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Gao W, Li H, Yang J, Zhang J, Fu R, Peng J, Hu Y, Liu Y, Wang Y, Li S, Zhang S. Machine Learning Assisted MALDI Mass Spectrometry for Rapid Antimicrobial Resistance Prediction in Clinicals. Anal Chem 2024; 96:13398-13409. [PMID: 39096240 DOI: 10.1021/acs.analchem.4c00741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Antimicrobial susceptibility testing (AST) plays a critical role in assessing the resistance of individual microbial isolates and determining appropriate antimicrobial therapeutics in a timely manner. However, conventional AST normally takes up to 72 h for obtaining the results. In healthcare facilities, the global distribution of vancomycin-resistant Enterococcus fecium (VRE) infections underscores the importance of rapidly determining VRE isolates. Here, we developed an integrated antimicrobial resistance (AMR) screening strategy by combining matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) with machine learning to rapidly predict VRE from clinical samples. Over 400 VRE and vancomycin-susceptible E. faecium (VSE) isolates were analyzed using MALDI-MS at different culture times, and a comprehensive dataset comprising 2388 mass spectra was generated. Algorithms including the support vector machine (SVM), SVM with L1-norm, logistic regression, and multilayer perceptron (MLP) were utilized to train the classification model. Validation on a panel of clinical samples (external patients) resulted in a prediction accuracy of 78.07%, 80.26%, 78.95%, and 80.54% for each algorithm, respectively, all with an AUROC above 0.80. Furthermore, a total of 33 mass regions were recognized as influential features and elucidated, contributing to the differences between VRE and VSE through the Shapley value and accuracy, while tandem mass spectrometry was employed to identify the specific peaks among them. Certain ribosomal proteins, such as A0A133N352 and R2Q455, were tentatively identified. Overall, the integration of machine learning with MALDI-MS has enabled the rapid determination of bacterial antibiotic resistance, greatly expediting the usage of appropriate antibiotics.
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Affiliation(s)
- Weibo Gao
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Hang Li
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Jingxian Yang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing 100039, China
| | - Jinming Zhang
- School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Rongxin Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
| | - Yechen Hu
- Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
| | - Yitong Liu
- Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
| | - Yingshi Wang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing 100039, China
| | - Shuang Li
- School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Shuailong Zhang
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- School of Integrated Circuits and Electronics, Beijing Institute of Technology, Beijing, 100081, China
- Zhengzhou Research Institute, Beijing Institute of Technology, Zhengzhou 100081, China
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Kiss CR, Ryan S, Meyer J, Kotsanas D, Cheng AC, Stuart RL. Impact of change in vancomycin-resistant Enterococcus infection prevention policy. Infect Control Hosp Epidemiol 2024; 45:691-692. [PMID: 38251664 DOI: 10.1017/ice.2023.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Affiliation(s)
- Christopher R Kiss
- Department of Infection Prevention and Epidemiology, Monash Health, Clayton, Victoria, Australia
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Susan Ryan
- Department of Infection Prevention and Epidemiology, Monash Health, Clayton, Victoria, Australia
| | - Jacky Meyer
- Department of Infection Prevention and Epidemiology, Monash Health, Clayton, Victoria, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Allen C Cheng
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Rhonda L Stuart
- Department of Infection Prevention and Epidemiology, Monash Health, Clayton, Victoria, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
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Telli Dizman G, Metan G, Zarakolu P, Tanrıverdi ES, Hazırolan G, Aytaç Ak H, Kılınçarslan D, Uzun M, Çelik Kavaklılar B, Arık Z, Otlu B, Ünal S. Cessation of Rectal Screening for Vancomycin-Resistant Enterococci: Experience from a Tertiary Care Hospital from Türkiye. Healthcare (Basel) 2023; 11:2641. [PMID: 37830678 PMCID: PMC10572918 DOI: 10.3390/healthcare11192641] [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: 08/14/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
OBJECTIVE Here, we compared the impact of different polices on the epidemiology of Vancomycin-resistant Enterococcus faecium bloodstream infections (VRE-BSIs) in a tertiary care hospital including two hospital buildings (oncology and adult hospitals) in the same campus. MATERIAL AND METHODS All patients who were hospitalized in high-risk units were screened weekly for VRE colonization via rectal swab between January 2006 and January 2013. After January 2013, VRE screening was only performed in cases of suspicion of VRE outbreak and during point prevalence studies to evaluate the epidemiology of VRE colonization. Contact precautions were in place for all VRE-positive patients. The incidence density rates of hospital-acquired (HA)-VRE-BSIs were compared between two periods. RESULTS While the rate of VRE colonization was higher in the second period (5% vs. 9.5% (p < 0.01) for the adult hospital, and 6.4% vs. 12% (p = 0.02 for the oncology hospital), there was no increase in the incidence rate HA-VRE BSIs after the cessation of routine rectal screening in either of the hospitals. CONCLUSION Screening policies should be dynamic and individualized according to the epidemiology of VRE as well as the workforce and cost. Periodical rectal screening of VRE can be discontinued if suspicion of an outbreak can be carefully monitored.
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Affiliation(s)
- Gülçin Telli Dizman
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye; (G.M.); (P.Z.); (M.U.); (S.Ü.)
