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Kiernan MA, Garvey MI, Norville P, Otter JA, Weber DJ. Is detergent-only cleaning paired with chlorine disinfection the best approach for cleaning? J Hosp Infect 2024; 148:58-61. [PMID: 38649119 DOI: 10.1016/j.jhin.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/25/2024]
Affiliation(s)
- M A Kiernan
- Richard Wells Research Centre, University of West London, Brentford, UK.
| | - M I Garvey
- Hospital Infection Research Laboratory, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - J A Otter
- Directorate of Infection, Guy's and St. Thomas NHS Foundation Trust, London, UK; National Institute for Healthcare Research Health Protection Research Unit (NIHR HPRU) in HCAI and AMR, Imperial College London, London, UK
| | - D J Weber
- Department of Infection Prevention, UNC Medical Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Lv G, Wang Y. Machine learning-based antibiotic resistance prediction models: An updated systematic review and meta-analysis. Technol Health Care 2024:THC240119. [PMID: 38875058 DOI: 10.3233/thc-240119] [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: 06/16/2024]
Abstract
BACKGROUND The widespread use of antibiotics has led to a gradual adaptation of bacteria to these drugs, diminishing the effectiveness of treatments. OBJECTIVE To comprehensively assess the research progress of antibiotic resistance prediction models based on machine learning (ML) algorithms, providing the latest quantitative analysis and methodological evaluation. METHODS Relevant literature was systematically retrieved from databases, including PubMed, Embase and the Cochrane Library, from inception up to December 2023. Studies meeting predefined criteria were selected for inclusion. The prediction model risk of bias assessment tool was employed for methodological quality assessment, and a random-effects model was utilised for meta-analysis. RESULTS The systematic review included a total of 22 studies with a combined sample size of 43,628; 10 studies were ultimately included in the meta-analysis. Commonly used ML algorithms included random forest, decision trees and neural networks. Frequently utilised predictive variables encompassed demographics, drug use history and underlying diseases. The overall sensitivity was 0.57 (95% CI: 0.42-0.70; p< 0.001; I2= 99.7%), the specificity was 0.95 (95% CI: 0.79-0.99; p< 0.001; I2 = 99.9%), the positive likelihood ratio was 10.7 (95% CI: 2.9-39.5), the negative likelihood ratio was 0.46 (95% CI: 0.34-0.61), the diagnostic odds ratio was 23 (95% CI: 7-81) and the area under the receiver operating characteristic curve was 0.78 (95% CI: 0.74-0.81; p< 0.001), indicating a good discriminative ability of ML models for antibiotic resistance. However, methodological assessment and funnel plots suggested a high risk of bias and publication bias in the included studies. CONCLUSION This meta-analysis provides a current and comprehensive evaluation of ML models for predicting antibiotic resistance, emphasising their potential application in clinical practice. Nevertheless, stringent research design and reporting are warranted to enhance the quality and credibility of future studies. Future research should focus on methodological innovation and incorporate more high-quality studies to further advance this field.
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Affiliation(s)
- Guodong Lv
- Department of STD and AIDS Prevention and Control, Langfang Center for Disease Prevention and Control, Langfang, Hebei, China
| | - Yuntao Wang
- Department of Pharmacy, Langfang Health Vocational College, Langfang, Hebei, China
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3
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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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4
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Goodman KE, Taneja M, Magder LS, Klein EY, Sutherland M, Sorongon S, Tamma PD, Resnik P, Harris AD. A multi-center validation of the electronic health record admission source and discharge location fields against the clinical notes for identifying inpatients with long-term care facility exposure. Infect Control Hosp Epidemiol 2024:1-6. [PMID: 38634555 DOI: 10.1017/ice.2024.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Identifying long-term care facility (LTCF)-exposed inpatients is important for infection control research and practice, but ascertaining LTCF exposure is challenging. Across a large validation study, electronic health record data fields identified 76% of LTCF-exposed patients compared to manual chart review. OBJECTIVE Residence or recent stay in a long-term care facility (LTCF) is an important risk factor for antibiotic-resistant bacterial colonization. However, absent dedicated intake questionnaires or resource-intensive chart review, ascertaining LTCF exposure in inpatients is challenging. We aimed to validate the electronic health record (EHR) admission and discharge location fields against the clinical notes for identifying LTCF-exposed inpatients. METHODS We conducted a retrospective study of 1020 randomly sampled adult admissions between 2016 and 2021 across 12 University of Maryland Medical System hospitals. Using study-developed guidelines, we categorized the following data for LTCF exposure: each admission’s history & physical (H&P) note, each admission’s EHR-extracted “Admission Source,” and (3) the EHR-extracted admission and discharge locations for previous admissions (≤90 days). We estimated sensitivities, with 95% CIs, of H&P notes and of EHR admission/discharge location fields for detecting “current” and “any recent” (≤90 days, including current) LTCF exposure. RESULTS For detecting current LTCF exposure, the sensitivity of the index admission’s EHR-extracted “Admission Source” was 46% (95% CI: 35%–58%) and of the H&P note was 92% (83%–97%). For detecting any recent LTCF exposure, the sensitivity of “Admission Source” across the index and previous admissions was 32% (24%–41%), “Discharge Location” across previous admission(s) was 57% (47%–66%), and of the H&P note was 68% (59%–76%). The combined sensitivity of admission source and discharge location for detecting any recent LTCF exposure was 76% (67%–83%). CONCLUSIONS The EHR-obtained admission source and discharge location fields identified 76% of LTCF-exposed patients compared to chart review but disproportionately missed currently exposed patients.
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Affiliation(s)
- Katherine E Goodman
- Department of Epidemiology and Public Health, The University of Maryland School of Medicine, Baltimore, MD, USA
- The University of Maryland Institute for Health Computing, Bethesda, MD, USA
| | - Monica Taneja
- The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Laurence S Magder
- Department of Epidemiology and Public Health, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eili Y Klein
- Department of Emergency Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark Sutherland
- Departments of Emergency Medicine and Internal Medicine, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Scott Sorongon
- Department of Epidemiology and Public Health, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Pranita D Tamma
- Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Philip Resnik
- Department of Linguistics and Institute for Advanced Computer Studies, The University of Maryland, College Park, College Park, MD, USA
| | - Anthony D Harris
- Department of Epidemiology and Public Health, The University of Maryland School of Medicine, Baltimore, MD, USA
- The University of Maryland Institute for Health Computing, Bethesda, MD, USA
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5
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Nasrollahian S, Graham JP, Halaji M. A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli. Front Cell Infect Microbiol 2024; 14:1387497. [PMID: 38638826 PMCID: PMC11024256 DOI: 10.3389/fcimb.2024.1387497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.
