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Filigheddu MT, Leonelli M, Varando G, Gómez-Bermejo MÁ, Ventura-Díaz S, Gorospe L, Fortún J. Using staged tree models for health data: Investigating invasive fungal infections by aspergillus and other filamentous fungi. Comput Struct Biotechnol J 2024; 24:12-22. [PMID: 38144574 PMCID: PMC10746417 DOI: 10.1016/j.csbj.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/26/2023] Open
Abstract
Machine learning models are increasingly used in the medical domain to study the association between risk factors and diseases to support practitioners in understanding health outcomes. In this paper, we showcase the use of machine-learned staged tree models for investigating complex asymmetric dependence structures in health data. Staged trees are a specific class of generative, probabilistic graphical models that formally model asymmetric conditional independence and non-regular sample spaces. An investigation of the risk factors in invasive fungal infections demonstrates the insights staged trees provide to support medical decision-making.
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Affiliation(s)
- Maria Teresa Filigheddu
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS (Instituto Ramón y Cajal de Investigación Sanitaria); Universidad de Alcalá, Madrid, Spain
| | | | - Gherardo Varando
- Image Processing Laboratory (IPL), Universitat de València, Valencia, Spain
| | | | - Sofía Ventura-Díaz
- Radiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Luis Gorospe
- Radiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Jesús Fortún
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS (Instituto Ramón y Cajal de Investigación Sanitaria); Universidad de Alcalá, Madrid, Spain
- Microbiology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
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Bienvenu AL, Leray V, Guichon C, Bourget S, Chapuis C, Duréault A, Pavese P, Roux S, Kahale E, Chaabane W, Subtil F, Maucort-Boulch D, Talbot F, Dode X, Ghesquières H, Leboucher G. ANTIFON-CLIC®, a new clinical decision support system for the treatment of invasive aspergillosis: is it clinically relevant? ANNALES PHARMACEUTIQUES FRANÇAISES 2024; 82:514-521. [PMID: 38000506 DOI: 10.1016/j.pharma.2023.11.002] [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: 10/31/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND Invasive aspergillosis (IA) is increasing especially in new groups of patients. Despite advances in management, morbidity and mortality related to IA remain high. Thus, Clinical Decision Support System (CDSS) dedicated to IA are needed to promote the optimal antifungal for each group of patients. PATIENTS AND METHODS This was a retrospective multicenter cohort study involving intensive care units and medical units. Adult patients who received caspofungin, isavuconazole, itraconazole, liposomal amphotericin B, posaconazole, or voriconazole, for the treatment of IA were eligible for enrollment. The primary objective was the concordance between the clinician's prescription and the prescription recommended by the CDSS. The secondary objective was the concordance according to different hospitals, departments, and indications. RESULTS Eighty-eight patients (n=88) from three medical hospitals were included. The overall concordance was 97% (85/88) including 100% (41/41) for center A, 92% (23/25) for center B, and 95% (21/22) for center C. There was no significant difference in concordance among the hospitals (P=0.973), the departments (P=1.000), and the indications (P=0.799). The concordance was 70% (7/10) for isavuconazole due to its use as an empirical treatment and 100% (78/78) for the other antifungals. DISCUSSION The concordance rate was high whatever the hospital, the department, and the indication. The only discrepancy was attributed to the use of isavuconazole as an empirical treatment which is a therapeutic option not included in the CDSS. CONCLUSIONS This new CDSS dedicated to IA is meeting the clinical practice. Its implementation in routine will help to support antifungal stewardship.
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Affiliation(s)
- A-L Bienvenu
- Service pharmacie, groupement hospitalier nord, hospices civils de Lyon, Lyon, France; Univ Lyon, Malaria Research Unit, SMITh, ICBMS UMR 5246, Lyon, France.
