empirical treatment of neonatal sepsis in many Asian countries. Alternative regimens must be studied to limit carbapenem consumption.
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Affiliation(s)
- Julia A Bielicki
- Paediatric Infectious Diseases Research Group, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
- Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Paediatric Pharmacology and Paediatric Infectious Diseases, University of Basel Children's Hospital, Basel, Switzerland
| | - Mike Sharland
- Paediatric Infectious Diseases Research Group, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - Paul T Heath
- Paediatric Infectious Diseases Research Group, Institute of Infection and Immunity, St George's University of London, London, United Kingdom
| | - A Sarah Walker
- Medical Research Council Clinical Trials Unit at University College London, London, United Kingdom
| | - Ramesh Agarwal
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Cambodia Oxford Medical Research Unit, Siem Reap, Cambodia
| | - David A Cromwell
- Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Feretzakis G, Loupelis E, Sakagianni A, Kalles D, Martsoukou M, Lada M, Skarmoutsou N, Christopoulos C, Valakis K, Velentza A, Petropoulou S, Michelidou S, Alexiou K. Using Machine Learning Techniques to Aid Empirical Antibiotic Therapy Decisions in the Intensive Care Unit of a General Hospital in Greece. Antibiotics (Basel) 2020; 9:E50. [PMID: 32023854 PMCID: PMC7167935 DOI: 10.3390/antibiotics9020050] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 11/18/2022] Open
Abstract
Hospital-acquired infections, particularly in the critical care setting, have become increasingly common during the last decade, with Gram-negative bacterial infections presenting the highest incidence among them. Multi-drug-resistant (MDR) Gram-negative infections are associated with high morbidity and mortality with significant direct and indirect costs resulting from long hospitalization due to antibiotic failure. Time is critical to identifying bacteria and their resistance to antibiotics due to the critical health status of patients in the intensive care unit (ICU). As common antibiotic resistance tests require more than 24 h after the sample is collected to determine sensitivity in specific antibiotics, we suggest applying machine learning (ML) techniques to assist the clinician in determining whether bacteria are resistant to individual antimicrobials by knowing only a sample's Gram stain, site of infection, and patient demographics. In our single center study, we compared the performance of eight machine learning algorithms to assess antibiotic susceptibility predictions. The demographic characteristics of the patients are considered for this study, as well as data from cultures and susceptibility testing. Applying machine learning algorithms to patient antimicrobial susceptibility data, readily available, solely from the Microbiology Laboratory without any of the patient's clinical data, even in resource-limited hospital settings, can provide informative antibiotic susceptibility predictions to aid clinicians in selecting appropriate empirical antibiotic therapy. These strategies, when used as a decision support tool, have the potential to improve empiric therapy selection and reduce the antimicrobial resistance burden.
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Affiliation(s)
- Georgios Feretzakis
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece;
- IT Department, Sismanogleio General Hospital, 15126 Marousi, Greece; (E.L.); (S.P.)
- Department of Quality Control, Research and Continuing Education, Sismanogleio General Hospital, 15126 Marousi, Greece
| | - Evangelos Loupelis
- IT Department, Sismanogleio General Hospital, 15126 Marousi, Greece; (E.L.); (S.P.)
| | - Aikaterini Sakagianni
- Intensive Care Unit, Sismanogleio General Hospital, 15126 Marousi, Greece; (A.S.); (K.V.); (S.M.)
| | - Dimitris Kalles
- School of Science and Technology, Hellenic Open University, 26335 Patras, Greece;
| | - Maria Martsoukou
- Microbiology Laboratory, Sismanogleio General Hospital, 15126 Marousi, Greece; (M.M.); (N.S.); (A.V.)
| | - Malvina Lada
- 2nd Internal Medicine Department, Sismanogleio General Hospital, 15126 Marousi, Greece;
| | - Nikoletta Skarmoutsou
- Microbiology Laboratory, Sismanogleio General Hospital, 15126 Marousi, Greece; (M.M.); (N.S.); (A.V.)
| | | | - Konstantinos Valakis
- Intensive Care Unit, Sismanogleio General Hospital, 15126 Marousi, Greece; (A.S.); (K.V.); (S.M.)
| | - Aikaterini Velentza
- Microbiology Laboratory, Sismanogleio General Hospital, 15126 Marousi, Greece; (M.M.); (N.S.); (A.V.)
| | | | - Sophia Michelidou
- Intensive Care Unit, Sismanogleio General Hospital, 15126 Marousi, Greece; (A.S.); (K.V.); (S.M.)