- Infection Control Committee, Hacettepe University Hospitals, Ankara 06800, Türkiye; (H.A.A.); (D.K.)
| | - Gökhan Metan
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye; (G.M.); (P.Z.); (M.U.); (S.Ü.)
- Infection Control Committee, Hacettepe University Hospitals, Ankara 06800, Türkiye; (H.A.A.); (D.K.)
| | - Pınar Zarakolu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye; (G.M.); (P.Z.); (M.U.); (S.Ü.)
| | - Elif Seren Tanrıverdi
- Molecular Microbiology Laboratory, Department of Medical Microbiology, Faculty of Medicine, İnönü University, Malatya 44280, Türkiye; (E.S.T.); (B.O.)
| | - Gülşen Hazırolan
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye;
| | - Hanife Aytaç Ak
- Infection Control Committee, Hacettepe University Hospitals, Ankara 06800, Türkiye; (H.A.A.); (D.K.)
| | - Dilek Kılınçarslan
- Infection Control Committee, Hacettepe University Hospitals, Ankara 06800, Türkiye; (H.A.A.); (D.K.)
| | - Mertcan Uzun
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye; (G.M.); (P.Z.); (M.U.); (S.Ü.)
| | - Başak Çelik Kavaklılar
- Department of Internal Medicine, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye;
| | - Zafer Arık
- Department of Internal Medicine, Section of Oncology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye;
| | - Barış Otlu
- Molecular Microbiology Laboratory, Department of Medical Microbiology, Faculty of Medicine, İnönü University, Malatya 44280, Türkiye; (E.S.T.); (B.O.)
| | - Serhat Ünal
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06800, Türkiye; (G.M.); (P.Z.); (M.U.); (S.Ü.)
- Infection Control Committee, Hacettepe University Hospitals, Ankara 06800, Türkiye; (H.A.A.); (D.K.)
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Chang E, Im D, Lee HY, Lee M, Lee CM, Kang CK, Park WB, Kim NJ, Choe PG, Oh M. Impact of discontinuing isolation in a private room for patients infected or colonized with vancomycin-resistant enterococci (VRE) on the incidence of healthcare-associated VRE bacteraemia in a hospital with a predominantly shared-room setting. J Hosp Infect 2023; 132:1-7. [PMID: 36473555 DOI: 10.1016/j.jhin.2022.11.017] [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: 09/09/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Isolating patients infected or colonized with vancomycin-resistant enterococci (VRE) in a private room or cohort room to prevent hospital transmission is controversial. AIM To evaluate the effect of a relaxed isolation policy for VRE-infected or colonized patients on healthcare-associated (HA) VRE bacteraemia in an acute care hospital with a predominantly shared-room setting. METHODS The incidence of HA VRE bacteraemia was compared during a private isolation era (October 2014-September 2017), a cohort isolation era (October 2017-June 2020), and a no isolation era (July 2020-June 2022). Using Poisson regression modelling, an interrupted time-series analysis was conducted to analyse level changes and trends in incidences of HA VRE bacteraemia for each era. FINDINGS The proportion of VRE-infected or -colonized patients staying in shared rooms increased from 18.3% in the private isolation era to 82.6% in the no isolation era (P < 0.001). There was no significant difference in the incidences of HA VRE bacteraemia between the private isolation era and the cohort isolation era (relative risk: 1.01; 95% confidence interval: 0.52-1.98; P = 0.977) or between the cohort isolation era and the no isolation era (0.99; 0.77-1.26; P = 0.903). In addition, there was no significant slope increase in the incidence of HA VRE bacteraemia between any of the eras. CONCLUSION In a hospital with predominantly shared rooms, the relaxation of isolation policy did not result in increased HA VRE bacteraemia, when other infection control measures were maintained.
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Affiliation(s)
- E Chang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - D Im
- Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - H Y Lee
- Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - M Lee
- Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - C M Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - C K Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - W B Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - N J Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
| | - P G Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea.
| | - M Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Center for Infection Control, Seoul National University Hospital, Seoul, Republic of Korea
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Should Perirectal Swab Culture Be Performed in Cases Admitted to the Neonatal Intensive Care Unit? Lessons Learned from the Neonatal Intensive Care Unit. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10020187. [PMID: 36832316 PMCID: PMC9955287 DOI: 10.3390/children10020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Serial perirectal swabs are used to identify colonization of multidrug-resistant bacteria and prevent spread. The purpose of this study was to determine colonization with carbapenem-resistant Enterobacterales (CRE) and vancomycin-resistant Enterococci (VRE). An additional purpose was to establish whether sepsis and epidemic associated with these factors were present in the neonatal intensive care unit (NICU), to which infants with hospital stays exceeding 48 h in an external healthcare center NICU were admitted. Perirectal swab samples were collected in the first 24 h by a trained infection nurse using sterile cotton swabs moistened with 0.9% NaCl from patients admitted to our unit after hospitalization exceeding 48 h in an external center. The primary outcome was positivity in perirectal swab cultures, and the secondary outcomes were whether this caused invasive infection and significant NICU outbreaks. A total of 125 newborns meeting the study criteria referred from external healthcare centers between January 2018 and January 2022 were enrolled. Analysis revealed that CRE constituted 27.2% of perirectal swab positivity and VRE 4.8%, and that one in every 4.4 infants included in the study exhibited perirectal swab positivity. The detection of colonization by these microorganisms, and including them within the scope of surveillance, is an important factor in the prevention of NICU epidemics.
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