| | - V Leray
- Service d'anesthésie-réanimation, groupement hospitalier centre, hospices civils de Lyon, Lyon, France
| | - C Guichon
- Service d'anesthésie-réanimation, groupement hospitalier nord, Hospices civils de Lyon, Lyon, France
| | - S Bourget
- Service pharmacie, CH de Valence, Valence, France
| | - C Chapuis
- Service de pharmacie, CHU de Grenoble, Grenoble-Alpes, France
| | - A Duréault
- Service des maladies infectieuses, centre hospitalier de Valence, Valence, France
| | - P Pavese
- Service des maladies infectieuses, CHU de Grenoble, Grenoble-Alpes, France
| | - S Roux
- Service des maladies infectieuses et tropicales, hospices civils de Lyon, Lyon, France
| | - E Kahale
- Direction de l'innovation, hospices civils de Lyon, Lyon, France
| | - W Chaabane
- Direction des services numériques, hospices civils de Lyon, Lyon, France
| | - F Subtil
- Service de biostatistique-bioinformatique, hospices civils de Lyon, Lyon, France
| | - D Maucort-Boulch
- Service de biostatistique-bioinformatique, hospices civils de Lyon, Lyon, France
| | - F Talbot
- Direction des services numériques, hospices civils de Lyon, Lyon, France
| | - X Dode
- Service pharmacie, groupement hospitalier est, hospices civils de Lyon, Lyon, France
| | - H Ghesquières
- Service d'hématologie, groupement hospitalier sud, hospices civils de Lyon, Lyon, France
| | - G Leboucher
- Service pharmacie, groupement hospitalier nord, hospices civils de Lyon, Lyon, France
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Rodriguez RCJ, Ganesan A, Shaikh F, Carson ML, Bradley W, Warkentien TE, Tribble DR. Combat-Related Invasive Fungal Wound Infections. Mil Med 2022; 187:34-41. [PMID: 35512377 DOI: 10.1093/milmed/usab074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION During Operation Enduring Freedom in Afghanistan, an outbreak of combat-related invasive fungal wound infections (IFIs) emerged among casualties with dismounted blast trauma and became a priority issue for the Military Health System. METHODS In 2011, the Trauma Infectious Disease Outcomes Study (TIDOS) team led the Department of Defense IFI outbreak investigation to describe characteristics of IFIs among combat casualties and provide recommendations related to management of the disease. To support the outbreak investigation, existing IFI definitions and classifications utilized for immunocompromised patients were modified for use in epidemiologic research in a trauma population. Following the conclusion of the outbreak investigation, multiple retrospective analyses using a population of 77 IFI patients (injured during June 2009 to August 2011) were conducted to evaluate IFI epidemiology, wound microbiology, and diagnostics to support refinement of Joint Trauma System (JTS) clinical practice guidelines. Following cessation of combat operations in Afghanistan, the TIDOS database was comprehensively reviewed to identify patients with laboratory evidence of a fungal infection and refine the IFI classification scheme to incorporate timing of laboratory fungal evidence and include categories that denote a high or low level of suspicion for IFI. The refined IFI classification scheme was utilized in a large-scale epidemiologic assessment of casualties injured over a 5.5-year period. RESULTS Among 720 combat casualties admitted to participating hospitals (2009-2014) who had histopathology and/or wound cultures collected, 94 (13%) met criteria for an IFI and 61 (8%) were classified as high suspicion of IFI. Risk factors for development of combat-related IFIs include sustaining a dismounted blast injury, experiencing a traumatic transfemoral amputation, and requiring resuscitation with large-volume (>20 units) blood transfusions. Moreover, TIDOS analyses demonstrated the adverse impact of IFIs on wound healing, particularly with order Mucorales. A polymerase chain reaction (PCR)-based assay to identify filamentous fungi and support earlier IFI diagnosis was also assessed using archived formalin-fixed, paraffin-embedded tissue specimens. Although the PCR-based assay had high specificity (99%), there was low sensitivity (63%); however, sensitivity improved to 83% in tissues collected from sites with angioinvasion. Data obtained from the initial IFI outbreak investigation (37 IFI patients) and subsequent TIDOS analyses (77 IFI patients) supported development and refinement of a JTS clinical practice guideline for the management of IFIs in war wounds. Furthermore, a local clinical practice guideline to screen for early tissue-based evidence of IFIs among blast casualties at the Landstuhl Regional Medical Center was critically evaluated through a TIDOS investigation, providing additional clinical practice support. Through a collaboration with the Uniformed Services University Surgical Critical Care Initiative, findings from TIDOS analyses were used to support development of a clinical decision support tool to facilitate early risk stratification. CONCLUSIONS Combat-related IFIs are a highly morbid complication following severe blast trauma and remain a threat for future modern warfare. Our findings have supported JTS clinical recommendations, refined IFI classification, and confirmed the utility of PCR-based assays as a complement to histopathology and/or culture to promote early diagnosis. Analyses underway or planned will add to the knowledge base of IFI epidemiology, diagnostics, prevention, and management.
