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Del Ben F, Da Col G, Cobârzan D, Turetta M, Rubin D, Buttazzi P, Antico A. A fully interpretable machine learning model for increasing the effectiveness of urine screening. Am J Clin Pathol 2023; 160:620-632. [PMID: 37658807 PMCID: PMC10691191 DOI: 10.1093/ajcp/aqad099] [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: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/05/2023] Open
Abstract
OBJECTIVES This article addresses the need for effective screening methods to identify negative urine samples before urine culture, reducing the workload, cost, and release time of results in the microbiology laboratory. We try to overcome the limitations of current solutions, which are either too simple, limiting effectiveness (1 or 2 parameters), or too complex, limiting interpretation, trust, and real-world implementation ("black box" machine learning models). METHODS The study analyzed 15,312 samples from 10,534 patients with clinical features and the Sysmex Uf-1000i automated analyzer data. Decision tree (DT) models with or without lookahead strategy were used, as they offer a transparent set of logical rules that can be easily understood by medical professionals and implemented into automated analyzers. RESULTS The best model achieved a sensitivity of 94.5% and classified negative samples based on age, bacteria, mucus, and 2 scattering parameters. The model reduced the workload by an additional 16% compared to the current procedure in the laboratory, with an estimated financial impact of €40,000/y considering 15,000 samples/y. Identified logical rules have a scientific rationale matched to existing knowledge in the literature. CONCLUSIONS Overall, this study provides an effective and interpretable screening method for urine culture in microbiology laboratories, using data from the Sysmex UF-1000i automated analyzer. Unlike other machine learning models, our model is interpretable, generating trust and enabling real-world implementation.
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Affiliation(s)
- Fabio Del Ben
- CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
| | - Giacomo Da Col
- KI4LIFE, Fraunhofer Austria Research, Klagenfurt, Austria
| | | | - Matteo Turetta
- CRO Aviano, National Cancer Institute, IRCCS, Aviano, Italy
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Benhamza N, Aarab A, Farih S, Saddari A, Yacoubi L, Benaissa E, Ben Lahlou Y, Elouennass M, Maleb A. Prediction of the bacterial shape in urinary tract infections with the Sysmex UF-1000i analyser: technical note. Ann Med Surg (Lond) 2023; 85:4877-4881. [PMID: 37811113 PMCID: PMC10552994 DOI: 10.1097/ms9.0000000000000701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/06/2023] [Indexed: 10/10/2023] Open
Abstract
Background The aim of our study was to explore the utility of the Sysmex UF-1000i analyzer as a rapid screening tool for urinary tract infections (UTI) and its ability to predict bacterial shape in order to help physicians choose the appropriate empiric treatment. Materials and methods This is a retrospective study, including 1023 urine cytobacteriological examinations. Urines were processed according to the recommendations of the medical microbiology reference system (REMIC). Using the Sysmex Uf-1000i analyzer, the authors evaluated bacteria forward scatter (B_FSC) and fluorescent light scatter (B_FLH) in a preliminary discrimination step for UTI caused by bacilli or cocci bacteria. Results The authors got 1023 positive samples. Comparing baccili and cocci bacteria, the authors observed a statistically significant difference for B_FSC but not for B_FLH. The values of B_FLH are very close for the four categories of microorganisms compared (bacilli, cocci, bacilli-cocci association, and yeasts). For these same categories, tests show different values for the B_FSC. A separate analysis of the B_FSC values for bacilli shows that their distribution is relatively homogeneous and exhibits a peak between 20 and 30 ch. Conclusion Dimensional parameters of bacteria generated by UF-1000i could be a rapid and useful tool for predicting the bacterial shape causing UTI.
