{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:45:02Z","timestamp":1760240702786,"version":"build-2065373602"},"reference-count":33,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T00:00:00Z","timestamp":1567641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JCM"],"abstract":"<jats:p>Clinical audit of invasive mold disease (IMD) in hematology patients is inefficient due to the difficulties of case finding. This results in antifungal stewardship (AFS) programs preferentially reporting drug cost and consumption rather than measures that actually reflect quality of care. We used machine learning-based natural language processing (NLP) to non-selectively screen chest tomography (CT) reports for pulmonary IMD, verified by clinical review against international definitions and benchmarked against key AFS measures. NLP screened 3014 reports from 1 September 2008 to 31 December 2017, generating 784 positives that after review, identified 205 IMD episodes (44% probable-proven) in 185 patients from 50,303 admissions. Breakthrough-probable\/proven-IMD on antifungal prophylaxis accounted for 60% of episodes with serum monitoring of voriconazole or posaconazole in the 2 weeks prior performed in only 53% and 69% of episodes, respectively. Fiberoptic bronchoscopy within 2 days of CT scan occurred in only 54% of episodes. The average turnaround of send-away bronchoalveolar galactomannan of 12 days (range 7\u201322) was associated with high empiric liposomal amphotericin consumption. A random audit of 10% negative reports revealed two clinically significant misses (0.9%, 2\/223). This is the first successful use of applied machine learning for institutional IMD surveillance across an entire hematology population describing process and outcome measures relevant to AFS. Compared to current methods of clinical audit, semi-automated surveillance using NLP is more efficient and inclusive by avoiding restrictions based on any underlying hematologic condition, and has the added advantage of being potentially scalable.<\/jats:p>","DOI":"10.3390\/jcm8091390","type":"journal-article","created":{"date-parts":[[2019,9,6]],"date-time":"2019-09-06T02:59:22Z","timestamp":1567738762000},"page":"1390","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Closing the Gap in Surveillance and Audit of Invasive Mold Diseases for Antifungal Stewardship Using Machine Learning"],"prefix":"10.3390","volume":"8","author":[{"given":"Diva","family":"Baggio","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne 3004, VIC, Australia"},{"name":"General Medical Unit, Alfred Health, Melbourne 3004, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trisha","family":"Peel","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne 3004, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2296-2126","authenticated-orcid":false,"given":"Anton Y.","family":"Peleg","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne 3004, VIC, Australia"},{"name":"Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton 3800, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sharon","family":"Avery","sequence":"additional","affiliation":[{"name":"Haematology and Bone Marrow Transplant Service, Alfred Health, Melbourne 3004, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Madhurima","family":"Prayaga","sequence":"additional","affiliation":[{"name":"General Medical Unit, Alfred Health, Melbourne 3004, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle","family":"Foo","sequence":"additional","affiliation":[{"name":"General Medical Unit, Alfred Health, Melbourne 3004, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gholamreza","family":"Haffari","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology, Monash University, Clayton 3800, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology, Monash University, Clayton 3800, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3665-9021","authenticated-orcid":false,"given":"Christoph","family":"Bergmeir","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology, Monash University, Clayton 3800, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7164-3108","authenticated-orcid":false,"given":"Michelle","family":"Ananda-Rajah","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne 3004, VIC, Australia"},{"name":"General Medical Unit, Alfred Health, Melbourne 3004, VIC, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,9,5]]},"reference":[{"key":"ref_1","unstructured":"Enoch, D., and Whitney, L. (2018). Antimicrobial Stewardship from Principles to Practice, British Society of Antimicrobial Chemotherapy."