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Affiliation(s)
- Sina Nasrollahian
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jay P. Graham
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, United States
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Microbiology and Biotechnology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
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6
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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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7
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Sansom SE, Shimasaki T, Dangana T, Lin MY, Schoeny ME, Fukuda C, Moore NM, Yelin RD, Bassis CM, Rhee Y, Cornejo Cisneros E, Bell P, Lolans K, Aboushaala K, Young VB, Hayden MK. Comparison of Daily versus Admission and Discharge Surveillance Cultures for Multidrug-Resistant Organism Detection in an Intensive Care Unit. J Infect Dis 2024:jiae162. [PMID: 38546721 DOI: 10.1093/infdis/jiae162] [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: 09/26/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a traditional approach to active surveillance, but its sensitivity for detecting colonization is uncertain. METHODS Daily rectal or fecal swab samples and clinical data were collected over 12 months from patients in one 25-bed intensive care unit (ICU) in Chicago, IL USA and tested for the following multidrug-resistant organisms (MDROs): vancomycin-resistant enterococci (VRE); third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL); and carbapenem-resistant Enterobacterales (CRE). MDRO detection by (1) admission/discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. RESULTS Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of incident MDRO colonization among medical ICU patients. Only a minority (7%) of MDRO carriers were identified by clinical cultures. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. CONCLUSION Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance.
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Affiliation(s)
- Sarah E Sansom
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Teppei Shimasaki
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Thelma Dangana
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Michael Y Lin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | | | - Christine Fukuda
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Nicholas M Moore
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Rachel D Yelin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Christine M Bassis
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
| | - Yoona Rhee
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Enrique Cornejo Cisneros
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Pamela Bell
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Karen Lolans
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Khaled Aboushaala
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI USA
| | - Mary K Hayden
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
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Li Y, Ma L, Ding X, Zhang R. Fecal carriage and genetic characteristics of carbapenem-resistant enterobacterales among adults from four provinces of China. FRONTIERS IN EPIDEMIOLOGY 2024; 3:1304324. [PMID: 38455926 PMCID: PMC10910981 DOI: 10.3389/fepid.2023.1304324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 03/09/2024]
Abstract
Carbapenem-resistant Enterobacterales (CRE) is a global concern. This study investigated the prevalence of fecal colonization carriage and clonal dissemination of CRE among population in four provinces of China. A total of 685 stool samples were collected from four provinces in China. Among these samples, 141 and 544 were obtained from healthy and hospitalized individuals, respectively. The overall fecal carriage rate was 9.6% (65/685) with 4.26% (95% CI: 0.9-7.6) in healthy individuals and 10.84% (95% CI: 8.2-13.5) in hospitalized patients. The highest prevalence was in Henan province (18.35%, 95% CI: 9%-18.7%). Sixty-six CRE isolates were identified in Escherichia coli (56.06%, 37/66), Klebsiella (15.15%, 10/66), Citrobacter (13.63%, 9/66), Enterobacter (12.12%, 8/66), and Atlantibacter (1.51%, 1/66). All CRE strains carried carbapenemase genes and multiple antibiotics resistance genes, blaNDM-5 (77.27%, 51/66) was the most common carbapenemase gene, followed by blaNDM-1 (19.69%, 13/66). Antibiotic resistance genes, including blaIMP-4, and the colistin colistin resistance (mcr-1) gene were also identified. All CRE isolates belonged to different sequence types (STs). ST206 (36.84%, 14/38) in E. coli and ST2270 (60%, 6/10) in Klebsiella were significantly dominant clones. The results indicated the prevalence of CRE fecal carriage among adults of China, mostly blaNDM-producing E coli, which pose significant challenges for clinical management. Screening for CRE colonization is necessary to control infection.
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Affiliation(s)
- Yuanyuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China
| | - Lan Ma
- Department of Clinical Laboratory, Second Affiliated Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Xinying Ding
- Department of Clinical Laboratory, Zibo First Hospital, Zibo, Shandong, China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
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Pople D, Kypraios T, Donker T, Stoesser N, Seale AC, George R, Dodgson A, Freeman R, Hope R, Walker AS, Hopkins S, Robotham J. Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting. BMC Med 2023; 21:492. [PMID: 38087343 PMCID: PMC10717398 DOI: 10.1186/s12916-023-03007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Globally, detections of carbapenemase-producing Enterobacterales (CPE) colonisations and infections are increasing. The spread of these highly resistant bacteria poses a serious threat to public health. However, understanding of CPE transmission and evidence on effectiveness of control measures is severely lacking. This paper provides evidence to inform effective admission screening protocols, which could be important in controlling nosocomial CPE transmission. METHODS CPE transmission within an English hospital setting was simulated with a data-driven individual-based mathematical model. This model was used to evaluate the ability of the 2016 England CPE screening recommendations, and of potential alternative protocols, to identify patients with CPE-colonisation on admission (including those colonised during previous stays or from elsewhere). The model included nosocomial transmission from colonised and infected patients, as well as environmental contamination. Model parameters were estimated using primary data where possible, including estimation of transmission using detailed epidemiological data within a Bayesian framework. Separate models were parameterised to represent hospitals in English areas with low and high CPE risk (based on prevalence). RESULTS The proportion of truly colonised admissions which met the 2016 screening criteria was 43% in low-prevalence and 54% in high-prevalence areas respectively. Selection of CPE carriers for screening was improved in low-prevalence areas by adding readmission as a screening criterion, which doubled how many colonised admissions were selected. A minority of CPE carriers were confirmed as CPE positive during their hospital stay (10 and 14% in low- and high-prevalence areas); switching to a faster screening test pathway with a single-swab test (rather than three swab regimen) increased the overall positive predictive value with negligible reduction in negative predictive value. CONCLUSIONS Using a novel within-hospital CPE transmission model, this study assesses CPE admission screening protocols, across the range of CPE prevalence observed in England. It identifies protocol changes-adding readmissions to screening criteria and a single-swab test pathway-which could detect similar numbers of CPE carriers (or twice as many in low CPE prevalence areas), but faster, and hence with lower demand on pre-emptive infection-control resources. Study findings can inform interventions to control this emerging threat, although further work is required to understand within-hospital transmission sources.