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Affiliation(s)
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA.,Walter Reed National Military Medical Center, Bethesda, MD 20852, USA
| | - Faraz Shaikh
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - M Leigh Carson
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - William Bradley
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | | | - David R Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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Cirks BT, Rajnik M, Madden KB, Otollini M. Pediatric Infectious Diseases Encountered During Wartime Part II: Infectious Diseases Complications in the Individual Pediatric Patient. Curr Infect Dis Rep 2021. [DOI: 10.1007/s11908-021-00771-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Princess I, Vadala R. Clinical Microbiology in the Intensive Care Unit: Time for Intensivists to Rejuvenate this Lost Art. Indian J Crit Care Med 2021; 25:566-574. [PMID: 34177177 PMCID: PMC8196372 DOI: 10.5005/jp-journals-10071-23810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We live in an era of evolving microbial infections and equally evolving drug resistance among microorganisms. In any healthcare facility, intensivists play the most pivotal role with critically ill patients under their direct care. Majority of the critically ill patients already harbor a microorganism at admission or acquire one in the form of healthcare-associated infections during their course of intensive care unit stay. It is therefore rather imperative for intensivists to possess sound knowledge in clinical microbiology. On a negative note, most clinicians have very meager and remote knowledge acquired during their undergraduate years. This knowledge is rather theoretical than applied and wanes over the years becoming nonbeneficial in intensive patient care. We, therefore, intend to explore important concepts in applied microbiology and infection control that intensivists should know and implement in their clinical practice on a day-to-day basis. How to cite this article: Princess I, Vadala R. Clinical Microbiology in the Intensive Care Unit: Time for Intensivists to Rejuvenate this Lost Art. Indian J Crit Care Med 2021;25(5):566–574.
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Affiliation(s)
- Isabella Princess
- Department of Microbiology, Apollo Speciality Hospitals, Vanagaram Branch, Chennai, Tamil Nadu, India
| | - Rohit Vadala
- Metro Centre for Respiratory Diseases, Metro Multispeciality Hospital, Noida, Uttar Pradesh, India
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Tribble DR, Ganesan A, Rodriguez CJ. Combat trauma-related invasive fungal wound infections. CURRENT FUNGAL INFECTION REPORTS 2020; 14:186-196. [PMID: 32665807 DOI: 10.1007/s12281-020-00385-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Purpose of review This review highlights research from the past five years on combat trauma-related invasive fungal wound infections (IFIs) with a focus on risk stratification to aid patient management, microbiology, and diagnostics. Recent Findings A revised classification scheme stratifies wounds into three risk groups: IFI, High Suspicion of IFI, and Low Suspicion of IFI. This stratification is based on persistence of wound necrosis and laboratory fungal evidence, presence of signs/symptoms of deep soft-tissue infections, and the need for antifungals. Use of this classification could allow for prioritization of antifungal therapy. Further, IFIs delay wound healing, particularly when caused by fungi of the order Mucorales. Lastly, molecular sequencing offers promising and complimentary results to the gold standard histopathology. Summary Optimal management of combat-related IFIs depends on early tissue-based diagnosis with aggressive surgical debridement and concomitant dual antifungal therapy. Further research on clinical decision support tools and rapid diagnostics are needed.
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Affiliation(s)
- David R Tribble
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Bethesda MD 20817.,Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889
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Ganesan A, Shaikh F, Bradley W, Blyth DM, Bennett D, Petfield JL, Carson ML, Wells JM, Tribble DR. Classification of Trauma-Associated Invasive Fungal Infections to Support Wound Treatment Decisions. Emerg Infect Dis 2020; 25. [PMID: 31441428 PMCID: PMC6711217 DOI: 10.3201/eid2509.190168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The proposed classification, based on diagnostic certainty, provides a framework for determining initial empiric and subsequent targeted therapy. To evaluate a classification system to support clinical decisions for treatment of contaminated deep wounds at risk for an invasive fungal infection (IFI), we studied 246 US service members (413 wounds) injured in Afghanistan (2009–2014) who had laboratory evidence of fungal infection. A total of 143 wounds with persistent necrosis and laboratory evidence were classified as IFI; 120 wounds not meeting IFI criteria were classified as high suspicion (patients had localized infection signs/symptoms and had received antifungal medication for >10 days), and 150 were classified as low suspicion (failed to meet these criteria). IFI patients received more blood than other patients and had more severe injuries than patients in the low-suspicion group. Fungi of the order Mucorales were more frequently isolated from IFI (39%) and high-suspicion (21%) wounds than from low-suspicion (9%) wounds. Wounds that did not require immediate antifungal therapy lacked necrosis and localized signs/symptoms of infection and contained fungi from orders other than Mucorales.