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Affiliation(s)
| | - Adnane Aarab
- Laboratory of Microbiology, Mohamed VI Teaching Hospital
| | - Soumya Farih
- Laboratory of Microbiology, Mohamed VI Teaching Hospital
| | | | - Loubna Yacoubi
- Laboratory of Microbiology, Mohamed VI Teaching Hospital
| | - Elmostapha Benaissa
- Department of Bacteriology, Mohammed V Teaching Military Hospital
- Epidemiology and Bacterial Resistance Research Team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Yassine Ben Lahlou
- Department of Bacteriology, Mohammed V Teaching Military Hospital
- Epidemiology and Bacterial Resistance Research Team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Mostafa Elouennass
- Department of Bacteriology, Mohammed V Teaching Military Hospital
- Epidemiology and Bacterial Resistance Research Team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy, University Mohammed V, Rabat, Morocco
| | - Adil Maleb
- Laboratory of Microbiology, Mohamed VI Teaching Hospital
- Research team ‘Cell Biology and Pharmacology Applied to Health Sciences’, Faculty of Medicine and Pharmacy, Mohammed First University, Oujda
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Szmulik M, Trześniewska-Ofiara Z, Mendrycka M, Woźniak-Kosek A. A novel approach to screening and managing the urinary tract infections suspected sample in the general human population. Front Cell Infect Microbiol 2022; 12:915288. [PMID: 36093203 PMCID: PMC9455924 DOI: 10.3389/fcimb.2022.915288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background Automated urine technology providing standard urinalysis data can be used to support clinicians in screening and managing a UTI-suspected sample. Fully automated urinalysis systems have expanded in laboratory practice. Commonly used were devices based on digital imaging with automatic particle recognition, which expresses urinary sediment results on an ordinal scale. There were introduced fluorescent flow cytometry analyzers reporting all parameters quantitatively. There is a need to harmonize the result and support comparing bacteria and WBC qualitative versus semiquantitative results. Methods A total of 1,131 urine samples were analyzed on both automated urinalysis systems. The chemical components of urinalysis (leukocyte esterase and nitrate reductase) and the sediment results (leukocytes and bacteria) were investigated as potential UTI indicators. Additionally, 106 specimens were analyzed on UF-5000 and compared with culture plating to establish cut-offs that can be suitable for standard urinalysis requirements and help to guide on how to interpret urinalysis results in the context of cultivation reflex. Results The medians of bacteria counts varies from 16.2 (absence), 43.0 (trace), 443.5 (few), 5,389.2 (moderate), 19,356.6 (many) to 32,545.2 (massive) for particular digital microscopic bacteriuria thresholds. For pyuria thresholds, the medians of WBC counts varies from 0.8 (absence), 2.0 (0-1), 7.7 (2-3), 21.3 (4-6), 38.9 (7-10), 61.3 (11-15) to 242.2 (>30). Comparing the culture and FFC data (bacterial and/or WBC counts) was performed. Satisfactory sensitivity (100%), specificity (83.7%), negative predictive value (100%), and positive predictive value (75%) were obtained using indicators with the following cut-off values: leukocytes ≥40/µl or bacteria ≥300/µl. Conclusions Accurate urinalysis gives information about the count of bacteria and leukocytes as useful indicators in UTIs, in general practice it can be a future tool to cross-link clinical and microbiology laboratories. However, the cut-off adjustments require individual optimization.
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Affiliation(s)
- Magdalena Szmulik
- Sysmex Poland Ltd, Scientific Aspect Prepared in Cooperation with Department of Laboratory Diagnostics, Military Institute of Medicine, Warsaw, Poland
- *Correspondence: Magdalena Szmulik, ; Agnieszka Woźniak-Kosek,
| | | | - Mariola Mendrycka
- Department of Nursing, Faculty of Medical Sciences and Health Sciences, Kazimierz Pulaski University of Technology and Humanities, Radom, Poland
| | - Agnieszka Woźniak-Kosek
- Department of Laboratory Diagnostics, Military Institute of Medicine, Warsaw, Poland
- *Correspondence: Magdalena Szmulik, ; Agnieszka Woźniak-Kosek,
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Martín-Gutiérrez G, Martín-Pérez C, Toledo H, Sánchez-Cantalejo E, Lepe JA. FlowUTI: An interactive web-application for optimizing the use of flow cytometry as a screening tool in urinary tract infections. PLoS One 2022; 17:e0277340. [PMID: 36346782 PMCID: PMC9642874 DOI: 10.1371/journal.pone.0277340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Due to the high prevalence of patients attending with urinary tract infection (UTI) symptoms, the use of flow-cytometry as a rapid screening tool to avoid unnecessary cultures is becoming a widely used system in clinical practice. However, the recommended cut-points applied in flow-cytometry systems differ substantially among authors, making it difficult to obtain reliable conclusions. Here, we present FlowUTI, a shiny web-application created to establish optimal cut-off values in flow-cytometry for different UTI markers, such as bacterial or leukocyte counts, in urine from patients with UTI symptoms. This application provides a user-friendly graphical interface to perform robust statistical analysis without a specific training. Two datasets are analyzed in this manuscript: one composed of 204 urine samples from neonates and infants (≤3 months old) attended in the emergency department with suspected UTI; and the second dataset including 1174 urines samples from an elderly population attended at the primary care level. The source code is available on GitHub (https://github.com/GuillermoMG-HUVR/Microbiology-applications/tree/FlowUTI/FlowUTI). The web application can be executed locally from the R console. Alternatively, it can be freely accessed at https://covidiario.shinyapps.io/flowuti/. FlowUTI provides an easy-to-use environment for evaluating the efficiency of the urinary screening process with flow-cytometry, reducing the computational burden associated with this kind of analysis.