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Affiliation(s)
- Diane Pople
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.
| | - Theodore Kypraios
- School of Mathematical Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Tjibbe Donker
- University Medical Center Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Breisacher Strasse, 79106, Freiburg im Breisgau, Germany
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare Associated Infections, University of Oxford and UKHSA, Oxford, UK
| | - Anna C Seale
- University of Warwick, Warwick, UK
- London School of Hygiene & Tropical Medicine, London, UK
- UK Health Security Agency, London, UK
| | - Ryan George
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew Dodgson
- UK Health Security Agency, Manchester Public Health Laboratory, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL, UK
| | - Rachel Freeman
- IQVIA, The Point, 37 North Wharf Road, London, W2 1AF, UK
| | - Russell Hope
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susan Hopkins
- NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare Associated Infections, University of Oxford and UKHSA, Oxford, UK
- UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
- Division of Infection and Immunity, UCL, Gower St, London, UK
| | - Julie Robotham
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
- NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare Associated Infections, University of Oxford and UKHSA, Oxford, UK
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Gouareb R, Bornet A, Proios D, Pereira SG, Teodoro D. Detection of Patients at Risk of Multidrug-Resistant Enterobacteriaceae Infection Using Graph Neural Networks: A Retrospective Study. HEALTH DATA SCIENCE 2023; 3:0099. [PMID: 38487204 PMCID: PMC10904075 DOI: 10.34133/hds.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 10/23/2023] [Indexed: 03/17/2024]
Abstract
Background: While Enterobacteriaceae bacteria are commonly found in the healthy human gut, their colonization of other body parts can potentially evolve into serious infections and health threats. We investigate a graph-based machine learning model to predict risks of inpatient colonization by multidrug-resistant (MDR) Enterobacteriaceae. Methods: Colonization prediction was defined as a binary task, where the goal is to predict whether a patient is colonized by MDR Enterobacteriaceae in an undesirable body part during their hospital stay. To capture topological features, interactions among patients and healthcare workers were modeled using a graph structure, where patients are described by nodes and their interactions are described by edges. Then, a graph neural network (GNN) model was trained to learn colonization patterns from the patient network enriched with clinical and spatiotemporal features. Results: The GNN model achieves performance between 0.91 and 0.96 area under the receiver operating characteristic curve (AUROC) when trained in inductive and transductive settings, respectively, up to 8% above a logistic regression baseline (0.88). Comparing network topologies, the configuration considering ward-related edges (0.91 inductive, 0.96 transductive) outperforms the configurations considering caregiver-related edges (0.88, 0.89) and both types of edges (0.90, 0.94). For the top 3 most prevalent MDR Enterobacteriaceae, the AUROC varies from 0.94 for Citrobacter freundii up to 0.98 for Enterobacter cloacae using the best-performing GNN model. Conclusion: Topological features via graph modeling improve the performance of machine learning models for Enterobacteriaceae colonization prediction. GNNs could be used to support infection prevention and control programs to detect patients at risk of colonization by MDR Enterobacteriaceae and other bacteria families.
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Affiliation(s)
- Racha Gouareb
- Department of Radiology and Medical Informatics,
University of Geneva, Geneva, Switzerland
| | - Alban Bornet
- Department of Radiology and Medical Informatics,
University of Geneva, Geneva, Switzerland
- HES-SO University of Applied Arts Sciences and Arts of Western Switzerland, Geneva, Switzerland
| | - Dimitrios Proios
- Department of Radiology and Medical Informatics,
University of Geneva, Geneva, Switzerland
- HES-SO University of Applied Arts Sciences and Arts of Western Switzerland, Geneva, Switzerland
| | | | - Douglas Teodoro
- Department of Radiology and Medical Informatics,
University of Geneva, Geneva, Switzerland
- HES-SO University of Applied Arts Sciences and Arts of Western Switzerland, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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11
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Yuan W, Xu J, Guo L, Chen Y, Gu J, Zhang H, Yang C, Yang Q, Deng S, Zhang L, Deng Q, Wang Z, Ling B, Deng D. Clinical Risk Factors and Microbiological and Intestinal Characteristics of Carbapenemase-Producing Enterobacteriaceae Colonization and Subsequent Infection. Microbiol Spectr 2022; 10:e0190621. [PMID: 36445086 PMCID: PMC9769896 DOI: 10.1128/spectrum.01906-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/24/2022] [Indexed: 12/03/2022] Open
Abstract
Gastrointestinal colonization with carbapenem-resistant Enterobacteriaceae (CRE) is always a prerequisite for the development of translocated infections. Here, we sought to screen for fecal carriage of CRE and identify the risk factors for CRE colonization as well as subsequent translocated pneumonia in critically ill patients admitted to the intensive care unit (ICU) of a university hospital in China. We further focused on the intestinal flora composition and fecal metabolic profiles in CRE rectal colonization and translocated infection patients. Animal models of gastrointestinal colonization with a carbapenemase-producing Klebsiella pneumoniae (carbapenem-resistant K. pneumoniae [CRKP]) clinical isolate expressing green fluorescent protein (GFP) were established, and systemic infection was subsequently traced using an in vivo imaging system (IVIS). The intestinal barrier, inflammatory factors, and infiltrating immune cells were further investigated. In this study, we screened 54 patients hospitalized in the ICU with CRE rectal colonization, and 50% of the colonized patients developed CRE-associated pneumonia, in line with the significantly high mortality rate. Upon multivariate analysis, risk factors associated with subsequent pneumonia caused by CRE in patients with fecal colonization included enteral feeding and carbapenem exposure. Furthermore, CRKP colonization and translocated infection influenced the diversity and community composition of the intestinal microbiome. Downregulated propionate and butyrate probably play important and multiangle roles in regulating immune cell infiltration, inflammatory factor expression, and mucus and intestinal epithelial barrier integrity. Although the risk factors and intestinal biomarkers for subsequent infections among CRE-colonized patients were explored, further work is needed to elucidate the complicated mechanisms. IMPORTANCE Carbapenem-resistant Enterobacteriaceae have emerged as a major threat to modern medicine, and the spread of carbapenem-resistant Enterobacteriaceae is a clinical and public health problem. Gastrointestinal colonization by potential pathogens is always a prerequisite for the development of translocated infections, and there is a growing need to assess clinical risk factors and microbiological and intestinal characteristics to prevent the development of clinical infection by carbapenem-resistant Enterobacteriaceae.