},{"key":"ref_2","first-page":"969","article-title":"Issues in antifungal stewardship: An opportunity that should not be lost","volume":"72","author":"Wattal","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1086\/651263","article-title":"Prospective surveillance for invasive fungal infections in hematopoietic stem cell transplant recipients, 2001\u20132006: Overview of the Transplant-Associated Infection Surveillance Network (TRANSNET) Database","volume":"50","author":"Kontoyiannis","year":"2010","journal-title":"Clin. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1128\/CMR.00091-13","article-title":"Molecular and nonmolecular diagnostic methods for invasive fungal infections","volume":"27","author":"Arvanitis","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1038\/bmt.2009.203","article-title":"Utility of early versus late fiberoptic bronchoscopy in the evaluation of new pulmonary infiltrates following hematopoietic stem cell transplantation","volume":"45","author":"Shannon","year":"2010","journal-title":"Bone Marrow Transplant."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1093\/jac\/dkx388","article-title":"A systematic review of interventions and performance measures for antifungal stewardship programmes","volume":"73","author":"Bienvenu","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1097\/QCO.0b013e32834e0680","article-title":"The case for antifungal stewardship","volume":"25","author":"Slavin","year":"2012","journal-title":"Curr. Opin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"459","DOI":"10.3324\/haematol.2011.051995","article-title":"Comparative clinical effectiveness of prophylactic voriconazole\/posaconazole to fluconazole\/itraconazole in patients with acute myeloid leukemia\/myelodysplastic syndrome undergoing cytotoxic chemotherapy over a 12-year period","volume":"97","author":"Grigg","year":"2012","journal-title":"Haematologica"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2268","DOI":"10.1093\/jac\/dks189","article-title":"Invasive fungal breakthrough infections, fungal colonization and emergence of resistant strains in high-risk patients receiving antifungal prophylaxis with posaconazole: Real-life data from a single-centre institutional retrospective observational study","volume":"67","author":"Auberger","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_10","unstructured":"Australian Commission on Safety and Quality in Health Care (2018). Antimicrobial Stewardship in Australian Health Care, ACSQHC."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e462","DOI":"10.3324\/haematol.2015.126698","article-title":"Epidemiology of invasive fungal disease in lymphoproliferative disorders","volume":"100","author":"Teng","year":"2015","journal-title":"Haematologica"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e28","DOI":"10.3324\/haematol.2014.114025","article-title":"Invasive fungal infections in patients with multiple myeloma: A multi-center study in the era of novel myeloma therapies","volume":"100","author":"Teh","year":"2015","journal-title":"Haematologica"},{"key":"ref_13","first-page":"1610","article-title":"Breakthrough fungal infections in leukemia patients receiving isavuconazole","volume":"67","author":"Rausch","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"O952","DOI":"10.1111\/1469-0691.12688","article-title":"Breakthrough invasive fungal disease in patients receiving posaconazole primary prophylaxis: A 4-year study","volume":"20","author":"Lerolle","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.diagmicrobio.2012.10.001","article-title":"Epidemiology, outcomes, and risk factors of invasive fungal infections in adult patients with acute myelogenous leukemia after induction chemotherapy","volume":"75","author":"Neofytos","year":"2013","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1111\/j.1469-0691.2011.03548.x","article-title":"Epidemiological trends in invasive aspergillosis in France: The SAIF network (2005\u20132007)","volume":"17","author":"Lortholary","year":"2011","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.3324\/haematol.2011.044636","article-title":"Invasive aspergillosis in patients with hematologic malignancies: Incidence and description of 127 cases enrolled in a single institution prospective survey from 2004 to 2009","volume":"96","author":"Nicolle","year":"2011","journal-title":"Haematologica"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Ananda-Rajah, M.R., Martinez, D., Slavin, M.A., Cavedon, L., Dooley, M., Cheng, A., and Thursky, K.A. (2014). Facilitating surveillance of pulmonary invasive mold diseases in patients with haematological malignancies by screening computed tomography reports using natural language processing. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0107797"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/j.jbi.2014.11.009","article-title":"Automatic detection of patients with invasive fungal disease from free-text computed tomography (CT) scans","volume":"53","author":"Martinez","year":"2015","journal-title":"J. Biomed. Inform."