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Schinkel M, Paranjape K, Nannan Panday RS, Skyttberg N, Nanayakkara PWB. Clinical applications of artificial intelligence in sepsis: A narrative review. Comput Biol Med 2019; 115:103488. [PMID: 31634699 DOI: 10.1016/j.compbiomed.2019.103488] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/25/2019] [Accepted: 10/05/2019] [Indexed: 12/27/2022]
Abstract
Many studies have been published on a variety of clinical applications of artificial intelligence (AI) for sepsis, while there is no overview of the literature. The aim of this review is to give an overview of the literature and thereby identify knowledge gaps and prioritize areas with high priority for further research. A literature search was conducted in PubMed from inception to February 2019. Search terms related to AI were combined with terms regarding sepsis. Articles were included when they reported an area under the receiver operator characteristics curve (AUROC) as outcome measure. Fifteen articles on diagnosis of sepsis with AI models were included. The best performing model reached an AUROC of 0.97. There were also seven articles on prognosis, predicting mortality over time with an AUROC of up to 0.895. Finally, there were three articles on assistance of treatment of sepsis, where the use of AI was associated with the lowest mortality rates. Of the articles, twenty-two were judged to be at high risk of bias or had major concerns regarding applicability. This was mostly because predictor variables in these models, such as blood pressure, were also part of the definition of sepsis, which led to overestimation of the performance. We conclude that AI models have great potential for improving early identification of patients who may benefit from administration of antibiotics. Current AI prediction models to diagnose sepsis are at major risks of bias when the diagnosis criteria are part of the predictor variables in the model. Furthermore, generalizability of these models is poor due to overfitting and a lack of standardized protocols for the construction and validation of the models. Until these problems have been resolved, a large gap remains between the creation of an AI algorithm and its implementation in clinical practice.
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Affiliation(s)
- M Schinkel
- Section Acute Medicine, Department of Internal Medicine, Amsterdam UMC, VU University Medical Center, De Boelelaan 1118, 1081HZ, Amsterdam, the Netherlands
| | - K Paranjape
- Section Acute Medicine, Department of Internal Medicine, Amsterdam UMC, VU University Medical Center, De Boelelaan 1118, 1081HZ, Amsterdam, the Netherlands
| | - R S Nannan Panday
- Section Acute Medicine, Department of Internal Medicine, Amsterdam UMC, VU University Medical Center, De Boelelaan 1118, 1081HZ, Amsterdam, the Netherlands
| | - N Skyttberg
- Department of Learning, Informatics, Management and Ethics, Health Informatics Centre, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - P W B Nanayakkara
- Section Acute Medicine, Department of Internal Medicine, Amsterdam UMC, VU University Medical Center, De Boelelaan 1118, 1081HZ, Amsterdam, the Netherlands.