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Affiliation(s)
- Wenli Yuan
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Jiali Xu
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Dali University, Dali, Yunnan Province, China
| | - Lin Guo
- Intensive Care Union, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Yonghong Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Jinyi Gu
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Huan Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Chenghang Yang
- Intensive Care Union, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Qiuping Yang
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Shuwen Deng
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Longlong Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Qiongfang Deng
- Intensive Care Union, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Zi Wang
- Department of Clinical Pharmacy, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Bin Ling
- Intensive Care Union, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
| | - Deyao Deng
- Department of Clinical Laboratory, The Affiliated Hospital of Yunnan University (The Second Hospital of Yunnan Province), Kunming, Yunnan Province, China
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12
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Papafotiou C, Roussos S, Sypsa V, Bampali S, Spyridopoulou K, Karapanou A, Moussouli A, Samarkos M, Daikos GL, Psichogiou M. Predictive score for patients with carbapenemase-producing enterobacterales colonization upon admission in a tertiary care hospital in an endemic area. J Antimicrob Chemother 2022; 77:3331-3339. [PMID: 36203392 DOI: 10.1093/jac/dkac321] [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: 05/02/2022] [Accepted: 08/30/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Carbapenemase-producing Enterobacterales (CPE) comprise important nosocomial pathogens worldwide. Colonized patients are the source of further dissemination in healthcare settings. Considering that timely detection of CPE carriers is pivotal but universal screening is unfeasible, we aimed to develop and validate a prediction score to detect patients harbouring CPE on hospital admission. METHODS The study was conducted in a tertiary care hospital located in a CPE endemic area. Rectal swabs were obtained from 2303 patients, screened shortly after hospital admission. The Enterobacterales isolated in cultures were examined for the presence of blaVIM, KPC, NDM, OXA-48 by PCR. Demographic data and patient history of the previous 6 months were recorded. Risk factors for CPE carriage were identified using a multivariable logistic regression model and a points-system risk score was developed. The discriminative ability of the risk score was assessed using the AUC and its predictive performance was validated in a second dataset of 1391 patients in a different time period. RESULTS Seven predictors were identified: previous CPE colonization or infection, prior hospitalization, stay in a long-term health care facility, history of ≥2 interventions, renal replacement therapy, diabetes with end-organ damage and Karnofsky score. The developed risk score in the derivation dataset ranged between 0 and 79 points, with an AUC of 0.84 in the derivation and 0.85 in the validation dataset. CONCLUSIONS This prediction tool may assist in identifying patients who are at risk of harbouring CPE on hospital admission in an endemic area and guide clinicians to implement prompt and appropriate infection control measures.
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Affiliation(s)
- Chrysanthe Papafotiou
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - Sotirios Roussos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sofia Bampali
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - Kalliopi Spyridopoulou
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - Amalia Karapanou
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - Anastasia Moussouli
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - Michael Samarkos
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - George L Daikos
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
| | - Mina Psichogiou
- First Department of Medicine, National and Kapodistrian University of Athens, Laikon General Hospital, 11527 Athens, Greece
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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: 11] [Impact Index Per Article: 5.5] [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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Papadimitriou-Olivgeris M, Bartzavali C, Karachalias E, Spiliopoulou A, Tsiata E, Siakallis G, Assimakopoulos SF, Kolonitsiou F, Marangos M. A Seven-Year Microbiological and Molecular Study of Bacteremias Due to Carbapenemase-Producing Klebsiella Pneumoniae: An Interrupted Time-Series Analysis of Changes in the Carbapenemase Gene's Distribution after Introduction of Ceftazidime/Avibactam. Antibiotics (Basel) 2022; 11:antibiotics11101414. [PMID: 36290072 PMCID: PMC9598502 DOI: 10.3390/antibiotics11101414] [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: 08/20/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Ceftazidime/avibactam (CZA) is a new option for the treatment of KPC-producing Klebsiella pneumoniae. The aim of this study was to determine resistance patterns and carbapenemase genes among K. pneumoniae (CP-Kp) bacteremic isolates before and after CZA introduction. Methods: K. pneumoniae from blood cultures of patients being treated in a Greek university hospital during 2015−21 were included. PCR for blaKPC, blaVIM, blaNDM and blaOXA-48 genes was performed. Results: Among 912 K. pneumoniae bacteremias: 725 (79.5%) were due to carbapenemase-producing isolates; 488 (67.3%) carried blaKPC; 108 (14.9%) blaVIM; 100 (13.8%) blaNDM; and 29 (4%) carried a combination of blaKPC, blaVIM or blaNDM. The incidence of CP-Kp bacteremias was 59 per 100,000 patient-days. The incidence of CP-Kp changed from a downward pre-CZA trend to an upward trend in the CZA period (p = 0.007). BSIs due to KPC-producing isolates showed a continuous downward trend in the pre-CZA and CZA periods (p = 0.067), while BSIs due to isolates carrying blaVIM or blaNDM changed from a downward trend in the pre-CZA to an upward trend in the CZA period (p < 0.001). Conclusions: An abrupt change in the epidemiology of CP-Kp was observed in 2018, due to the re-emergence of VIM-producing isolates after the suppression of KPC-producing ones via the use of CZA.
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Affiliation(s)
- Matthaios Papadimitriou-Olivgeris
- Division of Infectious Diseases, School of Medicine, University of Patras, 26504 Patras, Greece
- Infectious Diseases Service, Lausanne University Hospital, 1011 Lausanne, Switzerland
- Correspondence: ; Tel.: +41-79-556-5695
| | - Christina Bartzavali
- Department of Microbiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | | | - Anastasia Spiliopoulou
- Department of Microbiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ekaterini Tsiata
- Department of Pharmacy, University General Hospital of Patras, 26504 Patras, Greece
| | - Georgios Siakallis
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia 2408, Cyprus
| | | | - Fevronia Kolonitsiou
- Department of Microbiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Markos Marangos
- Division of Infectious Diseases, School of Medicine, University of Patras, 26504 Patras, Greece
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15
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Kang S, Jeong IS. Epidemiological characteristics of carbapenem-resistant Enterobacteriaceae and carbapenem-resistant Acinetobacter baumannii in a tertiary referral hospital in Korea. Osong Public Health Res Perspect 2022; 13:221-229. [PMID: 35820671 PMCID: PMC9263334 DOI: 10.24171/j.phrp.2022.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022] Open
Abstract
Objectives This study aimed to identify the epidemiological characteristics of patients with carbapenem-resistant Enterobacteriaceae and Acinetobacter baumannii (CRE/CRAB) isolates in a tertiary referral hospital in Korea. Methods We collected and analyzed data from 528 adults admitted to a tertiary referral hospital from August 1, 2018 to February 29, 2020. The CRE/CRAB isolates were confirmed as being present at the time of patients’ admission or acquired during hospitalization based on their medical records. The t-test, chi-square test, or Fisher exact test and stepwise multiple logistic regression were performed. Results While the proportion of community-acquired CRE/CRAB was low (6%), 20% of CRE/CRAB isolates were identified in patients at the time of hospitalization. The risk of CRAB isolation was positively associated with mechanical ventilator use (odds ratio [OR], 3.52; 95% confidence interval [CI], 1.96−6.33) and total parenteral nutrition use (OR, 3.64; 95% CI, 1.87−7.08). Conclusion Over 20% of CRE/CRAB isolates in a tertiary referral hospital in Korea were found at the time of patients’ admission. Furthermore, patients with mechanical ventilation and/or total parenteral nutrition tended to acquire CRAB more frequently. Thus, active surveillance for CRE/CRAB at the time of hospitalization is strongly required, particularly for patients who are expected to require mechanical ventilation or total parenteral nutrition.