},{"key":"ref_20","unstructured":"Liu, M., Haffari, G., Buntine, W., and Ananda-Rajah, M. (, January December). Leveraging linguistic resources for improving neural text classification. Proceedings of the Australasian Language Technology Association Workshop 2017, Brisbane, Australia. Available online: https:\/\/www.aclweb.org\/anthology\/U17-1004."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1097\/QCO.0b013e328348b2e1","article-title":"Imaging studies for diagnosing invasive fungal pneumonia in immunocompromised patients","volume":"24","author":"Marom","year":"2011","journal-title":"Curr. Opin. Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1086\/588660","article-title":"Revised definitions of invasive fungal disease from the European Organization for Research and Treatment of Cancer\/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC\/MSG) Consensus Group","volume":"46","author":"Walsh","year":"2008","journal-title":"Clin. Infect. Dis."},{"key":"ref_23","unstructured":"Ananda-Rajah, M., Tang, T., Josh, H., Ellis, S., Kam, A., Varma, D., Haffari, G., Liu, M., Seah, J., and Bergmeir, C. (2018, January 17\u201319). Deep learning based image analysis of invasive mold diseases on chest computed tomography in haematology-oncology patients. Proceedings of the International Immunocompromised Host Society Symposium, Athens, Greece."},{"key":"ref_24","first-page":"1","article-title":"Toward electronic surveillance of invasive mold diseases in hematology-oncology patients: An expert system combining natural language processing of chest computed tomography reports, microbiology, and antifungal drug data","volume":"1","author":"Bergmeir","year":"2017","journal-title":"JCO Clin. Cancer Inf."},{"key":"ref_25","first-page":"1621","article-title":"Breakthrough Invasive Mold Infections in the Hematology Patient: Current Concepts and Future Directions","volume":"67","author":"Lionakis","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1016\/j.cmi.2018.01.002","article-title":"Diagnosis and management of Aspergillus diseases: Executive summary of the 2017 ESCMID-ECMM-ERS guideline","volume":"24","author":"Ullmann","year":"2018","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_27","unstructured":"Liu, M., Haffari, G., and Buntine, W. Learning cascaded latent variable models for biomedical text classification, Proceedings of the Australasian Language Technology Association Workshop (ALTA)."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1111\/imj.12595","article-title":"Consensus guidelines for antifungal prophylaxis in haematological malignancy and haemopoietic stem cell transplantation, 2014","volume":"44","author":"Fleming","year":"2014","journal-title":"Intern. Med. J."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1007\/s40121-018-0203-4","article-title":"Systemic antifungal prophylaxis in patients hospitalized in hematology units in France: The AFHEM cross-sectional observational study","volume":"7","author":"Gangneux","year":"2018","journal-title":"Infect. Dis. Ther."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2359","DOI":"10.1093\/jac\/dkx133","article-title":"Randomized comparison of liposomal amphotericin B versus placebo to prevent invasive mycoses in acute lymphoblastic leukaemia","volume":"72","author":"Cornely","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1097\/QCO.0b013e328359a56e","article-title":"Making sense of posaconazole therapeutic drug monitoring: A practical approach","volume":"25","author":"Grigg","year":"2012","journal-title":"Curr. Opin. Infect. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/s41591-018-0300-7","article-title":"High\u2013performance medicine: The convergence of human and artificial intelligence","volume":"25","author":"Topol","year":"2019","journal-title":"Nat. Med."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"492.e1","DOI":"10.1016\/j.cmi.2015.01.013","article-title":"Antifungal stewardship in a tertiary\u2013care institution: A bedside intervention","volume":"21","author":"Valerio","year":"2015","journal-title":"Clin. Microbiol. Infect."}],"container-title":["Journal of Clinical Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2077-0383\/8\/9\/1390\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:17:07Z","timestamp":1760188627000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2077-0383\/8\/9\/1390"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,5]]},"references-count":33,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2019,9]]}},"alternative-id":["jcm8091390"],"URL":"https:\/\/doi.org\/10.3390\/jcm8091390","relation":{},"ISSN":["2077-0383"],"issn-type":[{"type":"electronic","value":"2077-0383"}],"subject":[],"published":{"date-parts":[[2019,9,5]]}}}