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Affiliation(s)
- Guillermo Martín-Gutiérrez
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Madrid, Spain
- * E-mail:
| | | | - Héctor Toledo
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Seville, Spain
| | | | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Parasitology, University Hospital Virgen del Rocío, Seville, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Madrid, Spain
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Gomez-Lopez N, Romero R, Galaz J, Xu Y, Panaitescu B, Slutsky R, Motomura K, Gill N, Para R, Pacora P, Jung E, Hsu CD. Cellular immune responses in amniotic fluid of women with preterm labor and intra-amniotic infection or intra-amniotic inflammation. Am J Reprod Immunol 2019; 82:e13171. [PMID: 31323170 DOI: 10.1111/aji.13171] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/05/2019] [Accepted: 07/15/2019] [Indexed: 12/12/2022] Open
Abstract
PROBLEM Preterm birth is commonly preceded by preterm labor, a syndrome that is causally linked to both intra-amniotic infection and intra-amniotic inflammation. However, the stereotypical cellular immune responses in these two clinical conditions are poorly understood. METHOD OF STUDY Amniotic fluid samples (n = 26) were collected from women diagnosed with preterm labor and intra-amniotic infection (amniotic fluid IL-6 concentrations ≥2.6 ng/mL and culturable microorganisms, n = 10) or intra-amniotic inflammation (amniotic fluid IL-6 concentrations ≥2.6 ng/mL without culturable microorganisms, n = 16). Flow cytometry was performed to evaluate the phenotype and number of amniotic fluid leukocytes. Amniotic fluid concentrations of classical pro-inflammatory cytokines, type 1 and type 2 cytokines, and T-cell chemokines were determined using immunoassays. RESULTS Women with spontaneous preterm labor and intra-amniotic infection had (a) a greater number of total leukocytes, including neutrophils and monocytes/macrophages, in amniotic fluid; (b) a higher number of total T cells and CD4+ T cells, but not CD8+ T cells or B cells, in amniotic fluid; and (c) increased amniotic fluid concentrations of IL-6, IL-1β, and IL-10, compared to those with intra-amniotic inflammation. However, no differences in amniotic fluid concentrations of T-cell cytokines and chemokines were observed between these two clinical conditions. CONCLUSION The cellular immune responses observed in women with preterm labor and intra-amniotic infection are more severe than in those with intra-amniotic inflammation, and neutrophils, monocytes/macrophages, and CD4+ T cells are the main immune cells responding to microorganisms that invade the amniotic cavity. These findings provide insights into the intra-amniotic immune mechanisms underlying the human syndrome of preterm labor.
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Affiliation(s)
- Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Immunology, Microbiology and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.,Detroit Medical Center, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yi Xu
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Bogdan Panaitescu
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Rebecca Slutsky
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA
| | - Kenichiro Motomura
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Navleen Gill
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Robert Para
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Percy Pacora
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Eunjung Jung
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chaur-Dong Hsu
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
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