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16
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Jeong IS, Song JY. Epidemiological Characteristics of Carbapenemase Producing Carbapenem-Resistant Enterobacteriaceae Colonization. Asian Nurs Res (Korean Soc Nurs Sci) 2022; 16:134-139. [PMID: 35605957 DOI: 10.1016/j.anr.2022.05.002] [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: 01/20/2022] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE This study identified the epidemiological characteristics, including the size and major strains, of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) and CP-CRE-related factors by comparing the characteristics of patients in the CP-CRE and non-CP-CRE groups and the CP-CRE and non-CRE groups. METHODS This secondary data analysis study included 24 patients in the CP-CRE group, 113 patients in the non-CP-CRE group, and 113 in the non-CRE group. The size and type of CP-CRE were analyzed in terms of frequency and percentage, and CP-CRE risk factors were identified using multiple logistic regression analysis. RESULTS The rate of CP-CRE positivity among patients with CRE was 17.5%, and the most common causative organism in the CP-CRE group was Klebsiella pneumoniae (81.8%). There were no significant differences between patients in the CP-CRE and non-CP-CRE groups. When compared with the non-CRE group, the isolation of multidrug-resistant organisms except for CRE, particularly vancomycin resistant Enterococcus, was confirmed as a major risk factor. CONCLUSION To prevent CP-CRE acquisition, patients with multidrug-resistant organisms require treatment with more thorough adherence to CRE prevention and management guidelines.
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Affiliation(s)
- Ihn Sook Jeong
- College of Nursing, Pusan National University, Republic of Korea
| | - Ju Yeoun Song
- Department of Nursing, Pusan National University Yangsan Hospital, Republic of Korea.
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17
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Liang Q, Zhao Q, Xu X, Zhou Y, Huang M. Early Prediction of Carbapenem-resistant Gram-negative Bacterial Carriage in Intensive Care Units Using Machine Learning. J Glob Antimicrob Resist 2022; 29:225-231. [DOI: 10.1016/j.jgar.2022.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/15/2022] Open
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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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StenoSCORE: Predicting Stenotrophomonas maltophilia Bloodstream Infections in the Hematologic Malignancy Population. Antimicrob Agents Chemother 2021; 65:e0079321. [PMID: 34060899 DOI: 10.1128/aac.00793-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Stenotrophomonas maltophilia bloodstream infections (BSI) are associated with considerable mortality in the hematologic malignancy population. Trimethoprim-sulfamethoxazole (TMP-SMX) is the treatment of choice; however, it is not routinely included in empirical treatment regimens, both because of its adverse event profile and the relative rarity of S. maltophilia infections. We developed a risk score to predict hematologic malignancy patients at increased risk for S. maltophilia BSI to guide early (TMP-SMX) therapy. Patients ≥12 years of age admitted to five hospitals between July 2016 and December 2019 were included. Two separate risk scores were developed, (i) a "knowledge-driven" risk score based upon previously identified risk factors in the literature in addition to variables identified by regression analysis using the current cohort, and (ii) a risk score based upon automatic variable selection. For both scores, discrimination (receiver operator characteristic [ROC] curves and C statistics) and calibration (Hosmer-Lemeshow goodness-of-fit test and graphical calibration plots) were assessed. Internal validation was assessed using leave-one-out cross-validation. In total, 337 unique patients were included; 21 (6.2%) had S. maltophilia BSI. The knowledge-driven risk score (acute leukemia, absolute neutrophil count category, mucositis, central line, and ≥3 days of carbapenem therapy) had superior performance (C statistic = 0.75; 0.71 after cross-validation) compared to that of the risk score utilizing automatic variable selection (C statistic = 0.63; 0.38 after cross-validation). A user-friendly risk score incorporating five variables easily accessible to clinicians performed moderately well to predict hematologic malignancy patients at increased risk for S. maltophilia BSI. External validation using a larger cohort is necessary to create a refined risk score before broad clinical application.
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20
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Seo SM, Jeong IS. [External Validation of Carbapenem-Resistant Enterobacteriaceae Acquisition Risk Prediction Model in a Medium Sized Hospital]. J Korean Acad Nurs 2021; 50:621-630. [PMID: 32895347 DOI: 10.4040/jkan.20137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE This study was aimed to evaluate the external validity of a carbapenem-resistant Enterobacteriaceae (CRE) acquisition risk prediction model (the CREP-model) in a medium-sized hospital. METHODS This retrospective cohort study included 613 patients (CRE group: 69, no-CRE group: 544) admitted to the intensive care units of a 453-beds secondary referral general hospital from March 1, 2017 to September 30, 2019 in South Korea. The performance of the CREP-model was analyzed with calibration, discrimination, and clinical usefulness. RESULTS The results showed that those higher in age had lower presence of multidrug resistant organisms (MDROs), cephalosporin use ≥ 15 days, Acute Physiology and Chronic Health Evaluation II (APACHE II) score ≥ 21 points, and lower CRE acquisition rates than those of CREP-model development subjects. The calibration-in-the-large was 0.12 (95% CI: - 0.16~0.39), while the calibration slope was 0.87 (95% CI: 0.63~1.12), and the concordance statistic was .71 (95% CI: .63~.78). At the predicted risk of .10, the sensitivity, specificity, and correct classification rates were 43.5%, 84.2%, and 79.6%, respectively. The net true positive according to the CREP-model were 3 per 100 subjects. After adjusting the predictors' cutting points, the concordance statistic increased to .84 (95% CI: .79~.89), and the sensitivity and net true positive was improved to 75.4%. and 6 per 100 subjects, respectively. CONCLUSION The CREP-model's discrimination and clinical usefulness are low in a medium sized general hospital but are improved after adjusting for the predictors. Therefore, we suggest that institutions should only use the CREP-model after assessing the distribution of the predictors and adjusting their cutting points.
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Affiliation(s)
- Su Min Seo
- Infection Control Unit, Dongeui Medical Center, Busan, Korea
| | - Ihn Sook Jeong
- College of Nursing, Pusan National University, Yangsan, Korea.