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Tribble DR, Murray CK, Lloyd BA, Ganesan A, Mende K, Blyth DM, Petfield JL, McDonald J. After the Battlefield: Infectious Complications among Wounded Warriors in the Trauma Infectious Disease Outcomes Study. Mil Med 2019; 184:18-25. [PMID: 31778199 PMCID: PMC6886670 DOI: 10.1093/milmed/usz027] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/04/2019] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION During recent wars in Iraq and Afghanistan, improved survivability in severe trauma corresponded with a rise in the proportion of trauma-related infections, including those associated with multidrug-resistant organisms (MDROs). Significant morbidity was reported in association with the infections. There is also concern regarding potential long-term impacts of the trauma-related infectious complications. Therefore, to meet the critical need of prospective collection of standardized infection-related data to understand the disease burden and improve outcomes of wounded personnel, the Trauma Infectious Disease Outcomes Study (TIDOS) was developed. Herein, we review accomplishments and key peer-reviewed findings of TIDOS. METHODS The TIDOS project is a multicenter observational study of short- and long-term infectious complications following deployment-related trauma. Wounded military personnel medevac'd to Landstuhl Regional Medical Center (LRMC; Germany) before transfer to a participating US military hospital between June 2009 and December 2014 were eligible for inclusion. An infectious disease module to supplement the Department of Defense Trauma Registry by collecting infection-related data from all trauma patients admitted to participating hospitals was developed. Specimens from trauma patients were also collected and retained in a microbiological isolate repository. During the initial hospitalization, patients were given the opportunity to enroll in a prospective follow-up cohort study. Patients who received Department of Veterans Affairs (VA) care were also given the opportunity to consent to ongoing VA follow-up. RESULTS A total of 2,699 patients transferred to participating military hospitals in the USA, of which 1,359 (50%) patients enrolled in the TIDOS follow-up cohort. In addition, 638 enrolled in the TIDOS-VA cohort (52% of TIDOS enrollees who entered VA healthcare). More than 8,000 isolates were collected from infection control surveillance and diagnostic evaluations and retained in the TIDOS Microbiological Repository. Approximately 34% of the 2,699 patients at US hospitals developed a trauma-related infection during their initial hospitalization with skin and soft-tissue infections being predominant. After discharge from the US hospitals, approximately one-third of TIDOS cohort enrollees developed a new trauma-related infection during follow-up and extremity wound infections (skin and soft-tissue infections and osteomyelitis) continued to be the majority. Among TIDOS cohort enrollees who received VA healthcare, 38% developed a new trauma-related infection with the incident infection being diagnosed a median of 88 days (interquartile range: 19-351 days) following hospital discharge. Data from TIDOS have been used to support the development of Joint Trauma System clinical practice guidelines for the prevention of combat-related infections, as well as the management of invasive fungal wound infections. Lastly, due to the increasing proportion of infections associated with MDROs, TIDOS investigators have collaborated with investigators across military laboratories as part of the Multidrug-Resistant and Virulent Organisms Trauma Infections Initiative with the objective of improving the understanding of the complex wound microbiology in order to develop novel infectious disease countermeasures. CONCLUSIONS The TIDOS project has focused research on four initiatives: (1) blast-related wound infection epidemiology and clinical management; (2) DoD-VA outcomes research; (3) Multidrug- Resistant and other Virulent Organisms Trauma Infections Initiative; and (4) Joint Trauma System clinical practice guidelines and antibiotic stewardship. There is a continuing need for longitudinal data platforms to support battlefield wound research and clinical practice guideline recommendation refinement, particularly to improve care for future conflicts. As such, maintaining a research platform, such as TIDOS, would negate the lengthy time needed to initiate data collection and analysis.
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Affiliation(s)
- David R Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814
| | - Clinton K Murray
- Brooke Army Medical Center, 3551 Roger Brooke Drive, JBSA Fort Sam Houston, TX 78234
- Current affiliation is 1st Area Medical Laboratory, Aberdeen Proving Ground, MD
| | - Bradley A Lloyd
- Landstuhl Regional Medical Center, Landstuhl, Germany, CMR 402, APO, AE, 09180
- Current affiliation is Wright Patterson Medical Center, OH
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814
- Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20852
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720 A Rockledge Drive, Bethesda, MD 20817
| | - Katrin Mende
- Infectious Disease Clinical Research Program, Preventive Medicine & Biostatistics Department, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814
- Brooke Army Medical Center, 3551 Roger Brooke Drive, JBSA Fort Sam Houston, TX 78234
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720 A Rockledge Drive, Bethesda, MD 20817
| | - Dana M Blyth
- Brooke Army Medical Center, 3551 Roger Brooke Drive, JBSA Fort Sam Houston, TX 78234
| | - Joseph L Petfield
- Landstuhl Regional Medical Center, Landstuhl, Germany, CMR 402, APO, AE, 09180
| | - Jay McDonald
- Veterans Affairs St. Louis Health Care System, 915 N Grand Blvd, St. Louis, MO 63106
- Washington University School of Medicine, 660 Euclid Ave, St. Louis, MO 63110
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