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Peiffer-Smadja N, Rawson TM, Ahmad R, Buchard A, Georgiou P, Lescure FX, Birgand G, Holmes AH. Machine learning for clinical decision support in infectious diseases: a narrative review of current applications. Clin Microbiol Infect 2019; 26:584-595. [PMID: 31539636 DOI: 10.1016/j.cmi.2019.09.009] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Machine learning (ML) is a growing field in medicine. This narrative review describes the current body of literature on ML for clinical decision support in infectious diseases (ID). OBJECTIVES We aim to inform clinicians about the use of ML for diagnosis, classification, outcome prediction and antimicrobial management in ID. SOURCES References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, biorXiv, ACM Digital Library, arXiV and IEEE Xplore Digital Library up to July 2019. CONTENT We found 60 unique ML-clinical decision support systems (ML-CDSS) aiming to assist ID clinicians. Overall, 37 (62%) focused on bacterial infections, 10 (17%) on viral infections, nine (15%) on tuberculosis and four (7%) on any kind of infection. Among them, 20 (33%) addressed the diagnosis of infection, 18 (30%) the prediction, early detection or stratification of sepsis, 13 (22%) the prediction of treatment response, four (7%) the prediction of antibiotic resistance, three (5%) the choice of antibiotic regimen and two (3%) the choice of a combination antiretroviral therapy. The ML-CDSS were developed for intensive care units (n = 24, 40%), ID consultation (n = 15, 25%), medical or surgical wards (n = 13, 20%), emergency department (n = 4, 7%), primary care (n = 3, 5%) and antimicrobial stewardship (n = 1, 2%). Fifty-three ML-CDSS (88%) were developed using data from high-income countries and seven (12%) with data from low- and middle-income countries (LMIC). The evaluation of ML-CDSS was limited to measures of performance (e.g. sensitivity, specificity) for 57 ML-CDSS (95%) and included data in clinical practice for three (5%). IMPLICATIONS Considering comprehensive patient data from socioeconomically diverse healthcare settings, including primary care and LMICs, may improve the ability of ML-CDSS to suggest decisions adapted to various clinical contexts. Currents gaps identified in the evaluation of ML-CDSS must also be addressed in order to know the potential impact of such tools for clinicians and patients.
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Affiliation(s)
- N Peiffer-Smadja
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK; French Institute for Medical Research (Inserm), Infection Antimicrobials Modelling Evolution (IAME), UMR 1137, University Paris Diderot, Paris, France.
| | - T M Rawson
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - R Ahmad
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | | | - P Georgiou
- Department of Electrical and Electronic Engineering, Imperial College, London, UK
| | - F-X Lescure
- French Institute for Medical Research (Inserm), Infection Antimicrobials Modelling Evolution (IAME), UMR 1137, University Paris Diderot, Paris, France; Infectious Diseases Department, Bichat-Claude Bernard Hospital, Assistance-Publique Hôpitaux de Paris, Paris, France
| | - G Birgand
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - A H Holmes
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
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Hijazi K, Joshi C, Gould IM. Challenges and opportunities for antimicrobial stewardship in resource-rich and resource-limited countries. Expert Rev Anti Infect Ther 2019; 17:621-634. [PMID: 31282277 DOI: 10.1080/14787210.2019.1640602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Inappropriate prescription practices, patient and provider knowledge and attitudes, variable availability of diagnostic and surveillance systems, and the unrestricted use of antimicrobials in animals and plants are contributory factors to the global crisis of antimicrobial resistance (AMR). Areas covered: Notwithstanding that interventions to revert AMR should be tailored to the socio-politico-economic landscape, there is a global consensus for the implementation and enhancement of antimicrobial stewardship strategies. Yet the implementation of Antimicrobial Stewardship Programs (ASPs) remains relatively limited within healthcare settings and faces complex challenges in resource-limited countries. The current review summarizes the limitations of current ASPs, translation challenges in resource-limited countries, and potential solutions. Expert opinion: Suboptimal ASP implementation in hospitals is multifactorial. Restriction of antimicrobial use should be informed by risk-benefit analyses, including the potential for substitute prescribing, and displacement of selection pressures. Thresholds in population use of antibiotics above which AMR increases may provide quantitative targets for ASPs. Horizontal and vertical collaborations involving policymakers and the general public are of paramount importance. While impactful prescribing changes require sustained engagement of the public and health-care professionals, we warn against over-estimating the benefits of behavioral interventions. We advocate for population-level stewardship interventions in addition to investment in structural factors that will aid ASP implementation.
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Affiliation(s)
- Karolin Hijazi
- a Institute of Dentistry, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen , Aberdeen , UK
| | - Chaitanya Joshi
- b Department of Medical Microbiology, Aberdeen Royal Infirmary , Aberdeen , UK
| | - Ian M Gould
- b Department of Medical Microbiology, Aberdeen Royal Infirmary , Aberdeen , UK
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