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21
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Wilson GM, Suda KJ, Fitzpatrick MA, Bartle B, Pfeiffer CD, Jones M, Rubin MA, Perencevich E, Evans M, Evans CT. Risk Factors Associated with Carbapenemase Producing Carbapenem-Resistant Enterobacteriaceae (CP-CRE) Positive Cultures in a Cohort of U.S. Veterans. Clin Infect Dis 2021; 73:1370-1378. [PMID: 33973631 DOI: 10.1093/cid/ciab415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Carbapenem-resistant Enterobacterales (CRE) cause approximately 13,100 infections with 8% mortality in the United States annually. The subset of carbapenemase-producing CRE (CP-CRE) infections have much higher mortality rates (40% -50%). There has been little research on characteristics unique to CP-CRE. The goal of this study was to assess differences between those with nonCP-CRE and CP-CRE cultures in U.S. Veterans. METHODS A retrospective cohort of Veterans with CRE cultures from 2013-2018 and their demographic, medical, and facility level covariates were collected. Clustered multiple logistic regression models were used to assess independent factors associated with CP-CRE. RESULTS 3,096 unique patients with cultures positive for either nonCP-CRE or CP-CRE were included. Being African American (Odds Ratio (OR)=1.44 (95% Confidence Interval (CI) 1.15,1.80), diagnosis in 2017 (OR=3.11 (95% CI 2.13,4.54)) or 2018 (OR=3.93 (95%CI 2.64,5.84)), congestive heart failure (OR=1.35 (95%CI 1.11,1.64)), and gastroesophageal reflux disease (OR=1.39 (95%CI 1.03,1.87)) were associated with CP-CRE cultures. 752 (24.3%) patients had no known antibiotic exposure in the year before culture; these individuals had a comparatively increased frequency of prolonged PPI use (17.3% vs 5.6%). DISCUSSION Among a cohort of patients with CRE, African Americans, individuals with congestive heart failure, and patients with gastroesophageal reflux disease had greater odds of having a CP-CRE culture. Roughly one in four patients with CP-CRE had no known antibiotic exposure in the year before their positive culture.
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Affiliation(s)
- Geneva M Wilson
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA
| | - Katie J Suda
- Center for Health Equity Research and Promotion, VA Pittsburgh Heath Care System, Pittsburgh, PA, USA.,University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, PA, USA
| | - Margaret A Fitzpatrick
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA.,Department of Medicine, Division of Infectious Diseases, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Brian Bartle
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA
| | - Christopher D Pfeiffer
- Department of Veterans Affairs, Portland VA Healthcare System, Portland, OR, USA.,Department of Medicine, Division of Infectious Diseases, Oregon Health Science University, Portland, OR, USA
| | - Makoto Jones
- Department of Veterans Affairs, VA Salt Lake City Healthcare System, Salt Lake City, UT, USA.,Department of Medicine, Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Michael A Rubin
- Department of Veterans Affairs, Center for Access & Delivery Research and Evaluation, Iowa City VA Health Care System, Iowa City, IA, USA.,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Eli Perencevich
- Department of Veterans Affairs, Center for Access & Delivery Research and Evaluation, Iowa City VA Health Care System, Iowa City, IA, USA.,Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Martin Evans
- Department of Veterans Affairs, Lexington VA Medical Center, Lexington, KY, USA
| | - Charlesnika T Evans
- Center of Innovation for Complex Chronic Healthcare (CINCCH), Hines Jr. Veterans Affairs Hospital, Hines, IL,USA.,Department of Preventive Medicine, Center for Health Services and Outcomes Research, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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22
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Nordmann P, Fournier C, Poirel L. A Selective Culture Medium for Screening Carbapenem Resistance in Pseudomonas spp. Microb Drug Resist 2021; 27:1355-1359. [PMID: 33877916 DOI: 10.1089/mdr.2020.0461] [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: 11/13/2022] Open
Abstract
Purpose: The SuperCP medium containing meropenem (2 mg/L) was evaluated for screening of carbapenem-resistant Pseudomonas species. Materials and Methods: It was evaluated using 29 meropenem-susceptible and 56 meropenem-nonsusceptible Pseudomonas-like clinical isolates, the latter exhibiting a variety of carbapenem-resistance mechanisms. Results: Its sensitivity and specificity of detection were found to be 91% and 100%, respectively. By testing spiked stools, an excellent performance of the medium was also observed for detection of carbapenem-resistant Pseudomonas aeruginosa, with a lowest detection limit ranging from 100 to 102 CFU/mL. Conclusion: This screening medium provides the opportunity to select carbapenem-resistant Pseudomonas and Pseudomonas-related isolates regardless of their resistance mechanism.
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Affiliation(s)
- Patrice Nordmann
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,INSERM European Unit (IAME), University of Fribourg, Fribourg, Switzerland.,Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland.,Institute for Microbiology, University of Lausanne and University Hospital Centre, Lausanne, Switzerland
| | - Claudine Fournier
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,INSERM European Unit (IAME), University of Fribourg, Fribourg, Switzerland.,Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
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23
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Seo SM, Jeong IS, Song JY, Lee S. Development of a Nomogram for Carbapenem-Resistant Enterobacteriaceae Acquisition Risk Prediction Among Patients in the Intensive Care Unit of a Secondary Referral Hospital. Asian Nurs Res (Korean Soc Nurs Sci) 2021; 15:174-180. [PMID: 33621701 DOI: 10.1016/j.anr.2021.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 02/04/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE This study aimed to identify the risk factors of carbapenem-resistant Enterobacteriaceae (CRE) acquisition to build a nomogram for CRE acquisition risk prediction and evaluate its performance. METHODS This unmatched case-control study included 352 adult patients (55 patients and 297 controls) admitted to the intensive care unit (ICU) of a 453-bed secondary referral hospital between January 1, 2018, and September 31, 2019, in Busan, South Korea. The nomogram was built with the identified risk factors using multiple logistic regression analysis. Its performance was analyzed using calibration-in-the-large, the slope of the calibration plot, concordance statistic (c-statistic), and the sensitivity and specificity of the training set, subsets, and a new test set. RESULTS The risk factors of CRE acquisition among ICU patients at a secondary referral hospital were Acute Physiology and Chronic Health Evaluation II score at the time of admission, use of a central venous catheter and a nasogastric tube, as well as use of cephalosporin antibiotics. At 20.0% of the predicted CRE acquisition risk in the training set, the calibration-in-the-large was 0, slope of the calibration plot was 1, c-statistic was .93, sensitivity was 85.5%, and specificity was 84.8%. The performance was relatively good in the subsets and new test set. CONCLUSION The nomogram can be used to monitor the CRE acquisition risk for ICU patients who have a similar case mix to patients in the study hospitals. Future studies need to involve more rigorous methodology and larger samples.
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Affiliation(s)
- Su Min Seo
- Ulsan Center for Infectious Control & Prevention, Ulsan, Republic of Korea.
| | - Ihn Sook Jeong
- College of Nursing, Pusan National University, Yangsan, Republic of Korea.
| | - Ju Yeoun Song
- Department of Nursing, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea.
| | - Sangjin Lee
- Graduate School, Department of Statistics, Pusan National University, Busan, Republic of Korea.
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24
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Adar A, Zayyad H, Azrad M, Libai K, Aharon I, Nitzan O, Peretz A. Clinical and Demographic Characteristics of Patients With a New Diagnosis of Carriage or Clinical Infection With Carbapenemase-Producing Enterobacterales: A Retrospective Study. Front Public Health 2021; 9:616793. [PMID: 33614584 PMCID: PMC7892593 DOI: 10.3389/fpubh.2021.616793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
Background: To examine the clinical, demographic, and microbiologic characteristics of new rectal carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) carriers vs. those with a clinical infection, hospitalized at Padeh-Poriya Medical Center between 2014 and 2017 and to examine the susceptibility profiles of isolates from clinical infections. Methods: In this retrospective, chart analysis, demographic and clinical data were collected from medical charts of 175 adult patients with either new- onset carbapenemase-producing Enterobacterales (CPE) carriage or clinical CPE infection. Collected data included age, ethnic group, place of residence, hospitalizations in the past 90 days, and 30-day mortality. Microbiological analyses considered bacterial genus, molecular resistance mechanism and antibiotic susceptibility. Results: A significantly higher percentage (42.4%) of CPE carriers were long-term care facility residents, and had been recently hospitalized (56.3%), as compared to patients with clinical CPE infection (29.2 and 45.9%, respectively). Additionally, we noted a high (58.3%) acquision of CPE in our hospital. The most common bacterial isolate was K. pneumoniae and the most common resistance mechanism was Klebsiella pneumoniae (K. pneumoniae) carbapenemases (KPC). High susceptibility rates to amikacin and chloramphenicol were also noted. Conclusions: This study reaffirmed the importance of CPE screening and infection control measures. The observed antibiotic susceptibility profile suggests amikacin and chloramphenicol as potential treatments for CPE infection.
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Affiliation(s)
- Assaf Adar
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Hiba Zayyad
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Infectious Disease Unit, The Baruch Padeh Medical Center, Tiberias, Israel
| | - Maya Azrad
- Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Tiberias, Israel
| | - Kozita Libai
- Infectious Disease Unit, The Baruch Padeh Medical Center, Tiberias, Israel
| | - Ilana Aharon
- Infectious Disease Unit, The Baruch Padeh Medical Center, Tiberias, Israel
| | - Orna Nitzan
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Infectious Disease Unit, The Baruch Padeh Medical Center, Tiberias, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Clinical Microbiology Laboratory, The Baruch Padeh Medical Center, Tiberias, Israel
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25
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Prolonged Carriage of Carbapenemase-Producing Enterobacteriaceae: Clinical Risk Factors and the Influence of Carbapenemase and Organism Types. J Clin Med 2021; 10:jcm10020310. [PMID: 33467637 PMCID: PMC7830152 DOI: 10.3390/jcm10020310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/29/2020] [Accepted: 01/12/2021] [Indexed: 12/25/2022] Open
Abstract
Prolonged carriage of carbapenemase-producing Enterobacteriaceae (CPE) constitutes a substantial epidemiologic threat. This study aimed to evaluate whether the types of carbapenemase and organism can affect the duration of carriage and to evaluate the clinical factors associated with prolonged carriage. We retrospectively reviewed data for patients admitted between May 2013 and August 2018 who were identified as CPE carriers. A total of 702 patients were identified; the major types of carbapenemase and organism were Oxacillinase (OXA)-48-like (n = 480, 68.4%) and Klebsiella pneumoniae (K. pneumoniae) (n = 584, 83.2%). The analyses of time to spontaneous decolonization using the Kaplan–Meier method showed that OXA-48-like and K. pneumoniae were significantly associated with prolonged carriage (log rank, p = 0.001 and p < 0.001). In multivariable logistic analysis to assess the risk factors for CPE prolonged carriage in the 188 patients with available follow-up culture data for 3 months, K. pneumoniae (adjusted odds ratio [aOR] 6.58; 95% confidence interval [CI], 1.05–41.27; p = 0.044), CPE positive clinical specimen (aOR 11.14; 95% CI, 4.73–26.25; p < 0.001), and concurrent Clostridioides difficile infection (CDI) (aOR 3.98, 95% CI 1.29–12.26; p = 0.016) were predictive of prolonged carriage. Our results suggest that CP-K. pneumoniae may have higher probability of prolonged carriage, while the effect of OXA-48-like CPE is inconclusive. Furthermore, patients with CP-K. pneumoniae who had positive clinical specimen or concurrent CDI can cause a vicious circle in prolonged carriage.
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26
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Vock I, Aguilar-Bultet L, Egli A, Tamma PD, Tschudin-Sutter S. Independent, external validation of clinical prediction rules for the identification of extended-spectrum β-lactamase-producing Enterobacterales, University Hospital Basel, Switzerland, January 2010 to December 2016. ACTA ACUST UNITED AC 2020; 25. [PMID: 32643598 PMCID: PMC7346366 DOI: 10.2807/1560-7917.es.2020.25.26.1900317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Algorithms for predicting infection with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) on hospital admission or in patients with bacteraemia have been proposed, aiming to optimise empiric treatment decisions. Aim We sought to confirm external validity and transferability of two published prediction models as well as their integral components. Methods We performed a retrospective case–control study at University Hospital Basel, Switzerland. Consecutive patients with ESBL-producing Escherichia coli or Klebsiella pneumoniae isolated from blood samples between 1 January 2010 and 31 December 2016 were included. For each case, three non-ESBL-producing controls matching for date of detection and bacterial species were identified. The main outcome measure was the ability to accurately predict infection with ESBL-PE by measures of discrimination and calibration. Results Overall, 376 patients (94 patients, 282 controls) were analysed. Performance measures for prediction of ESBL-PE infection of both prediction models indicate adequate measures of calibration, but poor discrimination (area under receiver-operating curve: 0.627 and 0.651). History of ESBL-PE colonisation or infection was the single most predictive independent risk factor for ESBL-PE infection with high specificity (97%), low sensitivity (34%) and balanced positive and negative predictive values (80% and 82%). Conclusions Applying published prediction models to institutions these were not derived from, may result in substantial misclassification of patients considered as being at risk, potentially leading to wrong allocation of antibiotic treatment, negatively affecting patient outcomes and overall resistance rates in the long term. Future prediction models need to address differences in local epidemiology by allowing for customisation according to different settings.
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Affiliation(s)
- Isabelle Vock
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Lisandra Aguilar-Bultet
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Pranita D Tamma
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sarah Tschudin-Sutter
- Department of Clinical Research, University Hospital Basel, Basel, Switzerland.,Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
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27
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Flores C, Bianco K, de Filippis I, Clementino MM, Romão CMC. Genetic Relatedness of NDM-Producing Klebsiella pneumoniae Co-Occurring VIM, KPC, and OXA-48 Enzymes from Surveillance Cultures from an Intensive Care Unit. Microb Drug Resist 2020; 26:1219-1226. [DOI: 10.1089/mdr.2019.0483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Claudia Flores
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde, Rio de Janeiro, Brazil
| | - Kayo Bianco
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde, Rio de Janeiro, Brazil
| | - Ivano de Filippis
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde, Rio de Janeiro, Brazil
| | | | - Célia Maria C.P.A. Romão
- Fundação Oswaldo Cruz, Instituto Nacional de Controle de Qualidade em Saúde, Rio de Janeiro, Brazil
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28
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Willems RPJ, van Dijk K, Ket JCF, Vandenbroucke-Grauls CMJE. Evaluation of the Association Between Gastric Acid Suppression and Risk of Intestinal Colonization With Multidrug-Resistant Microorganisms: A Systematic Review and Meta-analysis. JAMA Intern Med 2020; 180:561-571. [PMID: 32091544 PMCID: PMC7042870 DOI: 10.1001/jamainternmed.2020.0009] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE Acid suppressants inhibit gastric acid secretion and disrupt the intestinal microbiome. Whether acid suppression increases the risk of colonization with multidrug-resistant microorganisms (MDROs) is unclear. OBJECTIVES To systematically examine the association of use of acid suppressants with the risk of colonization with MDROs and to perform a meta-analysis of current evidence. DATA SOURCES PubMed, Embase, the Web of Science Core Collection, and the Cochrane Central Register of Controlled Trials were searched from database inception through July 8, 2019. STUDY SELECTION Study selection was performed independently by 2 authors (R.P.J.W. and C.M.J.E.V.-G.) on the basis of predefined selection criteria; conflicts were resolved by consensus or by an adjudicator (K.v.D.). Human observational studies (case control, cohort, and cross-sectional) and clinical trial designs were selected if they quantified the risk of MDRO colonization in users of acid suppressants in comparison with nonusers. DATA EXTRACTION AND SYNTHESIS The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) and Meta-analysis of Observational Studies in Epidemiology (MOOSE) recommendations were followed. Data were extracted independently by the same 2 authors, and adjudication was conducted when necessary. Risk of bias was assessed according to a modified Newcastle-Ottawa Scale. Pooled odds ratios (ORs) were estimated using random-effects models; heterogeneity was evaluated using the I2 method. MAIN OUTCOMES AND MEASURES The primary outcome measure was intestinal colonization with MDROs of the Enterobacterales order (producing extended-spectrum β-lactamases, carbapenemases, or plasmid-mediated AmpC β-lactamases), vancomycin-resistant enterococci, methicillin-resistant or vancomycin-resistant Staphylococcus aureus, or multidrug-resistant Pseudomonas or Acinetobacter species. RESULTS A total of 26 observational studies including 29 382 patients (11 439 [38.9%] acid suppressant users) met the selection criteria. Primary meta-analysis of 12 studies including 22 305 patients that provided adjusted ORs showed that acid suppression increased the odds of intestinal carriage of MDROs of the Enterobacterales order and of vancomycin-resistant enterococci by roughly 75% (OR = 1.74; 95% CI, 1.40-2.16; I2 = 68%). The odds were concordant with the secondary pooled analysis of all 26 studies (OR = 1.70; 95% CI, 1.44-1.99; I2 = 54%). Heterogeneity was partially explained by variations in study setting and the type of acid suppression. CONCLUSIONS AND RELEVANCE Acid suppression is associated with increased odds of MDRO colonization. Notwithstanding the limitations of observational studies, the association is plausible and is strengthened by controlling for confounders. In view of the global increase in antimicrobial resistance, stewardship to reduce unnecessary use of acid suppressants may help to prevent MDRO colonization.
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Affiliation(s)
- Roel P J Willems
- Amsterdam Infection and Immunity Institute, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Karin van Dijk
- Amsterdam Infection and Immunity Institute, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Johannes C F Ket
- Medical Library, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Amsterdam Infection and Immunity Institute, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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29
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Luz CF, Vollmer M, Decruyenaere J, Nijsten MW, Glasner C, Sinha B. Machine learning in infection management using routine electronic health records: tools, techniques, and reporting of future technologies. Clin Microbiol Infect 2020; 26:1291-1299. [PMID: 32061798 DOI: 10.1016/j.cmi.2020.02.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Machine learning (ML) is increasingly being used in many areas of health care. Its use in infection management is catching up as identified in a recent review in this journal. We present here a complementary review to this work. OBJECTIVES To support clinicians and researchers in navigating through the methodological aspects of ML approaches in the field of infection management. SOURCES A Medline search was performed with the keywords artificial intelligence, machine learning, infection∗, and infectious disease∗ for the years 2014-2019. Studies using routinely available electronic hospital record data from an inpatient setting with a focus on bacterial and fungal infections were included. CONTENT Fifty-two studies were included and divided into six groups based on their focus. These studies covered detection/prediction of sepsis (n = 19), hospital-acquired infections (n = 11), surgical site infections and other postoperative infections (n = 11), microbiological test results (n = 4), infections in general (n = 2), musculoskeletal infections (n = 2), and other topics (urinary tract infections, deep fungal infections, antimicrobial prescriptions; n = 1 each). In total, 35 different ML techniques were used. Logistic regression was applied in 18 studies followed by random forest, support vector machines, and artificial neural networks in 18, 12, and seven studies, respectively. Overall, the studies were very heterogeneous in their approach and their reporting. Detailed information on data handling and software code was often missing. Validation on new datasets and/or in other institutions was rarely done. Clinical studies on the impact of ML in infection management were lacking. IMPLICATIONS Promising approaches for ML use in infectious diseases were identified. But building trust in these new technologies will require improved reporting. Explainability and interpretability of the models used were rarely addressed and should be further explored. Independent model validation and clinical studies evaluating the added value of ML approaches are needed.
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Affiliation(s)
- C F Luz
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.
| | - M Vollmer
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - J Decruyenaere
- Ghent University, Ghent University Hospital, Department of Intensive Care, Ghent, Belgium
| | - M W Nijsten
- University of Groningen, University Medical Center Groningen, Department of Critical Care, Groningen, the Netherlands
| | - C Glasner
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - B Sinha
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
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30
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The Likelihood of Developing a Carbapenem-Resistant Enterobacteriaceae Infection during a Hospital Stay. Antimicrob Agents Chemother 2019; 63:AAC.00757-19. [PMID: 31138574 DOI: 10.1128/aac.00757-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/22/2019] [Indexed: 12/27/2022] Open
Abstract
Of 1,455 unique patients in U.S. intensive care units (ICUs), 4% were rectally colonized with CRE on admission. A total of 297 patients were initially negative for carbapenem-resistant Enterobacteriaceae (CRE) and remained in the ICU long enough to contribute additional swabs; 22% of these patients had a subsequent CRE-positive swab, with a median time to CRE colonization of 13 days (interquartile range, 7 to 21 days). Patients colonized with carbapenemase-producing CRE were more likely than those colonized with non-carbapenemase-producing CRE to develop CRE infections during their hospitalizations (36% versus 3%; P < 0.05).
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